Nature


Science


Nature


Nature

Infectious diseases science in Africa takes a leading place in the world.
de Oliveira T, The Lancet (2022), https://doi.org/10.1016/S0140-6736(22)00977-1I:.

Omicron infection enhances Delta antibody immunity in vaccinated persons.
Khan K, Karim F, Cele S, Reedoy K, San EJ, Lustig G, Tegally H, Rosenberg Y, Bernstein M, Jule Z, Ganga Y, Ngcobo N, Mazibuko M, Mthabela N, Mhlane Z, Mbatha N, Miya Y, Giandhari J, Ramphal Y, Naidoo T, Sivro A, Samsunder N, Kharsany A, Amoako D, Bhiman J, Manickchund N, Karim Q, Magula N, Abdool Karim SS, Gray G, Hanekom W, von Gottberg A, Milo R, Gosnell B, Lessells R, Moore P, de Olveira T, Moosa M-Y S, Sigal A, Nature (2022), https://doi.org/10.1038/s41586-022-04830-x:.

Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages.
Tegally H, Moir M, Everatt J, Giovanetti M, Scheepers C, Wilkinson E, Subramoney K, Moyo S, Amoako D, Althaus C, Anyaneji U, Kekana D, Viana R, Giandhari J, Maponga T, Maruapula D, Choga W, Mayaphi S, Mbhele N, Gaseitsiwe S, Msomi N, Naidoo Y, Pillay S, Sanko T, San J, Scott L, Singh L, Magini N, Smith-Lawrence P, Stevens W, Dor G, Tshiabuila D, Wolter N, Preiser W, Treurnicht F, Venter M, Davids M, Chiloane G, Mendes A, McIntyre C, O'Toole A, Ruis C, Peacock T, Roemer C, Williamson C, Pybus O, Bhiman J, Glass A, Martin D, Rambaut A, Gaseitsiwe S, von Gottberg A, Baxter C, Lessells R, de Oliveira T, medRxiv (2022), MEDRXIV-2022-274406v1-deOliveira:.

Effectiveness of the Ad26.COV2.S vaccine in health-care workers in South Africa (the Sisonke study): results from a single-arm, open-label, phase 3B, implementation study.
Bekker LG, Garrett N, Goga A, Fairall L, Reddy T, Yende-Zuma N, Kassanjee R, Collie S, Sanne I, Boulle A, Seocharan I, Engelbrecht I, Davies MA, Champion J, Chen T, Bennett S, Mametja S, Semenya M, Moultrie H, de Oliveira T, Lessells R, Cohen C, Jassat W, Groome M, Von Gottberg A, Le Roux E, Khuto K, Barouch D, Mahomed H, Wolmarans M, Rousseau P, Bradshaw D, Mulder M, Opie J, Louw V, Jacobson B, Rowji P, Peter JG, Takalani A, Odhiambo J, Mayat F, Takuva S, Corey L, Gray GE, Lancet (2022), 399(10330):1141-1153. doi: 10.1016/S0140-6736(22)00007-1:.

The geography and inter-community configuration of new sexual partnership formation in a rural South African population over fourteen years (2003–2016).
Kim H-Y, Cuadros D, Wilkinson E, Junqueira DM, de Oliveira T, Tanser F, PLoS Global Public Health (2022), https://doi.org/10.1371/journal.pgph.0000055:.

Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage.
Scheepers C, Everatt J, Amoako DG, Tegally H, Wibmer CK, Mnguni A, Ismail A, Mahlangu B, Lambson BE, Martin DP, Wilkinson E, San JE, Giandhari J, Manamela N, Ntuli N, Kgagudi P, Cele S, Richardson SI, Pillay S, Mohale T, Ramphal U, Naidoo Y, Khumalo ZT, Kwatra G, Gray G, Bekker LG, Madhi SA, Baillie V, Van Voorhis WC, Treurnicht FK, Venter M, Mlisana K, Wolter N, Sigal A, Williamson C, Hsiao NY, Msomi N, Maponga T, Preiser W, Makatini Z, Lessells R, Moore PL, de Oliveira T, von Gottberg A, Bhiman JN, Nature Commununications (2022), 13(1):1976. doi: 10.1038/s41467-022-29579-9:.

Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil.
Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San JE, Rodrigues ES, Vieira Santos E, Aburjaile F, Xavier J, Fritsch H, Ribeiro Adelino TE, Pereira F, Leal A, Campos de Melo Iani F, de Carvalho Pereira G, Vazquez C, Mercedes Estigarribia Sanabria G, de Oliveira EC, Demarchi L, Croda J, Dos Santos Bezerra R, Oliveira de Lima LP, Martins AJ, Dos Santos Barros CR, Marqueze EC, de Souza Todao Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Drummond Sampaio Corrêa Mariani P, Kitajima JP, Santos B, Proto-Siqueira R, Cantarelli VV, Tosta S, Brandão Nardy V, Reboredo de Oliveira da Silva L, Astete Gómez MK, Lima JG, Ribeiro AA, Guimarães NR, Watanabe LT, Barbosa Da Silva L, da Silva Ferreira R, F da Penha MP, Ortega MJ, Gómez de la Fuente A, Villalba S, Torales J, Gamarra ML, Aquino C, Martínez Figueredo GP, Fava WS, Motta-Castro ARC, Venturini J, do Vale Leone de Oliveira SM, Cavalheiro Maymone Gonçalves C, Debur Rossa MDC, Becker GN, Presibella MM, Marques NQ, Riediger IN, Raboni S, Coelho GM, Cataneo AHD, Zanluca C, Dos Santos CND, Assato PA, Allan da Silva da Costa F, Poleti MD, Chagas Lesbon JC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Tommasini Grotto RM, Souza-Neto JA, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, Bispo de Filippis AM, Venancio da Cunha R, Freitas C, Leonel Peterka CR, Rangel Fernandes CF, de Araújo WN, do Carmo Said RF, Almiron M, Campelo de Albuquerque E Melo CF, Lourenço J, de Oliveira T, Holmes EC, Haddad R, Sampaio SC, Elias MC, Kashima S, de Alcantara LCJ, Covas DT, medRxiv [Preprint] (2022), 28:2021.10.07.21264644. doi: 10.1101/2021.10.07.21264644:.

Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic.
Giovanetti M, Fonseca V, Wilkinson E, Tegally H, San EJ, Althaus CL, Xavier J, Nanev Slavov S, Viala VL, Ranieri Jerônimo Lima A, Ribeiro G, Souza-Neto JA, Fukumasu H, Lehmann Coutinho L, Venancio da Cunha R, Freitas C, Campelo de A E Melo CF, Navegantes de Araújo W, Do Carmo Said RF, Almiron M, de Oliveira T, Coccuzzo Sampaio S, Elias MC, Covas DT, Holmes EC, Lourenço J, Kashima S, de Alcantara LCJ, Virus Evolution (2022), doi: 10.1093/ve/veac024:.

Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function.
Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins GW, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A; NGS-SA, Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL, Mol Biol Evol. (2022), doi: 10.1093/molbev/msac061:.

Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021.
Bbosa N, Ssemwanga D, Namagembe H, Kiiza R, Kiconco J, Kayiwa J, Lutalo T, Lutwama J, Ssekagiri A, Ssewanyana I, Nabadda S, Kyobe-Bbosa H, Giandhari J, Pillay S, Ramphal U, Ramphal Y, Naidoo Y, Tshiabuila D, Tegally H, San EJ, Wilkinson E, de Oliveira T, Kaleebu P, Emerg Infect Dis (2022), doi: 10.3201/eid2805.220121:.

Targeted Sanger sequencing to recover key mutations in SARS-CoV-2 variant genome assemblies produced by next-generation sequencing.
Singh L, San JE, Tegally H, Brzoska PM, Anyaneji UJ, Wilkinson E, Clark L, Giandhari J, Pillay S, Lessells RJ, Martin DP, Furtado M, Kiran AM, de Oliveira T, Microb Genom. (2022), doi: 10.1099/mgen.0.000774:.

A Retrospective Overview of Zika Virus Evolution in the Midwest of Brazil..
Giovanetti M, Pereira LA, Adelino TÉR, Fonseca V, Xavier J, de Araújo Fabri A, Slavov SN, da Silva Lemos P, de Almeida Marques W, Kashima S, Lourenço J, de Oliveira T, Campelo de Albuquerque CF, Freitas C, Peterka CRL, da Cunha RV, Mendonça AF, Lemes da Silva V, Alcantara LCJ, Microbiol Spectr. (2022), e0015522. doi: 10.1128/spectrum.00155-22:.

The role of high-risk geographies in the perpetuation of the HIV epidemic in rural South Africa: A spatial molecular epidemiology study.
Cuadros DF, de Oliveira T, Graf T, Junqueira DM, Wilkinson E, Lemey P, Barnighausen T, Kim H-Y, Tanser F, PLoS Global Public Health (2022), https://doi.org/10.1371/journal.pgph.0000105:.

Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq.
Tshiabuila D, Giandhari J, Pillay S, Ramphal U, Ramphal Y, Maharaj A, Anyaneji UJ, Naidoo Y, Tegally H, San EJ, Wilkinson E, Lessells R, de Oliveira T, Research Square (2022), https://doi.org/10.21203/rs.3.rs-1249711/v1:.

Persistent SARS-CoV-2 infection with accumulation of mutations in a patient with poorly controlled HIV infection.
Maponga TG, Jeffries M, Tegally H, Sutherland A, Wilkinson E, Lessells R, Msomi N, van Zyl G, de Oliveira T, Preiser W, SSRN (2022), http://dx.doi.org/10.2139/ssrn.4014499:.

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.
Martin DP, Lytras S, Lucaci AG, Maier W, Grüning B, Shank SD, Weaver S, MacLean OA, Orton RJ, Lemey P, Boni MF, Tegally H, Harkins G, Scheepers C, Bhiman JN, Everatt J, Amoako DG, San JE, Giandhari J, Sigal A; NGS-SA, Williamson C, Hsiao NY, von Gottberg A, De Klerk A, Shafer RW, Robertson DL, Wilkinson RJ, Sewell BT, Lessells R, Nekrutenko A, Greaney AJ, Starr TN, Bloom JD, Murrell B, Wilkinson E, Gupta RK, de Oliveira T, Kosakovsky Pond SL, bioXriv (2022), 2022.01.14.476382. doi: 10.1101/2022.01.14.476382:.

Omicron infection of vaccinated individuals enhances neutralizing immunity against the Delta variant. .
Khan K, Karim F, Cele S, San JE, Lustig G, Tegally H, Rosenberg Y, Bernstein M, Ganga Y, Jule Z, Reedoy K, Ngcobo N, Miya Y, Mazibuko M, Mthabela N, Mhlane Z, Mbatha N, Giandhari J, Ramphal Y, Naidoo T, Manickchund N, Magula N, Karim SA, Gray G, Hanekom W, von Gottberg A, Milo R, Gosnell B, Lessells R, de Oliveira T, Moore P, Moosa YS, Sigal A., medRxiv (2022), 2021.12.27.21268439. doi: 10.1101/2021.12.27.21268439:.

T cell responses to SARS-CoV-2 spike cross-recognize Omicron.
Keeton R, Tincho MB, Ngomti A, Baguma R, Benede N, Suzuki A, Khan K, Cele S, Bernstein M, Karim F, Madzorera SV, Moyo-Gwete T, Mennen M, Skelem S, Adriaanse M, Mutithu D, Aremu O, Stek C, du Bruyn E, Van Der Mescht MA, de Beer Z, de Villiers TR, Bodenstein A, van den Berg G, Mendes A, Strydom A, Venter M, Giandhari J, Naidoo Y, Pillay S, Tegally H, Grifoni A, Weiskopf D, Sette A, Wilkinson RJ, de Oliveira T, Bekker LG, Gray G, Ueckermann V, Rossouw T, Boswell MT, Bihman J, Moore PL, Sigal A, Ntusi NAB, Burgers WA, Riou C, Nature (2022), doi: 10.1038/s41586-022-04460-3:.

Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests..
Rodgers MA, Olivo A, Harris BJ, Lark C, Luo X, Berg MG, Meyer TV, Mohaimani A, Orf GS, Goldstein Y, Fox AS, Hirschhorn J, Glen WB, Nolte F, Landay A, Jennings C, Moy J, Servellita V, Chiu C, Batra R, Snell LB, Nebbia G, Douthwaite S, Tanuri A, Singh L, de Oliveira T, Ahouidi A, Mboup S, Cloherty GA, J Clin Virol. (2022), 105080. doi: 10.1016/j.jcv.2022.105080:.

Reduced amplification efficiency of the RNA-dependent-RNA-polymerase target enables tracking of the Delta SARS-CoV-2 variant using routine diagnostic tests.
Valley-Omar Z, Marais G, Iranzadeh A, Naidoo M, Korsman S, Maponga T, Hussey H, Davies MA, Boulle A, Doolabh D, Laubscher M, Wojno J, Deetlefs JD, Maritz J, Scott L, Msomi N, Naicker C, Tegally H, de Oliveira T, Bhiman J, Williamson C, Preiser W, Hardie D, Hsiao NY, J Virol Methods (2022), 302:114471. doi: 10.1016/j.jviromet.2022.114471:.

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa.
Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, Anyaneji UJ, Bester PA, Boni MF, Chand M, Choga WT, Colquhoun R, Davids M, Deforche K, Doolabh D, du Plessis L, Engelbrecht S, Everatt J, Giandhari J, Giovanetti M, Hardie D, Hill V, Hsiao NY, Iranzadeh A, Ismail A, Joseph C, Joseph R, Koopile L, Kosakovsky Pond SL, Kraemer MUG, Kuate-Lere L, Laguda-Akingba O, Lesetedi-Mafoko O, Lessells RJ, Lockman S, Lucaci AG, Maharaj A, Mahlangu B, Maponga T, Mahlakwane K, Makatini Z, Marais G, Maruapula D, Masupu K, Matshaba M, Mayaphi S, Mbhele N, Mbulawa MB, Mendes A, Mlisana K, Mnguni A, Mohale T, Moir M, Moruisi K, Mosepele M, Motsatsi G, Motswaledi MS, Mphoyakgosi T, Msomi N, Mwangi PN, Naidoo Y, Ntuli N, Nyaga M, Olubayo L, Pillay S, Radibe B, Ramphal Y, Ramphal U, San JE, Scott L, Shapiro R, Singh L, Smith-Lawrence P, Stevens W, Strydom A, Subramoney K, Tebeila N, Tshiabuila D, Tsui J, van Wyk S, Weaver S, Wibmer CK, Wilkinson E, Wolter N, Zarebski AE, Zuze B, Goedhals D, Preiser W, Treurnicht F, Venter M, Williamson C, Pybus OG, Bhiman J, Glass A, Martin DP, Rambaut A, Gaseitsiwe S, von Gottberg A, de Oliveira T, Nature (2022), doi: 10.1038/s41586-022-04411-y:.

HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens..
Fischer W, Giorgi EE, Chakraborty S, Nguyen K, Bhattacharya T, Theiler J, Goloboff PA, Yoon H, Abfalterer W, Foley BT, Tegally H, San EJ, de Oliveira T, Network for Genomic Surveillance in South Africa (NGS-SA), Gnanakaran S, Korber B, Cell Host Microbe (2022), 29(7):1093-1110. doi: 10.1016/j.chom.2021.05.012:.

HIV-1 drug resistance in adults and adolescents on protease inhibitor-based antiretroviral treatment in KwaZulu-Natal Province, South Africa.
Chimukangara B, Lessells RJ, Sartorius B, Gounder L, Manyana S, Pillay M, Singh L, Giandhari J, Govender K, Samuel R, Msomi N, Naidoo K, de Oliveira T, Moodley P, Parboosing R, J Glob Antimicrob Resist. (2021), S2213-7165(21)00249-6. doi: 10.1016/j.jgar.2021.10.023. :.

Acquired HIV drug resistance and virologic monitoring in a HIV hyper-endemic setting in KwaZulu-Natal Province, South Africa..
Chimukangara B, Lessells RJ, Singh L, Grigalionyte I, Yende-Zuma N, Adams R, Dawood H, Dlamini L, Buthelezi S, Chetty S, Diallo K, Duffus WA, Mogashoa M, Hagen MB, Giandhari J, de Oliveira T, Moodley P, Padayatchi N, Naidoo K., AIDS Res Ther. (2021), 18(1):74. doi: 10.1186/s12981-021-00393-5:.

Temporal Changes in Vaginal Microbiota and Genital Tract Cytokines Among South African Women Treated for Bacterial Vaginosis.
Mtshali A, San JE, Osman F, Garrett N, Balle C, Giandhari J, Onywera H, Mngomezulu K, Mzobe G, de Oliveira T, Rompalo A, Mindel A, Abdool Karim SS, Ravel J, Passmore JS, Abdool Karim Q, Jaspan HB, Liebenberg LJP, Ngcapu S, Front Immunol. (2021), 12:730986. doi: 10.3389/fimmu.2021.730986.:.

Immunogenicity of SARS-CoV-2 infection and Ad26.CoV2.S vaccination in people living with HIV. .
Khan K, Lustig G, Bernstein M, Archary D, Cele S, Karim F, Smith M, Ganga Y, Jule Z, Reedoy K, Miya Y, Mthabela N, Magula NP, Lessells R, de Oliveira T, Gosnell BI, Karim SA, Garrett N, Hanekom W, Gail-Bekker L, Gray G, Blackburn JM, Moosa MS, Sigal A; COMMIT-KZN Team, Clin Infect Dis. (2021), 10:ciab1008. doi: 10.1093/cid/ciab1008:.

Escape from recognition of SARS-CoV-2 Beta variant spike epitopes but overall preservation of T cell immunity.
Riou C, Keeton R, Moyo-Gwete T, Hermanus T, Kgagudi P, Baguma R, Valley-Omar Z, Smith M, Tegally H, Doolabh D, Iranzadeh A, Tyers L, Mutavhatsindi H, Tincho MB, Benede N, Marais G, Chinhoyi LR, Mennen M, Skelem S, du Bruyn E, Stek C; SA-CIN†, de Oliveira T, Williamson C, Moore PL, Wilkinson RJ, Ntusi NAB, Burgers WA, Science Translational Medicine (2021), DOI: 10.1126/scitranslmed.abj6824:.

The political theatre of the UK’s travel ban on South Africa.
Mendelson M, Venter F, Moshabela M, Gray G, Blumberg L, de Oliveira T, Madhi SA, The Lancet (2021), https://doi.org/10.1016/ S0140-6736(21)02752-5:.

Track Omicron’s spread with molecular data.
Scott L, Hsiao NY, Moyo S, Singh L, Tegally H, Dor G, Maes P, Pybus OG, Kraemer MUG, Semenova E, Bhatt S, Flaxman S, Faria NR, de Oliveira T, Science (2021), DOI: 10.1126/science.abn4543 :.

Africa: tackle HIV and COVID-19 together.
Msomi N, Lessells RJ, Mlisana K, de Oliveira T, Nature (2021), 600, 33-36, doi: https://doi.org/10.1038/d41586-021-03546-8:.

SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection.
Cele S, Jackson L, Khoury DS, Khan K, Moyo-Gwete T, Tegally H, San JE, Cromer D, Scheepers C, Amoako DG, Karim F, Bernstein M, Lustig G, Archary D, Smith M, Ganga Y, Jule Z, Reedoy K, Hwa SH, Giandhari J, Blackburn JM, Gosnell BI, Abdool Karim SS, Hanekom W; NGS-SA; COMMIT-KZN Team, von Gottberg A, Bhiman JN, Lessells RJ, Moosa MS, Davenport MP, de Oliveira T, Moore PL, Sigal A, Nature (2021), doi: 10.1038/s41586-021-04387-1.:.

Rapid replacement of the Beta variant by the Delta variant in South Africa.
Tegally H, Wilkinson E, Althaus C, Giovanetti M, San J, Giandhari J, Pillay S, Naidoo Y, Ramphal U, Msomi N, Mlisana K, Amoako D, Everatt J, Mohale T, Nguni A, Mahlangu B, Ntuli N, Khumalo Z, Makatini Z, Wolter N, Scheepers C, Ismail A, Doolabh D, Joseph R, Strydom A, Mendes A, Davids M, Mayaphi S, Ramphal Y, Maharaj A, Karim W, Tshiabuila D, Anyaneji U, Singh L, Engelbrecht S, Fonseca V, Marais K, Korsman S, Hardie D, Hsiao N, Maponga T, van Zyl G, Marais G, Iranzadeh A, Martin D, Alcantara L, Bester P, Nyaga M, Subramoney K, Treurnicht F, Venter M, Goedhals D, Preiser W, Bhiman J, vonGottberg A, Williamson C, Lessells R, de Oliveira T, medRxiv (2021), MEDRXIV-2021-264018v1:.

The biological and clinical significance of emerging SARS- CoV-2 variants.
Tao T, Tzou1 PL, Nouhin J, Gupta RK, de Oliveira T, Pond SLK, Fera D, Shafer RW, Nature Reviews Genetics (2021), https://doi.org/10.1038/s41576-021-00408- x:.

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa .
Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, Martin DP, Rasmussen DA, Zekri AN, Sangare AK, Ouedraogo AS, Sesay AK, Priscilla A, Kemi AS, Olubusuyi AM, Oluwapelumi AOO, Hammami A, Amuri AA, Sayed A, Ouma AEO, Elargoubi A, Ajayi NA, Victoria AF, Kazeem A, George A, Trotter AJ, Yahaya AA, Keita AK, Diallo A, Kone A, Souissi A, Chtourou A, Gutierrez AV, Page AJ, Vinze A, Iranzadeh A, Lambisia A, Ismail A, Rosemary A, Sylverken A, Femi A, Ibrahimi A, Marycelin B, Oderinde BS, Bolajoko B, Dhaala B, Herring BL, Njanpop-Lafourcade BM, Kleinhans B, McInnis B, Tegomoh B, Brook C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Peyrefitte C, Daubenberger C, Morang'a CM, Nokes DJ, Amoako DG, Bugembe DL, Park D, Baker D, Doolabh D, Ssemwanga D, Tshiabuila D, Bassirou D, Amuzu DSY, Goedhals D, Omuoyo DO, Maruapula D, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong'era EM, Ngabana EN, Shumba E, El Fahime E, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Leendertz F, Ajili F, Enoch FO, Wasfi F, Abdelmoula F, Mosha FS, Takawira FT, Derrar F, Bouzid F, Onikepe F, Adeola F, Muyembe FM, Tanser F, Dratibi FA, Mbunsu GK, Thilliez G, Kay GL, Githinji G, van Zyl G, Awandare GA, Schubert G, Maphalala GP, Ranaivoson HC, Lemriss H, Anise H, Abe H, Karray HH, Nansumba H, Elgahzaly HA, Gumbo H, Smeti I, Ayed IB, Odia I, Ben Boubaker IB, Gaaloul I, Gazy I, Mudau I, Ssewanyana I, Konstantinus I, Lekana-Douk JB, Makangara JC, Tamfum JM, Heraud JM, Shaffer JG, Giandhari J, Li J, Yasuda J, Mends JQ, Kiconco J, Morobe JM, Gyapong JO, Okolie JC, Kayiwa JT, Edwards JA, Gyamfi J, Farah J, Nakaseegu J, Ngoi JM, Namulondo J, Andeko JC, Lutwama JJ, O'Grady J, Siddle K, Adeyemi KT, Tumedi KA, Said KM, Hae-Young K, Duedu KO, Belyamani L, Fki-Berrajah L, Singh L, Martins LO, Tyers L, Ramuth M, Mastouri M, Aouni M, El Hefnawi M, Matsheka MI, Kebabonye M, Diop M, Turki M, Paye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina M, Nwando M, Owusu M, Wiley MR, Youtchou MT, Ayekaba MO, Abouelhoda M, Seadawy MG, Khalifa MK, Sekhele M, Ouadghiri M, Diagne MM, Mwenda M, Allam M, Phan MVT, Abid N, Touil N, Rujeni N, Kharrat N, Ismael N, Dia N, Mabunda N, Hsiao NY, Silochi NB, Nsenga N, Gumede N, Mulder N, Ndodo N, Razanajatovo NH, Iguosadolo N, Judith O, Kingsley OC, Sylvanus O, Peter O, Femi O, Idowu O, Testimony O, Chukwuma OE, Ogah OE, Onwuamah CK, Cyril O, Faye O, Tomori O, Ondoa P, Combe P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Dussart P, Bester PA, Mbala PK, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Carr RAA, El Kabbaj S, Gargouri S, Masmoudi S, Sankhe S, Lawal SB, Kassim S, Trabelsi S, Metha S, Kammoun S, Lemriss S, Agwa SHA, Calvignac-Spencer S, Schaffner SF, Doumbia S, Mandanda SM, Aryeetey S, Ahmed SS, Elhamoumi S, Andriamandimby S, Tope S, Lekana-Douki S, Prosolek S, Ouangraoua S, Mundeke SA, Rudder S, Panji S, Pillay S, Engelbrecht S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Aanniz T, Mohale T, Le-Viet T, Schindler T, Anyaneji UJ, Chinedu U, Ramphal U, Jessica U, George U, Fonseca V, Enouf V, Gorova V, Roshdy WH, Ampofo WK, Preiser W, Choga WT, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Sall AA, Rebai A, von Gottberg A, Kouriba B, Williamson C, Bridges DJ, Chikwe I, Bhiman JN, Mine M, Cotten M, Moyo S, Gaseitsiwe S, Saasa N, Sabeti PC, Kaleebu P, Tebeje YK, Tessema SK, Happi C, Nkengasong J, de Oliveira T, Science (2021), DOI: 10.1126/science.abj4336:.

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages .
Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ; NGS-SA; COVID-19 Genomics UK (COG-UK), Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. , Cell (2021), https://doi.org/10.1016/j.cell.2021.09.003:.

Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing. .
Singh L, Anyaneji UJ, Ndifon W, Turok N, Mattison SA, Lessells R, Sinayskiy I, San EJ, Tegally H, Barnett S, Lorimer T, Petruccione F, de Oliveira T. , Scientific Reports (2021), 11(1):17793. doi: 10.1038/s41598-021-96934-z:.

Two doses of SARS-CoV-2 vaccination induce robust immune responses to emerging SARS-CoV-2 variants of concern.
Skelly DT, Harding AC, Gilbert-Jaramillo J, Knight ML, Longet S, Brown A, Adele S, Adland E, Brown H, Medawar Laboratory Team, Tipton T, Stafford L, Mentzer AJ, Johnson SA, Amini A, OPTIC, Tan TK, Schimanski L, Huang K-Y A, Rijal P, PITCH Study Group, C-MORE/PHOSP-C Group, Frater J, Goulder P, Conlon CP, Jeffery K, Dold C, Pollard AJ, Sigal A, de Oliveira T, Townsend AR, Klenerman P, Dunachie SJ, Barnes E, Carroll MW, James WS, Nature Communications (2021), https://doi.org/10.1038/s41467-021-25167-5:.

West Nile Virus in Brazil.
Costa WE, Giovanetti M, Silva Catenacci L, Fonseca V, Aburjaile FF, Chalhoub FLL, Xavier J, Campos de Melo Iani F, da Cunha E Silva Vieira MA, Freitas Henriques D, Medeiros DBA, Guedes MIMC, Senra Álvares da Silva Santos B, Gonçalves Silva AS, de Pino Albuquerque Maranhão R, da Costa Faria NR, Farinelli de Siqueira R, de Oliveira T, Ribeiro Leite Jardim Cavalcante K, Oliveira de Moura NF, Pecego Martins Romano A, Campelo de Albuquerque CF, Soares Feitosa LC, Martins Bayeux JJ, Bertoni Cavalcanti Teixeira R, Lisboa Lobato O, da Costa Silva S, Bispo de Filippis AM, Venancio da Cunha R, Lourenco J, Alcantara LCJ, Pathogens (2021), 10(7):896. doi: 10.3390/pathogens10070896:.

Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains.
Faulkner N, Ng KW, Wu MY, Harvey R, Margaritis M, Paraskevopoulou S, Houlihan C, Hussain S, Greco M, Bolland W, Warchal S, Heaney J, Rickman H, Spyer M, Frampton D, Byott M, de Oliveira T, Sigal A, Kjaer S, Swanton C, Gandhi S, Beale R, Gamblin SJ, McCauley JW, Daniels RS, Howell M, Bauer D, Nastouli E, Kassiotis G, Elife (2021), 10:e69317. doi: 10.7554/eLife.69317:.

Short Report: Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil.
Tosta S, Giovanetti M, Brandão Nardy V, Reboredo de Oliveira da Silva L, Kelly Astete Gomez M, Gomes Lima J, Wanderley Cardoso C, Oliveira Silva T, Sao Pedro Leal de Souza M, Presta Dia PH, Fonseca V, de Oliveira T, Lourenco J, Carlos Junior Alcantara L, Pereira F, Leal A, PLoS Negl Trop Dis. (2021), 15(7):e0009591. doi: 10.1371/journal.pntd.0009591:.

Molecular surveillance of the on-going SARS-COV-2 epidemic in Ribeirao Preto City, Brazil.
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Promoting Responsible Research and Innovation (RRI) During Brazilian Activities of Genomic and Epidemiological Surveillance of Arboviruses.
Giovanetti M, Alcantara LCJ, Dorea AS, Ferreira QR, Marques WA, Barros JJF, Adelino TER, Tosta S, Fritsch H, Iani FCM, Mares-Guia MA, Salgado A, Fonseca V, Xavier J, Lopes EN, Soares GC, Amarante MFC, Azevedo V, Kruger A, Matta GC, Paineiras-Domingos LL, Colonnello C, Filippis AMB, Montesano C, Colizzi V, Barreto FK, Front. Public Health (2021), v. 9, p. 1, 2021.:.

Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS-CoV-2 mitigation strategies.
Lopes EN, Fonseca V, Frias D, Tosta S, Salgado A, Vialle RA, Toscano PES, Barreto FK, Azevedo VA, Guarino M, Angeletti S, Ciccozzi M, Alcantara LCJ, Giovanetti M, J Med Virol (2021), 2021; 1- 5. DOI: 10.1002/jmv.27056:.

Short report: Introduction of chikungunya virus ECSA genotype into the Brazilian Midwest and its dispersion through the Americas.
de Oliveira EC, Fonseca V, Xavier J, Adelino T, Morales Claro I, Fabri A, Macario EM, Viniski AE, Souza CLC, Costa ESG, Sousa CS, Duarte FGD, Medeiros AC, Albuquerque CFC, Cunha RV, Moura NFO, Filippis AMB, de Oliveira T, Lourenço J, Abreu AL, Alcantara LCJ, Giovanetti M , PLoS Negl Trop Dis (2021), 2021; 15(4): e0009290. https://doi.org/10.1371/journal.pntd.0009290:.

Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil.
Nonaka CV, Franco M, Gräf T, Lorenzo BC, Avila MR, Sousa K, Neiva LMC, Fonseca V, Mendes AVA, Aguiar RS, Giovanetti M, Freitas BS., Emerg Infect Dis (2021), 2021;27(5):1522-1524.:.

Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil.
Adelino TÉR, Giovanetti M, Fonseca V, Xavier J, de Abreu ÁS, do Nascimento VA, Demarchi LHF, Oliveira MAA, da Silva VL, de Mello ALES, Cunha GM, Santos RH, de Oliveira EC, Júnior JAC, de Melo Iani FC, de Filippis AMB, de Abreu AL, de Jesus R, de Albuquerque CFC, Rico JM, do Carmo Said RF, Silva JA, de Moura NFO, Leite P, Frutuoso LCV, Haddad SK, Martínez A, Barreto FK, Vazquez CC, da Cunha RV, Araújo ELL, de Oliveira Tosta SF, de Araújo Fabri A, Chalhoub FLL, da Silva Lemos P, de Bruycker-Nogueira F, de Castro Lichs GG, Zardin MCSU, Segovia FMC, Gonçalves CCM, Grillo ZDCF, Slavov SN, Pereira LA, Mendonça AF, Pereira FM, de Magalhaes JJF, Dos Santos Júnior ACM, de Lima MM, Nogueira RMR, Góes-Neto A, de Carvalho Azevedo VA, Ramalho DB, Oliveira WK, Macario EM, de Medeiros AC, Pimentel V; Latin American Genomic Surveillance Arboviral Network, Holmes EC, de Oliveira T, Lourenco J, Alcantara LCJ, Nature Communications (2021), 12(1):2296. doi: 10.1038/s41467-021-22607-0.:.

SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy.
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Peer-mediated HIV assisted partner services to identify and link to care HIV-positive and HCV-positive people who inject drugs: a cohort study protocol.
Monroe-Wise A, Mbogo L, Guthrie B, Bukusi D, Sambai B, Chohan B, Scott J, Cherutich P, Musyoki H, Bosire R, Dunbar M, Macharia P, Masyuko S, Wilkinson E, De Oliveira T, Ludwig-Barron N, Sinkele B, Herbeck J, Farquhar C, BMJ Open (2021), 11(4):e041083. doi: 10.1136/bmjopen-2020-041083:.

Epidemiologic History and Genetic Diversity Origins of Chikungunya and Dengue Viruses, Paraguay.
Graf T, Vazquez C, Giovanetti M, de Bruycker-Nogueira F, Fonseca V, Claro IM, de Jesus JG, Gómez A, Xavier J, de Mendonça MCL, Villalba S, Torales J, Gamarra ML, Thézé J, de Filippis AMB, Azevedo V, de Oliveira T, Franco L, de Albuquerque CFC, Irala S, Holmes EC, Méndez Rico JA, Alcantara LCJ, Emerg Infect Dis (2021), 27(5):1393-1404. doi: 10.3201/eid2705.204244:.

Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant.
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Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2.
Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, Goes de Jesus J, Morales Claro I, Magalhaes Ferreira G, Crispim MAE, Brazil-UK CADDE Genomic Network, Singh L, Tegally H, Anyaneji UJ; Network for Genomic Surveillance in South Africa, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JR, Grubaugh ND, PLoS Biology (2021), DOI: 10.1371/journal.pbio.3001236:.

Genomic surveillance activities unveil the introduction of the SARS-CoV-2 B.1.525 variant of interest in Brazil: Case report.
Pereira F, Tosta S, Lima MM, Reboredo de Oliveira da Silva L, Nardy VB, Gomez MKA, Lima JG, Fonseca V, de Oliveira T, Lourenco J, Alcantara LC Jr, Giovanetti M, Leal A, J Med Virol (2021), doi: 10.1002/jmv.27086:.

Genomic evidence of SARS-CoV-2 reinfection case with the emerging B.1.2 variant in Brazil.
Fonseca V, de Jesus R, Adelino T, Reis AB, de Souza BB, Ribeiro AA, Guimaraes NR, Livorati MTFP, Neto DFL, Kato RB, Portela LMO, Dutra LH, Freitas C, de Abreu AL, Filizzola ERM, de Medeiros AC, Iani FCM, Carvalho G, Lourenco J, de Oliveira T, Alcantara LCJ, Giovanetti M, Journal of Infection (2021), DOI:https://doi.org/10.1016/j.jinf.2021.05.014:.

Transmission dynamics of SARS-CoV-2 within-host diversity in two major hospital outbreaks in South Africa.
San JE, Ngcapu S, Kanzi AM, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Nelson CW, Smidt W, Kiran AM, Chimukangara B, Pillay S, Singh L, Fish M, Gazy I, Martin DP, Khanyile K, Lessells R, de Oliveira T., Virus Evolution (2021), 7(1):veab041. doi: 10.1093/ve/veab041. eCollection 2021 Jan:.

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2.
O'Toole A, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbruck L, Stadler T, Swiss Viollier Sequencing Consortium, Parisi A, Bianco A, Garcia de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha Rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, SEARCH Alliance San Diego, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA), de Oliveira T, Faria N, Rambaut A, Kraemer MUG., Wellcome Open Res (2021), 6:121. doi: 10.12688/wellcomeopenres.16661.1. eCollection 2021.:.

SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse.
Konings F, Perkins MD, Kuhn JH, Pallen MJ, Alm EJ, Archer BN, Barakat A, Bedford T, Bhiman JN, Caly L, Carter LL, Cullinane A, de Oliveira T, Druce J, El Masry I, Evans R, Gao GF, Gorbalenya AE, Hamblion E, Herring BL, Hodcroft E, Holmes EC, Kakkar M, Khare S, Koopmans MPG, Korber B, Leite J, MacCannell D, Marklewitz M, Maurer-Stroh S, Rico JAM, Munster VJ, Neher R, Munnink BO, Pavlin BI, Peiris M, Poon L, Pybus O, Rambaut A, Resende P, Subissi L, Thiel V, Tong S, van der Werf S, von Gottberg A, Ziebuhr J, Van Kerkhove MD, Nature Microbiology (2021), https://doi.org/10.1038/s41564-021-00932-w:.

Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection.
Karim F, Moosa MYS, Gosnell BI, Cele S, Giandhari J, Pillay S, Tegally H, Wilkinson E, San JE, Msomi N, Mlisana K, Khan K, Bernstein M, Manickchund N, Singh L, Ramphal U, COMMIT-KZN Team, Hanekom W, Lessells RJ, Sigal A, de Oliveira T, medRxiv (2021), submitted, available on KRISP website.:.

Cross-Reactive Neutralizing Antibody Responses Elicited by SARS-CoV-2 501Y.V2 (B.1.351).
Moyo-Gwete T, Madzivhandila M, Makhado Z, Ayres F, Mhlanga D, Oosthuysen B, Lambson EB, Kgagudi P, Tegally H, Iranzadeh A, Doolabh D, Tyers L, Chinhoyi RL, Mennen M, Skelm S, Wibmer K C, Bhiman N J, Ueckermann V, Rossouw T, Boswell M, de Oliveira T, Williamson T, Burgers W, Ntusi N, Morris L, Moore P, NEJM (2021), DOI: 10.1056/NEJMc2104192:.

Multiple Early Introductions of SARS-CoV-2 to Cape Town, South Africa.
Engelbrecht S, Delaney K, Kleinhans B, Wilkinson E, Tegally H, Stander T, van Zyl G, Preiser W, de Oliveira T, Viruses (2021), 22;13(3):526. doi: 10.3390/v13030526:.

Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma..
Cele S, Gazy I, Jackson L, Hwa SH, Tegally H, Lustig G, Giandhari J, Pillay S, Wilkinson E, Naidoo Y, Karim F, Ganga Y, Khan K, Bernstein M, Balazs AB, Gosnell BI, Hanekom W, Moosa MS; NGS-SA; COMMIT-KZN Team, Lessells R, de Oliveira T, Sigal A., Nature (2021), DOI: 10.1038/s41586-021-03471-w:.

A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa.
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New SARS-CoV-2 Variants — Clinical, Public Health, and Vaccine Implications.
Karim SSA, de Oliveira T, NEJM (2021), DOI: 10.1056/NEJMc2100362:.

Appropriate names for COVID-19 variants.
Karim SSA, de Oliveira T, Loots G, Science (2021), http://science.sciencemag.org/content/371/6535/1215:.

Safety and efficacy of the ChAdOx1 nCoV-19 (AZD1222) Covid-19 vaccine against the B.1.351 variant in South Africa.
Madhi SA, Baillie VL, Cutland CL, Voysey M, KoenAL, Fairlie L, Padayachee SD, Dheda K, Barnabas SL, Bhorat QE, Briner C, Kwatra G, Ahmed K, Aley P, Bhikha S, Bhiman JN, Bhorat AE, du plessis J, Esmail A, Groenewald M, Horne E, Hwa S-H, Jose A, Lambe T, Laubscher M, Malahleha M, Masenya M, Masilela M, McKenzie S, Molapo K, Moultrie A, Oelofse S, Pate Fl, Pillay S, Rhead S, Rodel H, Rossouw L, Taoushanis C, Tegally H, Thombrayil A, van Eck S, Wibmer C, Durham NM, Kelly EJ, Villafana T, Gilbert S, Pollard AJ, de Oliveira T, Moore PL, Sigal A, Izu A, NGS-SA, Wits VIDA COVID vaccine trial group , NEJM (2021), https://doi.org/10.1056/NEJMoa2102214:.

Voices of Biotech Research.
Annabi N, Baker M, Boettiger A, Chakraborty D, Chen Y, Corbett K, Correia B, Dahlman J, de Oliveira T, Ertuerk A, Yanik M, Henaff E, Huch M, Iliev I, Jacobs T, Junca H, Keung A, Kolodkin-Gal I, Krishnaswamy S, Lancaster M, Macosko E, Martínez-Núñez M, Miura K, Molloy J, Cruz A, Platt R, Posey A, Shao H, Simunovic M, Slavov N, Takebe T, Vandenberghe L, Varshney R, Wang J, Nature Biotechnology (2021), https://doi.org/10.1038/s41587-021-00847-1:.

Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein.
Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana K, Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass A, Engelbrecht S, Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao M, Korsman S, Davies M, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer Cos, Sewell B, Lourenco J, Alcantara Ls, Kosakovsky Pond S, Weaver S, Martin D, Lessells R, Bhiman J, Williamson C, de Oliveira T, Nature (2021), https://doi.org/10.1038/s41586-021-03402-9:.

Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil.
Iani FCM, Giovanetti M, Fonseca V, Souza WM, Adelino TER, Xavier J, Jesus JG, Pereira MA, Silva MVF, Costa AVB, Silva EC, Mendes MCO, Filippis AMB, Albuquerque CFC, Abreu AL, Oliveira MAA, Alcantara LCJ, Faria NR., Infect Genet Evol (2021), S1567-1348(21)00082-4:.

SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma.
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Dengue Virus Serotype 2 Intrahost Diversity in Patients with Different Clinical Outcomes.
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Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil.
Xavier J, Fonseca V, Bezerra JF, Do Monte Alves M, Mares-Guia NA, Claro IM, De Jesus R, Adelino T, Araujo E, Cavalcante KRLJ, Tosta S, De Souza TR, Moreira Da Cruz FE, De Araujo Fabri A, de Oliveira EC, De Moura NFO, Do Carmo Said RF, De Albuquerque CFC, Azevedo V, de Oliveira T, De Filippis AMB, Venancio Da Cunha R, Luz KG, Giovanetti M, Alcantara L, IJID (2021), S1201-9712(21)00037-0:.

Sixteen novel lineages of SARS-CoV-2 in South Africa.
Tegally H, Wilkinson E, Lessells R, Giandhari J, Pillay S, Msomi N, Mlisana K, Bhiman J, Gottberg A, Walaza S, Fonseca V, Allam M, Ismail A, Engelbrecht S, Van Zyl G, Preiser W, Williamson C, Pettruccione F, Sigal A, Gazy I, Hardie D, Hsiao M, Martin D, York D, Goedhals D, San EJ, Giovanetti M, Lourenco J, Alcantara LCJ, de Oliveira T, Nature Medicine (2021), https://doi.org/10.1038/s41591-021-01255-3:.

Escape of SARS-CoV-2 501Y.V2 variants from neutralization by convalescent plasma.
Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, Giandhari J, Pillay S, Wilkinson E, Naidoo Y, Karim F, Ganga Y, Khan K, Balazs AB, Gosnell BI, Hanekom W, Moosa MYS, NGS-SA, COMMIT-KZN Team, Lessells R, de Oliveira T, Sigal A, medRxiv (2021), 250224v1-Sigal:.

Co-Circulation of Two Independent Clades and Persistence of CHIKV-ECSA Genotype during Epidemic Waves in Rio de Janeiro, Southeast Brazil. .
Fabri AA, Rodrigues CDS, Santos CC, Chalhoub FLL, Sampaio AS, Faria NRC, Torres MC, Fonseca V, Brasil P, Calvet G, Alcantara LCJ, Filippis AMB, Giovanetti M, Bruycker-Nogueira F., Pathogens (2020), 2020, 9(12), 984:.

Pan-genomics of virus and its applications.
Giovanetti M, Salgado A, Fonseca V, Tosta SFO, Xavier J, de Jesus JG, Iani FCM, Adelino TER, Barreto FK, Faria NR, De Oliveira T, Alcantara LCJ., Academic Press (2020), 2020; Pages 237-250:.

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa.
Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San E, Msomi N, Mlisana K, Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass A, Engelbrecht S, Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao M, Korsman S, Davies M, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer Cos, Sewell B, Lourenço J, Alcantara Ls, Kosakovsky Pond S, Weaver S, Martin D, Lessells R, Bhiman J, Williamson C, de Oliveira T, medRxiv (2020), https://doi.org/10.1101/2020.12.21.20248640:.

Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase.
Siedner MJ, Moorhouse MA, Simmons B, de Oliveira T, Lessells R, Giandhari J, Kemp SA, Chimukangara B, Akpomiemie G, Serenata Cm, Venter WDF, HillA, Gupta RK, Nature Communications (2020), https://doi.org/10.1038/s41467-020-19801-x:.

HIV infection alters SARS-CoV-2 responsive immune parameters but not clinical outcomes in COVID-19 disease.
Karim F, Gazy I, Cele S, Zungu Y, Krause R, Bernstein M, Ganga Y, Rodel H, Mthabela N, Mazibuko M, Khan K, Muema D, Ramjit D, Lustig G, Ndung'u T, Hanekom W, Gosnell BI, COMMIT-KZN Team, Wong E, de Oliveira T, Moosa MYS, Leslie A, Kløverpris H, Sigal A, medRxiv (2020), doi: https://doi.org/10.1101/2020.11.23.20236828:.

High Resolution analysis of Transmission Dynamics of Sars-Cov-2 in Two Major Hospital Outbreaks in South Africa Leveraging Intrahost Diversity.
San EJ, Ngcapu S, Kanzi A, Tegally H, Fonseca V, Giandhari J, Wilkinson E, Chimukangara B, Pillay S, Singh L, Fish M, Gazy I, Khanyile KS, Lessells R, de Oliveira T, medRxiv (2020), https://doi.org/10.1101/2020.11.15.20231993:.

Cost-effectiveness of public health strategies for COVID-19 epidemic control in South Africa: a microsimulation modelling study.
Reddy KP, Shebl FM, Foote JHA, Harling G, Scott JA, Panella C, Fitzmaurice KP, Flanagan C, Hyle EP, Neilan AM, Mohareb AM, Bekker L-G, Lessells R, Ciaranello AL, Wood R, Losina E, Freedberg KA, Kazemian P, Siedner MJ , Lancet Global Health (2020), https://doi.org/10.1016/S2214-109X(20)30452-6:.

Portable sequencing in the field and the classroom: a retrospective examination of the circulation of DENV1 and DENV2 in Brazil.
Adelino TER, Giovanetti M, Fonseca V, Xavier J, Salgado A, Nascimento V, Demarchi LH, Oliveira M, Silva V, Mello A, Muricy G, Santos R, Oliveira E, Junior JAC, Iani F, de Filippis AMB, Abreu AL, de Jesus R, Albuquerque CF, Rico J, Said R, Silva J, Moura N, Leite P, Vinhal L, Kashima S, Martinez AA, Khouri F, Vazquez C, Cunha R, Araujo E, Tosta S, Fabri A, Chalhoub F, Lemos P, de Bruycker-Nogueira F, Lichs G, Zardin M, Cardozo F, Goncalves C, Fernandez Z, Slavov S, Pereira LA, Mendonca AF, Pereira F, Magalhaes J, de Castro A, Lima M, Nogueira R, Goes A, Azevedo V, Ramalho D, Oliveira W, Medeiros A, Pimentel V, Latin American Genomic Surveillance Arboviral Network, Holmes EC, de Oliveira T, Lourenco J, Alcantara LCJ, medRxiv (2020), https://doi.org/10.1101/2020.09.01.20183301:.

Adding a Voice to the Unique Ethical Considerations in Molecular HIV Surveillance.
Mutenherwa F, Wassenaar D, de Oliveira T, The American Journal of Bioethics (2020), https://doi.org/10.1080/15265161.2020.1806399:.

Detection of Inducible Replication-Competent HIV-1 Subtype C Provirus Despite Long-Term Antiretroviral Treatment in Perinatally Infected Adolescents in Botswana.
Koofhethile CK, Moyo S, Kotokwe KP, Chang C, Mokgethi P, Muchoba L, Mokgweetsi S, Makhema J, Lockman S, Gaseitsiwe S, de Oliveira T, Essex M, Shapiro R, Kanki P, Novitsky V, AIDS Res Hum Retroviruses (2020), doi: 10.1089/AID.2020.0097:.

Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance.
Kanzi AM, San JE , Chimukangara B, Wilkinson E, Ramsuran V, de Oliveira T, Frontiers in Genetics (2020), 11: 1250, https://doi.org/10.3389/fgene.2020.544162:.

Impact of pretreatment low-abundance HIV-1 drug-resistant variants on virological failure among HIV-1/TB-co-infected individuals.
Chimukangara B, Giandhari J, Lessells J, Yende-Zuma N, Sartorius B, Samuel R, Khanyile KS, Stray-Pedersen B, Moodley P, Metzner KJ, Padayatchi N, Naidoo K, de Oliveira T, Journal of Antimicrobial Chemotherapy (2020), 75, 11:3319–3326, https://doi.org/10.1093/jac/dkaa343.

Unlocking the efficiency of genomics laboratories with robotic liquid-handling.
Tegally H, San JE, Giandhari J, de Oliveira T, BMC Genomics (2020), 729:https://doi.org/10.1186/s12864-020-07137-1.

Fatal outcome of chikungunya virus infection in Brazil.
Lima STS, Souza WM, Cavalcante JW, Candido DS, Fumagalli MJ, Carrera JP, Mello LMS, Araújo FMC, Ramalho ILC, Barreto FKA, Braga DNM, Simião AR, Silva MJM, Oliveira RMAB, Lima CPS, Lins CS, Barata RR, Melo MNP, Souza MPC, Franco LM, Távora FRF, Lemos DRQ, Alencar CHM, Jesus R, Fonseca V, Dutra LH, Abreu AL, Araújo ELL, Freitas ARR, Júnior JLSGV, Pybus OG, Figueiredo LTM, Faria NR, Nunes MRT, Cavalcanti LPG, Miyajima F., Clinical Infectious Diseases (2020), ciaa1038 DOI: https://doi.org/10.1093/cid/ciaa1038:.

Yellow fever transmission in non-human primates, Bahia, Northeastern Brazil.
Goes de Jesus J, Gräf T, Giovanetti M, Mares-Guia MA, Xavier J, Lima Maia M, Fonseca V, Fabri A, Santos RF, Pereira FM, Santos LFO, Silva LRO, Maia ZPG, Cerqueira JXG, Thèze J, Abade L, Cordeiro MCS, Torquato SSC, Santana EB, Silva NSJ, Dourado RSO, Alves AB, Guedes AS, Filho PMC, Faria NR, Campelo de Albuquerque CF, Abreu AL, Romano APM, Croda J, Said RFC, Cunha GM, Cerqueira JMF, Mello ALS, Filippis AMB, Alcantara LCJ., PLoS Negl Trop Dis (2020), 14(8): e0008405. https://doi.org/10.1371/journal.pntd.0008405:14(8): e0008405.

Accelerating genomics-based surveillance for COVID-19 response in Africa.
Tessema SK, Inzaule SC, Christoffels A, Kebede Y, de Oliveira T, Ouma AEO, Happi CT, Nkengasong JN, Lancet Microbe (2020), https://doi.org/10.1016/S2666-5247(20)30117-8:.

A genomics network established to respond rapidly to public health threats in South Africa.
Msomi N, Mlisana K, Willianson C, Bhiman JN, Goedhals D, Engelbrecht S, Van Zyl G, Preiser W, Hardie D, Hsiao M, Mulder N, Martin D, Christoffels A, York D, Giandhari J, Wilkinson E, Pillay S, Tegally H, James SE, Kanzi A, Lessells RJ, de Oliveira T, Lancet Microbe (2020), https://doi.org/10.1016/S2666-5247(20)30116-6:.

Exposure to waste sites and their impact on health: a panel and geospatial analysis of nationally representative data from South Africa, 2008–2015.
Tomita A, Cuadros DF, Burns JK, Tanser F, Slotow R, Lancet Planetary Health (2020), 4: e223–34:.

Neurocognitive functioning in MDR-TB patients with and without HIV in KwaZulu-Natal, South Africa.
Ramlall S, Lessells RJ, Naidu T, Mthembu SS, Padayatchi N, Burns JK, Tomita A, Tropical Medicine and International Health (2020), 25 (8), 919–927 :.

Opportunities and Challenges in HIV Treatment as Prevention Research: Results from the ANRS 12249 Cluster-Randomized Trial and Associated Population Cohort.
Tanser F, Kim H-Y, Vandormael A, Iwuji C, Barnighausen T, Current HIV/AIDS Reports (2020), 17:97–108 https://doi.org/10.1007/s11904-020-00487-1:.

Spatial clustering of food insecurity and its association with depression: a geospatial analysis of nationally representative South African data, 2008–2015.
Tomita A, Cuadros DF, Mabhaudhi T, Sartorius B, Ncama BP, Dangour AD, Tanser F, Modi AT, Slotow R, Burns JK , Scientific Reports (2020), (2020) 10:13771. https://doi.org/10.1038/s41598-020-70647-1:.

HIV incidence declines in a rural South African population: a G-imputation approach for inference.
Vandormael A, Cuadros D, Dobra A, Barnighausen T, Tanser F, BMC Public Health (2020), 20:1205 https://doi.org/10.1186/s12889-020-09193-4:.

Attitude and preferences towards oral and long-acting injectable antipsychotics in patients with psychosis in KwaZulu-Natal, South Africa.
Roopun KR, Tomita A, Paruk S, South African Journal of Psychiatry (2020), 6(0), a1509. https://doi.org/ 10.4102/sajpsychiatry. v26i0.1509:.

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic.
Pillay S, Giandhari J, Tegally H, Wilkinson E, Chimukangara B, Lessells R, Mattison S, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LCJ, de Oliveira T, Genes (2020), doi: https://doi.org/10.3390/genes11080949:11(8), 949.

Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report.
Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, Lourenço J, Chimukangara B, Lessells R, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LCJ, Petruccione F, de Oliveira T, IJID (2020), doi: https://doi.org/10.1016/j.ijid.2020.11.128:.

Protocol: Leveraging a demographic and health surveillance system for Covid-19 Surveillance in rural KwaZulu-Natal.
Siedner MJ, Harling G, Derache A, Smit T, Khoza T, Gunda R, Mngomezulu T, Gareta D, Majozi N, Ehlers E, Dreyer J, Nxumalo S, Dayi N, Ording-Jesperson G, Ngwenya N, Wong E, Iwuji C, Shahmanesh M, Seeley J, de Oliveira T, Ndung'u T, Hanekom W, Herbst K, Wellcome Open Research (2020), 5:109:.

The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing.
Xavier J, Giovanetti M, Adelino T, Fonseca V, da Costa AVB, Ribeiro AA, Felicio KN, Duarte CG, Silva MVF, Salgado A, Lima MT, de Jesus D, Fabri A, Zoboli CFS, Santos TGS, Iani F,de Filippis AMB, de Siqueira AMNT, de Abreu AL, de Azevedo V, Ramalho DBR, de Albuquerque CFC, de Oliveira T, Holmes EC, Lourenco J, Alcantara CLJ, Oliveira MAA, Emerging Microbes & Infections (2020), vol 9:.

Pervasive and non-random recombination in near full-length HIV genomes from Uganda.
Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa JM, Yebra G, Gomez LRE, Frampton D, Gall A, Kellam P, de Oliveira T, Bbosa N, Nsubuga RN, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh-Brown AJ, Virus Evolution (2020), veaa004, https://doi.org/10.1093/ve/veaa004:.

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
Mavian C, Pond SK, Marini S, Magalis BR, Vandamme A-M, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TTY, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M, Proceedings of the National Academy of Sciences (PNAS) (2020), doi:10.1073/pnas.2007295117:.

Priorities among HIV-positive individuals for tuberculosis preventive therapies.
Kim HY, Hanrahan CF, Dowdy DW, Martinson NA, Golub JE, Bridges JFP, Int J Tuberc Lung Dis (2020), 24(4):396-402. doi: 10.5588/ijtld.18.0740:.

Naturally Occurring Oxazole-Containing Peptides.
Mhlongo JT, Brasil E, de la Torre BG, Albericio F, Mar Drugs (2020), 18(4). pii: E203. doi: 10.3390/md18040203:.

New Genomes from The Congo Basin Expand History of CRF01_AE Origin and Dissemination.
Junqueira DM, Wilkinson E, Vallari AS, Deng XD, Achari A, Yu G, McArthur C, Kaptué L, Mbanya DN, Chiu C, Cloherty G, de Oliveira T, Rodgers MA, AIDS Res Hum Retroviruses (2020), doi: 10.1089/AID.2020.0031:.

Symptom and digital chest X-ray TB screening in South African prisons: yield and cost-effectiveness.
Kim HY, Zishiri V, Page-Shipp L, Makgopa S, Churchyard GJ, Dowdy D, Charalambous S, Hoffmann CJ, Int J Tuberc Lung Dis. (2020), 24(3):295-302. doi: 10.5588/ijtld.19.0214:.

Breaking a Couple: Disulfide Reducing Agents.
Mthembu SN, Sharma A, Albericio F, de la Torre BG, Chembiochem. (2020), doi: 10.1002/cbic.202000092:.

Protocol for synthesis of di- and tri-substituted s-triazine derivatives.
El-Faham A, Sharma A, Farooq M, Almarhoon Z, Alhameed RA, Wadaan MAM, de la Torre BG, Albericio F, MethodsX (2020), 7:100825. doi: 10.1016/j.mex.2020.100825:.

Assessing a diagnosis tool for bacterial vaginosis.
Singh R, Ramsuran V, Mitchev N, Niehaus AJ, Han KSS, Osman F, Ngcapu S, Karim SA, Rompalo A, Garrett N, Mlisana K, Eur J Clin Microbiol Infect Dis. (2020), doi: 10.1007/s10096-020-03862-3.:.

Impact of community piped water coverage on re-infection with urogenital schistosomiasis in rural South Africa.
Mogeni P, Vandormael A, Cuadros D, Appleton C, Tanser F, Elife (2020), 9. pii: e54012. doi: 10.7554/eLife.54012:.

Nine newly identified individuals refine the phenotype associated with MYT1L mutations.
Windheuser IC, Becker J, Cremer K, Hundertmark H, Yates LM, Mangold E, Peters S, Degenhardt F, Ludwig KU, Zink AM, Lessel D, Bierhals T, Herget T, Johannsen J, Denecke J, Wohlleber E, Strom TM, Wieczorek D, Bertoli M, Colombo R, Hempel M, Engels H, Am J Med Genet A. (2020), 182(5):1021-1031. doi: 10.1002/ajmg.a.61515:.

The Pharmaceutical Industry in 2019. An Analysis of FDA Drug Approvals from the Perspective of Molecules.
de la Torre BG, Albericio F, Molecules (2020), 25(3). pii: E745. doi: 10.3390/molecules25030745:.

Maternal variants within the apolipoprotein L1 gene are associated with preeclampsia in a South African cohort of African ancestry.
Thakoordeen-Reddy S, Winkler C, Moodley J, David V, Binns-Roemer E, Ramsuran V, Naicker T, Eur J Obstet Gynecol Reprod Biol. (2020), 246:129-133. doi: 10.1016/j.ejogrb.2020.01.034:.

Genome-wide Association Study Identifies HLA-DPB1 as a Significant Risk Factor for Severe Aplastic Anemia.
Savage SA, Viard M, O'hUigin C, Zhou W, Yeager M, Li SA, Wang T, Ramsuran V, Vince N, Vogt A, Hicks B, Burdett L, Chung C, Dean M, de Andrade KC, Freedman ND, Berndt SI, Rothman N, Lan Q, Cerhan JR, Slager SL, Zhang Y, Teras LR, Haagenson M, Chanock SJ, Spellman SR, Wang Y, Willis A, Askar M, Lee SJ, Carrington M, Gadalla SM, Am J Hum Genet. (2020), 106(2):264-271. doi: 10.1016/j.ajhg.2020.01.004:.

Migration and first-year maternal mortality among HIV-positive postpartum women: A population-based longitudinal study in rural South Africa.
Kim HY, Dobra A, Tanser F, PLoS Med (2020), https://doi.org/10.1371/journal.pmed.1003085:.

Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region.
Giovanetti M, Faria NR, Lourenco J, Goes de Jesus J, Xavier J, Claro IM, Kraemer MUG, Fonseca V, Dellicour S, Theze J, da Silva Salles F, Graef T, Silveira PP, Costa de Souza V, Alves do Nascimento V, Campos de Melo Iani F, Castilho-Martins EA, Cruz LN, Wallau G, Fabri A, Levy F, Quick J, de Azevedo V, Santana Aguiar R, de Oliveira T, Botto de Menezes C, da Costa Castilho M, Matos Terra T, Souza da Silva M, Bispo de Filippis M, Luiz de Abreu A, Kleber Oliveira W, Croda J, Campelo de Albuquerque CF, Nunes MRT, Cerdeira Sabino E, Loman N, Gomes Naveca F, Pybus O, Alcantara LC., Cell Reports (2020), https://doi.org/10.1016/j.celrep.2020.01.085:.

Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes.
Cleemput S, Dumon W, Fonseca V, Abdool Karim W, Giovanetti M, Alcantara LCJ, Deforche K, de Oliveira T, Bioinformatics (2020), btaa145, https://doi.org/10.1093/bioinformatics/btaa145:.

Genome-wide Association Study Identifies HLA-DPB1 as a Significant Risk Factor for Severe Aplastic Anemia.
Savage SA, Viard M, O'hUigin C, Zhou W, Yeager M, Li SA, Wang T, Ramsuran V, Vince N, Vogt A, Hicks B, Burdett L, Chung C, Dean M, de Andrade KC, Freedman ND, Berndt SI, Rothman N, Lan Q, Cerhan JR, Slager SL, Zhang Y, Teras LR, Haagenson M, Chanock SJ, Spellman SR, Wang Y, Willis A, Askar M, Lee SJ, Carrington M, Gadalla SM, Am J Hum Genet. (2020), pii: S0002-9297(20)30004-5. doi: 10.1016/j.ajhg.2020.01.004:.

Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls.
San EJ, Baichoo S, Kanzi A, Moosa Y, Lessells R, Fonseca V, Mogaka J, Power R, de Oliveira T, Front. Microbiol. (2020), https://doi.org/10.3389/fmicb.2019.03119:.

Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda.
Ratmann O, Kagaayi J, Hall M, Golubchick T, Kigozi G, Xi X, Wymant C, Nakigozi G, Abeler-Dörner L, Bonsall D, Gall A, Hoppe A, Kellam P, Bazaale J, Kalibbala S, Laeyendecker O, Lessler J, Nalugoda F, Chang LW, de Oliveira T, Pillay D, Quinn TC, Reynolds SJ, Spencer SEF, Ssekubugu R, Serwadda D, Wawer MJ, Gray RH, Fraser C, Grabowski MK, on behalf of the Rakai Health Sciences Program and the Pangea HIV Consortium, Lancet HIV (2020), https://doi.org/10.1016/ S2352-3018(19)30378-9:.

The state of the HIV epidemic in rural KwaZulu-Natal, South Africa: a novel application of disease metrics to assess trajectories and highlight areas for intervention.
Vandormael A, Cuadros D, Kim HY, Bärnighausen T, Tanser F, Int J Epidemiol. (2020), pii: dyz269. doi: 10.1093/ije/dyz269:.

HIV seroconcordance among heterosexual couples in rural KwaZulu-Natal, South Africa: a population-based analysis.
Kim HY, Harling G, Vandormael A, Tomita A, Cuadros DF, Bärnighausen T, Tanser F, J Int AIDS Soc. (2020), 23(1):e25432. doi: 10.1002/jia2.25432:.

Persistence of chikungunya ECSA genotype and local outbreak in an upper medium class neighborhood in Northeast Brazil.
Goes de Jesus J, da Luz Wallau G, Lima Maia M, Xavier J, Oliveira Lima MA, Fonseca V, Salgado de Abreu A, Fraga de Oliveira Tosta S, Ramos do Amaral H, Andrade Barbosa Lima I, Viana Silva P, Carlos Dos Santos D, Sousa de Oliveira A, Campos de Souza S, Barreto Falcão M, Cerqueira E, Ceschini Machado L, Sobral MC, Teodoro Rezende TM, Ribeiro Pereira M, Mota Pereira F, Pereira Gusmão Maia Z, Freitas de Oliveira França R, Luiz de Abreu A, Campelo de Albuquerque E Melo CF, Rodrigues Faria N, Venâncio da Cunha R, Giovanetti M, Alcantara LCJ, PLoS ONE (2020), 15(1):e0226098. doi: 10.1371/journal.pone.0226098:.

Return of the founder Chikungunya virus to its place of introduction into Brazil is revealed by genomic characterization of exanthematic disease cases..
Pereira Gusmão Maia Z, Mota Pereira F, do Carmo Said RF, Fonseca V, Gräf T, de Bruycker Nogueira F, Brandão Nardy V, Xavier J, Lima Maia M, Abreu AL, Campelo de Albuquerque CF, Kleber Oliveira W, Croda J, de Filippis AMB, Venancio Cunha R, Lourenço J, de Oliveira T, Faria NR, Junior Alcantara LC, Giovanetti M, Emerg Microbes Infect. (2020), 9(1):53-57. doi: 10.1080/22221751.2019.1701954:.

Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression.
Morais-Rodrigues F, Silv Erio-Machado R, Kato RB, Rodrigues DLN, Valdez-Baez J, Fonseca V, San EJ, Gomes LGR, Dos Santos RG, Vinicius Canário Viana M, da Cruz Ferraz Dutra J, Teixeira Dornelles Parise M, Parise D, Campos FF, de Souza SJ, Ortega JM, Barh D, Ghosh P, Azevedo VAC, Dos Santos MA, Gene (2020), 144168. doi: 10.1016/j.gene.2019.144168.:.

Depression, anxiety and stress symptoms in patients presenting with dyspepsia at a regional hospital in KwaZulu-Natal province.
Tshabalala SJ, Tomita A, Ramlall S , South African Journal of Psychiatry (2019), 2019;25(0), a1382. https://doi.org/10.4102/ sajpsychiatry.v25i0.1382:25(0), a1382. https://doi.org/10.4102/ sajpsychiatry.v25i0.1382.

Synthesis and Antimicrobial Activity of a New Series of Thiazolidine-2,4-diones Carboxamide and Amino Acid Derivatives.
Abd Alhameed R, Almarhoon Z, Bukhari SI, El-Faham A, de la Torre BG, Albericio F, Molecules (2019), 25(1). pii: E105. doi: 10.3390/molecules25010105:.

Emtricitabine-induced pure red cell aplasia.
Manickchund N, du Plessis C, John MA, Manzini TC, Gosnell BI, Lessells RJ, Moosa YS, South Afr J HIV Med (2019), 20(1):983. doi: 10.4102/sajhivmed.v20i1.983:.

The pharmacokinetic properties of HIV-1 protease inhibitors: A computational perspective on herbal phytochemicals..
Kehinde I, Ramharack P, Nlooto M, Gordon M, Heliyon (2019), 5(10):e02565. doi: 10.1016/j.heliyon.2019.e02565:.

Declines in HIV incidence among men and women in a South African population-based cohort.
Vandormael A, Akullian A, Siedner M, de Oliveira T, Bärnighausen T, Tanser F, Nature Communications (2019), 10(1):5482. doi: 10.1038/s41467-019-13473-y:.

Undetectable proviral deoxyribonucleic acid in an adolescent perinatally infected with human immunodeficiency virus-1C and on long-term antiretroviral therapy resulted in viral rebound following antiretroviral therapy termination: A case report with implications for clinical care.
Koofhethile CK, Moyo S, Kotokwe KP, Mokgethi P, Muchoba L, Mokgweetsi S, Gaolathe T, Makhema J, Shapiro R, Lockman S, Kanki P, Essex M, Gaseitsiwe S, de Oliveira T, Novitsky V, Medicine (Baltimore) (2019), 98(47):e18014. doi: 10.1097/MD.0000000000018014:.

Trends in HIV Prevention, Treatment, and Incidence in a Hyperendemic Area of KwaZulu-Natal, South Africa .
Kharsany ABM, Cawood C, Lewis L, Yende-Zuma N, Khanyile D, Puren A, Madurai S, Baxter C, George G, Govender K, Beckett S, Samsunder N, Toledo C, Ayalew KA, Diallo K, Glenshaw M, Herman-Roloff A, Wilkinson E, de Oliveira T, Abdool Karim SS, Abdool Karim Q, JAMA Network Open (2019), 2(11):e1914378. doi:10.1001/jamanetworkopen.2019.14378:.

Yellow fever virus re-emergence and spread in Southeast Brazil, 2016-2019.
Giovanetti M, Lima de Mendonça MC, Fonseca V, Mares-Guia MA, Fabri A, Xavier J, Goes de Jesus J, Gräf T, Damasceno Dos Santos Rodrigues C, Cardoso Dos Santos C, Alves Sampaio S, Lowen Levy Chalhoub F, Bruycker Nogueira F, Theze J, Pecego Martins Romano A, Garkauskas Ramos D, Luiz de Abreu A, Kleber Oliveira W, do Carmo Said RF, Campelo de Alburque CF, de Oliveira T, Fernandes CA, Ferreira Aguiar S, Chieppe A, Carvalho Sequeira P, Rodrigues Faria N, Venâncio Cunha R, Alcantara LCJ, Bispo de Filippis AM., Journal of Virology (2019), JVI.01623-19. doi: 10.1128/JVI.01623-19:.

Recent levels and trends in HIV incidence rates among adolescent girls and young women in ten high-prevalence African countries: a systematic review and meta-analysis.
Birdthistle I, Tanton C, Tomita A, de Graaf K, Schaffnit SB, Tanser F, Slaymaker E, Lancet Global Health (2019), 7: e1521–40:.

Ethical issues associated with HIV molecular epidemiology: a qualitative exploratory study using inductive analytic approaches.
Mutenherwa F, Wassenaar DR, de Oliveira T, BMC Medical Ethics (2019), 20:67, https://doi.org/10.1186/s12910-019-0403-9:.

Mosquito-Borne Viral Diseases: Control and Prevention in the Genomics Era.
Fonseca V, Xavier J, San EJ, de Oliveira T, de Filippis AMB, Alcantara LCJ, Giovanetti M, Current Topics in the Epidemiology of Vector-Borne (2019), DOI: 10.5772/intechopen.88769:.

Investigating Triorthogonal Chemoselectivity. Effect of Azide Substitution on the Triazine Core..
Sharma A, Sheyi R, Kumar A, El-Faham A, de la Torre BG, Albericio F., Org Lett. (2019), doi: 10.1021/acs.orglett.9b02878:.

The Role of Adverse Childhood Experiences on Perinatal Substance Use Behaviour in KwaZulu-Natal Province, South Africa..
Bhengu BS, Tomita A, Mashaphu S, Paruk S, AIDS Behav. (2019), doi: 10.1007/s10461-019-02661-y:.

Space-time clustering of recently diagnosed tuberculosis and impact of ART scale-up: Evidence from an HIV hyper-endemic rural South African population.
Tomita A, Smith CM, Lessells RJ, Pym A, Grant AD, de Oliveira T, Tanser F , Scientific Reports (2019), https://doi.org/10.1038/s41598-019-46455-7:.

Whole genome sequencing for drug-resistant tuberculosismanagement in South Africa: What gaps would this address andwhat are the challenges to implementation?.
Dlamini MT, Lessells R, Iketleng T, de Oliveira T, Journal of Clinical TB and Other Mycobacterial Dis (2019), https://doi.org/10.1016/j.jctube.2019.100115:.

The clinical presentation caused by truncating CHD8 variants..
Douzgou S, Liang HW, Metcalfe K, Somarathi S, Tischkowitz M, Mohamed W, Kini U, McKee S, Yates L, Bertoli M, Lynch SA, Holder S; Deciphering Developmental Disorders Study, Banka S, Clin Genet. (2019), 96(1):72-84. doi: 10.1111/cge.13554:.

Phylodynamic analyses of Brazilian antigenic variants of infectious bursal disease virus.
de Fraga AP, Graf T, Coltro VP, Ikuta N, Fonseca ASK, Majó N, Lunge VR, Infect Genet Evol. (2019), 73:159-166. doi: 10.1016/j.meegid.2019.04.020:.

Predictors of quality of life among community psychiatric patients in a peri-urban district of Gauteng Province, South Africa..
Mapatwana D, Tomita A, Burns JK, Robertson LJ, Int J Soc Psychiatry (2019), 65(4):322-332. doi: 10.1177/0020764019842291.

Bypassing Osmotic Shock Dilemma in a Polystyrene Resin Using the Green Solvent Cyclopentyl methyl Ether (CPME): A Morphological Perspective..
Al Musaimi O, El-Faham A, Almarhoon Z, Basso A, de la Torre BG, Albericio F, Polymers (Basel) (2019), 11(5). pii: E874. doi: 10.3390/polym11050874.:.

High rate of occult hepatitis B virus infection in hemodialysis units of KwaZulu-Natal, South Africa.
Msomi N, Ndlovu K, Giandhari J, Wilkinson E, Parboosing R, Zungu S, Mlisana K, J Med Virol. (2019), doi: 10.1002/jmv.25510:.

Circulation of chikungunya virus East/Central/South African lineage in Rio de Janeiro, Brazil.
Xavier J, Giovanetti M, Fonseca V, Thézé J, Gräf T, Fabri A, Goes de Jesus J, Lima de Mendonça MC, Damasceno Dos Santos Rodrigues C, Mares-Guia MA, Cardoso Dos Santos C, Fraga de Oliveira Tosta S, Candido D, Ribeiro Nogueira RM, Luiz de Abreu A, Kleber Oliveira W, Campelo de Albuquerque CF, Chieppe A, de Oliveira T, Brasil P, Calvet G, Carvalho Sequeira P, Rodrigues Faria N, Bispo de Filippis AM, Alcantara LCJ, PLoS One (2019), 14(6):e0217871:.

A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes.
Fonseca V, Libin PJK, Theys K, Faria NR, Nunes MRT, Restovic MI, Freire M, Giovanetti M, Cuypers L, Nowé A, Abecasis A, Deforche K, Santiago GA, Siqueira IC, San EJ, Machado KCB, Azevedo V, Filippis AMB, Cunha RVD, Pybus OG, Vandamme AM, Alcantara LCJ, de Oliveira T, PLoS Negl Trop Dis (2019), 13(5):e0007231: doi: 10.1371/journal.pntd.0007231.

Neurocognitive Impairment Risk Among Individuals With Multiple Drug-Resistant Tuberculosis and Human Immunodeficiency Virus Coinfection: Implications for Systematic Linkage to and Retention of Care in Tuberculosis/Human Immunodeficiency Virus Treatment..
Tomita A, Ramlall S, Naidu T, Mthembu SS, Padayatchi N, Burns JK, J Nerv Ment Dis (2019), 207(4):307-310.

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.
Ratmann O, Grabowski KM, Hall M, Golubchik T, Wymant C, Abeler-Dorner L, Bonsall D, Hoppe A, Leigh Brown A, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi G, Quinn TC, Wawer MJ, Laeyendecker O, Serwadda D, Gray RH, Fraser C, PANGEA Consortium and Rakai Health Sciences Program , Nature Communications (2019), 10:1411:https://doi.org/10.1038/s41467-019-09139-4.

Trends in Pretreatment HIV-1 Drug Resistance in Antiretroviral Therapy-naive Adults in South Africa, 2000–2016: A Pooled Sequence Analysis.
Chimukangara B, Lessells RJ, Rhee S-Y, Giandhari J, Kharsany ABM, Naidoo K, Lewis L, Cawood C, Khanyile D, Ayalew KA, Diallo K, Samuel R, Hunt G, Vandormael A, Stray-Pedersen B, Gordon M, Makadzange T, Kiepiela P, Ramjee G, Ledwaba J, Kalimashe M, Morris L, Parikh UM, Mellors JW, Shafer RW, Katzenstein D, Moodley P, Gupta RK, Pillay D, Karim SSA, de Oliveira T, EClinicalMedicine (Lancet) (2019), DOI:https://doi.org/10.1016/j.eclinm.2019.03.006:.

Effects of Migration on Risky Sexual Behavior and HIV Acquisition in South Africa: A Systematic Review and Meta-analysis, 2000-2017..
Dzomba A, Tomita A, Govender K, Tanser F, AIDS Behav. (2019), doi: 10.1007/s10461-018-2367-z:.

Major depression and household food insecurity among individuals with multidrug-resistant tuberculosis (MDR-TB) in South Africa..
Tomita A, Ramlall S, Naidu T, Mthembu SS, Padayatchi N, Burns JK, Soc Psychiatry Psychiatr Epidemiol. (2019), doi: 10.1007/s00127-019-01669-y:.

Effect of ART scale-up and female migration intensity on risk of HIV acquisition: results from a population-based cohort in KwaZulu-Natal, South Africa.
Dzomba A, Tomita A, Vandormael A, Govender K, Tanser F, BMC Public Health (2019), 19(1):196:doi: 10.1186/s12889-019-6494-x.

Effects of genetic variability on rifampicin and isoniazid pharmacokinetics in South African patients with recurrent tuberculosis.
Naidoo A, Chirehwa M, Ramsuran V, McIlleron H, Naidoo K, Yende-Zuma N, Singh R, Ncgapu S, Adamson J, Govender K, Denti P, Padayatchi N, Pharmacogenomics (2019), doi: 10.2217/pgs-2018-0166:.

Estimating trends in the incidence rate with interval censored data and time-dependent covariates.
Vandormael A, Tanser F, Cuadros D, Dobra A, Stat Methods Med Res (2019), 962280219829892. doi: 10.1177/0962280219829892:.

The Pharmaceutical Industry in 2018. An Analysis of FDA Drug Approvals from the Perspective of Molecules..
de la Torre B, Albericio F, Molecules (2019), 24(4): pii: E809. doi: 10.3390/molecules24040809..

Factors influencing HIV-1 phylogenetic clustering.
Junqueira DM, Sibisi Z, Wilkinson E, de Oliveira T, Curr Opin HIV AIDS (2019), doi: 10.1097/COH.0000000000000540:.

Early Genomic Detection of Cosmopolitan Genotype of Dengue Virus Serotype 2, Angola, 2018.
Hill SC, Neto de Vasconcelos J, Granja BG, Thézé J, Jandondo D, Neto Z, Mirandela M, Sebastião CDS, Cândido ALM, Clemente C, Pereira da Silva S, de Oliveira T, Pybus OG, Faria NR, Afonso JM, Emerg Infect Dis. (2019), 25(4):784-787.

The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis.
Wilkinson E, Junqueira DM, Lessells R, Engelbrecht S, van Zyl G, de Oliveira T, Salemi M, Scientific Reports (2019), 9:2640:https://doi.org/10.1038/s41598-018-37749-3.

Sociobehavioral and community predictors of unsuppressed HIV viral load: multilevel results from a hyperendemic rural South African population.
Tomita A, Vandormael A, Bärnighausen T, Phillips A, Pillay D, De Oliveira T, Tanser F, AIDS (2019), 33(3):559–569.

Spatial structure of depression in South Africa: A longitudinal panel survey of a nationally representative sample of households.
Cuadros DF, Tomita A, Vandormael A, Slotow R, Burns JK, Tanser F, Scientific Reports (2019), 9(1):979:doi.org/10.1038/s41598-018-37791-1.

Early detection of emergent extensively drug resistant tuberculosis (XDR-TB) by flow cytometry-based phenotyping and whole genome sequencing.
O'Donnell MR, Larsen MH, Brown TS, Jain P, Munsamy V, Wolf A, Uccellini L, Karim F, de Oliveira T, Mathema B, Jacobs WR, Pym A, Antimicrob Agents Chemother. (2019), pii: AAC.01834-18.:doi: 10.1128/AAC.01834-18.

Experts' Perspectives on Key Ethical Issues Associated With HIV Phylogenetics as Applied in HIV Transmission Dynamics Research.
Mutenherwa F, Wassenaar DR, de Oliveira T, J Empir Res Hum Res Ethics (2019), 1556264618809608. doi: 10.1177/1556264618809608:.

Moderate to high levels of pre-treatment HIV drug resistance in KwaZulu-Natal Province, South Africa.
Chimukangara B, Kharsany AB, Lessells RJ, Naidoo K, Rhee SY, Manasa J, Gräf T, Lewis L, Cawood C, Khanyile D, Diallo K, Ayalew KA, Shafer R, Hunt G, Pillay D, Abdool SK, de Oliveira T, AIDS Research and Human Retroviruses (2019), https://doi.org/10.1089/AID.2018.0202:.

Genome Detective: An Automated System for Virus Identification from High-throughput sequencing data..
Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara LC, Vanden Eynden E, Vandamme AM, Deforche K, de Oliveira T, Bioinformatics (2019), doi: 10.1093/bioinformatics/bty695:.

Phylodynamic analysis and molecular diversity of the avian infectious bronchitis virus of chickens in Brazil.
Fraga AP, Graf T, Pereira CS, Ikuta N, Fonseca ASK, Lunge VR, Infect Genet Evol. (2018), 61:77-83.

Spatiotemporal and demographic history of the HIV-1 circulating recombinant form CRF31_BC in Brazil.
Fritsch HM, Almeida SEM, Pinto AR, Graf T, Infect Genet Evol. (2018), 61:113-118.

2017 FDA Peptide Harvest.
Al Musaimi O, Al Shaer D, de la Torre BG, Albericio F, Pharmaceuticals (Basel) (2018), 11(2):doi: 10.3390/ph11020042.

Inferring population dynamics of HIV-1 subtype C epidemics in Eastern Africa and Southern Brazil applying different Bayesian phylodynamics approaches.
Mir D, Graf T, Esteves de Matos Almeida S, Pinto AR, Delatorre E, Bello G, Scientific Reports (2018), 8(1):877:doi: 10.1038/s41598-018-26824-4.

Exploiting the Thiobarbituric Acid Scaffold for Antibacterial Activity.
Sharma A, Noki S, Zamisa SJ, Hazzah HA, Almarhoon ZM, El-Faham A, de la Torre BG, Albericio F, ChemMedChem (2018), 13(18):1923-1930.

Formation of N?-terminal 2-dialkyl amino oxazoles from guanidinated derivatives under mild conditions.
Abdel Monaim SAH, Mhlongo JT, Kumar A, El-Faham A, Albericio F, de la Torre BG, Org Biomol Chem (2018), 16(31):5661-5666.

Bacteria Hunt Bacteria through an Intriguing Cyclic Peptide.
Abdel Monaim SAH, Somboro AM, El-Faham A, de la Torre BG, Albericio F, ChemMedChem (2018), 14(1):24-51.

Identification of patients with recent-onset psychosis in KwaZulu Natal, South Africa: a pilot study with traditional health practitioners and diagnostic instruments.
Veling W, Burns JK, Makhathini EM, Mtshemla S, Nene S, Shabalala S, Mbatha N, Tomita A, Baumgartner J, Susser I, Hoek HW, Susser E, Soc Psychiatry Psychiatr Epidemiol (2018), doi: 10.1007/s00127-018-1623-x:.

Exploring the Orthogonal Chemoselectivity of 2,4,6-Trichloro-1,3,5-Triazine (TCT) as a Trifunctional Linker With Different Nucleophiles: Rules of the Game..
Sharma A, El-Faham A, de la Torre BG, Albericio F, Front Chem. (2018), 6:516:doi: 10.3389/fchem.2018.00516.

Crystal structure, spectroscopic studies and theoretical studies of thiobarbituric acid derivatives: understanding the hydrogen-bonding patterns..
Sharma A, Zamisa SJ, Noki S, Almarhoon Z, El-Faham A, de la Torre BG, Albericio F., Acta Crystallogr C Struct Chem (2018), 74(Pt 12)::1703-1714.

Perfluorophenyl Derivatives as Unsymmetrical Linkers for Solid Phase Conjugation.
Alapour S, Sharma A, de la Torre BG, Ramjugernath D, Koorbanally NA, Albericio F, Front Chem (2018), 6:589: doi: 10.3389/fchem.2018.00589.

Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa.
Rasmussen DA, Wilkinson E, Vandormael A, Tanser F, Pillay D, Stadler T, de Oliveira T, Virus Evolution (2018), 4(2): vey037:.

Mycobacterium tuberculosis Next-Generation Whole Genome Sequencing: Opportunities and Challenges.
Iketleng T, Lessells R, Dlamini MT, Mogashoa T, Mupfumi L, Moyo S, Gaseitsiwe S, de Oliveira T, Tuberculosis Research and Treatment (2018), https://doi.org/10.1155/2018/1298542:.

Combining Phylogenetic and Network Approaches to Identify HIV-1 Transmission Links in San Mateo County, California.
Dalai SC, Junqueira DM, Wilkinson E, Mehra R, Kosakovsky Pond SL, Levy V, Israelski D, de Oliveira T, Katzenstein D, Front. Microbiol. (2018), https://doi.org/10.3389/fmicb.2018.02799:.

2018 update to the HIV-TRePS system: the development of new computational models to predict HIV treatment outcomes, with or without a genotype, with enhanced usability for low-income settings.
Revell AD, Wang D, Perez-Elias MJ, Wood R, Cogill D, Tempelman H, Hamers RL, Reiss P,, van Sighem AI, Rehm CA, Pozniak A, Montaner JSG, Lane HC, Larder BA, RDI Data and Study Group Collaborators: Reiss P, van Sighem A, Montaner J, Harrigan R, Rinke de Wit T, Hamers R, Sigaloff K, Agan B, Marconi V, Wegner S, Sugiura W, Zazzi M, Kaiser R, Schuelter E, Streinu-Cercel A, Alvarez-Uria G, Perez-Elias MJ, de Oliveira T, Gatell J, Lazzari E, Gazzard B, Nelson M, Pozniak A, Mandalia S, Smith C, Ruiz L, Clotet B, Staszewski S, Torti C, Lane C, Metcalf J, Rehm CA, Perez-Elias MJ, Vella S, Dettorre G, Carr A, Norris R, Hesse K, Vlahakis E, Tempelman H, Barth R, Wood R, Morrow C, Cogill D, Hoffmann C, Ene L, Dragovic G, Diaz R, Sucupira C, Sued O, Cesar C, Madero JS, Balavskrishnan P, Saravanan S, Emery S, Cooper D, Torti C, Baxter J, Monno L, Torti C, Gatell J, Clotet B, Picchio G, deBethune MP, Perez-Elias MJ, Emery S, Khabo P, Ledwaba L , J Antimicrob Chemother (2018), 73(8):2186–2196.

Community engagement with HIV drug adherence in rural South Africa: a transdisciplinary approach.
Treffry-Goatley A, Lessells RJ, Moletsane R, de Oliveira T, Gaede B, BMJ Med Humanit (2018), 44:239–246.

HIV drug resistance in sub-Saharan Africa: public health questions and the potential role of real-world data and mathematical modelling.
de waal R, Lessells R, Hauser A, Kouyos R, Davies M-A, Egger M, Wandeler G, for ieDeA-Southern Africa, Journal of Virus Eradication (2018), 4(Supplement 2): :55–58.

Predicted antiviral activity of tenofovir versus abacavir in combination with a cytosine analogue and the integrase inhibitor dolutegravir in HIV-1-infected South African patients initiating or failing first-line ART.
Derache A, Iwuji CC, Danaviah S, Giandhari J, Marcelin AG, Calvez V, de Oliveira T, Dabis F, Pillay D, Gupta RK, J Antimicrob Chemother. (2018), doi: 10.1093/jac/dky428:doi:10.1093/jac/dky428.

Intimate partner violence among HIV-serodiscordant couples in Durban, South Africa.
Mashaphu S, Wyatt GE, Gomo E, Tomita A, SAMJ (2018), 108(11):960-964.

Evidence on the Association Between Cigarette Smoking and Incident Depression From the South African National Income Dynamics Study 2008–2015: Mental Health Implications for a Resource-Limited Setting.
Tomita A, Manuel JI, Nicotine & Tobacco Research (2018), doi:10.1093/ntr/nty163:.

In Vitro Antibacterial Activity of Teixobactin Derivatives on Clinically Relevant Bacterial Isolates.
Ramchuran EJ, Somboro AM, Abdel Monaim SAH, Amoako DG, Parboosing R, Kumalo HM, Agrawal N, Albericio F, Torre BG, Bester LA, Front Microbiol. (2018), 9:1535.

Impact of next generation sequencing defined HIV pre-treatment drug resistance on virological outcomes in the ANRS 12249 treatment as prevention trial. .
Derache A, Iwuji CC, Baisley K, Danaviah S, Marcelin AG, Calvez V, de Oliveira T, Dabis F, Porter K, Pillay D, Clin Infect Dis (2018), doi: 10.1093/cid/ciy881:.

Pre-eclampsia: the role of highly active antiretroviral therapy and immune markers.
Phoswa WN, Naicker T, Ramsuran V, Moodley J, Inflamm Res. (2018), doi: 10.1007/s00011-018-1190-3:.

Recurrent tuberculosis among HIV-coinfected patients: a case series from KwaZulu-Natal.
Naidoo K, Dookie N, Naidoo K, Yende-Zuma N, Chimukangara B, Bhushan A, Govender D, Gengiah S, Padayatchi N, Infect Drug Resist (2018), 11:1413-1421.

Sexual trauma and post-traumatic stress among African female refugees and migrants in South Africa.
Mhlongo MD, Tomita A, Thela L, Maharaj V, Burns JK, S Afr J Psychiatr (2018), 24:1208:10.4102/sajpsychiatry.v24.i0.1208.

Genomic and epidemiological monitoring of yellow fever virus transmission potential.
Faria NR, Kraemer MUG, S C Hill, J Goes de Jesus, R S Aguiar, F C M Iani, J Xavier, J Quick, L du Plessis, S Dellicour, J Thézé, R D O Carvalho, G Baele, C-H Wu, P P Silveira, M B Arruda, M A Pereira, G C Pereira, J Lourenço1, U Obolski, L Abade, T I Vasylyeva, M Giovanetti, D Yi, D J Weiss, G R W Wint, F M Shearer, S Funk, B Nikolay, Fonseca V, T E R Adelino, M A A Oliveira, M V F Silva, L Sacchetto, P O Figueiredo, I M Rezende, E M Mello, R F C Said, D A Santos, M L Ferraz, M G Brito, L F Santana, M T Menezes, R M Brindeiro, A Tanuri, F C P dos Santos, M S Cunha, J S Nogueira, I M Rocco, A C da Costa, S C V Komninakis, V Azevedo, A O Chieppe, E S M Araujo, M C L Mendonça, C C dos Santos, C D dos Santos, A M Mares-Guia, R M R Nogueira, P C Sequeira, R G Abreu, M H O Garcia, A L Abreu, O Okumoto, E G Kroon, C F C de Albuquerque, K Lewandowski, S T Pullan, M Carroll, de Oliveira T, E C Sabino, R P Souza, M A Suchard, P Lemey, G S Trindade, B P Drumond, A M B Filippis, N J Loman, S Cauchemez, Alcantara LCJ, Pybus OG , Science (2018), DOI: 10.1126/science.aat7115:.

Patterns of genomic site inheritance in HIV-1M inter-subtype recombinants delineate the most likely genomic sites of subtype-specific adaptation.
Tongo M, de Oliveira T, Martin DP, Virus Evolution (2018), Volume 4, Issue 1, 1 January 2018, vey015:.

Dolutegravir for first-line antiretroviral therapy in low-income and middle-income countries: uncertainties and opportunities for implementation and research.
Dorward J, Lessells R, Drain PK, Naidoo K, de Oliveira T, Pillay Y, Karim SSA, Garrett N, Lancet HIV (2018), https://doi.org/10.1016/S2352-3018(18)30093-6:.

Renewing Felsenstein's phylogenetic bootstrap in the era of big data.
Lemoine F, Domelevo Entfellner JB, Wilkinson E, Correia D, Davila Felipe M, de Oliveira T, Gascuel O, Nature (2018), :doi:10.1038/s41586-018-0043-0.

Ethical issues associated with HIV phylogenetics in HIV transmission dynamics research: A review of the literature using the Emanuel Framework.
Mutenherwa F, Wassenaar DR, de Oliveira T, Developing World Bioethics (2018), https://doi.org/10.1111/dewb.12191:.

Spatial clustering of drug-resistant tuberculosis in Hlabisa subdistrict, KwaZulu-Natal, 2011-2015.
Smith CM, Lessells R, Grant AD, Herbst K, Tanser F, Int J Tuberc Lung Dis. (2018), 1;22(3):287-293. doi: 10.5588/ijtld.17.0457:.

Effect of genetic variation in UGT1A and ABCB1 on moxifloxacin pharmacokinetics in South African patients with tuberculosis.
Naidoo A, Ramsuran V, Chirehwa M, Denti P, McIlleron H, Naidoo K, Yende-Zuma N, Singh R, Ngcapu S, Chaudhry M, Pepper MS, Padayatchi N, Pharmacogenomics (2018), 19(1):17-29. doi: 10.2217/pgs-2017-0144:.

Case report: mechanisms of HIV elite control in two African women.
Moosa Y, Tanko RF, Ramsuran V, Singh R, Madzivhandila M, Yende-Zuma N, Abrahams MR, Selhorst P, Gounder K, Moore PL, Williamson C, Abdool Karim SS, Garrett NJ, Burgers WA, BMC Infect Dis (2018), 18(1):54. doi: 10.1186/s12879-018-2961-8:.

Epidemiological patterns of mental disorders and stigma in a community household survey in urban slum and rural settings in Kenya.
Mutiso VN, Musyimi CW, Tomita A, Loeffen L, Burns JK, Ndetei DM, Int J Soc Psychiatry (2018), 64(2):120-129. doi: 10.1177/0020764017748180:.

A Nationwide Panel Study on Religious Involvement and Depression in South Africa: Evidence from the South African National Income Dynamics Study.
Tomita A, Ramlall S, J Relig Health. (2018), doi: 10.1007/s10943-017-0551-5:.

Application of Decafluorobiphenyl (DFBP) Moiety as a Linker in Bioconjugation.
Alapour S, de la Torre BG, Ramjugernath D, Koorbanally NA, Albericio F, Bioconjug Chem (2018), 29(2):225-233. doi: 10.1021/acs.bioconjchem.7b00800:.

1,3,5-Triazino Peptide Derivatives: Synthesis, Characterization, and Preliminary Antileishmanial Activity.
Khattab SN, Khalil HH, Bekhit AA, Abd El-Rahman MM, de la Torre BG, El-Faham A, Albericio F, ChemMedChem. (2018), doi: 10.1002/cmdc.201700770:.

Solid-Phase Synthesis of Pyrrole Derivatives through a Multicomponent Reaction Involving Lys-Containing Peptides.
Jad YE, Gudimella SK, Govender T, de la Torre BG, Albericio F, ACS Comb Sci. (2018), doi: 10.1021/acscombsci.8b00006:.

The Pharmaceutical Industry in 2017. An Analysis of FDA Drug Approvals from the Perspective of Molecules.
de la Torre BG, Albericio F, Molecules (2018), 23(3). pii: E533:.

N-methylation in amino acids and peptides: Scope and limitations.
Sharma A, Kumar A, Abdel Monaim SAH, Jad YE, El-Faham A, de la Torre BG, Albericio F, Biopolymers (2018), doi: 10.1002/bip.23110:.

Impact of the scale-up of piped water on urogenital schistosomiasis infection in rural South Africa.
Tanser F, Azongo DK, Vandormael A, Barnighausen T, Appleton C, eLIFE (2018), 7:e33065:.

Unravelling the complicated evolutionary and dissemination history of HIV-1M subtype A lineages.
Tongo M, Harkins GW, Dorfman JR, Tovanabutra EBS, de Oliveira T, Martin DP, Virus Evolution (2018), 4(1) doi:vey003/4877091:.

Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells.
Ramsuran V, Vivek Naranbhai, Amir Horowitz, Ying Qi, Maureen P. Martin, Yuko Yuki, Xiaojiang Gao, Victoria Walker-Sperling, Gregory Q. Del Prete, Douglas K. Schneider, Jeffrey D. Lifson, Jacques Fellay, Steven G. Deeks, Jeffrey N. Martin, James J. Goedert, Steven M. Wolinsky, Nelson L. Michael, Gregory D. Kirk, Susan Buchbinder, David Haas, Thumbi Ndung'u, Philip Goulder, Peter Parham, Bruce D. Walker, Jonathan M. Carlson and Mary Carrington, Science (2018), 359:86-90.

Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1.
Martin MP, Naranbhai V, Shea PR, Qi Y, Ramsuran V, Vince N, Gao X, Thomas R, Brumme ZL, Carlson JM, Wolinsky SM, Goedert JJ, Walker BD, Segal FP, Deeks SG, Haas DW, Migueles SA, Connors M, Michael N, Fellay J, Gostick E, Llewellyn-Lacey S, Price DA, Lafont BA, Pymm P, Saunders PM, Widjaja J, Wong SC, Vivian JP, Rossjohn J, Brooks AG, Carrington M, J Clin Invest. (2018), pii: 98463. doi: 10.1172/JCI98463:.

HIV-1 drug resistance before initiation or re-initiation of first-line antiretroviral therapy in low-income and middle-income countries: a systematic review and meta-regression analysis.
Gupta RK, Gregson J, Parkin N, Haile-Selassie H, Tanuri A, Andrade Forero L, Kaleebu P, Watera C, Aghokeng A, Mutenda N, Dzangare J, Hone S, Hang ZZ, Garcia J, Garcia Z, Marchorro P, Beteta E, Giron A, Hamers R, Inzaule S, Frenkel LM, Chung MH, de Oliveira T, Pillay D, Naidoo K, Kharsany A, Kugathasan R, Cutino T, Hunt G, Avila Rios S, Doherty M, Jordan MR, Bertagnolio S., Lancet ID (2018), :http://dx.doi.org/10.1016/S1473-3099(17)30702-8.

Universal test and treat and the HIV epidemic in rural South Africa: a phase 4, open-label, community cluster randomised trial.
Iwuji CC, Orne-Gliemann J, Larmarange J, Balestre E, Thiebaut R, Tanser F, Okesola N, Makowa T, Dreyer J, Herbst K, McGrath N, Barnighausen T, Boyer S, de Oliveira T, Rekacewicz C, Bazin B, Newell ML, Pillay D, Dabis F, for the ANRS 12249 TasP Study Group, Lancet HIV (2018), :http://dx.doi.org/10.1016/S2352-3018(17)30205-9.

High percentage of undiagnosed HIV cases within a hyperendemic South African community: a population-based study.
Vandormael A, de Oliveira T, Tanser F, Barnighausen T, Herbeck JT, J Epidemiol Community Health (2018), :doi: 10.1136/jech-2017-209713.

Converting Teixobactin into a Cationic Antimicrobial Peptide (AMP).
Abdel Monaim SAH, Ramchuran EJ, El-Faham A, Albericio F, de la Torre BG, J Med Chem. (2017), 60(17):7476-7482.

Investigation of the N-Terminus Amino Function of Arg10-Teixobactin.
Monaim SAHA, Noki S, Ramchuran EJ, El-Faham A, Albericio F, Torre BG, Molecules (2017), 22(10):doi: 10.3390/molecules22101632.

Tuberculosis mortality and the male survival deficit in rural South Africa: An observational community cohort study.
Reniers G, Blom S, Lieber J, Herbst AJ, Calvert C, Bor J, Barnighausen T, Zaba B, Li ZR, Clark SJ, Grant AD, Lessells R, Eaton JW, Hosegood V, PLoS ONE (2017), 12(10):e0185692. doi: 10.1371/journal.pone.0185692:.

HIV assessment and testing for hospital in-patients: still a weak link in the cascade.
Iwuji CC, Lessells RJ, Public Health Action (2017), 21;7(4):243. doi: 10.5588/pha.17.0111:.

Green environment and incident depression in South Africa: a geospatial analysis and mental health implications in a resource-limited setting.
Tomita A, Vandormael AM, Cuadros D, Di Minin E, Heikinheimo V, Tanser F, Slotow R, Burns JK, Lancet Planetary Health (2017), 1:152?62.

Highlights of the second ISCB Student Council Symposium in Africa, 2017.
Rafael CN, Ashano E, Moosa Y, Shome S, DeBlasio D, F1000 Research (2017), 6(ISCB Comm J):2183 (doi: 10.12688/f1000research.13463.1).

Effect of population viral load on prospective HIV incidence in a hyperendemic rural African community.
Tanser F, Vandormael A, Cuadros D, Phillips AN, de Oliveira T, Tomita A, Barnighausen T, Pillay D, Science Translational Medicine (2017), 9:eaam8012.

Longitudinal trends in the prevalence of detectable HIV viremia: Population-based evidence from rural KwaZulu-Natal, South Africa.
Vandormael A, Barnighausen T, Herbeck J, Tomita A, Phillips A, Pillay D, de Oliveira T, Tanser F, Clin Infect Dis. (2017), :doi: 10.1093/cid/cix976.

Impact of point-of-care Xpert MTB/RIF on tuberculosis treatment initiation: a cluster randomised trial.
Lessells RJ, Cooke GS, McGrath N, Nicol MP, Newell ML, Godfrey-Faussett P, Am J Respir Crit Care Med (2017), :doi: 10.1164/rccm.201702-0278OC.

Hyperbilirubinemia in atazanavir-treated human immunodeficiency virus-infected patients: the impact of the UGT1A1*28 allele.
Naidoo A, Naidoo K, Ramsuran V, Reddy M, Padayatchi N, Pharmacogenomics and Personalized Medicine (2017), :doi: 10.2147/PGPM.S146787.

Rates of virological suppression and drug resistance in adult HIV-1-positive patients attending primary healthcare facilities in KwaZulu-Natal, South Africa.
Hunt GM, Dokubo EK, Takuva S, de Oliveira T, Ledwaba J, Dube N, Moodley P, Sabatier J, Deyde V, Morris L, Raizes E, Journal of Antimicrobial Chemotherapy (2017), :https://doi.org/10.1093/jac/dkx252.

Automated profiling of the human virome from raw metagenomic data.
Moosa Y, Vilsker M, Vanden Eyden E, Fonseca V, Nooij S, Deforche K, de Oliveira T, Virus Evolution (2017), : doi: 10.1093/ve/vew036.033.

Persistent circulation of highly divergent HIV-1M lineages in the Congo Basin Region.
Tongo M, Dorfman JR, de Oliveira T, Martin DP, Virus Evolution (2017), :doi: 10.1093/ve/vew036.039.

Genetic markers for protease inhibitor drug resistance in regions outside of the protease gene.
Giandhari J, Gordon M, van Vuuren C, Moodley P, de Oliveira T, Virus Evolution (2017), :doi: 10.1093/ve/vew036.018.

Sexual partnership age pairings and risk of HIV acquisition in rural South Africa.
Akulliana A, Bershteyna A, Kleina D, Vandormael A, Barnighausen T, Tanser F, AIDS (2017), :DOI:10.1097/QAD.0000000000001553.

Incidence rate estimation, periodic testing and the limitations of the mid-point imputation approach.
Vandormael A, Dobra A, Barnighausen T, de Oliveira T, Tanser F, International Journal of Epidemiology (2017), :doi.org/10.1093/ije/dyx134.

Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration.
Rhee SY, Varghese V, Holmes SP, Van Zyl GU, Steegen K, Boyd MA, Cooper DA, Nsanzimana S, Saravanan S, Charpentier C, de Oliveira T, Etiebet MA, Garcia F, Goedhals D, Gomes P, Gunthard HF, Hamers RL, Hoffmann CJ, Hunt G, Jiamsakul A, Kaleebu P, Kanki P, Kantor R, Kerschberger B, Marconi VC, D'amour Ndahimana J, Ndembi N, Ngo-Giang-Huong N, Rokx C, Santoro MM, Schapiro JM, Schmidt D, Seu L, Sigaloff KCE, Sirivichayakul S, Skhosana L, Sunpath H, Tang M, Yang C, Carmona S, Gupta RK, Shafer RW., EBioMedicine (2017), :doi: 10.1016/j.ebiom.2017.03.024.

High Rates of Transmission of Drug-resistant HIV in Aruba Resulting in Reduced Susceptibility to the WHO Recommended First-line Regimen in Nearly Half of Newly Diagnosed HIV-infected Patients.
Hofstra LM, Rivas ES, Nijhuis M, Bank LEA, Wilkinson E, Kelly K, Mudrikova T, Schuurman R, de Oliveira T, de Kort J, Wensing AMJ, Clinical Infectious Diseases (2017), :doi: 10.1093/cid/cix056.

Virological Outcomes of Second-line Protease Inhibitor-Based Treatment for Human Immunodeficiency Virus Type 1 in a High-Prevalence Rural South African Setting: A Competing-Risks Prospective Cohort Analysis.
Collier D, Iwuji C, Derache A, de Oliveira T, Okesola N, Calmy A, Dabis F, Pillay D, Gupta RK, for ANRS 12249 TasP Study Group, Clinical Infectious Diseases (2017), :doi: 10.1093/cid/cix015.

CD4+ T-cell count may not be a useful strategy to monitor antiretroviral therapy response in HTLV-1/HIV co-infected patients.
Vandormael A, Rego F, Danaviah S, Alcantara L, Boulware D, de Oliveira T, Current HIV Research (2017), :doi: 10.2174/1570162X15666170216114917.

Social disequilibrium and the risk of HIV acquisition: A multilevel study in rural KwaZulu-Natal Province, South Africa.
Tomita A, Vandormael AM, Barnighausen T, de Oliveira T, Tanser F, J Acquir Immune Defic Syndr. (2017), :10.1097/QAI.0000000000001349.

Sequence and Phylogenetic Analysis of the Untranslated Promoter Regions for HLA Class I Genes.
Ramsuran V, Hernandez-Sanchez PG, O'hUigin C, Sharma G, Spence N, Augusto DG, Gao X, Garcia-Sepulveda CA, Kaur G, Mehra NK, Carrington M,, J Immunol (2017), pii: 1601679:.

Primary HIV-1 Drug Resistant Minority Variants.
Chimukangara B, Samuel R, Naidoo K, de Oliveira T, AIDS Reviews (2017), 19(2):[Epub ahead of print].

Pairwise diversity and tMRCA as potential markers for HIV infection recency.
Moyo S, Wilkinson E, Vandormael A, Wang R, Weng J, Kotokwe KP, Gaseitsiwe S, Musonda R, Makhema J, Essex M, Engelbrecht S, de Oliveira T, Novitsky V , Medicine (Baltimore) (2017), 96:doi: 10.1097/MD.0000000000006041.

Sensitive next generation sequencing method reveals deep genetic diversity of HIV-1 in the Democratic Republic of the Congo.
Rodgers MA, Wilkerson E, Vallari A, McArthur C, Sthreshley L, Brennan CA, Cloherty G, de Oliveira T, Journal of Virology (2017), JVI.01841-16:doi: 10.1128/JVI.01841-16.

Complex subtype diversity of HIV-1 among drug users in major Kenyan cities.
Gounder K, Oyaro M, Padayachi N, Zulu TM,de Oliveira T, Wylie J, Ndung'u T, AIDS Res Hum Retroviruses (2017), :10.1089/AID.2016.0321.

Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study.
Kraemer MUG, Faria NR, Reiner Jr RC, Golding N, Nikolay B, Stasse S, Johansson MA, Salje H, Faye O, Wint GRW, Niedrig M, Shearer FM, Hill SC, Thompson RN, Bisanzio D, Taveira N, Nax HH, Pradelski BSR, Nsoesie EO, Murphy NR, Bogoch II, Khan K, Brownstein JS, Tatem AJ, de Oliveira T, Smith DL, Sall AA, Pybus OG, Hay SI, Cauchemez S, Lancet Infectious Diseases (2017), http://dx.doi.org/10.1016/S1473-3099(16)30513-8:.

Occult HIV-1 drug resistance to thymidine analogues following failure of first-line tenofovir combined with a cytosine analogue and nevirapine or efavirenz in sub Saharan Africa: a retrospective multi-centre cohort study.
Gregson J, Kaleebu P, Marconi VC, van Vuuren C, Ndembi N, Hamers RL, Kanki P, Hoffmann CJ, Lockman S, Pillay D, de Oliveira T, Clumeck N, Hunt G, Kerschberger B, Shafer RW, Yang C, Raizes E, Kantor R, Gupta RK, Lancet Infectious Diseases (2017), pii: S1473-3099(16)30469-8:http://dx.doi.org/10.1016/S1473-3099(16)30447-9.

Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa: a community-wide phylogenetic study.
de Oliveira T, Kharsany ABM, Graf T, Cawood C, Khanyile D, Grobler A, Puren A, Madurai S, Baxter C, Karim QA, Karim SSA, Lancet HIV (2017), http://dx.doi.org/10.1016/S2352-3018(16)30186-2:.

Microbial genome-wide association studies: lessons from human GWAS.
Power RA, Parkhill J, de Oliveira T, Nature Reviews Genetics (2017), nrg.2016.132:doi:10.1038/nrg.2016.132.

HIV drug resistance levels in adults failing first-line antiretroviral therapy in an urban and a rural setting in South Africa.
Rossouw TM, Nieuwoudt M, Manasa J, Malherbe G, Lessells RJ, Pillay S, Danaviah S, Mahasha P, van Dyk G, de Oliveira T, HIV Med. (2017), 2016 :doi: 10.1111/hiv.12400.

Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic.
Yebra G, Hodcroft EB1, Ragonnet-Cronin ML1, Pillay D2, Brown AJ1; , Scientific Reports (2016), 6:39489. doi: 10.1038/srep39489.

HLA-C Level Is Regulated by a Polymorphic Oct1 Binding Site in the HLA-C Promoter Region.
Vince N, Li H, Ramsuran V, Naranbhai V, Duh FM, Fairfax BP, Saleh B, Knight JC, Anderson SK, Carrington M, Am J Hum Genet (2016), 99(6):1353-1358.

HIV drug resistance testing among patients failing second line antiretroviral therapy-Comparison of in-house and commercial sequencing.
Chimukangara B, Varyani B, Shamu T, Mutsvangwa J, Manasa J, White E, Chimbetete C, Luethy R, Katzenstein D, J Virol Methods (2016), pii: S0166-0934(16)30289-0: doi: 10.1016/j.jviromet.2016.11.010.

HTLV-1aA introduction into Brazil and its association with the trans-Atlantic slave trade.
Amoussa AE, Wilkinson E, Giovanetti M, de Almeida Rego FF, Araujo TH, de Souza Goncalves M, de Oliveira T, Alcantara LC, Infection, Genetics and Evolution (2016), 48:doi: 10.1016/j.meegid.2016.12.005.

Genome-Wide Association Study of HIV Whole Genome Sequences Validated using Drug Resistance.
Power RA, Davaniah S, Derache A, Wilkinson E, Tanser F, Gupta RK, Pillay D, de Oliveira T, PLoS One (2016), 11(9):e0163746.

Contribution of Gag and Protease to HIV-1 Phenotypic Drug Resistance in Pediatric Patients Failing Protease Inhibitor-Based Therapy.
Giandhari J, Basson AE, Sutherland K, Parry CM, Cane PA, Coovadia A, Kuhn L, Hunt G, Morris L, Antimicrob Agents Chemother. (2016), 60(4):2248-56.

Comprehensive Characterization of HIV-1 Molecular Epidemiology and Demographic History in the Brazilian Region Most Heavily Affected by AIDS.
Graf T, Fritsch HM, de Medeiros RM, Junqueira DM, Almeida SEM, Pinto AR , Journal of Virology (2016), 90(18):8160-8168.

Analysis of Viral Diversity in Relation to the Recency of HIV-1C Infection in Botswana.
Moyo S, Vandormael A, Wilkinson E, Engelbrecht S, Gaseitsiwe S, Kotokwe, KP, Musonda R, Tanser F, Essex M, Novitsky V, de Oliveira T, PLoS One (2016), 11(8):DOI:10.1371/journal.pone.0160649.

Relationship between HIV serostatus, CD4 count and rehospitalisation: Potential implications for health systems strengthening in South Africa.
Moodley Y, Tomita A, Southern African Journal of Infectious Diseases (2016), 1(1):1-6.

Substance use and duration of untreated psychosis in KwaZulu-Natal, South Africa.
Davis GP, Tomita A, Baumgartner JN, Mtshemla S, Nene S, King H, Susser E and Burns JK, South African Journal of Psychiatry (2016), 22(1):p. 7.

Origin, imports and exports of HIV-1 subtype C in South Africa: A historical perspective.
Wilkinson E, Rasmussen D, Ratmann O, Stadler T, Engelbrecht S, de Oliveira T, Infection, Genetics and Evolution (2016), S1567-1348(16)30298-2:doi: 10.1016/j.meegid.2016.07.008.

Zika virus complete genome from Salvador, Bahia, Brazil.
Giovanetti M, Faria NR, Nunes MR, de Vasconcelos JM, Lourenco J, Rodrigues SG, Vianez JL Jr, da Silva SP, Lemos PS, Tavares FN, Martin DP, do Rosario MS, Siqueira IC, Ciccozzi M, Pybus OG, de Oliveira T, Alcantara LC Junior, Infection, Genetics and Evolution (2016), 41:142-145.

Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource .
Druce Megan, Hulo C, Masson P, Sommer P, Xenarios I, Le Mercier P, de Oliveira T, Database (2016), 2016:doi:10.1093/database/baw045.

Increasing HIV-1 drug resistance between 2010 and 2012 in adults participating in population-based HIV surveillance in rural KwaZulu-Natal South Africa.
Manasa J, Danaviah S, Lessells RJ, Elshareef M, Tanser F, Wilkinson E, Pillay S, Mthiyane H, Mwambi H, Pillay D, de Oliveira T, AIDS Res Hum Retroviruses (2016), 32(8):763-769.

Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study.
The TenoRes Study Group* Gregson J, Tang M, Ndembi N, Hamers RL, ..., de Oliveira T, ..., Shafer RW, Gupta KR, Lancet Infect Dis. (2016), 15:http://dx.doi.org/10.1016/S1473-3099(15)00536-8.

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt.
Mulder NJ, Christoffels A, de Oliveira T, Gamieldien J, Hazelhurst S, Joubert F, Kumuthini J, Pillay CS, Snoep JL, Tastan Bishop O, Tiffin N, PLoS Comput Biol (2016), 12(2):e1004395.

Understanding Specific Contexts of Antiretroviral Therapy Adherence in Rural South Africa: A Thematic Analysis of Digital Stories from a Community with High HIV Prevalence.
Treffry-Goatley A, Lessells R, Sykes P, Barnighausen T, de Oliveira T, Moletsane R, Seeley J., PLoS One (2016), 11(2):doi: 10.1371/journal.pone.0148801.

Analysis of Dominant HIV Quasispecies Suggests Independent Viral Evolution Within Spinal Granulomas Coinfected with Mycobacterium tuberculosis and HIV-1 Subtype C.
Danaviah S, de Oliveira T, Gordon M, Govender S, Chelule P, Pillay S, Naicker T, Cassol S, Ndung'u T, AIDS Research and Human Retroviruses (2016), :doi:10.1089/aid.2015.0189.

Brief Report: Virologic Monitoring Can Be a Cost-Effective Strategy to Diagnose Treatment Failure on First-Line ART.
Vandormael AM, Boulware DR, Tanser FC, Barnighuasen TW, Stott KE, de Oliveira T, J Acquir Immune Defic Syndr. (2016), 71(4):462?466.

Deep Sequencing Analysis of Human T Cell Lymphotropic Virus Type 1 Long Terminal Repeat 5' Region from Patients with Tropical Spastic Paraparesis/Human T Cell Lymphotropic Virus Type 1-Associated Myelopathy and Asymptomatic Carriers..
Rego FF, de Oliveira T, Giovanetti M, Galvao-Castro B, Goncalves MS, Alcantara LC., AIDS Research and Human Retroviruses (2016), 32(3):279-83.

HIV treatment cascade in tuberculosis patients.
Lessells RJ, Swaminathan S, Godfrey-Faussett P, Curr Opin HIV AIDS (2015), 10(6):439-46. doi: 10.1097/COH.0000000000000197:.

Epigenetic regulation of differential HLA-A allelic expression levels.
Ramsuran V, Kulkarni S, O'huigin C, Yuki Y, Augusto DG, Gao X, Carrington M, Hum Mol Genet (2015), 24(15):4268-75.

Epigenetic mechanisms, T-cell activation, and CCR5 genetics interact to regulate T-cell expression of CCR5, the major HIV-1 coreceptor.
Gornalusse GG, Mummidi S, Gaitan AA, Jimenez F, Ramsuran V, Picton A, Rogers K, Manoharan MS, Avadhanam N, Murthy KK, Martinez H, Molano Murillo A, Chykarenko ZA, Hutt R, Daskalakis D, Shostakovich-Koretskaya L, Abdool Karim S, Martin JN, Deeks SG, Hecht F, Sinclair E, Clark RA, Okulicz J, Valentine FT, Martinson N, Tiemessen CT, Ndung'u T, Hunt PW, He W, Ahuja SK., Proc Natl Acad Sci U S A (2015), 112(34):E4762-71.

Genetic Changes in HIV-1 Gag-Protease Associated with Protease Inhibitor-Based Therapy Failure in Pediatric Patients.
Giandhari J, Basson AE, Coovadia A, Kuhn L, Abrams AJ, Strehlau R, Morris L, Hunt GM, AIDS Res Hum Retroviruses (2015), 31(8):776-82.

Clinical, Virologic, Immunologic Outcomes and Emerging HIV Drug Resistance Patterns in Children and Adolescents in Public ART Care in Zimbabwe.
Makadzange AT, Higgins-Biddle M, Chimukangara B, Birri R, Gordon M, Mahlanza T, McHugh G, van Dijk JH, Bwakura-Dangarembizi M, Ndung'u T, Masimirembwa C, Phelps B, Amzel A, Ojikutu BO, Walker BD, Ndhlovu CE, PLoS One (2015), 10(12):DOI: 10.1371/journal.pone.0144057 .

History and origin of the HIV-1 subtype C epidemic in South Africa and the greater southern African region.
Wilkinson E, Engelbrecht S, de Oliveira T, Scientific Reports (2015), 5:16897. doi: 10.1038/srep16897.

HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing.
Rhee SY, Jordan MR, Raizes E, Chua A, Parkin N, Kantor R, Van Zyl GU, Mukui I, Hosseinipour MC, Frenkel LM, Ndembi N, Hamers RL, Rinke de Wit TF, Wallis CL, Gupta RK, Fokam J, Zeh C, Schapiro JM, Carmona S, Katzenstein D, Tang M, Aghokeng AF, de Oliveira T, Wensing AM, Gallant JE, Wainberg MA, Richman DD, Fitzgibbon JE, Schito M, Bertagnolio S, Yang C, Shafer RW., PLoS One (2015), 10(12):e0145772. doi: 10.1371/journal.pone.0145772.

The Art of HIV Elimination: Past and Present Science.
Iwuji CC, McGrath N, de Oliveira T, Porter K, Pillay D, Fisher M, Newport M, Newell M-L, AIDS & Clinical Research (2015), 6: 525. doi:10.4172/2155-6113.1000525 .

Identifying Recent HIV Infections: From Serological Assays to Genomics.
Moyo S, Wilkinson E, Novitsky V, Vandormael A, Gaseitsiwe S, Essex M, Engelbrecht S, de Oliveira T , Viruses (2015), 7:5508-5524; doi:10.3390/v7102887.

Long-range HIV genotyping using viral RNA and proviral DNA for analysis of HIV drug-resistance and HIV clustering.
Novitsky V, Zahralban-Steele M, McLane MF, Moyo S, Widenfelt E, Gaseitsiwe S, Makhema J, Essex M, Journal of Clinical Microbiology (2015), in press:in press .

The origin of HTLV-1 in southern Bahia by phylogenetic, mtDNA and Beta-globin analysis.
Aleluia MM, Mello MAG,Alcantara LCJ, Rego FFA, Santos LPS, Galvao-Castro B, Goncalves MS, de Oliveira T, Marin LJ, Sousa SMB, Gadelha SR, Virology Reports (2015), :dx.doi.org/10.1016/j.virep.2015.05.002.

PANGEA-HIV: phylogenetics for generalised epidemics in Africa.
Pillay D, Herbeck J, Cohen MS, de Oliveira T, Fraser C, Ratmann O, Brown A-L, Kellam P, on behalf of the PANGEA-HIV Consortium, Lancet Infect Dis. (2015), 15(3):259-61.

Evidence of Long-Lived Founder Virus in Mother-to-Child HIV Transmission.
Danaviah S, de Oliveira T, Bland R, Viljoen J, Pillay S, Tuaillon E, Van de Perre P, Newell ML, PLoS One (2015), 10(3):e0120389.

Sequencing and phylogenetic analysis of near full-length HIV-1 subtypes A, B, G and unique recombinant AC and AD viral strains identified in South Africa.
Wilkinson E, Holzmayer V, Jacobs G, de Oliveira T, Brennan C, Hackett J Jr, Janse van Rensburg E, Engelbrecht S., AIDS Research and Human Retroviruses (2015), in press:.

Impact of drug resistance-associated amino acid changes in HIV-1 subtype C on susceptibility to newer nonnucleoside reverse transcriptase inhibitors.
Basson AE, Rhee SY, Parry CM, El-Khatib Z, Charalambous S, De Oliveira T, Pillay D, Hoffmann C, Katzenstein D, Shafer RW, Morris L, Antimicrob Agents Chemother (2015), pii: AAC.04215-14:pii: AAC.04215-14.

Expression of the CCR5 HIV co-receptor in women with genital schistosomiasis.
Kleppa E, Ramsuran V, Zulu S, Karlsen GH, Bere A, Passmore JA, Ndhlovu P, Lillebo K, Holmen SD, Onsrud M, Gundersen SG, Taylor M, Kjetland EF, Ndung'u T, 16th ICID Abstracts / International Journal of Inf (2014), 21S:1-460.

Effect of female genital schistosomiasis and anti-schistosomal treatment on monocytes, CD4+ T-cells and CCR5 expression in the female genital tract.
Kleppa E, Ramsuran V, Zulu S, Karlsen GH, Bere A, Passmore JA, Ndhlovu P, Lillebo K, Holmen SD, Onsrud M, Gundersen SG, Taylor M, Kjetland EF, Ndung'u T, PLoS One (2014), 9(6):e98593.

Use of antiretroviral therapy in households and risk of HIV acquisition in rural KwaZulu-Natal, South Africa, 2004-12: a prospective cohort study.
Vandormael A, Newell ML, Barnighausen T, Tanser F, Lancet Global Health (2014), 2:e209-215.

Drug resistance mutations from whole blood proviral DNA among patients on antiretroviral drugs in Zimbabwe.
Chimukangara B, Gwanzura G, Mitchell R, Katzenstein D, Masimirembwa C , Curr HIV Res (2014), 12(5):309-16.

Detection of Transmission Clusters of HIV-1 Subtype C over a 21-Year Period in Cape Town, South Africa.
Wilkinson E, Engelbrecht S, de Oliveira T, PLoS One (2014), 9(10):doi:10.1371/journal.pone.0109296.

HIV Drug Resistance Patterns at the Epicentre of the HIV-1 Epidemic in Kwazulu-Natal, South Africa 2003-2013.
Kiepiela P, Manasa J, Moosa M-Y, Moodley P, Gordon M, Parikh UM, Sunpath H, de Oliveira T, Ramjee G, J AIDS Clin Res (2014), 5:doi: 10.4172/2155-6113.1000299.

Phylogenetic studies of transmission dynamics in generalized HIV epidemics: An essential tool where the burden is greatest?.
Dennis AM, Herbeck JT, Brown AL, Kellam P, de Oliveira T, Pillay D, Fraser C, Cohen MS, J Acquir Immune Defic Syndr. (2014), in press:.

HIV-1 adaptation to antigen processing results in population-level immune evasion and affects subtype diversification.
Tenzer S, Crawford H, Pymm P, Gifford R, Sreenu VB, Weimershaus M, de Oliveira T, Burgevin A, Gerstoft J, Akkad N, Lunn D, Fugger L, Bell J, Schild H, van Endert P, Iversen AK., Cell Reports (2014), 7:doi: 10.1016/j.celrep.2014.03.031.

Circulating Biomarkers of Immune Activation Distinguish Viral Suppression from Nonsuppression in HAART-Treated Patients with Advanced HIV-1 Subtype C Infection.
Malherbe G, Steel HC, Cassol S, de Oliveira T, Seebregts CJ, Anderson R, Cassol E, Rossouw TM., Mediators Inflamm. (2014), 2014:198413:doi: 10.1155/2014/198413.

HIV-1 Subtypes B and C Unique Recombinant Forms (URFs) and Transmitted Drug Resistance Identified in the Western Cape Province, South Africa.
Jacobs GB, Wilkinson E, Isaacs S, Spies G, de Oliveira T, Seedat S, Engelbrecht S , PLoS One (2014), 9(3):e90845. doi:10.1371/journal.pone.0090845.

Implementing antiretroviral resistance testing in a primary health care HIV treatment programme in rural KwaZulu-Natal, South Africa: early experiences, achievements and challenges.
Lessells RJ, Stott KE, Manasa J, Naidu KK, Skingsley A, Rossouw T, de Oliveira T, BMC Health Services Research (2014), 14:116:doi:10.1186/1472-6963-14-116.

Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa.
Manasa J, Lessells R, Rossouw T, Naidu K, Van Vuuren C, Goedhals D, Van Zyl G, Bester A, Skingsley A, Stott K, Danaviah S, Chetty T, Singh L, Moodley P, Iwuji C, McGrath N, Seebregts CJ, de Oliveira T, Database (Oxford) (2014), Vol. 2014 :bat082. doi: 10.1093/database/bat082.

Drug resistance in children at virological failure in a rural KwaZulu-Natal, South Africa, cohort.
Pillay S, Bland RM, Lessells RJ, Manasa J, de Oliveira T, Danaviah S., AIDS Res Ther. (2014), 11(1):3. doi: 10.1186/1742-6405-11-3.

Concentrated HIV subepidemics in generalized epidemic settings.
Tanser F, de Oliveira T, Maheu-Giroux M, Barnighausen T, Curr Opin HIV AIDS (2014), 9(2):115-125.

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings.
Manasa J, Danaviah S, Pillay S, Padayachee P, Mthiyane H, Seebregts C, Rinke De Wit TF, Viljoen J, Katzenstein D, De Oliveira T , Journal of Visualized Experiments (JoVE) (2014), (85):e51242, doi:10.3791/51242.

Genetic interplay between HLA-C and MIR148A in HIV control and Crohn disease.
Kulkarni S, Qi Y, O'hUigin C, Pereyra F, Ramsuran V, McLaren P, Fellay J, Nelson G, Chen H, Liao W, Bass S, Apps R, Gao X, Yuki Y, Lied A, Ganesan A, Hunt PW, Deeks SG, Wolinsky S, Walker BD, Carrington M, Proc Natl Acad Sci U S A (2013), 110(51):20705-10.

Implementing HIV-1 Genotypic Resistance Testing in Antiretroviral Therapy Programs in Africa: Needs, Opportunities, and Challenges.
Lessells RJ, Avalos A, de Oliveira T, AIDS Reviews (2013), 15:221-229.

An Investigation of Classification Algorithms for Predicting HIV Drug Resistance without Genotype Resistance Testing.
Brandt P, Moodley D, Pillay AW, Seebregts CJ, de Oliveira T, Lecture Notes in Computer Science (LNCS) (2013), 8315:236-253.

A Pragmatic Approach to HIV-1 Drug Resistance Determination in Resource-Limited Settings by Use of a Novel Genotyping Assay Targeting the Reverse Transcriptase-Encoding Region Only.
Aitken SC, Bronze M, Wallis CL, Stuyver L, Steegen K, Balinda S, Kityo C, Stevens W, Rinke De Wit TF & Schuurman R., J Clin Microbiol (2013), 51:1757-1761.

Dramatic increases in HIV prevalence after scale-up of antiretroviral treatment: a longitudinal population-based HIV surveillance study in rural Kwazulu-Natal.
Zaidi J, Grapsa E, Tanser F, Newell M-L, Barnighausen T, AIDS (2013), 27(14):2301-2305.

High coverage of ART associated with decline in risk of HIV acquisition in rural KwaZulu-Natal, South Africa.
Tanser F, Barnighausen T, Grapsa E, Zaidi J, Newell M-L., Science (2013), 339(6122):966-971.

A qualitative and quantitative histopathological analysis of the host immune response to TB of the spine in HIV-positive and negative patients.
Danaviah S, Sacks J, Taylor L, Govender S, Fallows D, Kumar KPS, Ndung'u T, Kaplan G. , Tuberculosis (2013), 93(4):432-41.

Pili contribute to biofilm formation in vitro in Mycobacterium tuberculosis.
Ramsugit S, Guma S, Pillay B, Jain P, Larsen MH, Danaviah S, Pillay M., Antonie Van Leeuwenhoek (2013), 104(2):DOI 10.1007/s10482-013-9981-6.

Combined antiretroviral and antituberculosis drug resistance following incarceration.
Stott KE, de Oliveira T, Lessells RJ, S Afr J HIV Med (2013), 14(3):135-137.

Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights.
Frias D, Monteiro-Cunha JP, Mota-Miranda AC, Fonseca V, de Oliveira T, Galvao-Castro B Alcantara LCJ, Bioinformatics and Biology Insights (2013), 7:1-11.

High-Levels of Acquired Drug Resistance in Adult Patients Failing First-Line Antiretroviral Therapy in a Rural HIV Treatment Programme in KwaZulu-Natal, South Africa.
Manasa J, Lessells RJ, Skingsley A, Naidu KK, Newell M-L, McGrath N, de Oliveira T, PLoS One (2013), 8(8):e72152.

High Level of HIV-2 False Positivity in KwaZulu-Natal Province: A Region of South Africa With a Very High HIV-1 Subtype C Prevalence.
Singh L, Parboosing R, Manasa J, Moodley P, de Oliveira T, Journal of Medical Virology (2013), Advanced Access:doi: 10.1002/jmv.23716.

Trends in Genotypic HIV-1 Antiretroviral Resistance between 2006 and 2012 in South African Patients Receiving First- and Second-Line Antiretroviral Treatment Regimens.
Van Zyl GU, Liu TF, Claassen M, Engelbrecht S, de Oliveira T, Preiser W, Wood NT, Travers S, Shafer RW, PLoS One (2013), 8(6):e67188.

Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools.
Pena ACP, Faria NR, Imbrechts S, Libin P, Abecasis AB, Deforche K, Gomez A, Camacho RJ, de Oliveira T, Vandamme A-M, Infectious Genetics and Evolution (2013), in press :.

Development and evaluation of an affordable real-time qualitative assay for determining HIV-1 virological failure in plasma and dried blood spots..
Aitken SC, Kliphuis A, Bronze M, Wallis CL, Kityo C, Balinda S, Stevens WS, Spieker N, de Oliveira T, Rinke de Wit TF, Schuurman R., J Clin Microbiol (2013), 29 (11):JCM.03305-12.

RegaDB: Community-driven data management and analysis for infectious diseases.
Libin P, Beheydt G, Deforche K, Imbrechts S, Ferreira F, Van Laethem K, Theys K, Carvalho AP, Cavaco Silva J, Lapadula G, Torti P, Assel M, Wesner S, Snoeck J, Ruelle J, De Bel A, Lacor P, De Munter P, Van Wijngaerden E, Zazzi M, Kaiser R, Ayouba A, Peeters M, de Oliveira T, Alcantara L, Grossman Z, Sloot P, Otelea D, Paraschiv S, Boucher C, Camacho R, and Vandamme AM, Bioinformatics (2013), 29 (11):1477-1480, doi: 10.1093/bioinformatics/btst162 .

HIV & TB Drug Resistance & Clinical Management Case Book.
Rossouw T, Lessells RJ, de Oliveira T, South African Medical Research Council Press (2013), ISBN 978-1-920014-91-9:.

Searching for Virus Phylotypes.
Chevenet F, Jung M, Peeters M, de Oliveira T, Gascuel O, Bioinformatics (2013), 29 (5):561-570.

Universal Amplification, Next-Generation Sequencing, and Assembly of HIV-1 Genomes.
Gall A, Ferns B, Morris C, Watson S, Cotten M, Robinson M, Berry N, Pillay D, Kellam P, Journal of Clinical Microbiology (2012), 50(12):doi:10.1128/JCM.01516-12.

In-house human immunodeficiency virus-1 genotype resistance testing to determine highly active antiretroviral therapy resistance mutations in Hong Kong.
Chen JH, Wong KH, Li PC, Chan KK, Lee MP, To SW, Yam WC , Hong Kong Med J (2012), 18:20-24.

Principles of HIV drug resistance for clinical management in South Africa.
Stott K, Michel J, de Oliveira T, HIV Nursing Matters (2012), 3(4):46-51.

The 2012 southern African ARV drug resistance testing guidelines.
Conradie F, Wilson D, Basson A, de Oliveira T, Hunt G, Joel D, Papathanasopoulos M, Preiser W, Klausner J, Spencer D, Stevens W, Venter F, van Vuuren C, S Afr J HIV Med (2012), 13(4):162-167.

Are subtype differences important in HIV drug resistance?.
Lessells RJ, Katzenstein DK, de Oliveira T, Current Opinion Virology (2012), 2(5):636-43.

Gender Differences in Survival among Adult Patients Starting Antiretroviral Therapy in South Africa: A Multicentre Cohort Study.
Cornell M, Schomaker M, Garone DB, Giddy J, Hoffmann CJ, Lessells R, Maskew M, Prozesky H, Wood R, Johnson LF, Egger M, Boulle A, Myer L For IeDEA-SA, PLoS Medicine (2012), 9(9):e1001304.

The tainted milk of human kindness.
Goedhals D, Rossouw I, Hallbauer U, Mamabolo M, de Oliveira T, Lancet (2012), 380:702.

WHO HIV drug resistance report 2012.
WHO ResNet, including - Jordan MR, Barcarolo J, Parkin N, de Oliveira T (analysis support), Bertagnolio S, WHO report (2012), ISBN 978 92 4 150393 8:.

Modeling HIV-1 Drug Resistance as Episodic Directional Selection.
Murrell B, de Oliveira T, Seebregts C, Kosakovsky-Pond SL, Scheffler K, on behalf SATuRN, PLoS Comput Biol (2012), 8(5):e1002507.

Primary drug resistance in South Africa - data from 10 years of surveys.
Manasa J, Katzenstein D, Cassol S, Newell ML, de Oliveira T, AIDS Res Hum Retroviruses (2012), 28(6):558-565.

Influence of variations in CCL3L1 and CCR5 on tuberculosis in a northwestern Colombian population.
Mamtani M, Mummidi S, Ramsuran V, Pham MH, Maldonado R, Begum K, Valera MS, Sanchez R, Castiblanco J, Kulkarni H, Ndung'u T, He W, Anaya JM, Ahuja SK, J Infect Dis (2011), 203(11):1590-4.

Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women.
Ramsuran V, Kulkarni H, He W, Mlisana K, Wright EJ, Werner L, Castiblanco J, Dhanda R, Le T, Dolan MJ, Guan W, Weiss RA, Clark RA, Karim SS, Ahuja SK, Ndung'u T, Clin Infect Dis. (2011), 52(10):1248-56.

Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings..
Zhou Z, Wagar N, Devos JR, Rottinghaus E, Diallo K, Nguyen DB, Bassey O, Ugbena R, Wadonda-Kabondo N, Mcconnell MS, Zulu I, Chilima B, Nkengasong J, Yang C , PLoS One (2011), 6:e28184.

Cumulative exposure to cell-free HIV in breast milk, rather than feeding pattern per se, identifies postnatally infected infants.
Neveu D, Viljoen J, Bland RM, Nagot N, Danaviah S, Coutsoudis A, Rollins NC, Coovadia HM, Van de Perre P, Newell ML. , Clin Infect Dis (2011), 52(6):819-25.

Use of dried blood spots for the determination of genetic variation of IL-10, Killer Immunoglobulin-like Receptor and HLA Class I genes.
Ndlovu BG, Danaviah S, Moodley E, Ghebremichael M, Bland R, Viljoen J, Newell M-L, Ndung'u T, and Carr WH, Tissue Antigens (2011), 79(2):114-22.

Surveillance of transmitted antiretroviral drug resistance among HIV-1 infected women attending antenatal clinics in Chitungwiza, Zimbabwe..
Tshabalala M, Manasa J, Zijenah LS, Rusakaniko S, Kadzirange G, Mucheche M, Kassaye S, Johnston E, Katzenstein D, PLoS ONE (2011), 6(6):e21241.

Cohort profile: Hlabisa HIV Treatment and Care Programme.
Houlihan C, Bland R, Mutevedzi P, Lessells R, Ndirangu J, Thulare H, Newell ML, Int J Epidemiol (2011), 40:318-26.

Retention in HIV care for individuals not yet eligible for antiretroviral therapy: rural KwaZulu-Natal, South Africa.
Lessells RJ, Mutevedzi PC, Cooke GS, Newell ML., J Acquir Immune Defic Syndr (2011), 56(3):e79-86.

Association of age with mortality and virological and immunological response to antiretroviral therapy in rural South African adults.
Mutevedzi PC, Lessells RJ, Rodger AJ, Newell ML, PLoS ONE (2011), 6(7):e21795.

Poor long-term outcomes for cryptococcal meningitis in rural South Africa.
Lessells RJ, Mutevedzi PC, Heller T, Newell ML, S Afr Med (2011), 101:251-2.

International spread of multidrug-resistant tuberculosis from Tugela Ferry, South Africa.
Cooke GS, Beaton RK, Lessells RJ, John L, Ashworth S, Kon OM, Williams OM, Supply P, Moodley P, Pym AS, Emerg Infect Dis (2011), 17:2035-2037.

Evaluation of tuberculosis diagnostics: establishing an evidence base around the public health impact.
Lessells RJ, Cooke GS, Newell ML, Godfrey-Faussett P, J Infect Dis (2011), 204:S1187-95.

Genetic Characteristics, Coreceptor Usage Potential and Evolution of Nigerian HIV-1 Subtype G and CRF02_AG Isolate.
Ajoge HO, Gordon ML, de Oliveira T, Green TN, Ibrahim S, Shittu OS, Olonitola SO, Ahmad AA, Ndung'u T, PLoS One (2011), 6(3):e17865.

Affordable in-house antiretroviral drug resistance assay with good performance in non-subtype B HIV-1.
Wallis CL, Papathanasopoulos MA, Lakhi S, Karita E, Kamali A, Kaleebu P, Sanders E, Anzala O, Bekker LG, Stevens G, De Wit TF, Stevens W , J Virol Methods (2010), 163:505-508.

Comparison of the Generic HIV Viral Load assay with the Amplicor HIV-1 monitor v1.5 and Nuclisens HIV-1 EasyQ v1.2 techniques for plasma HIV-1 RNA quantitation of non-B subtypes: the Kesho Bora preparatory study. .
Rouet F, Foulongne V, Viljoen J, Steegen K, Becquart P, Valea D, Danaviah S, Segondy M, Verhofstede C, Van de Perre P; WHO/ANRS 1289 Kesho Bora Study Group, Virol Methods (2010), 163(2):253-7.

Dried Blood Spot HIV-1 RNA Quantification Using Open Real-Time Systems in South Africa and Burkina Faso.
Viljoen J, Gampini S, Danaviah S, Valea D, Pillay S, Kania D, Meda N, Newell ML, Van de Perre P, Rouet F; for the World Health Organization/ANRS 1289 Kesho Bora Study Group, Acquir Immune Defic Syndr (2010), 55(3):290-8.

Community-based treatment for multidrug-resistant tuberculosis in rural KwaZulu-Natal, South Africa.
Heller T, Lessells RJ, Wallrauch C, Barnighausen T, Cooke GS, Mhlongo L, Master I, Newell ML, Int J TB Lung Dis (2010), 14:420-426.

The TB challenge in a rural South African HIV programme.
Houlihan C, Mutevedzi P, Lessells R, Cooke G, Tanser F, Newell ML, BMC Infect Dis (2010), 10:23.

Scale-up of a decentralised HIV treatment programme in rural KwaZulu- Natal, South Africa: does rapid expansion affect patient outcomes?.
Mutevedzi P, Lessells RJ, Heller T, Barnighausen T, Cooke G, Newell ML, Bull WHO (2010), 88:593-600.

Comparative performance of the REGA subtyping tool version 2 versus version 1.
Abecasis AB, Wang Y, Libin P, Imbrechts S, de Oliveira T, Camacho RJ, Vandamme AM, Infect Genet Evol. (2010), 10(3):380-5.

The HIV-1 Subtype C Epidemic in South America is Linked to the United Kingdom.
de Oliveira T, Pillay D, Gifford RJ; for the UK Collaborative Group on HIV Drug Resistance, PLoS One (2010), 19;5(2):e9311.

Public Database for HIV Drug Resistance in southern Africa.
de Oliveira T, Shafer WR, Seebregts C, for SATuRN, Nature (2010), 464(7289):673.

Molecular characterization of non-subtype C and recombinant HIV-1 viruses from Cape Town, South Africa.
Wilkinson E, Engelbrecht S, Infectious Genetics and Evolution (2009), 9:840-846.

The RNA virus database.
Belshaw R, de Oliveira T, Markowitz S, Rambaut A, Nucleic Acids Res (2009), 37(Database issue):D431-5.

Genetic variability of human immunodeficiency virus-1 in Bahia state, Northeast, Brazil: high diversity of HIV genotypes.
Monteiro JP, Alcantara LC, de Oliveira T, Oliveira AM, Melo MA, Brites C, Galvao-Castro B, J Med Virol (2009), 81(3):391-9.

Extensive HIV-1 intra-host recombination is common in tissues with abnormal histopathology.
Lamers SL, Salemi M, Galligan DC, de Oliveira T, Fogel GB, Granier SC, Zhao L, Brown JN, Morris A, Masliah E, McGrath MS, PLoS One (2009), 4(3):e5065.

Functional characteristics of HIV-1 subtype C compatible with increased heterosexual transmissibility.
Walter BL, Armitage AE, Graham SC, de Oliveira T, Skinhoj P, Jones EY, Stuart DI, McMichael AJ, Chesebro B, Iversen AK, AIDS (2009), 23(9):1047-57.

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences.
Alcantara LC, Cassol S, Libin P, Deforche K, Pybus OG, Van Ranst M, Galvao-Castro B, Vandamme AM, de Oliveira T, Nucleic Acids Res (2009), 37(Web Server issue):W634-42.

Prevalence of HIV type-1 drug-associated mutations in pre-therapy patients in the Free State, South Africa..
Huang KH, Goedhals D, Fryer H, van Vuuren C, Katzourakis A, De Oliveira T, Brown H, Cassol S, Seebregts C, McLean A, Klenerman P, Phillips R, Frater J; Bloemfontein-Oxford Collaborative Group., Antivir Ther. (2009), 14(7):975-84.

Evolution and Molecular Epidemiology of Subtype C HIV-1 in Zimbabwe.
Dalai SC, de Oliveira T, Harkins GH, Kassaye SG, Lint J, Manasa J, Johnston E, Katzenstein D, AIDS (2009), 23(18):2523-32.

Antiretroviral drug resistance surveillance among drug-naive HIV-1-infected individuals in Gauteng Province, South Africa in 2002 and 2004.
Pillay V, Ledwaba J, Hunt G, Rakgotho M, Singh B, Makubalo L, Bennett D E, Puren A, Morris L , Antivir Ther (2008), 13 Suppl 2:101-107.

In-house HIV-1 RNA real-time reverse transcription PCR assays: principle, available tests and usefulness in developing countries.
Rouet F, Menan H, Viljoen J, Ngo Giang Huong N, Mandaliya K, Valea D, Xuan L, Danaviah S, Rousset D, Ganon A and Nerrienet E, Expert Review of Molecular Diagnostics (2008), 8(5):635-650.

HIV and hepatitis B co-infection in Africa.
Lessells RJ, Main J, Cooke GS, Lancet Infectious Diseases (2008), 8:210-11.

Effect of the HIV epidemic on liver cancer in Africa.
Lessells RJ, Cooke GS, Lancet (2008), 371:1504.

High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania.
Salemi M, de Oliveira T, Ciccozzi M, Rezza G, Goodenow MM, PLoS One (2008), 3(1):e1390.

The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries.
Salemi M, Goodenow MM, Montieri S, de Oliveira T, Santoro MM, Beshkov D, Alexiev I, Elenkov I, Elenkov I, Yakimova T, Varleva T, Rezza G, Ciccozzi M, AIDS Res Hum Retroviruses (2008), 24(6):771-9.

Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences.
Armitage AE, Katzourakis A, de Oliveira T, Welch JJ, Belshaw R, Bishop KN, Kramer B, McMichael AJ, Rambaut A, Iversen AK, J Virol (2008), 82(17):8743-61.

Atypical mycobacterial spondylitis in HIV-negative patients identified by 16S rDNA genotyping.
Danaviah S, Govender S, Gordon ML, Cassol S. , J Bone Joint Surg Br. (2007), 89(3) :346-348.

Cervical spine tuberculosis in children.
Govender S, Ramnarain A, Danaviah S, Clin Orthop Relat Res. (2007), 460:50-5.

Evaluation of the Partec flow cytometer against the BD FACSCalibur system for monitoring immune responses of human immunodeficiency virus-infected patients in Zimbabwe.
Manasa J, Musabaike H, Masimirembwa C, Burke E, Luthy R, Mudzori J, Clin Vaccine Immunol (2007), 14(3):293-8.

Sequential broadening of CTL responses in early HIV-1 infection is associated with viral escape.
Karlsson AC, Iversen AK, Chapman JM, de Oliveira T, Spotts G, McMichael AJ, Davenport MP, Hecht FM, Nixon DF, PLos One (2007), 2(2):e225.

Re-mapping the molecular features of the human immunodeficiency virus type 1 and human T-cell lymphotropic virus type 1 Brazilian sequences using a bioinformatics unit established in Salvador, Bahia, Brazil, to give support to the viral epidemiology studies.
de Queiroz AT, Mota-Miranda AC, de Oliveira T, Moreau DR, Urpia Cde C, Carvalho CM, Galvao-Castro B, Alcantara LC, Mem Inst Oswaldo Cruz (2007), 102(2):133-9.

Evidence for recombination in natural populations of porcine circovirus type 2 in Hong Kong and mainland China.
Ma CM, Hon CC, Lam TY, Li VY, Wong CK, de Oliveira T, Leung FC, J Gen Virol (2007), 88(Pt 6):1733-7.

An outbreak of HIV-1 subtype G among Italian injecting drug users.
Ciccozzi M, Montieri S, Salemi M, De Oliveira T, Dorrucci M, Sinicco A, De Luca A, Giuliani M, Balotta C, Rezza G, AIDS (2007), 21(9):1213-5.

Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form.
Abecasis AB, Lemey P, Vidal N, de Oliveira T, Peeters M, Camacho R, Shapiro B, Rambaut A, Vandamme AM, J Virol (2007), 81(16):8543-51.

Libya should stop denying scientific evidence on HIV.
Colizzi V, de Oliveira T, Roberts RJ, Nature (2007), 448(7157):992.

Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1.
Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme AM, Kellam P, Pillay D; UK Collaborative Group on HIV Drug Resistance, J Virol (2007), 81(23):13050-6.

Mapping the molecular characteristics of Brazilian human T-cell lymphotropic virus type 1 Env (gp46) and Pol amino acid sequences for vaccine design.
Mota-Miranda AC, de Oliveira T, Moreau DR, Bomfim C, Galvao-Castro B, Alcantara LC Jr, Mem Inst Oswaldo Cruz (2007), 102(6):741-9.

A report of 3 unusual opportunistic bacterial infections of the spine.
Danaviah S, Govender S, Gordon M, Cassol S, SAOJ (2006), 5(3):12-16.

Out of Africa: The BioAfrica website.
de Oliveira T, BioTechniques (2006), 41:129.

Tracing the origin of Brazilian HTLV-1 as determined by analysis of host and viral genes.
Alcantara LC, de Oliveira T, Gordon M, Pybus O, Mascarenhas RE, Seixas MO, Goncalves M, Hlela C, Cassol S, Galvao-Castro B, AIDS (2006), 20(5):780-2.

Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity.
Gifford R, de Oliveira T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme AM, Kellam P, Pillay D; UK Collaborative Group on HIV Drug Resistance, AIDS (2006), 20(11):1521-9.

Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak.
de Oliveira T, Pybus OG, Rambaut A, Salemi M, Cassol S, Ciccozzi M, Rezza G, Gattinara GC, D'Arrigo R, Amicosante M, Perrin L, Colizzi V, Perno CF; Benghazi Study Group, Nature (2006), 444(7121):836-7.

Scourge of a Continent: The BioAfrica Website.
de Oliveira T, Cassol S (edited by M. Leslie), Science (2005), 310:1877.

BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools.
Doherty RS, de Oliveira T, Seebregts C, Danaviah S, Gordon M, Cassol S, Retrovirology (2005), 2:18.

Different epidemic potentials of the HIV-1B and C subtypes.
Salemi M, de Oliveira T, Soares MA, Pybus O, Dumans AT, Vandamme AM, Tanuri A, Cassol S, Fitch WM, J Mol Evol (2005), 60(5):598-605.

An automated genotyping system for analysis of HIV-1 and other microbial sequences.
de Oliveira T, Deforche K, Cassol S, Salminen M, Paraskevis D, Seebregts C, Snoeck J, van Rensburg EJ, Wensing AM, van de Vijver DA, Boucher CA, Camacho R, Vandamme AM, Bioinformatics (2005), 21(19):3797-800.

Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS.
Salemi M, Lamers SL, Yu S, de Oliveira T, Fitch WM, McGrath MS, J Virol (2005), 79(17):11343-52.

Management of hepatitis B co-infection in human immunodeficiency virus infected subjects.
Lessells R, Leen CLS, Eur J Clin Micro ID (2004), 23(5):366-374.

A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil.
Soares MA, De Oliveira T, Brindeiro RM, Diaz RS, Sabino EC, Brigido L, Pires IL, Morgado MG, Dantas MC, Barreira D, Teixeira PR, Cassol S, Tanuri A; Brazilian Network for Drug Resistance Surveillance, AIDS (2003), 17(1):11-21.

An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences.
De Oliveira T, Miller R, Tarin M, Cassol S, Bioinformatics (2003), 19(1):153-4.

Molecular characteristics of human immunodeficiency virus type 1 subtype C viruses from KwaZulu-Natal, South Africa: implications for vaccine and antiretroviral control strategies.
Gordon M, De Oliveira T, Bishop K, Coovadia HM, Madurai L, Engelbrecht S, Janse van Rensburg E, Mosam A, Smith A, Cassol S, J Virol (2003), 77(4):2587-99.

Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses.
Salemi M, De Oliveira T, Courgnaud V, Moulton V, Holland B, Cassol S, Switzer WM, Vandamme AM, J Virol (2003), 77(13):7202-13.

Variability at human immunodeficiency virus type 1 subtype C protease cleavage sites: an indication of viral fitness?.
de Oliveira T, Engelbrecht S, Janse van Rensburg E, Gordon M, Bishop K, zur Megede J, Barnett SW, Cassol S, J Virol (2003), 77(17):9422-30.

Prevalence, incidence and mother-to-child transmission of HIV-1 in rural South Africa.
Rollins NC, Dedicoat M, Danaviah S, Page T, Bishop K, Kleinschmidt I, Coovadia HM, Cassol SA, Lancet (2002), 360(9330):389.

Novel evolutionary analyses of full-length HIV type 1 subtype C molecular clones from Cape Town, South Africa.
zur Megede J, Engelbrecht S, de Oliveira T, Cassol S, Scriba TJ, van Rensburg EJ, Barnett SW, AIDS Res Hum Retroviruses (2002), 18(17):1327-32.

Molecular cloning and functional analysis of three type D endogenous retroviruses of sheep reveal a different cell tropism from that of the highly related exogenous jaagsiekte sheep retrovirus.
Palmarini M, Hallwirth C, York D, Murgia C, de Oliveira T, Spencer T, Fan H, J Virol (2000), 74(17):8065-76.

Sequence of the env gene of some KwaZulu-Natal, South African strains of HTLV type I.
Bhigjee AI, Tarin ML, Bill PL, De Oliveira T, York D, AIDS Res Hum Retroviruses (1999), 15(13):1229-33.

Postdoctoral Positions (x3) at CERI & KRISP: Molecular Epidemiology, Human and Pathogen Genomics and Bioinformatics

We are seeking to appoint three post-doctoral fellows with great potential and ambition to become leading scientists. These positions will work with some of the best genomics and bioinformatics scientists in the world. We aim to identify both pathogen and human genomic variation that are associated with the transmission and virulence of pathogens and the development of diseases.

ABBOTT- CERI/KRISP – Fellowship in Genomics (2-week short-term and 12-month long-term Fellowships)

Abbott are offering two long-term fellowships of 12 months and 5 short-term fellowships of 2 weeks. The fellowship will cover travel, accommodation, and a daily stipend.

26th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME)

The VEME workshop faculty includes international leading researchers in virus evolution, molecular epidemiology, and bioinformatics. VEME has run for 26 years and it became known as one of the best workshops in the world. This year it will be presented in Panama and applicants from developing countries have priority.

CERI & KRISP Talks: Context-specific emergence and spread of SARS-CoV-2 lineages

Presenter: Professor Moritz Kraemer, Oxford University, Date: 25 May 2022, Locations: STIAS, Manor House Library, Wallenberg Centre, Stellenbosch or *VIRTUALLY

CERI & KRISP Talks: Using next generation sequencing methods to enhance understanding of the epidemiology and treatment of drug resistant TB

Presenter: Professor Rob Warren, 11 May 2022, Locations: JN De Villiers Auditorium, Clinical Building, Tygerberg Campus, University of Stellenbosch or *VIRTUALLY

How global heating will increase virus swapping between species

A new modelling study published in the journal Nature is the first of its kind to project how global heating will increase virus swapping between species.

New versions of Omicron are masters of immune evasion

Vaccines and prior infection still prevent severe disease from new SARS-CoV-2 strains. Science, 10 May 2022.

Watch | ‘South Africa's 5th COVID Wave Is Very Different From the Earlier One'

BA.4 and BA.5 can easily break the immunity that was conferred by the earlier Omicron variants such as BA.1 and BA.2, says South African bioinformatics professor Tulio de Oliveira

Two new Omicron variants are spreading. Will they drive a new U.S. surge?

The subvariants BA.4 and BA.5 may dodge immunity, especially in unvaccinated people, possibly causing a spike in infections worldwide.

Are COVID surges becoming more predictable? New Omicron variants offer a hint

Omicron relatives called BA.4 and BA.5 are behind a fresh wave of COVID-19 in South Africa, and could be signs of a more predictable future for SARS-CoV-2.

South Africa’s latest surge is a possible preview of the pandemic’s next chapter.

The spread of two newly discovered subvariants has doctors watching closely. New York Times piece on our work, 4 May 2022.

CERI & KRISP Newsletter Apr/May 2022: Novel BA.4 and BA.5 Omicron lineages and the massive collaborative effort t in Africa

Please find CERI’s & KRISP’s newsletter. In our April/May issue of 2022, In this issue, we feature the recent research describing the novel BA.4 and BA.5 Omicron lineages in South Africa and the massive collaborative effort that provides insights on the evolving SARS-CoV-2 epidemic in Africa. We also highlight the New York Times article on how South Africa’s latest surge is a possible preview of the pandemic’s next chapter. We are also pleased to announce the availability of three Postdoctoral positions at CERI & KRISP and are excited to host Prof Rob Warren and Prof Moritz Kraemer at our upcoming seminar series for May.

Are new Omicron subvariants a threat? Here's how scientists are keeping watch

In South Africa, a network of researchers are studying whether new lineages BA.4 and BA.5 escape immunity from COVID-19 vaccines and prior infections.

Omicron’s new sub-lineages in SA: Continued evolution of the virus ‘entirely expected’

Two new sub-lineages of the Omicron variant have been detected in SA and some other countries. However, KRISP scientists say there is no cause for alarm at this stage. Known as BA.4 and BA.5, the team will continue to track their spread and study their properties. The detection of two new sub-lineages of the Omicron variant in South Africa serves as a reminder that the virus will continue to evolve and change over time.

'No cause for alarm' as scientists find two new Omicron strains in SA

South African scientists have discovered two new sublineages of the Omicron coronavirus variant, said Tulio de Oliveira, who runs gene-sequencing institutions in the country.

Prof Tulio de Oliveira: saving lives by searching for clues in pandemics

In Covid-19 history, Stellenbosch University (SU) bioinformatician Prof Tulio de Oliveira will be remembered for first detecting the Beta variant of SARS-CoV-2 in late 2020. In November 2021, a few months after moving from the University of KwaZulu-Natal (UKZN) to SU's School for Data Science and Computational Thinking, he also detected the Omicron variant.

SAMRC Scientific Merit Awards: Prof Tulio de Oliveira is awarded a Gold Medal

The South African Medical Research Council strongly supports excellence in health research and has established a set of medal awards to recognise world-class science. The Awards are among South Africa’s most prestigious and are dedicated to contributions to health research in South Africa.

CERI & KRISP Talks: Planning for research impact: lessons from a decade as director of the IDM at UCT

Presenter: Prof Valerie Mizrahi, 30 March 2022, Locations: STIAS, Breakaway Room, Wallenberg Centre, University of Stellenbosch or *VIRTUALLY

UKZN researchers scoop the 2022 National Batho Pele Excellence Awards

The University of KwaZulu-Natal has congratulated three members of their community who received the 2022 National Batho Pele Excellence Awards (NBPEA) on Thursday evening.

In an uncertain and rapidly changing world, research universities play a critical role in building a better future

Higher education is under pressure, but universities have a crucial role to play in helping society ‘build back better’ from Covid-19 and other existential challenges.

How should the world respond to the next pandemic?

As the WHO mulls when to call the Covid pandemic over, attention is turning to the future. Last November, having alerted the world to the new and highly transmissible Omicron variant of the Sars-CoV-2 virus, South Africa-based scientist Tulio de Oliveira saw that country hit with travel bans.

CERI & KRISP Talks: Host genetic susceptibility to infectious diseases

Presenter: Professor Marlo Moller, 9 March 2022, 12:00-1:00pm Locations: JN DE Villiers Auditorium, Clinical Building, Tygerberg Campus, University of Stellenbosch or *VIRTUALLY

CERI & KRISP Newsletter Feb/Mar 2022: WHO Director-General, Dr Tedros Adhanom Ghebreyesus visit CERI. We are also selected as one of the Ten Breakthro

In our February/March issue of 2022, we focus on the visit of Director-General, Dr Tedros Adhanom Ghebreyesus, Minister of Health Dr. Joe Phaahla, Higher Education, Science and Innovation Deputy Minister Buti Manamela, the Belgian Minister of Development Cooperation, Meryame Kitirto to CERI’s new facilities at Stellenbosch University. We also highlight our selection on the Ten Breakthrough Technologies of 2022 by MIT and the Abbott Pandemic Defense Coalition program to identify novel pathogens and respond to prevent and /or mitigate the impact of the next pandemic

Africa CDC - PUBLIC HEALTH GRAND ROUNDS: Omicron and other COVID-19 variants of concern – where are we now?

Join the next African Union and Africa CDC 2022 Lecture and Discussion Series of Omicron and other COVID-19 variants of concern –where are we now?, "A New Public Health Order in the 21st Century ", Tuesday, 1 March 2022 at 3:00 pm EAT.

No Real-World Evidence BA.2 Is More Severe

Concerns that BA.2 may be more severe than the original Omicron variant have been driven by a hamster study, but real-world data suggest the sublineage isn't more virulent, according to the World Health Organization (WHO).

How tracking coronavirus variants will prepare us for the next global public health threat

Genomic surveillance of SARS-CoV-2 is helping us spot new variants and figure out how to respond. What else could it help us do?

CERI & KRISP Talks: Embracing novel technologies in a pandemic: Experience of real-time genomics and big data analysis in Africa over the past 2 year

Presenter: Dr. Jennifer Giandhari and PhD Candidate, Houriiyah Tegally, 23 February 2022, Locations: STIAS, Breakaway Room, Wallenberg Centre, University of Stellenbosch or *VIRTUALLY

Fact Check: New BA.2 variant HAS NOT caused a spike in deaths for SA

‘Reported’ deaths in South Africa have increased substantially in the past week or so – but it’s got nothing to do with the BA.2 variant.

WHO’s director-general part of high-level delegation visiting SU genomics lab

Stellenbosch University’s (SU) Faculty of Medicine and Health Sciences (FMHS) hosted a high-level international delegation, led by the World Health Organisation’s (WHO) director-general, Dr Tedros Adhanom Ghebreyesus, at its Tygerberg campus in Cape Town on Friday.

WHO Public Health Laboratories knowledge sharing webinars - From SARS-CoV-2 sequences to actionable public health data

In this webinar, we will hear about the setting up of sequencing and bioinformatic pipelines for SARS-CoV-2, timeliness of data generated and the overall system coordination to inform public health action, with experiences and lessons learned from Denmark, South Africa and Argentina.

Africa’s first mRNA hub in Cape Town a potential ‘game changer’, says WHO boss

A collaborative partnership will ensure a boost in vaccine production capabilities in low to middle-income countries. WHO boss, Dr Tedros Ghebreyesus, visited the vaccine research sites in CT and said it was a 'strategic solution' to vaccine inequity.

CERI & KRISP Newsletter Jan/Feb 2022: President Cyril Ramaphosa and minister Dr. Blade Nzimande at CERI’s new facilities at SUN, Students graduate

In our January/February issue of 2022, we focus on the visit of our president Cyril Ramaphosa and minister Dr. Blade Nzimande to CERI’s new facilities at Stellenbosch University. We also highlight two students that graduated with a PhD and a MMedSci Cum Laude at KRISP at UKZN and the new papers and news about Omicron variant.

CERI & KRISP Talks: Collaboration in South Africa to lead the world on the discovery and characterisation of SARS-CoV-2 variants

Presenter: Prof Tulio de Oliveira, Date: 2 February 2022, Locations: JN de Villiers Auditorium, Clinical Building, University of Stellenbosch Tygerberg Campus & K-RITH Tower Building, Nelson R Mandela School of Medicine, UKZN.

Capacity Building in Africa: MMedSci Cum Laude

Congratulations to Ugochukwu (Jacob) Anyaneji. Mr Anyaneji, who has been awarded a Master of Medical Science (MMedSci) Cum Laude at the School of Laboratory Medicine and Medical Sciences College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal in January 2022.

Capacity Building in Africa: A New Doc to Change the World!

We would like to present to you Dr. Emmanuel James San. Dr. San has been awarded his Ph.D. in Medicine at the College of Health Sciences, Nelson R Mandela School of Medicine, University of KwaZulu-Natal in January 2022.

Twitter Science: The new way to quickly communicate scientific results! Please follow us for real-time updates

We at CERI and KRISP are very used to epidemic and pandemic responses. One of the crucial tools for fast communication of results across the scientific community, media, government, and general population is Twitter. Follow us for real-time updates

Covid-infected HIV patient developed 21 mutations, study shows

A South African woman suffering from inadequately treated HIV, and who harboured Covid-19 for nine months saw the respiratory virus develop at least 21 mutations while in her body, according to a study.

Where did Omicron come from? Three key theories

The highly transmissible variant emerged with a host of unusual mutations. Now scientists are trying to work out how it evolved. Nature news piece covering the original Omicron paper and the main theories of how the variant emerged.

South Africa Bolsters Genomics Capability to Hunt Deadly Disease

County secures funding to hire scientists, build laboratories. Other nations to get training to enhance sequencing capability

Ramaphosa lauds SU’s world-class research centre set to lead global epidemic response

President Cyril Ramaphosa, along with the Minister of Higher Education, Science and Technology, Blade Nzimande, and the biotech investor of NantAfrica (a division of NantWorks), Dr Patrick Soon-Shiong, visited the Stellenbosch University (SU) Biomedical Research Institute (BMRI) today (19 January 2022) to view the cutting-edge facilities of the Centre for Epidemic Response and Innovation (CERI), which will provide the genomic sequencing for the development and evaluation of vaccine therapies in South Africa. CERI is to be officially launched later this year.

How We Can Spot the Next COVID-19 Variant Even Faster

In Durban, South Africa, scientists led by Dr. Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University, were conducting routine genomic surveillance of SARS-CoV-2 from different regions when they noticed worrying variations in genomes clustered in Gauteng Province.

Nature’s 10: Ten people who helped shape science in 2021

An Omicron investigator, a Mars explorer and an AI ethics pioneer are some of the people behind the year’s big research stories. The Nature’s 10 list explores key developments in science this year and some of the people who played important parts in these milestones. Along with their colleagues, these individuals helped to make amazing discoveries and brought attention to crucial issues.

The Variant Hunters: Inside South Africa’s Effort to Stanch Dangerous Mutations.

Scientists in a cutting-edge laboratory at CERI and KRISP do part of the work. Local health workers on foot do the rest. Front Page NYTimes Sunday edition paper covering our work.

How South African Researchers Identified the Omicron Variant of COVID

Little is known about the Omicron variant, which was first detected in Southern Africa, but the nature of its mutations and its seemingly rapid emergence have concerned governments around the world. Interview with Prof. Tulio de Oliveira at the New Yorker.

BBC Take: Three people across Africa who made a difference in 2021

What do a seaweed farmer from Tanzania, a scientist in South Africa and a Senegalese influencer all have in common? The BBC's Malu Cursino looks back at how Kaije, Tulio de Oliveira and Khaby made their mark in 2021.

CERI: Why genomic sequencing is crucial in COVID-19 response

Cape Town - In December 2020, South Africa detected the Beta variant and in May 2021 the Delta variant, thanks to robust genomic surveillance. Professor Tulio De Oliveira, a renowned bioinformatician who identified the Beta variant, explains the criticality of genomic sequencing. Professor De Oliveira is the Director of the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) and Centre for Epidemic Response and Innovation (CERI) based in South Africa.

CERI: Realizing the Potential of Pathogen Genomics in Africa

The launch of a new genomics facility, CERI, in South Africa bolsters the continent’s epidemic and pandemic public health response

SA to expedite Covid-19, cancer vaccine development at largest genomics facility on continent

Billionaire Patrick Soon-Shiong has partnered with local universities. He has set up the biggest genomics facility in Africa at Stellenbosch University. He also set up centres of excellence at the universities to research cancer, Covid-19, HIV/AIDS and TB.

Vaccine: SA expat Dr Soon-Shiong launches R3 billion initiative

SA born billionaire and former local physician Dr. Patrick Soon-Shiong has announced an investment of R3 billion to advance vaccine research.

L.A. Times owner plans South Africa vaccine plant

South African-born biotech billionaire Patrick Soon-Shiong’s NantWorks has agreed to invest in a manufacturing plant and complex in the country’s Western Cape and aims to produce COVID-19 and cancer vaccines.

The Rockefeller Foundation Supports the Launch of the Centre for Epidemic Response and Innovation To Help Prevent Future Pandemics

CERI: Centre for Epidemic Response and Innovation to expand pathogen surveillance capability in Africa in partnership with the Rockefeller Foundation.

Ramaphosa to attend announcement by Dr Patrick Soon-Shiong of launch of NantAfrica Covid-19 and cancer vaccine

President Cyril Ramaphosa will be the guest of honour today, Thursday, 23 September 2021, at an announcement by Dr Patrick Soon-Shiong, founder of the multinational conglomerate, NantWorks LLC, of an initiative ambitious initiative to build capacity for advanced health care in Africa.

Unethical? Unnecessary? The COVID-19 vaccine booster debate intensifies

As United States reveals its plan to offer an extra dose of COVID-19 vaccine, equity and scientific questions abound

Stellenbosch University 2 Postdoctoral Positions on Pathogen Genomics, Cape Town

The Faculty of Medicine and Health Sciences at Stellenbosch University is seeking to appoint two molecular biologists with great potential and ambition to become leading scientists. These two positions will work with some of the best pathogen and bioinformatics genomics program in the world, which is currently focused on the COVID-19 response. These full-time contract positions are offered for a period of up to three years.

KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) 2 Postdoctoral Positions on Bioinformatics

KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at UKZN is seeking to appoint 2 Bioinformaticians with great potential and ambition to become leading scientists. Postdoctoral fellows will support researchers with genomic data management and analysis. These full-time contract positions are offered for a period of 3 years and will be affiliated to the School of Laboratory Medicine and Medical Sciences in the College of Health Sciences.

Stellenbosch University 2 Postdoctoral Positions on Bioinformatics, Cape Town or Stellenbosch

The School for Data Science and Computational Thinking at Stellenbosch University is seeking to appoint two Bioinformaticians with great potential and ambition to become leading scientists. These two positions will work with some of the best pathogen and bioinformatics genomics program in the world, which is currently focused on the COVID-19 response. These full-time positions are offered for a period of up to three years.

Six Postdoctoral Research Fellowships in Bioinformatics at Durban, Cape Town or Stellenbosch

Come work with one of the best pathogen research programs in the world, which is currently focused on the COVID-19 response. Twp positions at KRISP at UKZN & Four at Stellenbosch University.

SARS-CoV-2 whole-genome sequencing training using Illumina for the Mozambican Instituto Nacional de Saude (INS)

A senior scientist from the Instituto Nacional de Saude (INS) de Mozambique spent two weeks at KRISP labs at UKZN to receive training generating whole genomes of SARS-CoV-2.

Webinar Series on COVID-19 Genomic Surveillance in Africa - In collaboration with Africa CDC and African Union

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI have started a Webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data in Africa.

9th Webinar Series on COVID-19 Genomic Surveillance in Africa - Oxford Nanopore Technology (ONT) Sequencing of SARS-CoV-2 Genomes

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI have started a Webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data in Africa.

As COVID-19 collides with HIV/AIDS, the pandemic may be taking an ominous turn

As the world less affluent countries scramble for COVID-19 vaccine and contend with deadly surges of the disease, researchers in South Africa have just documented an ominous development: the collision of the pandemic with HIV/AIDS.

8th Webinar Series on COVID-19 Genomic Surveillance in Africa - How to make publication-ready professional-looking figures Part II

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: How to make publication-ready professional-looking figures Part II.

Coronavirus variants get Greek names, but will scientists use them?

From Alpha to Omega, the labelling system aims to avoid confusion and stigmatization. To quell such confusion and avoid geographical stigmas, everyone should now just call it Beta according to a naming scheme announced on 31 May by the World Health Organization (WHO) in Geneva and described in a forthcoming article in Nature Microbiology.

Jiving with Science to get South Africans in tune with Covid-19 science

What is better than music to simplify and spread the facts on a pandemic clouded by so much misinformation? Watch a video series between musicians and scientists aimed at decrease vaccine hesitancy.

7th Webinar Series on COVID-19 Genomic Surveillance in Africa - NGS genome assembly and quality control

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: NGS genome assembly and quality control.

6th Webinar Series on COVID-19 Genomic Surveillance in Africa - Ancestral state reconstruction and import/export analysis of viral lineages

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: Ancestral state reconstruction and import/export analysis of viral lineages.

5th Webinar Series on COVID-19 Genomic Surveillance in Africa - How to make publication-ready professional-looking figures Part I

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: How to make publication-ready professional-looking figures Part I.

Some Nations Could Wait Years for Covid Shots. That is Bad for Everyone

While richer places, such as the U.S., hope to vaccinate most of their citizens within months, poorer countries, like Kenya, expect to reach just small fractions of their populations in that time.

Rare COVID reactions might hold key to variant-proof vaccines

Some people mount an immune response able to fend off a menagerie of coronavirus variants. Nature news covering four of our recent papers on the variant, neutralisation of plasma and Vaccines (Novavax and Astrazeneca)

What’s unique about the body’s response to the 501Y.V2 variant? Find out

New research from South Africa’s genomic surveillance network shows that people infected with the 501Y.V2 variant are also immune to other forms of the virus. The team found the protection against the 501Y.V2 variant could also extend to the original virus circulating the country and the variant first identified in Brazil.

We Now Can See a Virus Mutate Like Never Before

Tracking the coronavirus’s evolution, letter by letter, is revolutionizing pandemic science.In the beginning, there was one. The first genome for the virus causing a mysterious illness we had not yet named COVID-19 was shared by scientists on January 10, 2020. That single genome alerted the world to the danger of a novel coronavirus.

Antibodies from S Africa COVID variant may offer cross-protection

The 501Y.V2 variant reportedly produces a high number of antibodies, providing protection against infection by other variants. The findings in laboratory studies offer hope that COVID-19 vaccines based on the 501Y.V2 variant first identified late last year could protect against multiple variants circulating in different parts of the world

A Virus Variant by Any Other Name - Please

B.1.351 may sound sweet to a molecular epidemiologist, but what is the alternative, other than stigmatizing geographical names? News piece at NY Times highlighting our work with WHO on a new nomenclature system for COVID-19 variants

Another coronavirus variant detected in SA, but no reason to panic

A new SARS-CoV-2 variant, which has dominated Covid-19 infections in Uganda and Rwanda, has been detected in South Africa. The announcement was made by Professor Tulio de Oliveira, director of the KRISP lab. However, de Oliveira told Health24 that is not a variant of concern, and that genome surveillance will monitor this and other variants

Covid variants: What are they and will vaccines work?

A variant of concern first identified in Brazil has now been found in the UK. Public health officials are investigating the six cases and are deploying more testing to see if it has spread to more people. Some variants, like this one, appear to be more contagious and there are concerns vaccines may not work quite so well against them.

Coronavirus variants update: One has spread to over 90 countries, two on WHO watchlist

Scientists worldwide have been closely monitoring the emergence of coronavirus variants. Although there are a large number of variants, some of them have turned out to be more alarming. Professor Tulio de Oliveira provided an update on the spread of three of these, and said that two more have been placed on the WHO's watchlist.

South African scientists on pandemic’s frontline

South Africa’s pause of its rollout of the Oxford/AstraZeneca vaccine in response to concern about a local coronavirus variant sparked global debate —and shone a spotlight on how the country’s science has become vital to understanding where the pandemic may go next.

All These Mutant Virus Strains Need New Code Names

As potentially more dangerous variants of Covid-19 spread, scientists are taking a crack at giving them clearer names that’ll help in the fight. Another very interesting piece of The Wired magazine one SARS-CoV-2 variants' names

Worrisome New Coronavirus Strains Are Emerging. Why Now?

Across the globe, SARS-CoV-2 is evolving ways to evade the immune system and become more infectious. Blown pandemic response plans are to blame. Really interesting but funny piece at The Wired magazine.

Fast-spreading COVID variant can elude immune responses

Evidence that a variant of the coronavirus identified in South Africa might compromise immunity sparks concerns about vaccine effectiveness.

Genome Detective Coronavirus variant typing tool

Phylogenetic identification of variants 501Y.V1, 501Y.V2, 501Y.V3 (B.1.1.7, B.1.351, P.1 / Nextstrain 20I, 20H, 20J). Tool also determines nucleotide (NT), amino acids (AA) and codon (CDS) mutations. The mutations list are provided in html and excel formats.

Alarming COVID variants show vital role of genomic surveillance

Efforts to track SARS-CoV-2 sequences have helped identify worrying variants - but researchers are blind to emerging mutations in some regions.

‘A bloody mess': Confusion reigns over naming of new COVID variants

As more lineages emerge, researchers are struggling with a patchwork of nomenclature.

As Coronavirus Mutates, the World Stumbles Again to Respond

A South African tip led to the discovery of mutations around the world. With infections skyrocketing, 'it's a race against time.'. Doctors and nurses at a South African hospital group noticed an odd spike in the number of Covid-19 patients in their wards in late October...

Will vaccines work against the new COVID variants? Scientists race to find out

One year later and the new coronavirus is still posing new questions for researchers. The recent emergence of new COVID-19 variants across the world has left scientists searching for answers once again as they try to understand what these changes mean for the pandemic - and vaccine roll-outs. As South Africa awaits the arrival of its first shipment of COVID vaccines there are growing concerns about a new coronavirus variant - known as 501Y.V2 - circulating in the country, and what the changes in the virus could mean for how well the jabs work.

Answers to 9 crucial questions about the coronavirus variants spreading around the world

Experts worldwide are urgently studying three coronavirus variants to understand what risks they pose. One variant first identified in the UK, one in South Africa, and one in Japan are probably more contagious than the original strain. They have caused cases to surge and the three nations to lock down. Here are nine key questions about the variants, answered.

Could new COVID variants undermine vaccines? Labs scramble to find out

Researchers race to determine why lineages identified in Britain and South Africa spread so quickly and whether they'll compromise vaccines.

KRISP COVID-19 Scientific News Coverage

KRISP believes that open and independent scientific information is represented by good journalism that determines its value to the society it serves. Read news at KRISP COVID-19 Scientific News Coverage.

WHO calls for new names for Covid variants to avoid country stigma

Countries that conduct a lot of genetic sequencing are more likely to find new strains, say experts

Third concerning coronavirus variant should be a 'wake up call' to the world, experts warn

A variant identified in Japan in arrivals from Brazil shares 'concerning' characteristics with mutations detected in the UK and South Africa

The New Covid-19 Strain in South Africa: What We Know

Researchers warn that the new variant may spread faster and could reduce the efficacy of vaccines

As the coronavirus mutates, the world stumbles to respond - Brief on NY Times live blog

The coronavirus has evolved as it has made its way across the world, as any virus is expected to do. But experts have been startled by the pace at which significant new variants have emerged.

South African variant unlikely to fully negate COVID vaccines, scientist says

JOHANNESBURG (Reuters) - A variant of the coronavirus first detected in South Africa is unlikely to completely negate the immunising effects of vaccines, a researcher studying it told Reuters.

South African Covid variant may affect vaccine efficacy, warn scientists

Mutation reduces ability of antibodies to bind to virus and could make some shots less effective.

Boris Johnson Tightens U.K. Lockdown, Citing Fast-Spreading Version of Virus

The variant is up to 70 percent more transmissible than earlier versions, officials said. People in southeast England, including London, were told to stay at home.

Fast-spreading virus variants raise alarms

Scientists are scrambling to better understand effects of a series of worrisome mutations from in the U.K. and South Africa variants.

Pr Tulien de Oliveira: 'Si le virus continue à circuler librement, le risque qu'il s'adapte mieux augmente'

'Si nous permettons au virus de continuer à circuler librement, nous lui donnons une grande marge de manœuvre pour mieux s'adapter à la transmission chez l'homme', déclare Tulio de Oliveira, le Brésilien à l'origine de la découverte d'une nouvelle mutation "plus transmissible" du coronavirus qui suscite des inquiétudes dans le monde entier.

South Africa hits 1 million coronavirus cases as new variant spreads rapidly

President Cyril Ramaphosa expected to announce new restrictions in attempt to slow the surge

Coronavírus: brasileiro que descobriu mutação de covid-19 explica nova variante

Tulio de Oliveira, o brasileiro por trás da descoberta de uma nova mutação "mais transmissível" do coronavírus que vem causando preocupação ao redor do mundo, diz à BBC News Brasil que "se o vírus continuar circulando livremente, o risco dele se adaptar melhor aumenta".

South African Covid-19 variant may be 'more effective at spreading

Research still to confirm threat posed but variant does not appear to provoke more serious symptoms

Variants put spotlight on immunocompromised patients' role in the COVID-19 pandemic

In June, Ravindra Gupta, a virologist at the University of Cambridge, heard about a cancer patient who had come into a local hospital the month before with COVID-19 and was still shedding virus. The patient was being treated for a lymphoma that had relapsed and had been given rituximab, a drug that depletes antibody-producing B cells. That made it hard for him to shake the infection with SARS-CoV-2.

Got questions about the new Covid-19 variant in South Africa? Health department has lots of answers

The new variant of SARS-CoV-2 detected in SA has left scientists working round the clock to unravel its mysteries, the health department said on December 19 2020. The department of health issued a lengthy list of questions and answers on Saturday after announcing that the virus that causes Covid-19 has evolved into a new variant.

KRISP produces over 1000 HIV-1 genomes in record time

Durban, 3 December 2020. The KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal has produced over 1000 HIV-1 genomes in record time in South Africa, a significant scientific endeavor to understand how drug resistance has developed to a new and potent antiretroviral (ARV) treatment.

How many people are catching Covid in hospital?

Prof Carl Heneghan & Tom Jefferson write at the Spectator about nosocomial infection in the U.K. In this article they mention our genomics and outbreak response (Lessells, Moosa & de Oliveira 2020) work on a large hospital outbreak in South Africa.

The KZN Covid-19 Research Consortium

The KZN Covid-19 Research Consortium invites researchers, scientists, and clinicians to submit an abstract for its upcoming virtual conference. Abstracts should relate to KZN-specific Covid-19 research findings and/or experiences and practice. An example of experience/practice may include experiences of working in hospital or clinic settings; or what the challenges were in clinical research conduct.

16 new lineages of SARS-CoV-2 emerge in South Africa despite lockdown

Published in a recent medRxiv* paper, researchers from South Africa, the United Kingdom, and Brazil found that these mutations in SARS-CoV-2 lineages are localized to South Africa. These unique strains, not found elsewhere in the world, are thought to have contributed around 42% to the country's total infection rate.

SPARK South Africa: Novel Diagnostics Grant Application 2020

Proposals will be reviewed by a selection committee composed of KRISP, UKZN, eThekwini, Stanford and SPARK Global faculty and commercial and industry experts. Based on the compiled rankings, finalists will be invited to present an oral pitch to the review panel in early December, 2020. Approximately 3-5 proposals selected for awards (number dependent on available funding) will be notified before the end of December, 2020.

28th Weekly Press Briefing on the Coronavirus disease outbreak - Dr John Nkengasong & Prof. Tulio de Oliveira

WHAT: Weekly interaction with members of the media to share critical updates on steps taken to implement key aspects of the joint continental strategy for COVID-19 response; and to also highlight the coordinated efforts by African Union Member States to combat the pandemic in their respective countries.

4th Webinar Series on COVID-19 Genomic Surveillance in Africa - Main Routes of Entry and Genomic Diversity of SARS-CoV-2 in Uganda

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: Main Routes of Entry and Genomic Diversity of SARS-CoV-2 in Uganda .

Accelerating genomics-based surveillance for COVID-19 response in Africa

The use of genomics to support the response to COVID-19 and containment of the virus in Africa is currently low. To address this suboptimal use of genomics, the Africa Centres for Disease Control and Prevention (CDC) Institute of Pathogen Genomics, in consultation with the Africa CDC led African Task Force for Coronavirus Preparedness and Response (AFTCOR) laboratory technical working group.

How a team of scientists worked tirelessly to help the COVID-19 response in Africa

Ahead of the emergence of the SARS-CoV -2 outbreak in South Africa KRISP started preparing for it. KRISP really rose to the occasion in the fight against COVID-19 pandemic in Africa. In the process, KRISP trained 1000s of health care workers, produced genomic protocols & capacitated dozens of laboratories in Africa to respond to the COVID-19 pandemic

3rd Webinar Series on COVID-19 Genomic Surveillance in Africa - SARS-CoV-2 whole genome sequencing and quality control

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: SARS-CoV-2 whole genome sequencing and quality control .

2nd Webinar Series on COVID-19 Genomic Surveillance in Africa - PHA4GE and Public Health

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: Public Health Alliance for Genomic Epidemiology (PHA4GE): Strengthening Bioinformatics in Public Health .

South Africa 59% excess deaths imply hidden Covid-19 toll

South Africa witnessed some 17000 extra deaths from natural causes or 59% more than would normally be expected between early May and mid-July, scientists said, suggesting many more people are dying of Covid-19 than shown in official figures.

Excess deaths increase but we are ‘still in the dark'

There have been 17090 more deaths in the country than there were in previous years during the same period. But the official number of Covid-19 deaths is about 6000. There is a significant departure from the historical trends, even under these abnormal circumstances.

Webinar Series on COVID-19 Genomic Surveillance in Africa #1

The Africa Union and AfricaCDC, in partnership with SANBI, KRISP, H3AbioNet and the Africa Centre of Excellence for Genomics of Infectious Diseases have started a weekly Webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data in Africa.

South Africa Data May Underreport Virus Deaths, Experts Say

The official number of deaths linked to Covid-19 in South Africa doesn't reflect the true scale of the crisis, with provinces that have been hit hardest by the outbreak showing a surge in fatalities, health experts say.

Experts question ‘underreported' virus deaths in South Africa

The official number of deaths linked to Covid-19 in South Africa doesn't reflect the true scale of the crisis, with provinces that have been hit hardest by the outbreak showing a surge in fatalities, health experts say.

South Africa joins 'Big 5' COVID-19 countries

South Africa has joined the United States, Brazil, India, and Russia as the countries with the most recorded COVID-19 cases. On Saturday, Health Minister Dr Zweli Mkhize announced the country has 350,879 confirmed COVID-19 cases.

Initial COVID-19 Infections In CT Came From Europe, Researchers Find

CAPE TOWN - Genome sequencing, by colleagues at Stellenbosch University and the Network for Genomic Surveillance, was used to trace most of the very first COVID-19 cases reported in the Western Cape back to Europe.

Scientists found who may have triggered the coronavirus crisis in Cape Town

There were multiple — possibly hundreds — of introductions of the novel coronavirus virus to Cape Town from foreign travellers and return citizens, scientists found.

SA's first Covid-19 vaccine trial brings hope

Durban - The newly launched Africa Centres for Disease Control and Prevention Consortium for Covid-19 vaccine clinical trial by the AU Commission is a glimmer of hope as the first vaccine trial gets under way in South Africa.

Early transmission of SARS-CoV-2 in South Africa

The Network for Genomic Surveillance in South Africa (NGS-SA) presents a molecular epidemiological study of the first twenty-one SARS-CoV-2 whole genomes sampled in the first port of entry, KwaZulu-Natal (KZN), during the first month of the epidemic.

Snapshot of African SARS-CoV-2 Diversity

This report focuses on the first SARS-CoV-2 388 genomes from Africa. These genomes were accessed from GISAID and analysed against a backdrop of reference sequences. By comparing our viral genomes against others, we can infer how and when SARS-CoV-2 was introduced into Africa and how it has spread within the continent.

Network for Genomic Surveillance in South Africa (NGS-SA)

KRISP is a founding member of the Network for Genomic Surveillance in South Africa. A network of laboratories, scientists and academic institutions that have joined forces to ensure the public health responses to COVID-19 in South Africa have access to the best possible scientific data.

5fm Catch Up: Dexamethasone (Professor Tulio de Oliveira, Dr Richard Lessells and Prof Yunus Moosa)

Nick Hammer chats to Prof Tulio De Oliveira, Dr. Richard Lessells and Prof Yunus Moosa about the trial on the UK of Dexamethasone for COVID-19.

South Africa: How to get the best readings from thermometers

Experts weigh in on how to avoid inaccurate results during Covid-19 testing. Distance, hair and sweat can all affect the reading of the temperature scans you've been experiencing at work, shopping malls and schools.

SA accelerating towards virus peak without capacity, experts warn

With Covid-19 now growing by leaps and bounds in South Africa, a Mail & Guardian survey has spotlighted the nationwide shortage of staff, equipment and facilities needed to cope with the infected people who are set to flood the healthcare system when the outbreak hits its peak.

Dexamethasone study hailed a game changer in fight against COVID-19

Results of a study conducted in the United Kingdom have been hailed as a game-changer in the fight against COVID-19. A University of Oxford study has shown that the drug, dexamethasone, has been proven to reduce one in eight deaths in critically ill patients on ventilators.

En Afrique du Sud, l'espoir ténu du BCG, « boosteur » du système immunitaire contre le Covid-19

L'Afrique apporte sa pierre à la science (9). Cinq cents personnes du Cap, foyer de l'épidémie de coronavirus en Afrique du Sud, participent à une étude en double aveugle sur le vaccin contre la tuberculose.

Study tells ‘remarkable story' about COVID-19's deadly rampage through a South African hospital

On 9 March, a patient who had recently traveled to Europe and had symptoms of COVID-19 visited the emergency department of St. Augustine's, a private hospital in Durban, South Africa. Eight weeks later, 39 patients and 80 staff linked to the hospital had been infected, and 15 patients had died—fully half the death toll in KwaZulu-Natal province at that time.

En Afrique du Sud, des chercheurs remontent la piste du coronavirus

L'Afrique apporte sa pierre à la science (3). Dans une étude saluée par la revue « Science », le laboratoire Krisp établit avec une rare finesse la chaîne de contamination dans un hôpital de Durban.

South Africa: Protecting Healthcare Workers 'Not Rocket Science'

An investigation into the first major outbreak of Covid-19, at a Durban hospital, shows that staff members spread the virus, raising concerns about the safety of healthcare workers as infections rise.

Coronavirus in South Africa: Eight lessons for the rest of the continent

South Africa leads this continent in many ways. Right now, it is poised to lead Africa into the next, most dangerous phase of the pandemic, as the country braces itself for a dramatic rise in infections that will almost certainly overwhelm its relatively well-resourced healthcare system.

Full report: How 135 people at St Augustine's Hospital in Durban got COVID-19

The report outlines in detail how SARS-CoV-2, which causes COVID-19, spread through Netcare's 149-bed facility in Durban. This piece in Bhekisisa also contains simple take-away messages and recommendations on how to protect health care workers and hospitals from COVID-19. Download the full investigative report here.

The South African COVID-19 Pregnancy Outcomes Study

The South African Obstetric Surveillance System Consortium in partnership with the SA MRC Maternal and Infant Health Strategies Unit and KRISP/UKZN invites clinicians from South African obstetric institutions to participate in this national study.

Three ‘detectives', a virus and the patient who infected an entire hospital | Future Planet

Durban, South Africa, March 9. A man goes to the emergency room of the San Agustín hospital. He coughs, his head hurts. They admit him and share a stay with a woman who has had a heart attack. That man has just come from Europe, the lady lives in a nursing home.

Lockdown has stopped SA's flu season in its tracks - it's now several weeks late

South Africa's lockdown seems to have stopped the winter influenza outbreak in its tracks. School closures and travel bans are likely to have prevented seasonal flu from taking hold. A mild flu season will help in the fight against Covid-19, but lifting lockdown could result in flu resurging.

Between two devils: Why hospitals must act fast to prevent health worker deaths

A new investigative report details the rapid spread of coronavirus disease in St Augustine's Hospital in Durban, and how it could have been prevented. The study, which Bhekisisa has seen, was conducted by researchers at the University of KwaZulu-Natal's (UKZN) Nelson R. Mandela School of Medicine and the KwaZulu?Natal Research Innovation & Sequencing Platform, KRISP.

Southern Africa: COVID-19 Roundup | Back to School

As schools get ready to reopen, models suggest the country will still not have enough ICU beds at the virus peak. In the meantime, court battles rage while unions fight to keep miners safe.

Report into a nosocomial outbreak of coronavirus disease 2019 (COVID-19) at Netcare St. Augustine's Hospital

This report presents the findings and recommendations of an investigation into a nosocomial outbreak of coronavirus disease 2019 (COVID-19) at St. Augustine's Hospital in Durban, South Africa. The investigation began on 4 April after the identification of a number of confirmed COVID-19 cases and three deaths at the hospital. Investigation methods included medical record reviews, ward visits, and interviews with health care workers and management. A detailed timeline of patient cases was constructed to generate hypotheses as to the spread of infection through the hospital. In addition, DNA sequencing of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) nucleic acid extracted from nasopharyngeal and oropharyngeal swab samples was performed and phylogenetic analysis was conducted.

14% OF KZN COVID-19 CASES CAN BE TRACED TO ST AUGUSTINE'S HOSPITAL - REPORT

The report by a University of KwaZulu-Natal-led research team was made public on Wednesday following an investigation at the facility. A new report shows that 14% of all COVID-19 cases in KwaZulu-Natal can be traced to the coronavirus outbreak at Netcare's St Augustine's Hospital in Durban

Investigation report reveals single source of infection caused St Augustine virus outbreak

A newly released investigation report revealed there were a total of 15 patient deaths and 119 confirmed Coronavirus cases at the Netcare St Augustine Hospital.

University probe finds over 100 COVID-19 cases at St Augustine's Hospital

An investigation has found there were 119 confirmed cases of coronavirus identified at Durban's St Augustine's Hospital by the end of last month. The probe into the COVID-19 outbreak at the hospital was led by a team at UKZN.

Investigation into Covid-19 outbreak at Durban hospital reveals virus spread through patient to patient transfer

Durban - An investigation into the Covid-19 outbreak at Durban's St. Augustine's Hospital has found the cluster outbreak was as a result of patient to patient transfer after both were admitted to the hospital around the same time.

More than 100 infections and 15 patient deaths in Covid-19 outbreak at St Augustine's Hospital

The Covid-19 outbreak at St Augustine's Hospital in Durban which forced health authorities to close it down, resulted in 119 people testing positive and 15 patient deaths.

How one Covid-19 case at St Augustine's Hospital led to 135 infections within 51 days

The outbreak of coronavirus disease at the Netcare St. Augustine's Hospital in Durban, that led to the infection of at least 135 patients and staff in the hospital complex and people in a nursing home, was caused by a single patient admitted to the facility's emergency department early in March, a new report has found. The virus spread so fast in the hospital that infections caused by the outbreak in the hospital constituted almost 14% of Covid-19 cases in KwaZulu-Natal by the end of April.

Netcare welcomes findings into Covid-19 outbreak at St Augustine's Hospital

Durban - The Netcare group has welcomed the findings of a report which investigated the outbreak of Covid-19 at the St Augustine's Hospital. On Wednesday, the investigative report was released and showed that between March 9 and April 30, there were 119 people – among them 39 patients and 80 staff members – who had confirmed cases identified at the hospital. Fifteen of the 39 patients died.

University probe finds over 100 Covid-19 cases at St Augustine's Hospital

An investigation has found there were 119 confirmed cases of coronavirus at Durban's St Augustine's Hospital by the end of last month. The probe into the Covid-19 outbreak at the hospital was led by a team at University of KwaZuu-Natal.

How one COVID-19 case at St Augustine's Hospital led to 135 infections within 51 days - report

The coronavirus spread rapidly through Netcare St. Augustine's Hospital and beyond and made up 14% of KwaZulu-Natal's infections by the end of April. The study, seen by Bhekisisa, was conducted by researchers at the University of KwaZulu-Natal's (UKZN) Nelson R. Mandela School of Medicine and the KwaZulu?Natal Research Innovation & Sequencing Platform, Krisp.

PRESS RELEASE: Findings and recommendations of the investigation into the Covid-19 outbreak at Netcare St Augustine's Hospital led by UKZN team

The investigation found that between 9 March and 30 April 2020, there were 119 confirmed cases identified at St. Augustine's Hospital (39 patients and 80 staff). Fifteen of the 39 patients died (case fatality rate 38.5%). The most plausible explanation for the outbreak is that there was a single introduction of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2)

‘Small fires' drive rise in Covid cases

As President Cyril Ramaphosa eases restrictions on one of the most stringent lockdowns in the world, the number of Covid-19 daily infections has continued to rise. Up to 700 people a day tested positive this week.

Cape Town Becomes Center of South Africa's Virus Pandemic

Clusters of infections contribute to surge in the Western Cape. Contrary to projections, Gauteng has seen slow rise in numbers. By Pauline Bax and Prinesha Naidoo, Bloomberg.

SAfm Sunrise, 15 May Professor Tulio de Oliveira argues that the value of lockdown cannot be underestimated

Since Lockdown began on the evening of 26 March 2020, South Africa is yet to see the flattening of the Curve. Professor Tulio de Oliveira has argued that the value of lockdown cannot be underestimated.

Nick Hammer, 5FM, chats to the director at KZN Research Innovation and Sequencing Platform (KRISP), UKZN, about how the government's interventions

Nick Hammer chats to Prof Tulio De Oliveira about how the government's interventions, including the travel ban and lockdown, potentially averted the death of at least 20 000 people.

Can you get Covid-19 from pets or poultry? East Coast Radio Breakfast Show with Darren Maule

Professor Tulio de Oliveira is the director of the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at UKZN. He joins us for another Covid-19 information session.

Researcher explains how early SA lockdown has saved at least 20,000 lives

Comparative trajectory analysis from the day of 100th infection shows SA on 11,000 cases, while UK at that point on 161,000

The Western Cape now accounts for more than half of South Africa's coronavirus cases

The coronavirus outbreak in South Africa has hit hardest in the Western Cape, home to the city of Cape Town.

A Lockdown may Have Averted 20,000 Deaths, Says Bio-Information Expert

As the nation debates about whether lockdown restrictions must be eased, Professor Tulio de Oliveira argues that its value cannot be underestimated.

Lockdown and other interventions potentially saved 20 000 lives

Government interventions, including the travel ban and lockdown, have potentially averted at least 20 000 deaths, says a top scientist

UKZN's Professor Tulio de Oliveira talks Covid-19 to East Coast Radio Breakfast Show

UKZN's Professor Tulio de Oliveira is a bioinformatician from the KwaZulu-Natal's Research, Innovation and Sequencing Platform (KRISP) faculty - and he spoke to us this morning.

KRISP Newsletter Apr/May 2020: Highlight our work on the current COVID-19 pandemic.

In our April/May issue of 2020, We have worked very hard to produce and analyse COVID-19 data in real time. We have also sequenced many SARS-CoV-2 genomes in South Africa that showed how the virus was introduced in the country. We also worked with the media to help to translate scientific results to the general public. KRISP believes that open and independent scientific information is represented by good journalism that determines its value to the society it serves.

KRISP has produced most of the COVID-19 viral genomes in South Africa & created a Big Data Analysis team at UKZN

KwaZulu Natal's Research, Innovation and Sequencing Platform (KRISP) and the Big Data Flagship Program of the University of KwaZulu-Natal (UKZN) has a multi-disciplinary team of world-renowned experts which mainly focuses on analysis and control of viral outbreaks and genomic analysis.

SA's confirmed Covid-19 cases rise to 5 951, with 13 deaths on Day 1 of level 4 lockdown

Cape Town - Confirmed Covid-19 infections in South Africa have risen to 5 951, with 13 deaths recorded in the past 24 hours, Health Minister Zweli Mkhize announced on Friday. This is an increase of 304 confirmed cases on Thursday's figures.

Covid-19: Infections could rise by 10% per day after lockdown lifts - top scientists

The Covid-19 infection rate could jump from 5% to 10% per day as South Africa emerges from a five-week hard lockdown from Friday. Scientists are expecting a "rapid rise" in infections ahead of the disease hitting its peak in summer.

Coronavirus: 27 patients on ventilators as SA edges towards the end of 'hard' lockdown

As South Africa edges towards the end of the so-called hard lockdown, and with an expected spike in Covid-19 cases around the corner, just 27 Covid-19 patients are on ventilator support in hospital, seemingly in line with government's projections. Sarah Evans from News24 highlights our Big Data COVID-19 analysis of in South Africa.

Human trials for vaccine begins

Many deaths are still likely to hapen because of the coronavirus, but a promising vaccine against Covid-19, developed by the University of Oxford, started human trials this week. UKZN scientists warn many deaths still likely before virus is conquered

The Pros and Cons of high-speed science

Scientific research on Covid-19 has been published at an unprecedented scale and speed, but some fear that this is at the cost of scientific rigour. Adele Baleta explores the pros and cons of high-speed science. By Adele Baleta for Spotlight, Daily Maverick and News24, 24 April 2020

Data science sees gold rush to create COVID-19 breakthroughs

The use of data science has become a critical 'gold rush' as research scientists across the globe partner on scientific breakthroughs, to better understand the novel coronavirus (COVID-19) and recommend strategies to help address its complexities

SA scientists on breaking the Covid-19 code

Durban - A team of world renowned scientists based at the University of KwaZulu-Natal has launched a fundraising campaign to support the analysis of Covid-19 data - which could provide vital research and insight on the spread of the virus across both South Africa and globally as the world battles to contain the devastating pandemic.

Scientists launch fundraising campaign to support analysis of COVID-19 data in real time

They have produced five of the six COVID-19 viral genomes in the country, which clearly showed how the virus was introduced into South Africa. KwaZulu Natal's Research, Innovation and Sequencing Platform (KRISP) and the Big Data Flagship Programme of UKZN collaborate in a fund raising campaign.

KwaZulu-Natal researchers seeking to research Covid-19 outbreak in South Africa

Scientists at the University of KwaZulu-Natal (UKZN) have launched a fundraising campaign to finance independent research into the Covid-19 outbreak in South Africa. Donors will qualify for Section 18A tax certificates, issued by the UKZN Foundation.

Support South Africa's COVID-19 Scientists on the Frontline

The countries which have had some of the best responses to the COVID-19 pandemic, Singapore and South Korea, have closely followed scientific advice. Our government has already used our results to show that South Africa is flattening the curve. We need your support to ensure that we can keep producing high-level scientific information to guide our national response.

Big Data, Bioinformatics & Artificial Intelligence to fight COVID-19 epidemic in South Africa

KRISP has partnered with the Pro-Vice Chancellor of Big Data Analysis at UKZN, Prof. Francesco Petruccione to put together a team with more than 20 researchers, including computer scientists, mathematicians, statisticians, bioinformaticians, infectious diseases clinicians, theoretical physicists and quantum computing scientists to analyze the COVID-19 outbreak in South Africa.

Big Data presentations on COVID-19 by Profs. Salim Abdool Karim, Tulio de Oliveira, Richard Lessells and Francesco Petruccione

Watch the full videos of the Big Data, Genomics and Clinical Medicine presentations of COVID-19 by experts. Full videos of Prof. Salim Abdool Karim, Prof. Tulio de Oliveira and Dr. Richard Lessells in April 2020. Data@breakfast organised by Prof. Francesco Petruccione of UKZN Big Data Flagship program.

SA government plans for Covid-19 to peak in September but questions about data remain

The extended five-week national lockdown has postponed South Africa's worst-case Covid-19 scenario to September, a government projection shows. March was arguably the busiest month for President Cyril Ramaphosa in his tenure as head of state. Every other day, the President is putting out fires.

Covid-19 will change us in many ways, says UKZN war room specialist

A UKZN seminar series has been moved online in the face of the COVID-19 epidemic. IT was a logical step for UKZN Pro Vice-Chancellor for Big Data and Informatics, Professor Francesco Petruccione, to turn to the online world to continue with his monthly data@breakfast seminar series in a time of national Covid-19 lockdown.

There is no magic bullet: the town that turned the tide against HIV. Lessons learned in Eshowe are being used against coronavirus.

Lessons learned in Eshowe, South Africa, one of the areas worst hit by the HIV pandemic, are being used against coronavirus. Jason Burke in Eshowe writes to The Guardian about KRISP and UKZN work.

Masks - to wear or not to wear

Durban - Conflicting information and misinformation about whether to wear a mask or not during the Covid-19 pandemic has left many people confused.The World Health Organisation (WHO) has recommended people not wear a mask unless they are sick with Covid-19 or caring for someone who has the virus.

Public warned about 'rapid' coronavirus test kits

Durban - ONLY polymerase chain reaction (PCR) tests are being used to test for the coronavirus in South Africa, which can detect infection before patients become symptomatic, and not rapid serological tests, which are not recommended by experts for public use.

Single mom makes living sewing face masks amid Covid-19 mask shortage

A young single mother has started her own business making masks, which she distributes in rural areas. Currently there's a huge debate on the subject of a face mask's efficiency, with the World Health Organisation saying there is no evidence to suggest it curbs the spread. However, some experts believe it does indeed work, as studies into other coronaviruses proved masks can reduce the risk.

Odd drop in how Covid-19 numbers grow

Speaking to the media on Wednesday night, Health Minister Zweli Mkhize said, We will only fight coronavirus with facts and evidence-based strategies, not fake news. Mail and Guardian news, 2 April, 2020.

Four reasons to be hopeful about South Africa's coronavirus testing plan

South Africa stands at a crossroads in the fight against the new coronavirus — and winning the battle will hinge on the decisions we make now about how quickly and how broadly we begin to test for the virus. In a grim news cycle, Health Minister Zweli Mkhize's announcement yesterday that the country is evaluating rapid tests for the new coronavirus is something to celebrate. Bhekisisa opinion piece by Dr. Richard Lessells and Prof. Mosa Moshabela.

African countries unprepared to respond to coronavirus outbreak

Durban - An infectious disease specialist says that although the world is much more prepared to deal with a pandemic than in previous years, African countries are still unable able to respond adequately to a respiratory virus like Covid-19.

Testing to be ramped up and new tests in pipeline for COVID-19

South Africa's strategy to defeat Covid-19 is to lock down the country and scale-up testing to quickly identify people who may have been infected with the SARS-CoV-2 virus. Health journalism by Adele Baleta for Spotlight 31 March 2020.

Am Kap geht es erst los

Südafrika hat die meisten Corona-Fälle in Afrika. Auch wenn die Zahlen denen in Europa noch hinterherhängen, warnen Experten vor einer rasanten Ausbreitung des Virus. Von Julia Jaki, Kapstadt, 27. März 2020

What you need to know about Covid-19 to protect yourself

There is much we do not understand about the virus and how it will affect our bodies, especially after Minister of Health Zweli Mkhize said that 60% to 70 % of people could be infected by Covid-19. The Mail & Guardian asked different experts — including disease specialist Dr Richard Lessells, the National Institute for Communicable Diseases, and the World Health Organisation (WHO) — for information about this coronavirus.

Big Data update for COVID-19 in Africa: Epidemiology & Genomics

Together with the Big Data group of UKZN, we started a daily update of the data on COVID-19 in South Africa and a weekly update on cases, deaths and genomic data in Africa. All of the scripts for generation of the data is deposited open in repositories as all any data developed by our team.

M&G's latest Covid-19 projections

Three thousand people have died in Italy as a result of Covid-19, with more than 35000 infected. Three weeks ago, the country passed the 150 mark for infected people. It took three weeks to get to that number. In South Africa, we passed the 150 mark on Thursday, two weeks after the first local positive test. Mail and Guardian, 19 March 2020.

KRISP is Helping the Response to Coronavirus in Africa. See our activities and please support us...

The University of KwaZulu Natal's Research Innovation and Sequencing Platform (KRISP) boasts state-of-the-art laboratory facilities and scientific expertise and capacity not commonly found in Africa. This places our multidisciplinary team in the ideal position of being able to play a critical role in supporting the public health response to the COVID-19 pandemic. The team has placed all current research activities and services on hold to focus full-time on helping with this outbreak. Please help to fund it by donating to our activities here.

Coronavirus testing: How it works, what it costs and when you need a test

The National Institute for Communicable Diseases can run hundreds of tests at the same time but ultimately the number of tests South Africa will be able to carry out for the new coronavirus depends on the machines, people and testing supplies available.

UKZN to launch health war room to tackle coronavirus

To bolster these efforts, the university has created an email address: covid19@ukzn.ac.za and the hashtag: #ukzncovid19 that staff and students can make enquiries to. The university is in the process of creating a hotline, which will aid in communicating with its stakeholders about the virus.

KRISP open a CRISPR-Cas9 laboratory with Thermo Fisher Scientific in South Africa

KRISP flew two international specialists from Thermo Fisher Scientific to start our new CRISPR-Cas9 laboratory! We also received advanced training on genetic and epigenetic editing techniques in our own lab. KRISP has now all of the equipment to growth, edit and analyse cell lines. The lab is available for scientific service and it is a major development that will help to keep Africa at the cutting-edge of science.

Innovation Festival 2020, Durban, South Africa, 5-7 March 2020

KRISP has an exhibition space at the Innovation Festival, Durban, 5-7 march 2020. We will also be participating in the Cities of the Future discussion session, where we will present BioDurban vision to make Durban the Biotech capital of Africa. Please come visit us and learn more about Biotech, Innovation, Genomics, Epigenetics, Bioinformatics, Precision Medicine and DNA testing...

KRISP work to produce a bioinformatics software for coronavirus COVID-19 rapid identification and characterization

We developed an rapid bioinformatics tool for the identification and characterization of novel coronavirus genomes. The tool was released in January 2020 and published in Bioinformatics in February 2020 as an open access tool to help to characterise genomes of COVID-19 viruses.

KRISP Newsletter Feb 2020: Publication of a Genome Detective software for rapid identification of coronavirus genomes. Award from UKZN VC

In our February/March issue of 2020, we highlight our work on the current coronavirus outbreak. We published a software application for rapid identification and characterization of novel coronavirus genomes. Our quick response was lauded by the national and international media. In this issue, we also cover the award from UKZN vice-chancellor to Dr. Veron Ramsuran, launched a CRISPR-Cas9 laboratory and organized talks, exhibitions and training workshops.

World Birth Defects Day, Inkosi Albert Luthuli Central Hospital (IALCH), 3 March 2020

Inkosi Albert Luthuli Central Hospital (IALCH), KRISP and Genetic Alliance SA joins nearly 200 national and global organizations in observing the sixth annual World Birth Defects Day (WBBD) on March 3, 2020. Launched in 2015, the WBBD movement aims to raise awareness around the serious global issue of birth defects and to urge improved surveillance, research, prevention, and care for affected individuals and families.

4th Industrial Revolution (4IR) UNIX/Linux Training, Durban, South Africa, 2-3 March, 2020

Learn UNIX/Linux from our experienced KRISP bioinformaticians. This 2-day course will teach you the basic UNIX/Linux commands that you will need to manage data. This is the first of five bioinformatics courses that KRISP is presenting in 2020.

KRISP scientists quick action lauded by Nature

KRISP was in the front and second page of Saturday Independent newspaper, including an article on how a reporter from nature has followed our hard work to produce and release the Genome Detective Coronavirus Tool in January 2020.

UKZN scientists make the African Academy of Science's Top 40 List

High-impact researchers at the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), based at the University of KwaZulu-Natal (UKZN), Dr Veron Ramsuran and honorary senior lecturer, Dr Lenine Liebenberg, have been selected as African Academy of Sciences (AAS) Fellows.

UKZN professor & KRISP Group Leader Bags Prestigious Award

Durban - University of KwaZulu-Natal's (UKZN's) high impact researcher, Dr Veron Ramsuran, was awarded the prestigious UKZN Vice-Chancellor's annual award. This award is the most prestigious award given at UKZN.

Coronavirus- Durban man shares eerie encounter

As news of the deadly Coronavirus spreads across the globe, a Durban man, teaching English in Hangzhou, describes the eerie streets of a city on lockdown and researchers at the University of KwaZulu-Natal (UKZN) prepare for the potential of a Coronavirus outbreak in Durban.

Social media helped scientists with coronavirus

The huge amount of knowledge gathered in six short weeks on the coronavirus outbreak (Covid19 or SarsCoV2) was a first for the global scientific community. That was the opinion of University of KwaZulu-Natal Professor Tulio De Oliveira from the KZN Research Innovation and Sequencing Platform (KRISP) at a public talk attended by 120 people at the Nelson Mandela Medical School, 15 feb 2020.

Novel Coronavirus (2019-nCoV) Outbreak: Genomics & Epidemiology

KRISP Talks by Prof. Tulio de Oliveira (KRISP UKZN & CAPRISA), Novel Coronavirus (2019-nCoV) Outbreak: Genomics & Epidemiology. This page summaries resources for coronavirus COVID-19 in KZN and South Africa and internationally. It also present our work on the creation of a genomics and bioinformatics pipeline for fast and accurate analysis of coronavirus genomes. KRISP is bases at K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa.

KRISP Newsletter Jan 2020: Reversing brain drain and training the next generation of scientists in South Africa and abroad.

This month, we launch our bioinformatics training program for 2020 and highlight as one of our key researchers become affiliate to the African Academy of Science. We also join the international community to fight the new coronavirus (2019-nCoV) pandemic, published a key paper on understanding HIV transmission hotspots and renewed our partnership with Thermo Fisher Scientific to provide very affordable sequencing in Africa

KRISP Service Brochure 2020

KRISP expanded its genomics service offers. Our DNA sequencing services incorporate internal quality control (IQC), external quality assurance (EQA) and procedures are validated and performed by HPCSA-accredited scientists. Here you can access a detailed brochure of the genomics services we provide in Africa.

KRISP Join Stanford SPARK Global Program and creates Durban SPARK Innovation Breakfast Monthly Meeting

KRISP at UKZN partner with Stanford University on a global innovation program: SPARK GLOBAL: Translational Scientists without borders. As part of this program we run a monthly meeting (first Wednesday of EVERY MONTH) to discuss innovation, select and mentor start-ups that can produce translational research.

New study shows 43% drop in rate of new HIV infections

New research from the Africa Health Research Institute (AHRI) in collaboration with KRISP shows a 43% decrease in the rate of new HIV infections between 2012 and 2017 in the Hlabisa area of northern KwaZulu-Natal (KZN), South Africa.

Science Through the Lens of Photography

Lifeblood, an exhibition of photographs by Mr Samora Chapman at the Community Art Gallery in Durban. Curated by UKZN Professor and Director of the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) Tulio de Oliveira, it aimed to highlight the diversity of humans, plants and animals in South Africa.

KRISP Newsletter Dec 2019: Conservation Genomics and big decline in the overall HIV incidence rate in northern KZN!

This month, we report on a Nature Communications paper with AHRI that report a 43% decline in the overall HIV incidence rate in northern KZN. We also hosted a leading conservation genomics scientist and organized many talks and events. We went to Drakensberg for our strategic meeting, released the KRISP Wellness program and even went to Hamburg, Germany, to compete in the finals of the Upgrade my NGS Competition.

KRISP Newsletter Dec 2019: Conservation Genomics and big decline in the overall HIV incidence rate in northern KZN!

This month, we focus on a key Nature Communications paper that report a 43% decline in the overall HIV incidence rate in northern KZN. We also hosted a leading conservation genomics scientist and organized many talks and events. We went to Drakensberg for our strategic meeting, released the KRISP Wellness program and even went to Hamburg, Germany, to compete in the finals of the Upgrade my NGS Competition.

KRISP and Genomics Africa hosted a leading Conservation Geneticist in South Africa

Prof. Frandsen, who published a paper in Science on conservation genomics in Nov 2019, has worked with KRISP & Genomics Africa to identify DNA sequencing services that we offer the conservation community in Africa.

KRISP Wellness

In today's world, health and wellness are critical components of a productive work environment and a happy workforce. To often, these topics are misunderstood or ignored in an organisation's drive for results and profit. Health and wellness can also not be viewed in isolation of each other, as each feeds into and supports the other. Health is a state of body, and wellness is a state of being

KRISP 2020 - Strategy Meeting

At the end of November, the KRISP team traded their lab coats and laptops for hiking boots and hats, as they travelled up to the Sani Pass Premier Resort for a three-day strategy session

KRISP Talks: Dr. Richard Lessells, Can we stop worrying about HIV drug resistance with the roll-out of dolutegravir?

UKZN African Health Flagship Talks by Dr. Richard Lessells (KRISP UKZN & CAPRISA), Can we stop worrying about HIV drug resistance with the roll-out of dolutegravir? Tuesday, 26 Nov 2019 (12:00pm - 1:00pm), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

KRISP at UKZN is reversing brain drain in Africa and achieving scientific excellence!

KRISP at UKZN challenges the status quo to create a scientific environment in South Africa that delivers high level science, creates innovations and reverses the brain drain. This vision is starting to pay off, and we are happy to say that in just three years, we published > 15 papers in Nature, Science and Lancet journals, which are some of the most respected scientific journals in the word.

KRISP Talks: Dr. Benjamin Chimukangara, Increasing levels of HIV pretreatment drug resistance in South Africa

UKZN African Health Flagship and KRISP Talks by Dr. Benjamin Chimukangara (Phd Graduation Talk, Post-Fellow at KRISP, UKZN) - Increasing levels of HIV pretreatment drug resistance in South Africa. Tuesday, 19 Nov 2019 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

Promotion Sanger Sequencing at KRISP - Jan to Dec 2020

KRISP is running a Sanger Sequencing promotion to celebrate the launch of two new Sanger Sequencers (ABI 3730xl and 3500). Unbelievable prices for 2020. Capillary electrophoresis only – R 25 (per sample well). Sequencing of PCR purified amplicons – R 45 (per primer). Sequencing of PCR unpurified amplicons – R 75 (per primer).

International Virus Bioinformatics Meeting 2020

We have been invited to give a keynote speech in the International Virus Bioinformatics Meeting (IVBM) 2020, Bern, Switzerland. IVBM 2020 is jointly organized by the European Virus Bioinformatics Center, the University of Bern and the Swiss Institute of Bioinformatics.

KRISP Newsletter Nov 2019: Art & Science output of KRISP: Decline in HIV Incidence in Young Women & Ethics of HIV phylogenetics

This month, we focus on the art & science output of KRISP. This month we published many manuscripts including a key papers with CAPRISA that show a significant decline in HIV incidence in young women in KZN. We also participated in a large study that track HIV incidence in 10 African countries. We have also published a manuscript on the Ethics of HIV-1 molecular research and phylogenetics and worked with Brazilian collaborators to track the dissemination of viruses outbreaks in Brazil.

Request for Applications (RFA) Pharmacogenomics in Precision Medicine by SAMRC in collaboration with KRISP & DIPLOMICS labs

The SAMRC, through its Strategic Health Innovation Partnership (SHIP) programme, is seeking to fund five highly collaborative projects in the areas of pharmacogenomics with reference to failure of treatments with drugs (or drug classes) for Non-Communicable diseases, specifically Hypertension, Cardiovascular, Diabetes and Cancer in (South) Africa. Total Budget ZAR 12-14 million, which genomics data generation should be done in a DIPLOMICS laboratory, such as KRISP, in South Africa.

KRISP Bioinformatics Services and Expertises

KRISP is a competence centre in bioinformatics and computational biology. The group employs skilled personnel that provides infrastructure, support and technological R&D for life sciences and clinical research.

Women in Bioinformatics: Keynote start of the X-meeting 2019

The X-metting 2019 starts with a special session of Women in Bioinformatics. KRISP is >60% women and it is very exciting to participate in this section. We will cover the tweets to highlight how women can drive in this exciting field.

KRISP is present at the X-Meeting 2019: 15th International Conference of the Brazilian Bioinformatics Society AB3C

KRISP is giving a keynote speech at the X-Meeting. The X-Meeting is a Brazilian event with international reach which has an average of 300 participants. The Conference is an opportunity for students, researchers and companies to interact and diffuse knowledge.

KRISP Talks: Prof. Tulio de Oliveira Pharmacogenomics in Precision Medicine RFA by SAMRC with DIPLOMICS: 15 million rands of funding available!

KRISP and DIPLOMCIS Talks by Prof. Tulio de Oliveira (KRISP, UKZN) - Pharmacogenomics in Precision Medicine RFA by SAMRC with DIPLOMICS: 15 million rands of funding available! Monday, 28 Oct 2019 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome and Talk can be remotely attended: https://zoom.us/j/360942224

LIFEBLOOD - Photography Exhibition by Samora Chapman, Community Art Gallery, Durban, 24 Oct 2019

KRISP has partnered with a great photographer (Samora Chapman) to highlight the human and biodiversity life in South Africa. The photographic exhibition was curated by Tulio de Oliveira and highlight many of the genomics aspects that make us so similar and interesting at genotypic and phenotypic level.

KRISP Talks: Dr. Helen Malherbe, Estimating the Burden of Congenital Disorders in South Africa: Recommendations for a Relevant Public Health Respo

UKZN African Health Flagship Talks by Dr. Helen Malherbe (Post-Doctoral Fellow at KRISP, UKZN) - Estimating the Burden of Congenital Disorders in South Africa: Recommendations for a Relevant Public Health Response. Wednesday, 23 Oct 2019 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

KRISP is running a Phylogenetics workshop at the 28th International Workshop on HIV Drug Resistance and Treatment Strategies

KRISP has been invited to present a Phylogenetics workshop as part of the international HIV drug resistance meeting. The workshop will happen in the first day of the conference and will focus on the use of HIV-1 Pol data to identify transmission networks.

KRISP Newsletter Oct 2019: BioDurban & KRISP walkabout to Sydney to participate in the top translational program in the world: the SPARK Global progra

This month, we focus on the launch of we focus on KRISP launching a Biotech Incubator in Durban - BioDurban. KRISP team walkabout to Sydney to participate in the top translational program in the world: the SPARK Global program. In our newsletter, we also highlight some of our fun activities, including three travel blogs, a Photo Exhibition with a great photographer and the publication of a Open Access Book on genomics and bioinformatics for viral outbreaks.

Open Access Book Chapter - Mosquito-Borne Viral Diseases: Control and Prevention in the Genomics Era

We have published together with colleagues from FioCruz Foundation in Brazil a book on the use of genomics to control and prevent viral diseases. This book focus on some of the genomics methods and bioinformatics tools that we have developed for arboviruses (i.e. Zika, Chikungunya, Dengue and Yellow Fever).

Three Blogs from KRISP trip to SPARK Global Meeting in Australia, is this the best and most ethical translational program in the world?

KRISP fantastic team (Dr. Thulile Nlapo, Dr. Benjamin Chimukangara, Dr. Richard Lessells and Gugulethu Mhkize) travel to attend a very inspiring translational science program in Australia. Read these cool blogs and see their personal view on one of the best and most ethical translational science program in the world.

KRISP participation at BioAfrica 2019 in Review

Once again, this three-day conference hosted at the Durban ICC did not disappoint, attracting delegates and exhibitors from over 30 African countries and beyond. Most encouraging was the collective emphasis on innovation and the need to focus Africa's efforts in harnessing the untapped resources and scientific discoveries that the continent still has to offer.

KRISP Newsletter Sept 2019: KRISP Sale Brochure 2019-2020 and the launch of KRISP Business Development Unit

This month, we focus on the launch of KRISP Sale Brochure 2019-2020 and the launch of KRISP Business Development Unit. These two initiatives aim to provide access to high-quality, output-driven, customer-centric and cost-effective genomics services in Africa.

Groundbreaking study on KZN community gives new hope to fight TB

A ground breakin study conducted by scientist from the University of KwaZulu-Natal (UKZN), the KwaZulu-Natal Research Innovation & Sequencing Platform (KRISP) and the Africa Health Research Institute (AHRI) has given new hope to policy makers on the frontline of the fighting the disease that proves that scaling up antiretroviral therapy (ART) coverage can reduce the cases of TB.

SASBi August Newsletter 2019: KRISP & Genomics Africa are featured in the South African Society of Bioinformatics (SASBi) Newsletter

This month at the SASBi newsletter KRISP at UKZN is featured as a key organization that is reversing brain drain in Africa and achieving scientific excellence! The newsletter also highlights Genomics Africa, our initiative with DIPLOMICS, the SASBi student council updates and some of the wild-cats' scientists (Yumna Moosa, San Emmanuel James and Upasana Ramphal) at KRISP. This is the coolest part of the newsletter and we really encourage you to read it...

KRISP Newsletter July/August 2019: Genomics Africa provide access to high-quality, output-driven, customer-centric and affordable sequencing in Africa

This month, we focused our newsletter we focus on the launch of Genomics Africa, a KRISP & DIPLOMICS initiative to provide access to high-quality, output-driven, customer-centric and cost-effective genomics services in Africa . In our newsletter, we highlight the Genomics Africa activities on Human Genomes, Animals & Plants and Pathogens & Microbes. We want to challenge the status quo and allow the genomics revolution to benefit Africa.

The potential for personalized microRNA therapeutics in cancer - KRISP & African Health Flagship Talk

KRISP & African Health Flagship Talk by Prof. Frank Slack, Shields Warren Mallinckrodt Professor & Director of the Institute for RNA Medicine, BIDMC, Harvard University, USA, Tuesday, 30 July 2019 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

Clinical Pharmacogenomics: Developments & Opportunities for Efficacious Use of Medicines in African Populations - Durban SPARK Innovation Breakfast

Durban SPARK Innovation Breakfast presentation by Prof. Collen Masimirembwa, President and Chief Scientific Officer: African Institute of Biomedical Science & Technology, Tuesday, 30 July 2019(7:30am - 8:30), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

KRISP Road Shows Westville & Pietermaritzburg UKZN Campuses

In order to showcase our services and promote collaboration and we are doing road shows at two other UKZN campus in July. We will be at the Westville campus (29-30 July) and at the Pietermaritzburg Campus (30-31 July).

New technologies in Africa: Opentrons Robotic Pipetting Hackatron, Durban, 20 July-3 August 2019

Hackatron to code Opentrons pipetting robots for DNA amplicons and libraries for Sanger, Illumina & ONT Minion sequencing. Opentrons are open-source pipetting robots for biologists. Flexible, accessible & affordable lab robots allow life scientists to do more science & less pipetting. Programming of the robots use python language. Protocols are coded as open-source and available for the community.

Decoding the South African Indian Genome for Health Risk

Diabetes is a growing problem in South Africa, but South African Indians are at three times the risk of other race groups. What is more, Diabetes and Ischaemic Heart disease occur at least a decade younger in Indians than in other populations in South Africa. Both these diseases are the leading cause of death within the Indian population. Apart from poor diet and exercise there is a genetic component that leads to increased disease risk.

KRISP mobile team tracking viral outbreaks in real-time in Brazil

KRISP, FioCruz, Brazilian Ministry of Health, the Pan American Organization and research centres from UK (Oxford, Birmingham and Edinburgh) established a network for real-time genomic surveillance.

HIV-1 genotyping service in Africa: rapid, reliable, and cost-effective

KRISP, Applied Biosystems and Thermo Fisher Scientific collaborate to bring Africa one step closer to realizing the 90-90-90 target by introducing a rapid, reliable, and cost-effective HIV-1 genotyping service in Africa. As part of the introduction, we are running a promotion of ZAR800 (US$ 55) per genotyping test (Jul-Dec 2019). Test can be done in plasma or DBS samples, turn-around time is seven working days.

KRISP Newsletter June/July 2019: KRISP on the road. We are criss-crossing the country to showcase our new DNA sequencing and bioinformatics capacity.

This month, we focused our newsletter on KRISP on the road. We are criss-crossing the country to showcase our new DNA sequencing and bioinformatics capacity. . In the newsletter, we also cover our high-throughput Sanger and Illumina sequencing services, arapid, reliable and cost effective HIV-1 Drug Resistance Service in Africa and many of our publications on viral outbreaks, mental health and industrial biotechnology.

Bioinformatics tools: Computational methods for the identification of Dengue, Zika, Chikungunya and Yellow Fever Virus species and genotypes

We recently produced open access phylogenetic typing tools to classify Arboviruses, including Dengue, Zika, Chikungunya and Yellow Fever Virus. These tools are been widely used by the scientific community and were published in Science (2018) and PLoS NTD (2019).

SPARK GLOBAL Program & Its value Proposition in Africa - Durban SPARK Innovation Breakfast, 27 June 2019

Durban SPARK Innovation Breakfast presentation by Professor Michael Wallach, KRISP Director SPARK Sydney and Regional Director of SPARK Oceania, University of Technology Sydney (UTS), Thursday, 27 June 2019(7:30am - 8:30), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

Capillary Electrophoresis (i.e. Sanger Sequencing) Workshop II, Durban, South Africa, 27-28 June 2019

UKZN African Health Flagship, KRISP, DIPLOMICS & Thermo Education Program on Capillary Electrophoresis (i.e. Sanger Sequencing. . Thermo-KRISP Lab, Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 27-28 June 2019. Training is open to University Post-Graduate Students & Technical Staff of Commercial and Academic laboratories. Scholarships available to previously disadvantaged South African learners.

Capillary Electrophoresis (i.e. Sanger Sequencing) Training Workshop, Durban, South Africa, 24-25 June 2019

UKZN African Health Flagship, KRISP, DIPLOMICS & Thermo Education Program on Capillary Electrophoresis (i.e. Sanger Sequencing) . Thermo-KRISP Lab, Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 24-25 June 2019. Training is open to University Post-Graduate Students & Technical Staff of Commercial and Academic laboratories. Scholarships available to previously disadvantaged South African learners.

STEM Education: Training II - Quantitative PCR (qPCR), KRISP and ThermoScientific Workshop, Durban, South Africa, 21 June 2019

Science Technology Engineering and Maths (STEM) training II on quantitative PCR (qPCR). Thermo-KRISP Lab, Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 21 June 2019. Training is open to post-graduate students and for technical staff of commercial and academic laboratories.

KRISP Newsletter May/June 2019: KRISP participation in BIO 2019, the largest biotechnology innovation convention in the world

This month, we focused our newsletter on KRISP participation in the largest biotechnology innovation convention in the world, BIO2019. KRISP is part of the official South African delegation and is profiled as an inspiring organization for economic development in South Africa. In the newsletter, we also cover our high-throughput Sanger and Illumina sequencing services, growing bioinformatics team and KRISP & Thermo Fisher Scientific training program in Africa.

STEM Education: Training I - Quantitative PCR (qPCR), KRISP and ThermoScientific Workshop, Durban, South Africa, 20 June 2019

Science Technology Engineering and Maths (STEM) training II on quantitative PCR (qPCR). Thermo-KRISP Lab, Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 20 June 2019. Training is open to post-graduate students and for technical staff of commercial and academic laboratories.

UKZN secures grant for joint study into mental health

Scientists from UKZN's College of Health Sciences and KRISP have received a R12,8 million grant from the South African Medical Research Council and the UK Medical Research Council/Newton Fund for a UK-South Africa joint initiative on mental health.

BIO 2019: KRISP is profiled as an inspiring organization for Economic Development in South Africa

KRISP is taking part of the BIO 2019 as part of the official South African Delegation. KRISP is also profiled as an inspiring and Bio-innovative organization for Economic and Social Development in South Africa in an official booklet of the South African government.

BIO 2019: KRISP is part of the official South Africa Delegation at BIO 2019

KRISP takes part of the South African delegation attending the Bio International Convention. In addition, the delegation will include senior representatives of the DST, SAMRC, TIA, CPGR and DIPLOMICS. Together, we will showcase South Africa in the BIO 2019 as one of the most sophisticated, diverse and dynamic emerging market that is open to investment.

KRISP Newsletter Apr/May 2019: Genomics, bioinformatics and artificial intelligence technologies at KRISP and ThermoFisher Workshops

This month, we focused our newsletter on Genomics, bioinformatics and artificial intelligence at KRISP. This month newsletter also highlights our travel to the Wellcome Trust Sanger Institute and a prestigious Royal Society Award to KRISP. We also cover our recent publication on TB and mental health in South Africa and four new training workshops organized with ThermoFisher Scientific.

KRISP Talks: Funding Opportunities: FLAIR Fellowship & SAMRC-NIH Calls 2019

UKZN African Health Flagship Grants Support Unit discuss about new funding opportunities: AAS and Royal Society FLAIR Fellowship & SAMRC-NIH Calls 2019. Wednesday, 24 April 2019 (1:00pm - 2:00pm), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

SAFM Interview Story Telling for Health Research following our BMJ Medical Humanities 2019 paper

Radio interview by Dr. Astrid Treffry-Goatley about the use of story telling of our BMJ Medical Humanities 2019 paper entitled: Community engagement with HIV drug adherence in rural South Africa: a transdisciplinary approach.

KRISP at IndabaX Deep Learning and Artificial Intelligence Conference, South Africa 2019

The IndabaX is a means with which to experiment with the ways in which we strengthen African machine learning, artificial intelligence and its local communities. KRISP is a sponsor of the Deep Learning IndabaX 2019, 14 to 17 April, South Africa.

KRISP among the first awards of The African Academy of Sciences and Royal Society £25M FLAIR scheme

KRISP Team Leader Dr. Veron Ramsuran is one of 30 leading scientists to receive the prestigious AAS and UK Royal Society FLAIR Fellowship. The 2019 FLAIR funded scientists were selected from a competitive pool of more than 700 applicants. Their research is diverse, ranging from providing renewable energy solutions and addressing climate change, to tackling food security and targeting health and environmental problems that are most acute for people living in African countries.

KRISP provide access to qPCR and TaqMan Arrays

KRISP has invested in two high-throughput qPCR equipment (QuantStudio 7 Flex Real Time PCR Systems. We have validated qPCR TaqMan Array Card for many common pathogens and pathogens including panels for Gastrointestinal Panel (38 pathogens), Sexually Transmitted Infections (STI) Panel (12 pathogens) and Respiratory Diagnostic Panel (34 pathogens).

KRISP provide access to high-throughput Illumina sequencing services

KRISP has invested in a new Illumina DNA sequencer, providing access to NGS services using Miseq, NextSeq and HiSeq DNA sequencers. We are now in the position to generate NGS sequencing data at similar price, quality and speed as the international leading genomics centres.

KRISP provide access to high-throughput Sanger sequencing services

KRISP has invested in two new Sanger DNA sequencers, including the ABI3730xl, which is the largest and most automated Sanger machine in the world. This equipment has 96 capillaries and it is able to produce over 1,500 sequences a day.

KRISP Newsletter Mar/Apr 2019: New services & technologies available at KRISP, educational events and publications on drug resistance & phylogenetics

This month, we focused our newsletter on the new services and technologies available at KRISP. The newsletter also highlights our educational events (Talks, Wet-Lab and Dry-Lab workshops) and publications, including a paper on the increase of HIV-1 drug resistance in South Africa and another on the use of deep-sequence phylogenies to infer HIV-1 transmission networks

KRISP & Thermo Fisher Scientific complete their 5th STEM training workshop in Africa

KRISP partner with Thermo Fisher Scientific on an educational program in Africa. As part of this program we organized 5 training workshops on STEM subjects in 2018 and 2019, ranging from PCR, qPCR, DNA sequencing and bioinformatics techniques.

KRISP Talks: Lynn Woolfrey, Opening up data for social well-being research in South Africa

UKZN African Health Flagship Talks by Lynn Woolfrey (DataFirst, University of Cape Town) - Opening up data for social well-being research in South Africa. Thursday, 11 April 2019 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

KRISP Workshop: Neville Naidoo, Protection of Personal Information Act (POPIA), South Africa

UKZN African Health Flagship Workshop by Neville Naidoo (University of KwaZulu-Natal Legal Services) - Protection of Personal Information Act (POPIA), South Africa. Thursday, 4 April 2019 (9:00am - 12:30pm), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

KRISP Newsletter Feb/Mar 2019: Partnership with University of Washington, postgraduate training and translational science workshop

This month, we focused our newsletter on KRISP partnership with the Department of Global Health at University of Washington in Seattle. We also focus on our new post-graduate training workshops. This month, we also have many publications on African Health, including on HIV and TB phylogenetic and drug resistance analysis.

Research Ethics and Conflicts of Interest Workshop, Durban, South Africa, 1st April 2019

UKZN African Health Flagship Postgraduate Training Program present the Research Ethics and Conflicts of Interest Workshop. Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 1 April 2019. Training is open to University Post-Graduate Students & Post-Doctoral Fellows.

KRISP Talks: Prof. Michael Pepper ASSAf Consensus Study on Ethical, Legal and Social Implications of Genetics & Genomics in South Africa

UKZN African Health Flagship Talks by Prof. Michael Pepper (University of Pretoria & SAMRC Unit for Stem Cell Research & Therapy) - the Academy of Science of South Africa (ASSAf) Consensus Study on the Ethical, Legal and Social Implications of Genetics & Genomics in South Africa. Tuesday, 7 May 2019 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

24th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME)

24th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME), The University of Hong Kong, Hong Kong, China, 4-9 August, 2019. The VEME workshop is recognised as one of the best international virus bioinformatics courses.

DNA Sequencing Fragment Analysis (i.e Microsatellite) Workshop, Durban, South Africa, 28-29 March 2019

UKZN African Health Flagship, KRISP, DIPLOMICS & Thermo Education Program on DNA Sequencing Fragment Analysis Workshop . Thermo-KRISP Lab, Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 28-29 March 2019. Training is open to University Post-Graduate Students & Technical Staff of Commercial and Academic laboratories. Scholarships available to previously disadvantaged South African learners.

Capillary Electrophoresis (i.e. Sanger Sequencing) Training Workshop, Durban, South Africa, 24-25 March 2019

UKZN African Health Flagship, KRISP, DIPLOMICS & Thermo Education Program on Capillary Electrophoresis (i.e. Sanger Sequencing) . Thermo-KRISP Lab, Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 25-26 March 2019. Training is open to University Post-Graduate Students & Technical Staff of Commercial and Academic laboratories. Scholarships available to previously disadvantaged South African learners.

Workshop in Translational Research, Health Innovation & Commercialization

KRISP is presenting at the UCL/UKZN workshop on translational research, Health Innovation and Commercialisation. The workshop starts 19th March, Tuesday, at 12pm, finishes 20th March, Wednesday, at 2pm in Durban, South Africa.

KRISP Talks: Dr. Maryam Fish, Cancer Genomics at KRISP, Friday, 15 March 2019

UKZN African Health Flagship Talk by Dr. Maryam Fish - Cancer Genomics at KRISP will cover some of the genomics tests and bioinformatics pipelines for the analysis of whole exome sequencing (WES) and cancer panels from Thermo Fisher Scientific, Illumina and other sequencing methods. Friday, 15 March 2019 (8:30am - 9:30am), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

Z to A: List of Grants Proposals from KRISP

This is a password protected section of the website that provide access, to internal members, to previous grants applications submitted by KRISP.

KRISP Grants Unit Introduction

KRISP challenges the status quo to create a scientific environment in (South) Africa that delivers the highest level of science, creates innovations and reverses the brain drain. This vision is starting to pay off, and we are happy to say that in just two years, we have been awarded over twenty grants to produce and analyze omics data in the African continent. Please contact us to discuss collaborative grants applications.

The Grant Process - B) Post-Award Process

The Post-Award process is the step that we want to get to. However, it can be quite complicated for new PIs. Here we provide a summary of the process you should follow, along with contact information for the people who can provide immediate assistance as you proceed to grant application.

KRISP Talks: Prof Tulio de Oliveira, Power of Diversity: Being Inclusive Gives Teams a Competitive Edge In Science, 31 Jan 2019

UKZN African Health Flagship Talks by Prof Tulio de Oliveira, Power of Diversity. Nature editorial covers a variety of studies that have tracked different types of diversity — ethnic, gender, nationality and scientific discipline — and suggest that particularly diverse groups publish a higher number of papers and receive more citations per paper than average. Thursday, 31 January 2019 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

NextStrain & Genome Detective Workshop, KRISP, Durban, South Africa, 24-25 January 2019

From NGS data to real-time tracking of viruses' outbreaks: NextStrain and Genome Detective workshop. KRISP, Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 24-25 January. Training is free to post-graduate students of UKZN and members of the H3AbioNet Bioinformatics Network.

KRISP Newsletter January 2019: Training the next generation of scientists, positions available for PhDs and Post-Docs in Durban South Africa

This month, we focused our newsletter on KRISP training the next generation of scientists and positions available for PhDs and Post-Doctoral fellows at a Flagship program of UKZN. We also highlight publications on TB next generation sequencing and diagnostics, ethics and trans-disciplinary perspectives of HIV research and new phylodynamics models to characterize viral outbreaks.

Post-Doc and PhD positions available at the Afrocentric Precision Approach to Control Health Epidemics Flagship Project of UKZN

We invite applications from ambitious Post-Docs (x10) and PhD (x10) students, to undertake research in a Flagship programme of UKZN in Durban and Pietermaritzburg, South Africa. In this Flagship, leading investigators from different disciplines come together to develop cutting-edge research ideas on precision medicine, precision public health and translational science.

Post-Doc (x2) & PhD (x2) Scholarships available - Establishment of Zebrafish Models for Human Disease and Toxicology, Pietermaritzburg, South Africa

We invite applications from ambitious Post-Docs and PhD students, to undertake research in a Flagship programme of the UKZN in Pietermaritzburg, South Africa. This project aims to establish Zebrafish Models for Human Disease and Toxicology, including the development of genetic models for non-communicable diseases (NCD) such as Type 2 Diabetes and for pollutants and contaminants of emerging concern (CEC).

Post-doctoral Fellowship available - Precision Public Health, Durban, South Africa

We invite applications from ambitious post doctoral scientists, to undertake research in a Flagship programme of the UKZN and the MRC in Durban, South Africa. This Fellowship aims to generate large geographically indexed HIV, TB and cancer datasets in South Africa. The fellow will apply advanced geospatial analysis techniques and molecular epidemiology and geographical analysis techniques to identify “hotspots” in space-time and describe the characteristics of HIV, TB and HPV transmission networks and its impact on the development of cancer.

Postdoc Fellowship available - Precision Medicine, Durban, South Africa

We invite applications from ambitious post doctoral scientists, to undertake research in a Flagship programme of the UKZN and the MRC in Durban, South Africa. This project aims to identify factors associated with the acquisition and progression of HIV and the development of HIV drug resistance. The postdoctoral fellow will use human and viral genetic data combined with high quality clinical and epidemiological data to characterize genetic and epigenetic factors that are associated with health outcomes.

PhD (x2) Scholarships available - Precision Medicine and Public Health, Durban, South Africa

We invite applications from ambitious post students, to undertake a PhD in a Flagship programme of the UKZN and the MRC in Durban, South Africa. This project exemplifies how analysis of genomic, clinical, social and epidemiological data could directly impact human health in Africa. PhD fellows will receive outstanding training and be mentored by leading scientists, who commonly publish in some of of the top biomedical journals

KRISP & Thermo qPCR Solutions for Infectious Disease Seminar

KRISP & Thermo Seminar and Lab Tour qPCR Solutions for Infectious Disease Seminar, 11 December 2018 (9:30 - 11:30), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

KRISP Talks: Assessment of Proviral Reservoir: Synergistic Combination of Reporter Cell based Assay and Viral Diversity

KRISP Talks by Dr Sikhulile Moyo & Dr Catherine Koofhethile, Harvard School of Public Health & Botswana Harvard Partnership (BHP), 10 December 2018 (11:00 - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

KRISP Newsletter - Oct/Nov 2018 - New technologies and preparing the next generation of scientists

This month, we focused our newsletter on KRISP learning about new technologies and preparing the next generation of scientists. This month, we also have many publications on African Health, including on HIV drug resistance, antimicrobial activity, pre-eclampsia and smoking and depression.

The Technology Innovation Agency (TIA), Funding Activities and Success, Durban SPARK Innovation Breakfast, 7 Nov 2018

Durban SPARK Innovation Breakfast by Barlow Manilal, CEO TIA, Wednesday, 7 November 2018 (7:30am - 8:30), KRISP, K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

Alain, Andrew and Wilbert together taught PBHLJ11 for UKZN Master of Public Health in 2018.

KRISP Faculty teach Health Measurement Descriptive course at School of Nursing and Public Health. The aim of the course is to provide learners with skills to collect, analyse and use health information. In addition, this course provide students with an understanding of the basic principles and methods of descriptive epidemiology, descriptive biostatistics and demography.

KRISP Preparing Next Generation Scientists

UKZN's KwaZulu-Natal Research Innovations and Sequencing Platform (KRISP) in collaboration with Thermo Fisher Scientific held a one-day Science, Technology, Engineering and Maths (STEM) training session for Grade 11 pupils and students on basic Polymerase Chain Reaction (PCR)

In Epicenter of Global HIV Crisis, Multiple Partners and Age Disparity Part of Problem

VULINDLELA, South Africa—Sweat streams from the young men's faces as they pursue a soccer ball across a sun-baked pitch of red dust.

KRISP Talks: Prof Caroline Tiemessen (NICD), Models for the study of HIV remission: elite and post-treatment controllers

KRISP Talks by Prof. Caroline Tiemessen, Models for the study of HIV remission: elite and post-treatment controllers, UKZN, Tuesday, 9 October 2018 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

STEM Education: Training II - Quantitative PCR (qPCR), KRISP and ThermoScientific Workshop, Durban, South Africa, 4 October 2018

Science Technology Engineering and Maths (STEM) training II on quantitative PCR (qPCR). Thermo-KRISP Lab, Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 4 October 2018. Training is open to post-graduate students and for technical staff of commercial and academic laboratories.

SPARK Innovation Breakfast: Disruptive Financial Instruments, Entrepreneurship & Social Enterprise, 3 October 2018

SPARK Innovation Breakfast by Patrick Schofield, Uprise.Africa, Disruptive Financial Instruments, Entrepreneurship & Social Enterprise, Wednesday, 3 October 2018 (7:30am - 8:30), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

STEM Education: Sample to PCR Training Workshop, KRISP and ThermoScientific Workshop, Durban, South Africa, 2 October 2018

Science Technology Engineering and Maths (STEM) training on Sample to PCR. Thermo-KRISP Lab, Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 2 October 2018. Training is open to High-school and University Students and scholarships available to previously disadvantaged South African students.

KRISP presents a new cutting-edge DNA sequencing, Precision Medicine and Bioinformatics Scientific Service Platform

A critical function of KRISP is to make cutting edge genomics, precision medicine and bioinformatics technology accessible to academic, industrial and commercial users. KRISP uses a hybrid model that includes a research team and a commercial laboratory.

KRISP Join Thermo Fisher Scientific to creates a STEM education program in South Africa

KRISP at UKZN partner with Thermo Fisher Scientific on a educational program in Africa. As part of this program we run many training workshops on STEM subjects, ranging from PCR, qPCR, DNA sequencing and CRISPR techniques. We have also produced a short video that shows the state-of-art training facilities in Durban, South Africa

Capacitating frontline health care workers in the hearth of the HIV & TB epidemic: KRISP & CAPRISA trained 2,000 health care workers in South Africa

At KRISP, we recognize the importance of strengthening the health system if we are to achieve the goals of ending the HIV and TB epidemics. We have a particular passion for training frontline health care workers. Through our partnership with the CAPRISA Advanced Clinical Care Programme in the last four years, we have contributed to training of over 2000 health care workers in KwaZulu-Natal Province, South Africa.

KRISP host a Data Carpentry Training Workshop

KRISP in conjunction with the University Capacity Development Fund (UCDP) are conducting a two-day data carpentry training on the 27th and 28th of September, 2018 in Durban. In this workshop 35 researchers will be equipped with fine skills to perform data organization and analysis.

KRISP is hosting the H3Africa Bioinformatics Network Introduction to Bioinformatics Course, 2018

Bioinformatics embodies a set of critical skills necessary to derive insights from biological datasets in a cost effective and lab free manner. Such skills are not readily accessible in the African context. To address this challenge, KRISP as part of the H3Africa initiative is hosting a class for the introduction to bioinformatics course (IBT).

The necessity of good corporate governance principles on research projects - KRISP Talks, 19 Sept 2018

KRISP Talks by Erick Nsikayezwe Sithole, Governance, Strategy and Innovation , UKZN, Wednesday, 19 September 2018 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

Advancing scientific education on the African continent

Thermo Fisher Scientific in partnership with the KwaZulu Natal Research Innovation and Sequencing Platform (KRISP) at University of KwaZulu-Natal (UKZN) in South Africa has developed an educational programme on PCR which has been offered to high school and tertiary students.

Quasi-companies in Biotechnology - Durban SPARK Innovation Breakfast, 5 Sept 2018

Durban SPARK Innovation Breakfast presentation by Fernando Albericio, KRISP Research Scientist, UKZN Professor, Wednesday, 5 September 2018 (7:30am - 8:30), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

KRISP exhibition at the BIOAFRICA convention, Durban, South Africa

KRISP showcase its bio innovations at the BIOAFRICA Convention held on 27 - 29 August 2018 at Durban ICC. Under the theme, Africa - Open for business - Together building the Bio-Economy. KRISP had an exhibition booth under the large TIA pavilion that displayed precision medicine technologies, bioinformatics services as well as a range of genomics services and capacity development program.

Tracking the evolution and transmission of yellow fever

A pioneering research collaboration into yellow fever virus (YFV) has shed new light on the exceptional recent outbreak in Brazil and how the virus spreads. The findings have implications for monitoring viral transmission and could potentially contribute to a strategy for eliminating YFV worldwide

Yellow fever virus detective work could help target vaccination campaigns

Science paper in 2018 that uses genomic sequencing of a recent yellow fever outbreak in Brazil has traced it back to its source.

KRISP was selected to take part on an exhibition for 15,000 students in Durban as part of the 100 scarce skill career Indaba!

The South African Government has identified 100 scarce skills nationally in the workplace and KRISP has taken this opportunity to empower the youth and contribute towards education by taking the 100 Scarce Skills Campaign Indaba in Durban - 31 July to 2 August 2018.

Challenges & barriers to implement point-of-care diagnostics in resource-limited settings - KRISP Talks, 15 Aug 2018

KRISP Talks by Dr Tivani Mashamba-Thompson, PhD, Academic Leader, School of Nursing and Public Health (SNPH), UKZN, Wednesday, 15 August 2018 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

Thermo Fisher Scientific in conjunction with KRISP, cordially invite you to a genetics solutions application seminar - 8 Aug 2018

The event will give you insight into the exciting world of scientific research in the field of genetics but also give you a chance to visit the state of the art laboratory at the KRISP unit in Durban, South Africa

KRISP Newsletter - July 2018 - KRISP public engagement initiatives & genetic solutions with Thermo Fisher Scientific

KRISP public engagement initiatives & genetic solutions with Thermo Fisher Scientific. This month, we have participated in many events and engaged with the general and scientific public! We have even participated in the BRICS summit and have been inspired by translational research.

KRISP & CAPRISA participated in the BRICS Health Summit 2018

KRISP participated in high-level meeting of the BRICS summit in South Africa, 28 July 2018. Participants include South African Deputy General (DG) of Health, Ms Malebona Precious Matsoso, the special advisor to the Minister of International Affairs in Brazil, Fabio Rocha Frederico, the HIV/AIDS programme leader of Russia and seniors representatives of the World Health Organization (WHO).

Boston, Berlin, Brazil & SPARK Global Successful model - Durban SPARK Innovation Breakfast, 1 Aug 2018

Durban SPARK Innovation Breakfast presentation by Tulio de Oliveira, KRISP Research Scientist, UKZN Professor, Wednesday, 1 August 2018 (7:30am - 8:30), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

The hazards of unseen HIV: implications for statistical inference - KRISP Talks, 31 Jul 2018

KRISP Talks by Dr. Alain Vandormael, PhD, KRISP Research Scientist, UKZN Lecture, Tuesday, 31 July 2018 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

KRISP attends the 2018 SPARK GLOBAL meeting in Berlin, Germany

KRISP team attended the 3rd SPARK GLOBAL meeting, which took place in Berlin, 21 and 22 July 2018. We have been inspired by this meeting and we are working with SPARK GLOBAL partners to replicate their successful model in South Africa

STEM Education: Sample to PCR Training Workshop, KRISP and ThermoScientific Workshop, Durban, South Africa, 6 July 2018

Science Technology Engineering and Maths (STEM) training on PCR. Thermo-KRISP Lab, Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 6 July 2018. Training is open to High-school and University Students and scholarships available to previously disadvantaged South African students.

Durban Spark Innovation Breakfast Meeting - Fintech & Project UBU - 4 July 2018, Durban, South Africa

In partnership with Stanford University, KRISP will host its 6th Durban Spark Innovation breakfast meeting on the 4 July at 7h30-8h30 K-RITH Tower Building. The keynote address focus on Fintech & Project UBU by Viroshan Naicker, Mathematician & Economist, North Quotient.

KRISP Newsletter - June 2018 - KRISP at the Innovation Festival, STEM training with ThermoScientific, two research awards and LancetHIV paper

KRISP participated in the Innovate Durban 2018 Festival, Sample to PCR KRISP and Thermo-Fisher Scientific Workshop, KRISP gets two awards at SANTHE DELTA initiative and Lancet HIV paper on Dolutegravir for first line therapy in developing countries

Innovation Festival 2018, Durban, South Africa, 28-30 June 2018.

KRISP has an exhibition space at the Innovation Festival, The Barn, Durban, 28-29 June. Please come visit us and learn more about Genomics, Epigenetics, Bioinformatics, Precision Medicine and DNA testing.

KRISP gets two awards at SANTHE DELTA initiative

KRISP researchers Upasana Ramphal and Dr. Marcel Tongo scooped two of the three awards at the Wellcome Trust DELTAS SANTHE research day held on the 6 - 7 June 2018 at Crinkly Bottom in Waterfall, South Africa.

KRISP and South Africa have a large exhibition at the most prestigious biotechnology event, the BIO Convention 2018, please come visit us!

KRISP and the South African DST, SAMRC and TIA showcase South Africa in the BIO 2018 as one of the most sophisticated, diverse and dynamic emerging market that is open to investment...

5th Durban Spark Innovation breakfast meeting - Diagnostic Innovations: Gaps & Opportunities - 6 June 2018, Durban, South Africa

In partnership with Stanford University, KRISP will host its 5th Durban Spark Innovation breakfast meeting on the 6 June at 7h30-8h30 K-RITH Tower Building. The keynote address focus on Diagnostic Innovations: Gaps & Opportunities by Dr. Richard Lessells & Dr. Veron Ramsuran,Group Leaders at KRISP.

KRISP Newsletter - May 2018 - KRISP learning about innovation in Boston as part of South African delegation to BIO and new services area

KRISP on the official South African delegation of the BIO international convention in Boston, Global SPARK meeting, new services and online quote section of website, genome detective, inovation breakfast and talks.

KRISP DNA sequencing, cancer genomics, ddPCR, NGS, Exomes, HLA and other services in Africa

A critical function of KRISP is to make genomics, NGS, epigenetics and bioinformatics services accessible to academic, industrial and commercial users. Services include on-demand next generation sequencing (NGS), cancer genomics, drug resistance testing, Human Exomes, HLA typing and absolute quantification (ddPCR)

KRISP Cautions about Intellectual Property when Fostering Innovation and Entrepreneurship

By Lihle Sosibo, Durban, 24-May-18. Understanding Intellectual Property (IP) allows people and businesses to harness creations of the human mind and realise their economic potential through commercialisation. It is important to know what constitutes intellectual property, who owns the intellectual property and what protection and advantages are afforded to intellectual property owners.

Integrating Computer-Aided Drug Design into Infectious Disease Drug Discovery

KRISP Talks by Prof. Joe Eyermann, Drug Discovery and Development Centre (H3D) - UCT, University of Cape Town (UCT), 9 May 2018 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

4th Durban Spark Innovation breakfast meeting - 2nd May, Durban, South Africa

In partnership with Stanford University, KRISP will host its 4th Durban Spark Innovation breakfast meeting on the 2 May at 7h30-8h30 K-RITH Tower Building. The keynote address focus on Intellectual Property (IP) & Patents and it is presented byTyron Grant, MSc (Genetics) & Patent Attorney, Partner, Spoor & Fisher.

KRISP Newsletter - April 2018: KRISP, FioCruz & Oxford, reversing brain drain & scientific excellence, Nature paper, sparking innovation...

KRISP partner with FioCruz and Oxford on real-time outbreak analysis, reversing brain drain and achieving scientific excellence, Nature paper, KRISP talks and innovation events arising

KRISP team goes to Brazil to work with FioCruz & Oxford on Yellow Fever Outbreak

KRISP team spent 10 days in Brazil working with Prof. Luiz Carlos Alcantara group to use Oxford Nanopore sequencing device to analyse the current Yellow fever outbreak in Brazil

University-Industry-Government Co-operation Needed for Entrepreneurial Success

By MaryAnn Francis, Durban, 11-April-18. A partnership involving academia, industry and government is needed for innovation and entrepreneurship to blossom, says Deputy Vice-Chancellor of Research at UKZN, Professor Deresh Ramjugernath at the Durban Spark Innovation Breakfast

Nature paper: Renewing Felsenstein's phylogenetic bootstrap in the era of big data

KRISP Nature paper with Pasteur Institute on a new phylogenetic method to analyse large HIV and mammalian DNA sequence datasets!

An era of both peril and promise

Sunday Tribune, 1st April 2018 - The impact of the Fourth Industrial Revolution, an age of unprecedented advances, is under the spotlight at UKZN this week, writes A dire need to cultivate entrepreneurship and innovation in SA

Thought Leadership Workshop on Biomedical Innovation and Entrepreneurship - 10 April 2018, Pretoria, South Africa

The Department of Science and Technology (DST) funded Technology Innovation Agency (TIA) in collaboration with KRISP invites academics, government, clinicians, investors, law-makers, entrepreneurs and industrialists to an intellectually engaging exchange of ideas on the establishment of an innovative bio-incubation system. 10 April 2018, Pretoria, South Africa.

Laboratory-free virology research: Computational approaches for evolutionary hypothesis testing

KRISP Talks by Prof. Darren P Martin, IDMM, University of Cape Town (UCT), 9 April 2018 (12:00 - 13:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

KRISP Newsletter - March 2018: Partnership with TIA, DST and SAMRC on a Thought Leadership Workshop in Pretoria, News, Publications and Collaborators

In our third issue of 2018, we would like to bring attention to a partnership with TIA, DST and SAMRC to deliver a Thought Leadership Workshop on Bio-Innovation. We also highlight some of our publications, collaborators and capacity building workshops

3rd Durban Spark Innovation breakfast meeting - 4th April at 7h30-8h30, Durban, South Africa

In partnership with Stanford University in the United States, UKZN's KZN Research Innovation and Sequencing Platform (KRISP) will host its 3rd Durban Spark Innovation breakfast meeting on the 4th April at 7h30-8h30 K-RITH Tower Building. The keynote address at the third breakfast is Professor Deresh Ramjugernath, UKZN's Deputy Vice-Chancellor of Research.

A dire need to cultivate entrepreneurship and innovation in SA

1 APRIL 2018, by FRED KOCKOTT. South Africa needs to up its game in the world of innovation and entrepreneurship, says University of KwaZulu-Natal deputy vice chancellor: research, Professor Deresh Ramjugernath.

Training the trainee - KRISP & KZN Science Center workshop on HIV/AIDS knowledge

The KZN Science Centre (KZNSC) team attended a HIV/AIDS training on the 8-9th of March 2018 that was hosted by KRISP at UKZN. The training equipped the team with a solid background and knowledge on HIV/AIDS which enabled the KZNSC educational facilitators to give informative presentations on HIV/AIDS to young grade 9 female learners in disadvantage communities.

2nd Durban Spark Innovation Breakfast Meeting - March Meeting Sparking Innovation on UKZN's Medical School Campus

By MaryAnn Francis, 15 March 2018, Durban. The Technology Innovation Agency (TIA)-funded KZN Research Innovation and Sequencing Platform (KRISP) recently hosted its second Durban Spark Innovation breakfast featuring UKZN's A-rated scientist Professor Fernando Albericio as the keynote speaker.

Renewing Felsenstein's Phylogenetic Bootstrap in the Era of Big Data

KRISP Talks by Dr. Eduan Wilkinson, KRISP, UKZN, 6th March 2018 (15:00 - 16:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

KRISP Newsletter - Feb 2018: Partnership with SPARK Global Program at Stanford, innovation meeting, news, publications, training

In our second issue of 2018, we would like to bring attention to a partnership with SPARK Global Program at Stanford, innovation meeting, news, publications, collaborators and capacity building workshops

The Grant Process - A) Pre-Award Process

Here we provide a summary of the process you should follow, along with contact information for the people who can provide immediate assistance as you proceed to grant application. This assay focus on the pre-award process.

1st Durban Spark Innovation Breakfast Meeting - February meeting in Durban to foster innovation between Universities, Government and Industrial Sector

The development of innovation, small businesses and entrepreneurship should be the cornerstones of development in order to alleviate poverty and improve health on the African continent. In order to respond to these challenges, KRISP and UKZN have partnered with some of the world's leading innovative organizations to learn from the successful innovation in the Silicon Valley.

Videos - Grants management and collaborative research at KRISP, UKZN Durban, South Africa

KRISP video highlighting the important role that grants and project management play in allowing researchers to achieve scientific excellence in South Africa.

Find Funding - List of Agencies in South Africa and abroad

KRISP maintains a list of selected funding sources and databases. In addition, our grants managers maintain an email list for KRISP, APACHE and UKZN interested researchers that highlights new opportunities.

KRISP researchers presented at the CAPRISA Strategic Meeting

CAPRISA annual strategic meeting was presented at the International Conference Centre (ICC) in Durban. We were present and two of our manuscripts (Lancet HIV 2017 and Science 2018) were presented.

Effect of DNA methylation on HIV disease

KRISP Talks by Dr. Veron Ramsuran, KRISP, UKZN & CAPRISA, 26 January 2018 (15:00 - 16:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

Our Paper on Green Environment & Depression Selected as One of the 20 Most Influential Conservation Ecology Papers of 2017 by F1000!

F1000 has produced another retrospective list of the top 20 influential conservation papers of 2017 as assessed by experts in the field. The manuscript by Tomita, Vandormael et al. Lancet Planetary Health 2017 on green environment and depression made this influencial list...

Why some HIV-positive people develop AIDS quicker than others is now clearer

The study, published in the prestigious journal Science (Ramsuram et al. 2018), was led by South African scientists who, together with an international research team, discovered that a specific-type human leucocyte antigen (HLA) gene helps infected cells to evade the body's first line of defence

SA study reveals important link between genes and Aids

HIV/AIDS researchers have never understood why people infected with HIV developed Aids at different times? but now they suspect that it all has to do with their genes. A study by South African and US researchers (Ramsuran et al. Science 2018) has shed new light on how specific genes in people can lead to the faster progression of Aids-related illnesses in people living with HIV who are not on treatment.

Science Discovery: Biomarkers for HIV treatment

Mercury Reporter, Durban, KwaZulu-Natal, 19 Jan 2018: Scientists led an in ternational research team which discovered new genetic markers that identify why the onset of Aids appears to occur so quickly in some people after they are infected with HIV The study published in the journal Science (Ramsuran et al. Science 2018), sheds new light on how specific human genes can lead to a faster deterioration for people living with HIV who are not on treatment.

Science Editorial: Inhibiting natural killer cells in AIDS

The human leukocyte antigen (HLA) gene complex varies enormously among individuals and helps explain individual variation in immunity to infectious diseases. Ramsuran et al. (Science 2018) examined data from almost 10,000 HIV infections.

Why KRISP? KRISP challenges the status quo to create a scientific environment in South Africa that drives innovations & reverses the brain drain.

The Technology Innovation Agency (TIA) and UKZN have signed an agreement for the establishment of KRISP - the KwaZulu-Natal Research and Innovation Sequencing Platform.

Science TM Editorial: Status is not everything

Many parameters are examined to try to understand HIV transmission in endemic areas. Tanser et al. (Science TM 2017) use longitudinal population-based data from rural South Africa to show that population viral load indices incorporating geographical location and local HIV prevalence can be used to infer HIV transmission potential.

Scientists develop new prediction methods for HIV infection rates

The Mercury, 14 December 2017, KwaZulu-Natal-based medical research organisations have developed an improved method to accurately predict where the highest rate of new HIV infections will likely occur in a community. Press coverage of our KRISP paper by Tanser et al. (Science TM 2017)

Even with easy access to ARVs, only one in three HIV-positive people will seek them

By Katharine Child, 05 December 2017. SA's policy to reduce HIV infections is to do what the UN recommends, which is to get 90% of people tested, 90% of HIV-positive people taking antiretrovirals and 90% of those on treatment taking it properly so they are not infectious. Press coverage of our KRISP paper Iwuji et al. (Lancet HIV 2017).

South Africans with HIV miss out on the benefits of early treatment due to a fear of stigma

By Linda Nordling, 2 December 2017, Quartz Africa. Antiretrovirals 'the drugs used to keep HIV in check' don't only prevent people from getting AIDS; they also keep virus levels low, making those taking them less likely to pass the infection to others. Press coverage of our KRISP paper Iwuji et al. (Lancet HIV 2017).

We have designed a tool to track HIV infection rates cheaply and accurately

By Sikhulile Moyo, 1 December 2017. The conversation, press coverage of our KRISP paper Moyo et al. (PLoS One HIV 2016). A critical part of reaching zero new HIV infections by 2030 as the 'UN's Sustainable Development Goal aims to do' is to be able to track accurately when specific high risks groups become infected with the virus.

HIV drug resistance is on the rise, notes research

Drug resistance in HIV is rising to more than 10% in people with HIV who are preparing to start (or re-start) first-line antiretroviral therapy, according to a recently published meta-analysis. Press coverage of our KRISP paper Gupta et al. (Lancet ID 2017).

Rising levels of HIV drug resistance

HIV drug resistance is approaching and exceeding 10% in people living with HIV who are about to initiate or reinitiate first-line antiretroviral therapy, according to the largest meta-analysis to date on HIV drug resistance. Press coverage of Gupta et al. (Lancet ID 2017).

Prevention of HIV transmission by antiretroviral therapy

Commentary by Jens Lundgren & Andrew Phillips, Lancet HIV, 30 November 2017.

Integrating Assisted Partner Services and Phylogenetics for HIV and Hepatitis C Prevention in Nairobi

KRISP Talks by Dr. Aliza Monroe-Wise, University of Washington, 16 November 2017 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

Real-time genomic epidemiology for outbreak response: Lessons and insights from the 2014-2016 Ebola virus epidemic

KRISP Talks by Prof. Andrew Rambaut, Edinburgh University, 15 November 2017 (15:00 - 16:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

Five (5) KRISP positions open in Durban! Grants Manager, Office Admin, Molecular Technologist, DNA Data & Laboraroty Quality administrators.

KRISP staff are based in a state of the art building in Durban and have access to fast advancing technologies such as genomics, epigenetics, bioinformatics and epidemiology.

Improving the estimation of temporal trends in HIV incidence by calibrating agent-based simulation models to multiple data sources

KRISP Talks by Dr. Wim Delva, SACEMA (Stellenbosch), 23 October 2017 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

X-meeting - 13th International Conference of the AB3C, Sao Pedro, Brazil, Oct 4-6, 2017

Bioinformatics is now a strategic area for Brazil and all Latin America and, therefore, it is also strategic to the development of Science, Technology and Economy. The X-Meeting is a Brazilian event with international reach which has an average of 400 participants.

Paediatric HIV Infection: Elite Control, Remission and Cure

KRISP Talks by Prof. Philip Goulder, Oxford University, 20 September 2017 (14:00 - 15:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

11th Annual Workshop on Advanced Clinical Care - AIDS (AWACC), Durban, South Africa, 6-7 Sep 2017

The workshop is targeted at 400 clinicians, clinical virologists and nurses working in the public sector who are currently involved in the treatment of patients with HIV and TB in KwaZulu-Natal, South Africa.

22nd International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME), Lisbon, Portugal

The workshop provides both theoretical and practical training in phylogenetic inference and evolutionary hypothesis testing. It is recognized as one of the best international virus bioinformatics courses. It covers sequence analysis, phylogenetics, phylodynamics methods and large scale methods for next-generation sequencing (NGS) analytics

A multi-centre analysis of internal migration and AIDS/TB and NCD-related mortality in Kenya and South Africa

KRISP Talks by Dr Carren Ginsburg, SAMRC/Wits Rural Public Health & Health Transitions Research Unit (Agincourt), 23 August 2017 (11am - midday), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!

KRISP Newsletter - July 2017: news, videos, blogs, publications and training events

The concept behind this newsletter is that anyone with 15 minutes to spare can learn about KRISP work. In this July 2017 issue of our newsletter, we have included interesting news, videos, blogs, reports, tweets, publications and training events of KRISP

Enabling Infectious Disease Transmission Research

KRISP Researcher and Fulbright scholar Dr. Eduan Wilkinson news from the US: HiPerGator supercomputer is enabling infectious disease transmission research in UF's Emerging Pathogens Institute.

KRISP & SANTHE trainee wins Best Abstract at DELTAS Africa meeting

Friday, 7 July, 2017, Dr Marcel Tongo Passo, a SANTHE Post-doctoral trainee, has won a "Best Abstract" award at the DELTAS (Developing Excellence in Leadership, Training and Science) Africa Annual Grantees Meeting 2017, held in Accra, Ghana, between 3 to 5 July. Passo is based at KRISP (KwaZulu-Natal Research and Innovation Sequencing Platform) and HPP (HIV Pathogenesis Programme) at the University of KwaZulu-Natal, South Africa.

Durban at the forefront of DNA research - KwaZulu-Natal Research and Innovation Sequencing Platform - KRISP

By Arthi Gopi, Independent on Saturday Newspaper - KRISP atrracts the brightest - Durban is leading the way in DNA research, having attracted some of the brightest minds in the science field, in a new state-of-the-art lab in the city.

KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP) Established

The Technology Innovation Agency (TIA) and UKZN have signed an agreement for the establishment of KRISP - the KwaZulu-Natal Research and Innovation Sequencing Platform.

Seminar: Can the type of jeans you wear determine your treatment response?

KRISP Talks by Professor Bonga Chiliza, Discipline of Psychiatry: College of Health Sciences, UKZN, 23 June 2017, K-RITH building, Nelson R Mandela School of Medicine, Durban, South Africa. All welcome!

Newsletter, Jan-Mar 2017: 'Alarming' drug resistance levels, novel next generation sequencing method and the origin of HIV, SATuRN & CAPRISA workshop

The concept behind this newsletter is that anyone with 15 minutes to spare can learn about our research work. In this Jan-Mar 2017 issue of our newsletter, we have included interesting open access publications, news, blogs, reports, tweets, and training information produced by our group.

KRISP/SATuRN & CAPRISA 2017: HIV & TB Drug Resistance and Advanced Care Workshop

The workshop is targeted at clinicians, clinical virologists and nurses working in the public sector who are currently involved in the treatment of patients with HIV and TB in KwaZulu-Natal, South Africa.

CD4+ Count Not Useful to Assess ART Response in HTLV-1/HIV Coinfection

Patients coinfected with human T-cell lymphotropic virus 1 (HTLV-1) and HIV continue to have elevated CD4+ T-cell counts, even though there is no difference in their HIV viral load levels after antiretroviral therapy when compared with patients who just have HIV (Curr HIV Res 2017).

CD4+ T-cell count useful to assess antiretroviral therapy response in HTLV-1/HIV patients?

News coverage and clinical management implication of our recent HIV/HTLV co-infection manuscript, Current HIV Research, 2017

Perspective: Extreme high-level of drug resistance in Aruba: We need ITI-based regimens available globally now!

Perspective by Carlos del Rio, MD Professor of medicine, division of infectious diseases, Emory University School of Medicine on our recent CID manuscript on high-level transmitted resistance epidemic in Aruba.

Prevalence of drug-resistant HIV reaches 'alarming levels' in Aruba

The prevalence of resistance to nonnucleoside reverse transcriptase inhibitors among HIV-infected individuals has increased to 'alarming levels' in Aruba, reaching 45% in 2015, see our recent publication at CID.

Seminar: Microbial genome-wide association studies: lessons from human GWAS

KRISP Talks by Prof. Tulio de Oliveira, College of Health Sciences, UKZN & CAPRISA Research Associate, 17 March 2017, K-RITH building, Nelson R Mandela School of Medicine, Durban, South Africa

We have been awarded a collaborative grant from SANTHE/Wellcome Trust programme in Africa

The Wellcome Trust DELTAS funded SANTHE program awarded seven grants to develop collaborative research projects to address critical challenges to African capacity in HIV and/or TB clinical, social/behavioural, and biomedical science.

Swiss South African Symposium on Pathogen Genomics

The National Research Foundation and Swiss National Science Foundation through their Swiss-South Africa programme, have funded a project entitled: A context-based knowledge resource integrating HIV and Mtb molecular biology with host-pathogen and drug-resistance data. As part of the project, the University of Cape Town Computational Biology Division and our research group at UKZN are hosting a symposium on pathogen genomics.

Seminar: Differential HLA-A Expression Levels and the Effect on HIV

KRISP Talks by Dr Veron Ramsuran, Senior Lecturer: College of Health Sciences, UKZN, 27 January 2017, K-RITH building, Nelson R Mandela School of Medicine, Durban, South Africa

Newsletter, Dec 2016: Ethics & phylogenetics, HIV transmission cycle, UNAIDS Report, Drug resistance increases in Africa

The concept behind this newsletter is that anyone with 15 minutes to spare can learn about our research work. In this December 2016 issue of our newsletter, we have included interesting news, blogs, reports, tweets, publications and training information produced by our group.

Ethics and Viral Genomics: An Exploration of Ethical Issues Associated with HIV Phylogenetics

This is a half-day interactive workshop, which seeks to explore and deliberate on key ethical issues associated with HIV phylogenetic analysis as applied in our understanding of HIV transmission dynamics, particularly in African settings. Keynote presentations will be followed by plenary discussions led by the speakers.

Time to get serious with HIV-1 resistance in sub-Saharan Africa

In The Lancet Infectious Diseases, John Gregson and colleagues report the results of a meta-analysis investigating HIV-1 drug resistance in 20 studies from sub-Saharan Africa.

Two manuscripts featured in the Lancet website front webpage on AIDS day.

Two of our recently published manuscripts (de Oliveira et al. Lancet HIV 2016 & Gregson et al Lancet Infectious Diseases 2016) are highlighed in the Lancet website front webpage...

Unrelenting spread of HIV amongst Adolescent girls and young women in rural and urban KwaZulu-Natal

By Professor Ayesha Kharsany, December 1, 2016, Durban - Globally, over 1.6 billion people are in the age group 12-24 years, the largest generation of adolescents and young people. However, almost 42% of new HIV infections occur in this age group, nearly 80% of these live in sub-Saharan Africa and more than 70% of these infections occur in adolescent girls and young women. Not only do these adolescent girls and young women have higher rates of HIV, they also acquire infection 5-7 years earlier than their male peers.

More than 18 million on HIV treatment, a million more than 2015: UNAIDS 2016 Report

More than 18 million people now have access to life-saving AIDS treatment, 1.2 million more than at the end of last year, the United Nations said on Monday. With detailed data showing some of the many complexities of the HIV epidemic, the report found that people are particularly vulnerable to HIV at certain points in their lives (de Oliveira et al. Lancet HIV 2016). It called for 'life-cycle; approach to offer help and prevention measures for everyone at every stage of life.

UNAIDS Report 2016 - Get on the Fast-Track - The life-cycle approach to HIV

In this report, UNAIDS is announcing that 18.2 million people now have access to HIV treatment. The Fast-Track response is working. Increasing treatment coverage is reducing AIDS-related deaths among adults and children. But the life-cycle approach, which highlight our phylogenetics manuscript (de Oliveira et al. Lancet HIV 2016), has to include more than just treatment.

10th Annual Workshop on Advanced Clinical Care - AIDS (AWACC)

This AWACC annual workshop is in the 10th edition and it is organized as a joint effort of the Centre for AIDS research (CFAR) of Harvard Medical School, SATuRN, CAPRISA, UKZN and the KwaZulu-Natal Department of Health. AWACC objecitve is to translate the latest evidence-based research and apply best practice models of care into good clinical practice, specifically for resource constrained areas.

SATuRN Newsletter, 3rd quarter, 2016: SATuRN/CAPRISA, Rural vs Urban resistance levels, PhD fellowships, AWACC workshop

The concept behind this newsletter is that anyone with 15 minutes to spare can learn about the work of SATuRN. In this third 2016 issue of our newsletter we have included interesting news, blogs, reports, tweets, publications and training information produced by our network. We hope you enjoy it and find it informative. We welcome any feedback about content or format.

4th Joint Congress of the South African Society for Bioinformatics (SASBi) and the South African Genetics Society (SAGS)

The biennial SASBi and SAGS congresses are the premier national scientific meetings on bioinformatics and genetics in South Africa. In total, 187 participats delivered 40 oral presentations and 65 posters in SASBi-SAGS-2016. This congress provided an exciting opportunity to learn about cutting-edge research in both disciplines, and to network with members of the two societies and with leading international scientists.

PhD Fellowships: 2x postions at CAPRISA on Genomics, Bioinformatics, HIV-1 Drug resistance and/or Phylogenetics

The Professional Development Programme (PDP) of the Department of Science and Technology (DST) and the National Research Foundation (NRF) at CAPRISA aims to develop and retain South African scientists and professionals of the highest calibre.

PhD Fellowship II: Genomics, Bioinformatics, Epidemioloy and Phylogenetics

The Professional Development Programme (PDP) at CAPRISA aims to develop and retain South African scientists and professionals of the highest calibre. The genomics and bioinformatics project in HIV-1 phylogenetics and molecular epidemiology is inter-disciplinary in nature and involves collaboration between the CAPRISA's MRC HIV-TB Pathogenesis and Treatment Research Unit and the Flagship Program of the MRC, which are two of the most prestigious research programs in South Africa.

PhD Fellowship I: Genomics, Bioinformatics & Drug Resistance

The Professional Development Programme (PDP) at CAPRISA aims to develop and retain South African scientists and professionals of the highest calibre. The genomics and bioinformatics project in HIV-1 drug resistance is inter-disciplinary in nature and involves collaboration between the CAPRISA's MRC HIV-TB Pathogenesis and Treatment Research Unit and the Flagship Program of the MRC, which are two of the most prestigious research programs in South Africa.

Social cycle aids HIV spread

Nature (Vol. 535, pp. 335, 2016) report our recent results on the use of genetic sequences to uncover HIV-1 transmission patterns in young woman in South Africa (de Oliveira et al. Lancet HIV 2016). The paper was presented as a Keynote at AIDS 2016 conference.

Studies Offer Fresh Hope in Fight Against HIV/AIDS in South Africa.

Researchers with the Centre for the AIDS Programme of Research in South Africa, or CAPRISA, a consortium of South African and North American scientists, analyzed genetic codes (de Oliveira et al. Lancet HIV 2016) from study subjects in South Africa to try to pinpoint biological factors that may contribute, along with behavioral factors, to the large number of infections.

South Africa's bid to end AIDS

Science magazine (Vol. 353, Issue 6294, pp. 18-21, 2016). This issue was published before the AIDS conference in Durban 2016 and highlights some of our research, including our treatment as prevention trial (TasP) as well our phylogenetic analysis (de Oliveira et al. Lancet HIV 2016).

First two South African MSc students graduate from the MRC Flagship Program: Inspiring blogs about their experiences and achievements

Megan Druce and Sthembiso Msweli are two very bright South Africans who have successfully completed their MSc as part of the UKZN Flagship program at the MRC. They both wrote inspiring blogs, the first is about a Cum Laude degree which allowed the award of a scholarship for a PhD in Germany, the second is about the history of a laboratory technologist from rural KZN, who after graduating was promoted to laboratory manager...

SATuRN Newsletter, 2016: SATuRN/CAPRISA, Increase transmitted resistance, TDF global resistance

The concept behind this newsletter is that anyone with 15 minutes to spare can learn about the work of SATuRN. In this first 2016 issue of our newsletter we have included interesting news, blogs, reports, tweets, publications and training information produced by our network. We hope you enjoy it and find it informative. We welcome any feedback about content or format.

21st International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME)

The 21st International Workshop on Virus Evolution and Molecular Epidemiology (VEME2016) will be hosted by the Korea University College of Medicine, 14-19 August, Seoul, Republic of Korea. Abstract deadline: 15 March 2016

Seminar: A phylodynamic view of the HIV epidemic in KwaZulu-Natal

KRISP Talks by Dr David Rasmussen, Postdoc Research Fellow, ETH Zurich, 11 March 2016, K-RITH building, Nelson R Mandela School of Medicine, Durban, South Africa

Seminar: Sources of HIV infection among men having sex with men and implications for prevention

KRISP Talks by Oliver Ratmann, Research Fellow, Department Infectious Disease Epidemiology, Imperial College of London & UKZN MRC Research Fellow, 06 February 2016, K-RITH building, Nelson R Mandela School of Medicine, Durban, South Africa

SATuRN & AWACC workshop - 19-20 November 2015, Durban, South Africa

The SATuRN 10th Southern African HIV & TB Drug Resistance and Treatment Monitoring Workshop will be run together with the Annual Workshop on Advanced Clinical Care - AIDS (AWACC) - Durban, South Africa, 19 to 20 November 2015

Positions open! Bioinformatics Software Developer & Scientific Manager

Africa Centre through its European Commission Virogenesis Project & MRC Flagship Programmer wish to recruit a 1) Software Developer & 2) Bioinformatics Scientific Manager.

Seminar: Is HIV-1 subtype C more pathogenic than other subtypes?

We cordially invites you to a seminar presented by Prof Thumbi Ndungu from K-RITH and HPP/UKZN, 21 August 2015, K-RITH building, Nelson R Mandela School of Medicine, Durban, South Africa

Research travel grants: Doctoral or post-doctoral students to Wellcome Trust Africa Centre, South Africa

Introduction: This is an excellent opportunity for outstanding and motivated individuals to access one of the most comprehensive population-based HIV surveillance and genomics datasets in the world at the Wellcome Trust Africa Centre for Health and Population Studies based in KwaZulu-Natal, South Africa.

Seminar: The Molecular Epidemiology of HIV in Rakai Uganda

The Wellcome Trust Africa Centre Genomics & Bioinformatics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Prof. Oliver Laeyendecker Assistant Professor of Medicine, Johns Hopkins University,19 June 2015, K-RITH building, Nelson R Mandela School of Medicine, Durban, South Africa

Seminar: Clinical Impressions of HIV Pathogenesis & Vaccine Research

The Wellcome Trust Africa Centre Genomics & Bioinformatics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Dr Nigel Garrett from CAPRISA, 19 June 2015, K-RITH building, Nelson R Mandela School of Medicine, Durban, South Africa

MOLECULAR EPIDEMIOLOGY: HIV family trees reveal viral spread.

By John Cohen, Science, 12 June 2015. New studies could aid public health efforts. Last week at the New York Academy of Sciences in New York City, researchers, public health specialists, and HIV/AIDS advocates discussed how to exploit the potential of the technique, called phylogenetic analysis - and the thorny ethical and legal issues it raises...

Feature story: Understanding HIV through phylogenetic research

Phylogenetic research 'the analysis of molecular sequencing data to study evolutionary relationships among groups and organisms' needs to be scaled up to end the AIDS epidemic, according to the participants at a symposium held on 4 June at the New York Academy of Sciences called HIV 2015: Using Phylogenetics to Enhance the HIV Response.

HIV 2015: Using Phylogenetics to Enhance the HIV Response, New York, June 4, 2015

A discussion meeting presented by the Joint United Nations Programme on HIV/AIDS (UNAIDS) and the Microbiology & Infectious Diseases Discussion Group at the New York Academy of Sciences on the use of phylogenetics to enhance HIV response.

Seminar: Near Full Length Sequencing to Understand HIV & TB Epidemics In Africa In Real Time

The Wellcome Trust Africa Centre Genomics & Bioinformatics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Prof. Tulio de Oliveira, 30 April 2015, K-RITH building, Nelson R Mandela School of Medicine, Durban, South Africa

Ground-breaking PhD Study helps Rural Doctors monitor HIV Drug Resistance

Dr Justen Manasa graduated with a PhD after completing ground-breaking research in the Hlabisa District of KwaZulu-Natal that resulted in a low cost genotyping method envisaged to help doctors monitor and evaluate drug resistance among HIV-infected patients in resource-limited settings.

Report on the SATuRN & CAPRISA HIV & TB Advanced Clinical Care Workshop

The Southern Africa Treatment and Resistance Network (SATuRN) and the Centre for the AIDS Programme of Research in South Africa (CAPRISA) organized a HIV & TB Advanced Clinical Care Workshop. This workshop is funded by the Centers for Disease Control and Prevention (CDC) & PEPFAR program in South Africa.

Our genomics and bioinformatics research program was selected as a keynote presentation in the 1st South African Illumina User Group Meeting, 2015

By: Tulio de Oliveira, Franschoek, South Africa, 31 March 2015 - Continuing advances in next generation genomic analysis are rapidly changing the way we approach our research. The setup of our high-throughput genomics facility at the Nelson R Mandela School of Medicine, in collaboration with Africa Centre and Health and Population Studies allowed our research group to produce HIV-1 complete genomes at an unprecedented scale.

Seminar: Whole genome sequence interrogation of drug resistant Mycobacterium tuberculosis

The Wellcome Trust Africa Centre Genomics & Bioinformatics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Prof. Samantha Sampson, 20 February 2015, K-RITH building, Nelson R Mandela School of Medicine, Durban, South Africa

Seminar: Virus and host genetics: where and how to look in big data for associations with infectious disease

The Wellcome Trust Africa Centre Genomics & Bioinformatics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Prof. Paul Kellam, 13 February 2015, K-RITH building, Nelson R Mandela School of Medicine, Durban, South Africa

Seminar: An Unexpected Influence of Genome Secondary Structure on Recombination in HIV

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Prof. Darren Martin, 9 January 2015, K-RITH building, Nelson R Mandela School of Medicine, Durban

Seminar: Whole genome sequence interrogation of drug resistant Mycobacterium tuberculosis

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Samantha Sampson, 21 November 2014, Susser & Stein Seminar Room, K-RITH building, Nelson R Mandela School of Medicine, Durban

AWACC & SATuRN conference a success! Please see twitter summary

SATuRN annual workshop run in partnership with AWACC (UKZN, NDoH & Harvard). In total 346 participants attended the two days workshop. The workshop discussions were also very good. Here, we summarize the Tweeter coverage of the event, which contains information on the topics discussed and questions raised.

Seminar: Transcriptional profiling in human tuberculosis

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Prof. Robert J Wilkinson, 10 October 2014, K-RITH building, Nelson R Mandela School of Medicine, Durban

Doris Duke Annual Seminar for Medical Students from Harvard and UKZN

Each year during AWAAC, the Doris Duke International Research Fellowship at Harvard Medical School sponsors a special seminar for medical students who will be attending the conference. During the seminar, invited faculty members discuss journals article that they select with a group of medical students from the US who are engaging in research in sub-Saharan Africa and a group of South African medical students from UKZN. This year 20-25 students will attend the seminar.

Seminar: ARV Therapy Initiated Before 2-Months-of-Age Reduces Transcriptionally Active HIV-1 DNA Persistence

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Prof. Gert Van Zyl, 19 September 2014, K-RITH building, Nelson R Mandela School of Medicine, Durban

Seminar: Nanotechnology and the Treatment of HIV Infection

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Dr. Louis Chonco Jimenez, 22 August 2014, K-RITH building, Nelson R Mandela School of Medicine, Durban

Postdoc Fellowship available - HIV Genomics & Bioinformatics I

We invite applications from ambitious post doctoral scientists, to undertake research in a Flagship programme of the Wellcome Trust & MRC in South Africa.This Fellowship aims to apply and develop bioinformatics software applications to analyze large datasets of complete HIV-1 genomes.

Postdoc Fellowship available - HIV Bioinformatics & Phylogenetics II

We invite applications from ambitious post doctoral scientists, to undertake research in a Flagship programme of the Wellcome Trust & MRC in South Africa.This Fellowship aims to develop and/or apply phylogenetic software applications to create a framework to identify epidemiologically important HIV strains.

Postdoc Fellowship available - HIV & HTLV Bioinformatics & Phylogenetics III

We invite applications from ambitious post doctoral scientists, to undertake research in a collaborative programme of the the Wellcome Trust Africa Centre and the FioCruz Foundation in South Africa and Brazil.This fellowship aims to apply and develop bioinformatics software applications to analyze large datasets of HIV-1 and HTLV-1 complete genomes

SATuRN Newsletter, Jul 2014: Annual HIVDR Workshop, News, Publications & Blogs

The newsletter idea is that anyone with 15 minutes to spare can learn about our work and its application in everyday life. In our second issue of 2014 (Vol. 3 Num. 2), we advertise our annual workshop, which will be presented as part of the Annual Workshop on Advanced Clinical Care - AIDS (AWACC), Durban, 8-9 Oct 2014. We also included interesting news, blogs and publications produced by our network and partners.

NICD accredited by WHO for HIVDR testing using DBS specimens

By Anna Salimo, South Africa, 20 July 2014. The NICD laboratory in Johannesburg has been performing HIV-1 drug resistance (HIVDR) testing for surveillance purposes using plasma or serum specimens. The World Health Organization (WHO) have adjusted their requirements for accreditation to include HIVDR testing on dried blood spots (DBS) due to their ease of collection, handling, transportation and storage.

Postdoctoral Research Fellows in HIV

We invite applications from ambitious clinical or non-clinical postdoctoral scientists, to undertake research in a Flagship programme of the Wellcome Trust & MRC in South Africa

Seminar: Genome-wide association study indicates two novel resistance loci for severe malaria

KRISP Talks by Prof. Andreas Ziegler, 1 August 2014, Council Chambers, Westville Campus, UKZN, Durban.

Inaugural Lecture: Bioinformatics, Genomics and HIV Research in Africa: A Brief Personal History

The Vice-Chancellor and Principal Professor Malegapuru Makgoba cordially invites you and your spouse/partner to attend an inaugural lecture presented by Professor Tulio de Oliveira, 30 July 2014, K-RITH, Durban

Seminar: Genomics & Bioinformatics: The need to engage biologists, mathematicians & computer scientists.

The Wellcome Trust Africa Centre Genomics Programme, the UKZN MRC Flagship project and School of Mathematics, Statistics and Computer Science, UKZN, cordially invites you to a seminar presented by Prof. Tulio de Oliveira, 7 July 2014, UKZN, Pietermaritzburg, South Africa

Bioinformatics in the Tropics blog: Molecular Evolution & Phylogenetics Workshop Entebbe Uganda 7th-10th April 2014

By: Deogratius Ssemwanga, Jonathan Kayondo, Siva Danaviah and Jaffer Zaidi. The bioinformatics in the tropics series is part of a south-to-south capacity building programme to develop the next generation of bioinformaticians in Africa and Latin America.

Seminar: Cause-specific mortality: Standardised measurements and comparisons

The Wellcome Trust Africa Centre Deputy Director iShare Programme cordially invites you to a seminar presented by Prof. Peter Byass, 09 April 2014, Africa Centre headquarters, Mtubatuba

SATuRN Newsletter, Mar 2014: News, publications, videos & new seminar series!

The newsletter idea is that anyone with 15 minutes to spare can learn about our work and its application in everyday life. In our first issue of 2014 (Vol. 3 Num. 1) our newsletter we focus on our new seminar series and publications and results from SATuRN partners. We also included interesting news, blogs, reports, tweets and training information produced by our network.

Seminar: Old and new challenges for HIV control

The Wellcome Trust Africa Centre for Health and Population Studies and the University of KwaZulu-Natal (UKZN) cordially invites you to a seminar presented by Prof. Peter Piot, 1 April 2014, Africa Centre headquarters, Mtubatuba

Seminar: Next-generation sequencing for identifying drug resistance in Mycobacterium Tuberculosis

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a seminar, 28 March 2014, Durban

From sample to sequencing: an introduction to Longhorn's primesuite of technologies

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a presentation, 28 March 2014, Durban

Seminar: Unlocking the potential of TB genomics

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Dr. Siva Danaviah, 26 March 2014, Africa Centre headquarters, Mtubatuba

Seminar: Trends and causes of hospitalisation in adults receiving ART

The Wellcome Trust Africa Centre Population Epidemiology Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Dr. Portia Mutevedzi, 19 March 2014, Africa Centre headquarters, Mtubatuba

Interactive Biostatistics Course, Durban, 26-30 may 2014

K-RITH is offering an innovative course in the biostatistical methods used in medical research. This hands-on course is taught by Harvard biostatistician, Dr. Lori Chibnik.

Seminar: Multi-step inhibition explains HIV-1 protease inhibitor pharmacodynamics and resistance

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Dr. Justen Manasa, 12 March 2014, Africa Centre headquarters, Mtubatuba

Seminar: HIV-1 Transmission during Early Infection in Men Who Have Sex with Men: A Phylodynamic Analysis

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Dr. Eduan Wilkinson, 19 February 2014, Africa Centre headquarters, Mtubatuba

Seminar: 30 years of HIV diversity research: a personal perspective

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Prof. Susan Engelbrecht, 31 January 2014, Durban

PhD and/or MSc Scholarship available - Computer Science

The causes and consequences of HIV transmission and drug resistance - Computer Science PhD and/or MSc studentships available at UKZN/CSIR Meraka Centre for Artificial Intelligence Research (CAIR) in collaboration with Wellcome Trust Africa Centre for Health and Population Studies. Funded by a MRC Flagship research project. Potential Supervisors: Dr. Deshen Moodley & Prof. Hugh Murrell, CAIR, UKZN

Seminar: Implementing HIV-1 Genotypic Resistance Testing in Antiretroviral Therapy Programs in Africa: Needs, Opportunities, and Challenges.

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Prof. Tulio de Oliveira, 15 January 2014, Africa Centre headquarters, Mtubatuba

SATuRN Newsletter, Dec 2013: News, workshops, manuscripts & PhD/MSC positions available!

The newsletter idea is that anyone with 15 minutes to spare can learn about our work and its application in everyday life. In our last issue of 2013 our newsletter we focus on our capacity building programme. We also advertise 7 PhDs and 4 MScs positions in this issue!

Bioinformatics in the Tropics Uganda 2014, UVRI, Entebbe, Uganda, 7th to 10th April 2014

This is a series of four workshops, which will be presented in Brazil (2013 & 2014), South Africa (2013) and Uganda (2014) as part of a south to south capacity building programme to develop the next generation of bioinformaticians in Africa and Latin America. The objective is to train post-doctoral researchers to become trainers and post-graduate students to use bioinformatics and phylogenetic software applications needed for their research.

PhD and/or MSc Scholarship available - Social Sciences

The causes and consequences of HIV transmission and drug resistance - Social Sciences PhD and/or MSc studentships available at HEARD/UKZN Genetics department in collaboration with Wellcome Trust Africa Centre for Health and Population Studies. Funded by a MRC Flagship research project. Potenital Supervisors: Dr Kaymarlin Govender, Ms Samantha Willan & Mr. Andrew Gibbs, HEARD, UKZN.

PhD and/or MSc Scholarship available - Human Genetics

The causes and consequences of HIV transmission and drug resistance - Human Genetics PhD and/or MSc studentships available at UKZN Genetics department in collaboration with Wellcome Trust Africa Centre for Health and Population Studies. Funded by a MRC Flagship research project. Supervisors: Dr. Paula Sommer, Genetics Department, UKZN & Prof. Tulio de Oliveira, Africa Centre, UKZN

PhD Scholarship available - Genomics, Bioinformatics & Epidemiology I - HIV Drug Resistance

The causes and consequences of HIV transmission and drug resistance - HIV Drug resistance PhD studentship at Wellcome Trust Africa Centre for Health and Population Studies, University of KwaZulu-Natal (UKZN). Funded by a MRC Flagship research project. Supervisors: Prof. Tulio de Oliveira & Prof. Frank Tanser, Africa Centre, UKZN

PhD Scholarship available - Genomics, Bioinformatics & Epidemiology II - HIV dynamics

The causes and consequences of HIV transmission and drug resistance - PhD studentship available for Genomics, Epidemiology and Bioinformatics at UKZN for the MRC Flagship research project. Supervisors: Prof. Tulio de Oliveira & Prof. Frank Tanser, Africa Centre, UKZN

SA Medical Research Council Scientific Awards

In his address to MRC award and grant winners at a prestigious ceremony in Cape Town, outgoing MRC Chairperson Professor Lizo Mazwai described the South African Medical Research Council (MRC) as 'richer, more focused, more efficient and better placed to deliver a healthy nation through research.'

Heroes in the battle for health

There have been major successes in the fight agains the disease since it was first identified in 1983. Bianca Capazorio speaks to some young South Africans at the forefront of work in the field.

Putting the I into HIV - World Aids Day UKZN

Leading scientists in HIV/AIDS research discussed the diversity of the HIV epidemic, new scientific evidence and the promising interventions on the horizon to tackle it.

'An HIV-1 vaccine is possible' says Prof Thumbi Ndung'u at UKZN AIDS Day 2013

Ahead of World AIDS Day 2013, leading HIV/AIDS researchers in Durban have urged society to focus on insights, innovation and integrity in the journey into an HIV-free future and to put people at the centre of health services.

SATURN-PASER unites international minds & reveals potential resistance free HIV drug

By Inez Rossouw, 26 Nov 2013, Bloemfontein - Dolutegravir, a drug aimed against the human immunodeficiency virus (HIV), might not elicit any resistance to it. This was revealed at the Southern African HIV/TB drug resistance and monitoring workshop hosted by the Southern African Treatment and Resistance Network (SATuRN) at the Medical School of the University of the Free State.

DNA sequencer launched at the University of Free State

The University of the Free State (UFS) can now collect immensely valuable data on drug resistance in HIV/Aids and TB with the new DNA sequencer that was launched recently at the International workshop on HIV/AIDS and TB drug resistance at the Bloemfontein Campus.

International Workshop in Bloemfontein to Translate Research and Clinical Knowledge into Clinical Practice to Fight HIV & TB Drug Resistance in Africa

BLOEMFONTEIN, 21 November 2013. Today, a large intentional workshop on HIV & TB drug resistance starts, which will bring some of the top international researchers, clinicians and policy makers to the University of the Free State in order to discuss strategies to manage and prevent drug resistance in Africa.

A UKZN panel discussion: Bringing the 'I' into HIV - New approaches in developing person-centred interventions to fight the HIV epidemic

A UKZN panel discussion on 26 November 2013: 'Bringing the 'I' into HIV - New approaches in developing person-centred interventions to fight the HIV epidemic' as part of World AIDS Day 2013 activities.

SAFM Radio Interview with Prof. Tulio de Oliveira on their HIV Drug Resistance and Transmission Research and Award

Radio interview by Sisanda Jonas at SAfm weekend pmlive show 3 Nov 2013

The SA Medical Research Council announces funding of R190 million for high impact research projects

The MRC has established a new high-profile R190 million funding opportunity for Medical Schools and Universities to undertake 'Flagship Projects' aimed at addressing South Africa's key health problems. The winning projects, led by some of South Africa's most accomplished scientists, were announced at a media briefing at the MRC in Cape Town on Wednesday evening.

16.5 million rand to convert cutting-edge HIV research in rural South Africa into national policy

Professor Salim Abdool Karim and Health Minister, Dr Aaron Motsoaledi, awarded a R16.5 million grant to fight HIV drug resistance and transmission in rural KwaZulu-Natal.

Multi-million rand award to UKZN scientists for Cutting-Edge HIV Research

Professor Frank Tanser and Professor Tulio de Oliveira from UKZN's Africa Centre for health and Population studies were recently awarded a large grant to fight HIV drug resistance and transmission in rural KwaZulu-Natal. The grant, funded by the Medical Research Council (MRC) Flagship Projects is part of the MRC's strategy to sustain vibrant medical research in South Africa.

BioMedical research is undergoing a revolution

'Intensive', 'Comprehensive', 'Fulfilling' and 'Exciting' were just some of the words used by students to describe the first Bioinformatics course hosted by the KwaZulu-Natal Research Institute for TB and HIV (K-RITH) in partnership with the US-based Broad Institute and the NIH recently.

Newsletter, Oct 2013: News, blogs, manuscripts & Youtube videos!

The concept behind this newsletter is that anyone with 15 minutes to spare can learn about the work of SATuRN. In this third issue of 2013 our newsletter we focus on our digital videos activities. We have also included interesting news, blogs, reports, tweets, publications and training information produced by our network.

New Director named for leading HIV research centre in South Africa

Deenan Pillay, Professor of Virology at UCL (University College London), is today named as the new Director of the Africa Centre for Health and Population Studies, one of the Wellcome Trust's major overseas programmes.

SATuRN Newsletter, Aug 2013: Special Edition - Training and Capacity Building

The concept behind this newsletter is that anyone with 15 minutes to spare can learn about the work of SATuRN. The newsletter is presented as a PDF document with links to complete articles at the bioafrica.net website.

BOOK REVIEW - HIV & TB Drug Resistance & Clinical Management Case Book

by Sigaloff & Hamers, The Southern African Journal of HIV Medicine, Book Review on the HIV & TB Drug Resistance & Clinical Management Case Book by Rossouw, Lessells and de Oliveira

Bioinformatics in the tropics II: Large data sets analysis workshop: HIV phylogenetics and drug resistance, Durban, South Africa, 23-26 Sept 2013

This is the second workshop of the bioinformatics in the tropics series, which will be presented by the Wellcome Trust Africa Centre for Health and Population Studies at K-RITH at the University of KwaZulu-Natal, Durban, South Africa, 23 to 27 September 2013. The bioinformatics in the tropics series is part of a south to south capacity building programme to develop the next generation of bioinformaticians in Africa and Latin America.

Bioinformatics in the tropics I: 1st International Bioinformatics & Molecular Viral Evolution Workshop, Salvador, Bahia, Brazil, 22-26 July 2013

This is the first workshop of the bioinformatics in the tropics series, which will be presented at the Oswaldo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil, 22 to 26 July 2013.

Bioinformatics in the tropics workshop series 2013-2014

This is a series of four workshops, which will be presented in Brazil (2013 & 2014), South Africa (2013) and Uganda (2014) as part of a south to south capacity building programme to develop the next generation of bioinformaticians in Africa and Latin America.

Infectious Disease Genomics and Global Health Wellcome Trust Conference

We are pleased to announce that we are presenting at the Sixth Infectious Disease Genomics and Global Health conference, Cambridge, U.K, 16-18 October 2013. The focus of this meeting is the application of genomic technologies to the problems of infectious disease in a global health context.

The Network Marker

Drug resistance poses significant potential problems in the fight against HIV and TB, but little is known about how best to tackle it. Dr Tulio de Oliveira heads a network that aims to fill this knowledge gap.

Case book tackles HIV and TB drug resistance

By Jonathan Davis, 15 April 2013 - Researchers from the Africa Centre for Health and Population Research near Mtubatuba have published a important book to help rural doctors, nurses and pharmacists working on the frontline of the country's interlinked HIV and tuberculosis (TB) pandemics manage increasing levels of resistance to the drugs needed to fight the diseases.

SATuRN Newsletter, Mar 2013: News, blogs, events, publications and a case book on HIV/TB drug resistance

The concept behind this newsletter is that anyone with 15 minutes to spare can learn about the work of SATuRN. The newsletter is presented as a PDF document with links to complete articles at the bioafrica.net website.

SATuRN will have a session at the 17th Rural Health Conference

The 17th Annual Rural Health Conference will be held in St. Lucia, KwaZulu-Natal, South Africa, from 8 to 10 August 2013. SATuRN will have a session (approximately 2-3 hours) in the conference and will distribute the HIV & TB Drug Resistance and Clinical Management Case Book.

Casebook aims to curb drug resistance

Pretoria News - 19 March 2013, DOCTORS from the University of Pretoria (UP) and University of KwaZulu-Natal (UKZN) have stepped up to the challenge of providing a clinical management casebook for health care workers treating patients with HIV and TB drug resistance.

University of Pretoria and partners launch a book

By Sanku Tsunke, Pretoria, 19 March 2013. Drug resistance is one of the main challenges confronting HIV and TB programmes in Africa. Facing these challenges requires an understanding of how drug resistance develops, as well as up-to-date knowledge of how to diagnose and manage drug resistance in HIV and TB patients.

BOOK ON MANAGEMENT OF HIV AND TB DRUG RESISTANCE LAUNCHED

HIV and TB: Drug Resistance and Clinical Management Case Book - a book co-authored by two academics from the Africa Centre for Health and Population Studies - has been presented to frontline health workers at a workshop in northern KwaZulu-Natal.

Universiteit van Pretoria en vennote stel boek vry oor weerstand teen middels wat gebruik word om MIV en tuberkulose te bekamp

Weerstand teen medikasie is een van die belangrikste struikelblokke wat programme om MIV en tuberkulose in Afrika te bestry te bowe moet kom. Om hierdie uitdagings die hoof te bied, word 'n begrip vereis van hoe weerstand teen die middels tot stand kom, sowel as vertroudheid met die jongste metodes om weerstand teen die medikasie in MIV- en tuberkulosepasiente te diagnoseer en bestuur.

Transferring Critical Knowledge and Skills to Frontline Medical Personnel Fighting the HIV & TB epidemics in rural South Africa

UKZN's Africa Centre for Health and Population Studies, based in the College of health Sciences, has once again made huge strides in HIV management. Recently, the Centre's, Dr Richard Lessells and Dr Tulio de Oliveira together with the University of Pretoria's, Dr. Theresa Rossouw; launched a book entitled, 'HIV and TB: Drug Resistance and Clinical Management Case Book'.

PRESS RELEASE: Book Launch: HIV and TB Drug Resistance & Clinical Management Case Book

Prof Eric Buch, Dean of the Faculty of Health Sciences at the University of Pretoria, in partnership with European Delegation to South Africa, MRC Inflammation and Immunity Unit and the Africa Centre for Health and Population Studies, UKZN, invite members of the media to attend the launch of the 'HIV and TB Resistance & Clinical Management Case Book' that is authored by Dr Theresa Rossouw of UP and Drs Richard Lessells and Tulio de Oliveira of the Africa Centre for Health and Population Studies. The details are as follows:

Invitation to the launch of the HIV and TB drug resistance & clinical management case book

University of Pretoria invites you to attend the launch of the publication HIV and TB resistance & clinical management case book. The invitation is writen in three official South African languages: Afrikaans, English and Sepedi.

18th International Bioinformatics Workshop on Virus Evolution & Molecular Epidemiology, USA, 25-30 Aug 2013

We are announcing the organization of the international workshop on Virus Evolution and Molecular Epidemiology (VEME) in 2013, hosted by the Emerging Pathogens Institute in the warm city of Gainsville and sponsored by several local partners.

Africa Centre major scientific achievements! Two Science papers showing that antiretroviral therapy increases life expectance and reduces transmission

Africa Centre, South Africa, 22 February 2013 - Today, colleagues from the Wellcome Trust Africa Centre for Health and Population Studies have published two breakthrough scientific manuscripts at Science.

HIV/TB Drug Resistance and Clinical Management Workshop & Book Launch, Ghost Mountain Inn, Mkuze, South Africa, 7-8 Mar 2013

Organised by the Africa Centre for Health and Population Studies and Southern African Treatment and Resistance Network (SATuRN) in collaboration with the uMkhanyakude District Health Office. This workshop is aimed at developing knowledge and skills around the prevention and management of drug resistance and treatment failure in both HIV and TB.

Searching for Virus Phylotypes

Viral phylogenies have wide use: studying evolution, tracing the origin of epidemics, establishing dominant mode of transmission, identifying the apparition of drug resistance, even tracking individual body compartments.

Practical Course on Quality Assurance of HIV-1 Drug Resistance Interpretation in Sequence Editing and Data Management Processes

The African Centre for Integrated Laboratory Training (ACILT) present the HIV-1 drug resistance practical course, 22-26 April, Johannesburg, South Africa.

The 2012 Southern African ARV drug resistance testing guidelines

Antiretroviral therapy (ART) has converted HIV infection from an almost universally fatal illness to a chronic manageable disease. Adherence to therapy is essential for full viral suppression and optimal immune reconstitution.

The Machine That Will Help End TB

By Jon Cohen on December 11, 2012 - Nearly 1.5 million people die from tuberculosis every year, even though most cases can be cured with routine antibiotic treatments. One country's fight to get the ancient scourge under control has an unlikely hero: a simple diagnostic test.

Comminit News: Scientific Community Engagement Activities in Rural KwaZulu-Natal, South Africa

BioAfrica, Southern African Treatment and Resistance Network (SATuRN), and the Africa Centre Bioinformatics Unit use art to present scientific facts in Rural KwaZulu-Natal, South Africa. They are involved in many community engagement activities, presenting to African communities about the origin of HIV, the causes and consequences of drug resistance development, and how to successfully manage HIV and tuberculosis (TB) treatment.

UKZN Research Centres Collaborate to Celebrate World AIDS Day

The Health Economics and HIV and AIDS Research Division (HEARD) in collaboration with CAPRISA, SATuRN/Africa Centre and the University of KwaZulu-Natal Press hosted Getting to Zero: Showcasing KZN Research on HIV and AIDS on 14 November at the KZNSA Gallery.

SATuRN at the 43rd Union World Conference on Lung Health

KUALA LUMPUR, MALAYSIA, 14-17 Nov 2012, SATuRN researchers Dr. Richard Lessells and Dr. Tulio de Oliveira had a very successful TB conference. In this post we cover their presentations, workshops participation and tweeter coverage.

SATuRN/Africa Centre, CAPRISA and HEARD/UKZN: An event showcasing KZN research on HIV and AIDS

DURBAN, SOUTH AFRICA, 14 Nov 2012. We have organized and presented an event at the KZN National Art Gallery that portrait our DNA sequencing and Art & Science work.

HIV and TB bioinformatics presentation and tweet coverage at K-RITH opening, 9-11 October 2012

SATuRN is presenting a talk at the KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH) opening. This symposium has a fantastic scientific program, with some of the leading researchers and funders in the world! Please follow our tweeter coverage!

SATuRN activities at the London School of Hygiene and Tropical Medicine TB Centre

SATuRN activities were highlighted at the LSHTM TB Centre Annual Retreat, which was held in Downing College, Cambridge.

Dissecting diagnostics - TB drug resistance in rural South Africa

Researchers based in northern KwaZulu-Natal in rural South Africa are exploring the impact of novel molecular tuberculosis diagnostic system on clinical outcomes for patients with multidrug-resistance TB.

SATuRN Newsletter, Sept 2012, News, blogs, conferences, publications on HIV/TB drug resistance and phylogenetics

In this third issue of our newsletter we have included interesting news, blogs, reports, tweets, publications and training information produced by our network. We hope you enjoy it and find it informative. We welcome any feedback about content or format.

'Tainted milk' from wet nurse HIV risk

By BIANCA CAPAZORIO - A BABY girl who contracted HIV after being breast-fed by a well-meaning aunt has become the first proven case in SA to have contracted HIV from a surrogate feeder or 'wet nurse'.

Tainted Milk from Surrogate Feeder

A baby girl who contracted HIV after being breast-fed by a well-meaning aunt has become the first proven case in South Africa to have contracted HIV from a surrogate feeder or 'wet nurse'. The case contained in new research highlights the importance of HIV testing of mothers and surrogate feeders at a time when the government is phasing out free infant formula in its clinics.

Local centre proves 'surrogate' HIV infection

The Africa Centre for Health and Population Studies, Zululand's HIV-AIDS research hub based near Mtubatuba, has revealed the first proven HIV surrogate transmission case in South Africa.

DNA sequencing confirms HIV transmission through surrogate breastfeeding

DNA sequencing has provided evidence of HIV-1 transmission from an infected woman breastfeeding her niece in South Africa, drawing attention to infant feeding practices and the need for HIV testing of all breastfeeding surrogates as well as mothers.

Breastfeeding in the spotlight

A case where an aunt infected her niece with HIV through breastfeeding has drawn attention to feeding practices in South Africa. The case was published in the medical journal Lancet and highlighted the risk of HIV transmission from a surrogate carer, the Africa Centre for Health and Population Studies said today.

Collaboration to Undertake HIV Resistance Testing in Africa

Sequencing-based diagnostics for human immunodeficiency virus (HIV)-infected individuals will be carried out in Africa in order to determine resistance to antiretroviral drugs.

Creating access to HIV/TB drug resistance testing

During July, the acclaimed researcher, Dr Tulio de Oliveira from the Southern African Treatment Research Network (SATuRN), was invited to CAPRISA to visit CAPRISA's eThekwini Clinical Research Site. He also presented latest developments on affordable HIV and TB drug resistance testing and open access, public, drug resistance databases to CAPRISA's management team, followed by discussions on possible opportunities for collaboration.

Drug Resistance After Failure of First-Line ART Increasing in Rural South Africa: Presented at AIDS 2012

By Nancy A. Melville - WASHINGTON, DC - July 27, 2012 - As antiretroviral therapy (ART) for HIV becomes widely accessible in Southern Africa, the risk for drug resistances is on the rise, and as many as 1 in 6 adults show acquired drug resistance to standard second-line drug regimens, researchers said here on July 24 at the 19th International AIDS Conference.

Life Tech, SATuRN Collaborate on Dx for Antiretroviral Resistance in HIV in Africa

NEW YORK (GenomeWeb News) - Life Technologies today announced a collaboration with the Southern African Treatment and Resistance Network (SATuRN) covering sequencing-based diagnostics for HIV patients in Africa.

Life Technologies and SATuRN Collaborate to Increase Access to HIV Testing in Africa

Life and Southern African Treatment and Resistance Network (SATuRN) Partner in Sequencing-Based Surveillance of Drug Resistance

Life Technologies Corporation And Southern African Treatment and Resistance Network Collaborate To Increase Access To HIV Testing In Africa

Life Technologies Corporation announced a collaboration with the Southern African Treatment and Resistance Network (SATuRN) on sequencing-based diagnostics for HIV-infected individuals in Africa.

HIV drug resistance is spreading in Africa, experts say

WASHINGTON (By Erin Loury, LA Times) - Scaling up the distribution of HIV medication over the last decade has vastly increased the number of people receiving treatment around the world. An estimated 8 million infected people received the antiretroviral drugs in 2011, compared to just 400,000 in 2003.

Drug-resistant HIV 'on increase' in sub-Saharan Africa

Drug-resistant HIV has been increasing in parts of sub-Saharan Africa over the last decade, according to experts writing in the Lancet

SATuRN meeting, presentations & tweet coverage at the XIX International AIDS 2012 Conference, Washington

WASHINGTON, 22-27 July 2012 - We are hosting a meeting, presenting many talks and posters and tweeting on the XIX International AIDS 2012 Conference.

SAHIVSOC'S First Conference, 25-28 November 2012, Cape Town ICC

The Southern African HIV Clinicians Society will be hosting its first Conference: Striving for Clinical Excellence, 25-28 November 2012 at the Cape Town ICC.

SATuRN Newsletter V.1 Num.2 (Apr-Jun 2012) - Featured partners, news, blogs, tweets & publications

In this second issue of our newsletter we have included interesting news, blogs, reports, tweets, publications and training information produced by our network. We hope you enjoy it and find it informative. We welcome any feedback about content or format.

SATuRN's tweet coverage about drug resistance at the 3rd SA TB conference

We participated, presented and tweeted about the 3rd South African TB conference, 12-15 June 2012, ICC, Durban. We had covered all the sessions that present TB drug resistance results. Please find below our tweets from our participation in our national TB conference.

BioAfrica Art & Science section is open!

In this exciting new section of bioafrica.net art we feature creative projects that celebrate, investigate and/or communicate biomedical science. Here, we share blogs, news articles, tweets, audio and audiovisual media to increase public awareness of innovative collaborations between art and science.

SATuRN Newsletter Vol. 1 Number 1, Jan-Mar 2012

The newsletter idea is that anyone with 15 minutes to spare can learn about our work and its application in everyday life.

Open letter on urgent need for compassionate use of bedaquiline for XDR-TB and pre-XDR-TB in South Africa

BioAfrica & SATuRN Supports this Open Letter!

Open letter to the Medicines Control Council and Ministry of Health on urgent need for compassionate use of bedaquiline for XDR-TB and pre-XDRTB in South Africa.

Transmitted Drug Resistance Rate Remains Below 5% in South Africa

by Mark Mascolini - Analysis of South Africans with newly diagnosed, untreated HIV infection indicates low levels of transmitted antiretroviral-resistant HIV across the country through 2010 and no evidence of transmitted drug-resistant HIV in rural KwaZulu Natal

Highly Specialized Team to Tackle HIV Drug Resistance Problem in Southern Africa

DURBAN, SOUTH AFRICA, 24-26 FEB 2012 - A small, highly specialized multidisciplinary team of doctors and statisticians from South Africa, Botswana, the USA and the UK will meet in Durban this weekend with the express purpose of pooling their resources, knowledge and expertise in an attempt to improve understanding the problem of HIV drug resistance in southern Africa.

New and interactive section of BioAfrica and SATuRN website

One of our main aims for this development is for users and collaborators to become more involved in the website. It has added over 100 new webpages to bioafrica.net, including blogs, open access publications, media coverage, clinical cases tutorials and twitter. It has also increased the number of people collaborating in the development of our website!

Alarm bells on HIV-drug resistance - Study raises fears as patients develop immunity to antiretroviral therapy

JOHANNESBURG - The prevalance of HIV-positive people who have developed a resistance to life-prolonging antiretroviral treatment (ART) is a cause for concern for South Africa, scientists warn.

Botswana hosts Africa HIV/TB drug resistance workshop

GABARONE - For the first time, Botswana is hosting the Africa HIV/TB Drug Resistance and Clinical Management workshop. The two-day workshop started yesterday at the University of Botswana (UB). Scientists, public health officials and physicians from across the world are attending the event to discuss the growing problem of HIV and TB drug resistance in Southern Africa.

Meeting to Discuss the Growing Threat of HIV & TB Drug Resistance in South Africa and Botswana

JOHANNESBURG - A group of renowned HIV and TB scientists, public health officials and physicians will meet at the University of Botswana in Gaborone, this coming Monday and Tuesday (7th & 8th of November) to discuss the growing problem of HIV and TB drug resistance in southern Africa.

Drug Resistance Increasing in Children

Indeed, drug resistance is emerging in children on ART in South Africa.

Public database for HIV drug resistance in southern Africa

PRETORIA - We would like to draw attention to an HIV-1 drug resistance database, a scientific resource for regional and global HIV research that will enhance surveillance programmes in southern Africa.The database was established by investigators from the Southern African Treatment and Resistance Network (SATuRN), in collaboration with researchers from the United States & Europe. SAT- uRN will provide national de- partments of health with high quality, up-to-date information to guide delivery of antiretroviral ther- apy, helping to ensure the long -term success of antiretroviral treatment programmes.

Taxis on board - Spreading the word while jiving

Jiving with Science is a new public engagement initiative of the Africa Centre for Health and Population Studies. Africa Centre is an international HIV research facility with a partnership HIV testing, treatment and care programme run jointly with the KZN Department of Health. The Mtubatuba-based centre is where the HIV epidemic is one of the most severe in the world, with nearly one in two adults aged 35-40 being infected.

Jiving with Science is a new public engagement initiative of the Africa Centre for Health and Population Studies

Jiving with Science is a new public engagement initiative of the Africa Centre for Health and Population Studies. The Africa Centre, a joint project of the University of KwaZulu-Natal (UKZN) and the Medical Research Council of Southern Africa, is an international HIV research facility with a partnership HIV testing, treatment and care programme run jointly with the KwaZulu-Natal Department of Health.

JIVING WITH SCIENCE - Music CDs

Jiving with Science is a new public engagement initiative of the Africa Centre for Health and Population Studies. The Africa Centre, a joint project of the UKZN and the Medical Research Council of Southern Africa, is an international HIV research facility with a partnership HIV testing, treatment and care programme run jointly with the KZN Department of Health. It is based in rural, northern KwaZulu-Natal where the HIV epidemic is one of the most severe in the world with nearly one in two adults aged 35-40 being infected.

Stirring students with science

RICHARDS BAY - A team from Africa Centre for Health and Population Studies explained the origins of Human Immunodeficiency Virus (HIV) for scholars of the Aiglon Society at Grantleigh College last Tuesday. The challenge to incorporate high-level bioinformatics and molecular evolutionary analysis into a high-school format of genetic variation and HIV life cycle was facilitated by senior researcher, Dr Tulio de Oliveira.

The Race Against Drug Resistance

by Rachel Nugent, Emma Back, and Alexandra Beith - In an increasingly interconnected world, drug resistance does not stop at a patient's bedside, it threatens global health. It has slowed gains against the fatal ravages of childhood dysentery and pneumonia, drastically increased the costs of fighting tuberculosis and malaria, and imperiled efforts to effectively treat people living with HIV/AIDS. Tens of millions of lives are at stake; quality of life for scores of millions more is under threat.

Believe in ART, get tested please

CAPE TOWN - Believe that anti-retroviral treatment (ART) medication works and get yourself tested. People who are infected with the virus are able to live longer, healthier lives, provided they use their medication and seek treatment early enough. This was the key message Dr. Tulio de Oliveira, a bio-informatics researcher from SATuRN wanted to be convey to the general public.

High noon in Libya

This week sees yet another crisis point in the Libyan case of six foreign health professionals sentenced to death on charges of injecting hundreds of children with HIV. Declan Butler traces the efforts of scientists to help establish the truth.

World-class scientist due to join UWC team tackling HIV/Aids treatment in SA.

CAPE TOWN - A world-class molecular biologist whose research on HIV and anti-retrovirals (ARVs) could dramatically improve the treatment of HIV/Aids in South Africa. Doctor Tulio de Oliveira, an expert in bioinformatics at Oxford University, will join the SA National Bioinformatics Institute at UWC.

New evidence in Libyan HIV trial

New and compelling scientific evidence has emerged in support of five Bulgarian nurses and a Palestinian doctor accused of deliberately spreading HIV to 426 Libyan children in 1998.

Genetic Analysis Clears Accused Medics

A new molecular study provides the strongest scientific evidence yet that six foreign medics held in Libya are innocent of charges that they deliberately infected more than 400 children with HIV. Accumulated mutations in the virus genomes reveal that the outbreak began well before the medics arrived in the country. The Libyan supreme court is set to decide on 19 December whether to execute the medics. It is unclear whether the new study will influence its verdict.

Libya sentences medics to death

A Libyan court has sentenced five Bulgarian nurses and a Palestinian doctor to death for knowingly infecting hundreds of Libyan children with HIV.

Medics face death while Libya uses HIV children as diplomatic pawns

Alex Duval Smith The Observer, Sunday 17 December 2006 13.12 GMT - The death in Libya six weeks ago of nine-year-old Marwa Annouiji from Aids was much more than just another developing world statistic. In her short, life, dominated by illness, the frail child was a pawn in a high-level game of international relations. Marwa, from al-Bayda on the Mediterranean coast, was the 52nd Libyan child to die as a result, Libya claims, of a deliberate operation by foreign medical workers to pump HIV-infected blood into 426 girls and boys at the al-Fatah Hospital in Benghazi.

New Evidence Disputes Libya Case in H.I.V. Trial

LONDON, Dec. 6 (Reuters) - Scientists have produced new evidence that casts doubt on charges against five Bulgarian nurses and a Palestinian doctor accused by Libya of deliberately infecting 426 children with the virus that causes AIDS in 1998.

New scientific evidence in Libya HIV death penalty case

OXFORD - New molecular evidence from Oxford Zoology Department casts significant doubt on charges against six medical workers who are facing execution in Libya. The medical workers are charged with deliberately contaminating more than 400 children with HIV in 1998.However, new evidence published online in Nature from the Evolutionary Biology Group at Oxford, in collaboration with several European universities, shows that the subtype of HIV involved began infecting patients well before the medical workers arrived in Libya.

Molecular HIV evidence backs accused medics

International experts in DNA forensics say that a paper published online by Nature this week provides a firm alibi for the six medical workers facing the death penalty in Libya. The workers have been charged with deliberately infecting more than 400 children with HIV in 1998.

Study backs Libya HIV case medics

LONDON - Scientists have cast doubt on charges that five Bulgarian nurses and a Palestinian doctor deliberately infected Libyan children with HIV. The medics could face the death penalty if found guilty by a court in Tripoli later this month.

challenging the status quo

Epidemic
Research & Innovation
in Africa!

01

A coalition from global south to effectively respond to epidemics…

Vision:

Our vision is to effectively respond to epidemics through pathogen genomics surveillance to enhance biomedical discovery, improving the treatment, diagnosis and prevention of human disease and generating economic opportunities for Africa.

We use our expertise in genomics to identify new variants of pathogens and advance basic and translational science to improve prevention, treatment and vaccines to human disease in Africa.

02

Genomics & Digital Biology

CERI will bring together world-class research organizations under the leadership of Prof. Tulio de Oliveira,  who joined forces to create the Network for Genomic Surveillance in South Africa (NGS-SA). Through the NGS-SA, this has led to South Africa being one of the leading examples in the world of the application of genomics surveillance to SARS-CoV-2.

0
Pathogen genomes

0
IDEAS

0
PATHOGENS

0
WORKING HOURS & COFFEE

03

Genotype-to-phenotype

The Institute will have access to advanced P3+ biosafety level laboratories and animal models to determine pathogens’ phenotypes.

Vaccine Evaluation

In collaboration with Prof. Alex Sigal group, we evaluate the effectiveness of vaccines on the neutralization of variants.

Antimicrobial Resistance

We also focus on the identification of antimicrobial resistance and the evaluation of the most appropriate diagnostics and therapies for resistance pathogens.

RECENT PUBLICATIONS:

Big Data, Epidemiology & AI

CERI has a scientific team that specializes in epidemiology, big data, computational intelligence, and bioinformatics. These analytical skills are necessary to understand how pathogen genetic variation affects the transmission, diagnosis, treatment, and vaccination. We are able to analyze large datasets and provide information on how to guide public health response.

We Can Help Preparing to
Future Epidemics
Now

Computational Intelligence

We are building a team at the School for Data Science and Computational Intelligence to continue use advanced algorithms to identify the first signs of epidemics in Africa..

Largest automated Bio-repository in Africa

We have a Hamilton BIOS, which is a fully automated -80C biorepository that can store over 3 million samples. It also allows quick access to samples for genotyping and phenotyping.

OUR WORK ON THE NEWS: