// Research Output

Publications

2026
‘The not talking is actually what kills you’– young South African women’s communication barriers about sexual health

Hartley F, Trappler J, Gill K, Bekker L, MacKenny V, Knight L, Passmore J

Culture, Health & Sexuality
1-12
2026
Identification and genomic characterisation of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa

Dor G, Kekana D, Hisner R, Martin D, Korber B, Ernst T, Levy A, Speers D, Turville S, Sintchenko V, Basile K, Sullivan G, Rockett R, Kok J, Schoenmakers J, Gueli F, Lessels R, Baxter C, Wolter N, Gottberg A, Tegally H, de Oliveira T

Virus Evolution
2026
Human MERS-CoV cases are falling but pose an ongoing pandemic threat

Subissi L, Otieno J, Shah A, Abu-Raddad L, Agrawal A, Mehairi A, Albarraq A, Barakat A, Bashir I, Caly L, Chand M, Drosten C, Faria N, Fowotade A, von Gottberg A, Haagmans B, Huang B, Kindrachuk J, Koopmans M, Korber B, Leo Y, Mbala-Kingebeni P, Melhem N, Munster V, Ngere I, Njenga M, de Oliveira T, Palacios G, Peiris M, Rambaut A, Resende P, Saha S, Suzuki T, Yadav P, von Dobschuetz S, Azhar E, Van Kerkhove M

Nature Health
2026
VIBRANT: A phase 1 randomized trial of multi-strain vaginal L. crispatus live biotherapeutic products in people with bacterial vaginosis

Potloane D, Symul L, Ngcapu S, Lewis L, France M, Vermeren L, Elsherbini J, Chetty C, Mafunda N, Polliah A, Mtshali A, Kama A, Magini N, Mitchev N, Mzobe G, Khan A, Demidkina B, Goldenberg M, Xu J, Rutt L, Shirtliff B, Cook S, Murthy M, Hussain F, Passmore J, Jaspan H, Kullin B, Happel A, Liebenberg L, Relman D, Holmes S, Kwon D, Ravel J, Mitchell C

Cell Host & Microbe
2026
Faecal Coliforms and Escherichia coli Contamination in Drinking Water Sources in Cholera Hotspot Areas of Lusaka District, Zambia: A Cross-Sectional Study

Ng’ombe H, Luchen C, Phiri B, Ngosa D, Kapikila R, Sakanya S, Sakala C, Mbewe N, Liswaniso F, Chilengi R, Wilkinson E, Liebenberg L, Khan W, Thomson N, Sack D, Bosomprah S, Chisenga C

Microorganisms
14:420
2026
Cross-platform protocol for HTLV-1 whole-genome sequencing using nanopore and Illumina technologies

Lima A, de Moraes L, Amorim R, Cucco M, Silva R, Giovanetti M, Rego F, Araújo T, Fonseca V, Khouri R, Alcantara L, Santos L, Barreto F

Next Research
3:101110
2026
Spatiotemporal patterns of Rift Valley fever virus in Africa: a retrospective genomic epidemiology and phylodynamic modelling study

Juma J, Tegally H, Konongoi S, Roesel K, Sang R, de Oliveira T, Njenga M, Christoffels A, Bett B, Dellicour S, Oyola S

The Lancet Microbe
7:101251
2026
Robust mission-driven responses to infectious disease threats delivered by the Abbott pandemic defense coalition

Rodgers M, Averhoff F, Berg M, Anderson M, Strobel C, Inostroza J, Moy J, Mera J, Utz P, Weaver S, Chiu C, De Arcos J, Anzinger J, Henrys J, Hernandez-Ortiz J, Torres K, Mendes-Correa M, Gonçalves N, Kallas E, Mboup S, N’jai A, Mbanya J, de Oliveira T, Kaleebu P, El-Sayed M, Alkhazashvili M, Khan E, Khan R, Suputtamongkol Y, Osorio J, Cloherty G

International Journal of Infectious Diseases
162:108162
2026
Enhancing SARS-CoV-2 response capacity in Africa and other centers for research in emerging infectious diseases centres through a collaborative training programme

Ahouidi A, Padane A, Gaye A, Sakuntabha A, Deme A, Cisse B, de Oliveira C, Weldon C, Diedhiou C, Ndiaye D, Gottlieb G, McOwen H, Dia I, Xavier J, Siddle K, Andersen K, Barrett L, Paye M, Diallo M, Tilles S, Weaver S, Wohl S, de Oliveira T, Junior Alcantara L, Van Voorhis W, Mboup S, Wilkinson E, Giovanetti M

Clinical Microbiology and Infection
32:192-195
2026
CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation

Tagliamonte M, Sharma A, Riva A, Moir M, Salemi M, Baxter C, de Oliveira T, Mavian C, Wilkinson E

Bioinformatics
42
2026
Ancient Pathogen Genomics in Africa – Current Evidence and Future Directions

Vukovikj M, Mavian C, Wang H, Gifford R, de Oliveira T, Schlebusch C

Preprints.org
2026
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

Hunt M, Hinrichs A, Anderson D, Karim L, Dearlove B, Knaggs J, Constantinides B, Fowler P, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, Kotzen B, de Maio N, Amenga-Etego L, Amuzu D, Avaro M, Awandare G, Ayivor-Djanie R, Barkham T, Bashton M, Batty E, Bediako Y, De Belder D, Benedetti E, Bergthaler A, Boers S, Campos J, Carr R, Chen Y, Cuba F, Dattero M, Dejnirattisai W, Dilthey A, Duedu K, Endler L, Engelmann I, Francisco N, Fuchs J, Gnimpieba E, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao N, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki K, Kurkela S, Lappalainen M, Lataretu M, Lemieux J, Liu C, Malavige G, Mashe T, Mongkolsapaya J, Montes B, Mora J, Morang’a C, Mvula B, Nagarajan N, Nelson A, Ngoi J, da Paixão J, Panning M, Poklepovich T, Quashie P, Ranasinghe D, Russo M, San J, Sanderson N, Scaria V, Screaton G, Sessions O, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson R, Williamson C, Zair X, Biere B, Dürrwald R, Mache C, Oh D, Schulze J, Wedde M, Wolff T, Fuchs S, Semmler T, Paraskevopoulou S, Kerber R, Kröger S, Haas W, Bode K, Corman V, Erren M, Finzer P, Grosser R, Haffner M, Hermann B, Kiel C, Krumbholz A, Lorentz T, Meinck K, Nitsche A, Petzold M, Schwanz T, Szabados F, Tewald F, Tiemann C, de Oliveira T, Peto T, Crook D, Corbett-Detig R, Iqbal Z

Nature Methods
23:653-662
2026
Chikungunya virus

Ramphal Y, de Oliveira T

Nature Ecology & Evolution
10:610-610
2026
Re-emergence of DENV-3 in Paraguay After Two Decades: A Genomic and Epidemiological Investigation

Cantero C, Vazquez C, Gonzalez S, Rojas A, Fleitas F, Barrios J, Gomez de la Fuente A, Villalba S, Torales M, Ijeda A, Fonseca V, Junior Alcantara L, Giovanetti M

Emerging Microbes & Infections
2025
Differences in HIV risk factors between South African adolescents and adult women and their association with sexually transmitted infections

Mkhize P, Mehou-Loko C, Maphumulo N, Radzey N, Abrahams A, Sibeko S, Harryparsad R, Manhanzva M, Meyer B, Radebe P, Liebenberg L, Ngcapu S, Ahmed N, Busakwe F, Mqaba N, Archary D, Sivro A, Samsunder N, Potloane D, Horsnell W, Jordan C, Abdool Karim Q, Bekker L, Passmore J, Jaspan H, Humphries H, Masson L

Sexually Transmitted Infections
101:174-182
2025
Effect of the vaginal live biotherapeutic LACTIN-V (Lactobacillus crispatus CTV-05) on vaginal microbiota and genital tract inflammation among women at high risk of HIV acquisition in South Africa: a phase 2, randomised, placebo-controlled trial

Hemmerling A, Mitchell C, Demby S, Ghebremichael M, Elsherbini J, Xu J, Xulu N, Shih J, Dong K, Govender V, Pillay V, Ismail N, Casillas G, Moodley J, Bergerat A, Brunner T, Liebenberg L, Ngcapu S, Mbano I, Lagenaur L, Parks T, Ndung’u T, Kwon D, Cohen C

The Lancet Microbe
6:101037
2025
Circulating Short-Chain Fatty Acids: Association with Vaginal Microbiota, Genital Inflammation, and HIV Acquisition

Shivakoti R, Letsoalo M, Lewis L, Mckinnon L, Passmore J, Karim S, Liebenberg L

AIDS Research and Human Retroviruses
41:559-566
2025
Advancing the course of HIV genomics research in Africa

Agamah F, Arbuthnot P, Tindana P, Munung N, Kasule M, Ghansah A, Mosepele M, Gaolathe T, Kekitiinwa A, Nduati E, Jumare J, Gómez-Olivé F, Liebenberg L, Dandara C, Osawe S, Julius R, Muzambi T, Natus T, Omumbo J, Mayne E, Abimiku A, Richardson S, Matshaba M, Skelton M

BMJ Global Health
10:e019094
2025
Randomized trial of multi-strain Lactobacillus crispatus vaginal live biotherapeutic products after antibiotic therapy for bacterial vaginosis: study protocol for VIBRANT (vaginal lIve biotherapeutic RANdomized trial)

Chetty C, Mafunda N, Happel A, Khan A, Cooley Demidkina B, Yende-Zuma N, Saidi Y, Mahabeer Polliah A, Lewis L, Osman F, Radebe P, Passmore J, Kwon D, Ravel J, Ngcapu S, Liebenberg L, Symul L, Holmes S, Mitchell C, Potloane D

Contemporary Clinical Trials Communications
48:101554
2025
Genomic analysis and antimicrobial resistance of Vibrio cholerae isolated during Zambia’s 2023 cholera epidemic

Ng'ombe H, Luchen C, Bote L, Kasonde M, Musonda K, Mwape K, Kuntawala D, Silwamba S, Chibuye M, Chibesa K, Mbewe N, Bosomprah S, Khan W, Liebenberg L, de Oliveira T, Wilkinson E, Dorman M, Coghlan A, Simuyandi M, Chilengi R, Chisenga C, Thomson N

Microbial Genomics
11
2025
Reemergence of yellow fever virus in forest and periurban settings in Brazil

das Graças Dantas Andrade V, Ribeiro Adelino T, Fonseca V, Melo Farias Moreno K, Ribeiro Tomé L, Pereira L, Lima de La-Roque D, Bispo de Filippis A, Garkauskas Ramos D, Brock Ramalho D, de Lima Furtado K, Borges G, Martins L, Frutuoso L, Oliveira Lamounier L, Guimarães N, Sayuri Sato Barros P, Souza de Almeida P, de Souza da Silva P, Giesbrecht Pinheiro R, Guerino Stabeli R, Moreira da Silva Chagas S, Sousa Pietra Pedroso S, Kashima S, Gonçalves Penante S, Santini de Oliveira M, Lemes da Silva V, Van Voorhis W, Holmes E, Lourenço J, de Melo Iani F, Simões Jorge Júnior A, Giovanetti M, Junior Alcantara L

Communications Medicine
6:35
2025
Detection of Lymphocytic Choriomeningitis Virus in House Mouse (Mus musculus) in Brazil

Cavalcanti G, Fernandes J, Santos F, Teixeira B, Guterres A, Brignone J, Levis S, Lucio C, Costa-Neto S, Fonseca V, Giovanetti M, Alcantara L, D’Andrea P, de Lemos E, Oliveira R

Viruses
17:1544
2025
VAMPIRE: ALGORITMO PARA ANÁLISE DE DADOS DE NGS E IDENTIFICAÇÃO DE VARIANTES GENÉTICAS DO SISTEMA SANGUÍNEO RH

Galdino D, Rodrigues E, Lenz A, Chagas L, Laroque D, Santos F, Kashima S, Calado R, Fonseca V, Frias D

Hematology, Transfusion and Cell Therapy
47:105690
2025
Genomic surveillance of SARS-CoV-2 in the State of Mato Grosso, Midwest Brazil

da Silva S, Vasconcelos K, Almeida J, Guimarães N, Tomé L, Fonseca V, Júnior D, Giovanetti M, de Oliveira E, Alcântara L

Gene Reports
41:102361
2025
Uncovering DENV, CHIKV, and ZIKV in Urban Wastewater in Brazil Through Genomic and Molecular Screening

de Araujo J, Carvalho A, Adelino T, Iani F, Guimaraes N, Santos S, Leal C, Natividade M, Lima M, Almada M, Bertuce A, Guerra A, Costa M, Saia F, Fonseca V, Giovanetti M, Frutuoso L, Alcantara L

Microorganisms
13:2164
2025
Identifying genomic surveillance gaps in Africa for the global public health response to West Nile virus: a systematic review

Moir M, Sitharam N, Hofstra L, Dor G, Mwanyika G, Ramphal Y, Reichmuth M, San J, Gifford R, Wilkinson E, Tshiabuila D, Preiser W, Konou A, Bitew M, Onoja A, Paganotti G, Abera A, Maror J, Kayiwa J, Abuelmaali S, Lusamaki E, de Oliveira T, Alcantara L, Holmes E, Padane A, Musa A, Abera A, Campbell A, Ssemaganda A, Ahouidi A, Muianga A, Samson A, Onoja A, Alemu B, Foka C, Baxter C, van Zyl D, de Castro Silva D, Martin D, Wilkinson E, Kouma E, Simo F, Mwanyika G, Godebo G, D’or G, Tegally H, Omara I, Maror J, Poonagavan J, Juma J, Oludele J, Xavier J, Lourenco J, Fokam J, Maeka K, Singh L, Chabuka L, Issaka M, Hofstra M, Giovanetti M, Faye M, Koffi M, Owusu M, Dikongo M, Alimohamed M, Bitew M, Moir M, Kraemer M, Sitharam N, Jerome N, Mbhele N, Miantsatian Andry N, Tomori O, Magalutcheemee R, Guimaraes R, Oyola S, Abuelmaali S, Golubchik T, Fonseca V, Preiser W, Ramphal Y, Venter M, Burt F, Baxter C, Lessells R, de Oliveira T, Tegally H

The Lancet Microbe
6:101176
2025
Understanding the emergence expansion and impact of oropouche virus

Santos S, Adelino T, Cella E, Slavov S, Kashima S, Ciccozzi M, Tomé L, Guimarães N, Iani F, Alcantara L, Fonseca V, Giovanetti M

Discover Viruses
2
2025
CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation

Tagliamonte M, Sharma A, Riva A, Moir M, Salemi M, Baxter C, de Oliveira T, Mavian C, Wilkinson E

Bioinformatics
42
2025
Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples

de Campos G, Clemente L, Lima A, Cella E, Fonseca V, Ximenez J, Nishiyama M, de Carvalho E, Sampaio S, Giovanetti M, Elias M, Slavov S

Virology Journal
22
2025
Establishing a dengue genomic monitoring in Cuba: uncovering virus dynamics to enhance local response

Pérez M, Álvarez M, Perez L, Benitez A, Serrano S, Adelino T, Fonseca V, Resik S, Kouri V, Gresh L, Franco L, Rico J, Lourenço J, Alcantara L, Giovanetti M, Guzman M

IJID Regions
16:100683
2025
Tracing the spatial origins and spread of SARS-CoV-2 Omicron lineages in South Africa

Dor G, Wilkinson E, Martin DP, Moir M, Tshiabuila D, Kekana D, Ntozini B, Joseph R, Iranzadeh A, Nyaga MM, Goedhals D, Maponga T, Maritz J, Laguda-Akingba O, Ramphal Y, MacIntyre C, Chabuka L, Pillay S, Giandhari J, Baxter C, Hsiao NY, Preiser W, Bhiman JN, Davies MA, Venter M, Treurnicht FK, Wolter N, Williamson C, von Gottberg A, Lessells R, Tegally H, de Oliveira T

Nature Communications
28;16(1):4937. doi: 10.1038/s41467-025-60081-0
2025
Genomic Surveillance of Climate-Amplified Cholera Outbreak, Malawi, 2022–2023

Chabuka L, Choga W, Mavian C, Moir M, Morgenstern C, Tegaly H, Sharma A, Wilkinson E, Naidoo Y, Inward R, Bhatt S, WilliamWint G, Khan K, Bogoch I, Kraemer M, Lourenço J, Baxter C, Tagliamonte M, Salemi M, Lessells R, Mitambo C, Chitatanga R, Bitilinyu-Bango J, Chiwaula M, Chavula Y, Bukhu M, Manda H, Chitenje M, Malolo I, Mwanyongo A, Mvula B, Nyenje M, de Oliveira T, Kagoli M

Emerging Infectious Diseases
31(6):. doi: 10.3201/eid3106.240930.
2025
Importance of outbreak response research in bridging knowledge gaps on emerging infectious diseases

Breiman R, Osoro E, Reithinger R, Wang D, Diamond M, Van Voorhis W, Wasserheit J, Rabinowitz P, Mboup S, Hemingway-Foday J, de Oliveira T, Boon A, Schieffelin J, Sempowski G, Moody M, Vasilakis N, Hanley K, Nasimiyu C, Situma S, Ngere I, Kyobe Bosa H, Nyakarahuka L, Bakamutumaho B, Woodson S, Njenga M

BMJ Global Health
10(6):e018297. doi: 10.1136/bmjgh-2024-018297.
2025
Artificial intelligence for modelling infectious disease epidemics

Kraemer M, Tsui J, Chang S, Lytras S, Khurana M, Vanderslott S, Bajaj S, Scheidwasser N, Curran-Sebastian J, Semenova E, Zhang M, Unwin H, Watson O, Mills C, Dasgupta A, Ferretti L, Scarpino S, Koua E, Morgan O, Tegally H, Paquet U, Moutsianas L, Fraser C, Ferguson N, Topol E, Duchêne D, Stadler T, Kingori P, Parker M, Dominici F, Shadbolt N, Suchard M, Ratmann O, Flaxman S, Holmes E, Gomez-Rodriguez M, Schölkopf B, Donnelly C, Pybus O, Cauchemez S, Bhatt S

Nature
2025
Spatiotemporal disease suitability prediction for Oropouche virus and the role of vectors across the Americas

Poongavanan J, Dunaiski M, D’or G, Kraemer M, Giovanetti M, Lim A, Brady O, Baxter C, Fonseca V, Alcantara L, de Oliveira T, Tegally H

medRxiv
doi: 10.1101/2025.02.28.25323068.
2025
Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population

Lugano D, Mwangi K, Mware B, Kibet G, Osiany S, Kiritu E, Dobi P, Muli C, Njeru R, de Oliveira T, Njenga M, Routh A, Oyola S

medRxiv
doi: 10.1101/2025.03.03.25323296.
2025
Unveiling novel features and phylogenomic assessment of indigenous Priestia megaterium AB-S79 using comparative genomics

Adeniji A, Chukwuneme C, Conceição E, Ayangbenro A, Wilkinson E, Maasdorp E, de Oliveira T, Babalola O

Microbiology Spectrum
doi: 10.1128/spectrum.01466-24.
2025
Genomic Characterization of Circulating Dengue Virus, Ethiopia, 2022–2023

Abera A, Tegally H, Tasew G, Wilkinson E, Ali A, Regasa F, Bitew M, Belachew M, Chabuka L, Mwanyika G, Tshiabuila D, Giandhari J, Pillay S, Poogavanan J, Moir M, Kraemer M, Khan K, Huber C, Tollera G, de Wit T, Baxter C, Lessells R, Wolday D, Beyene D, de Oliveira T,

Emerging Infectious Diseases
31(3):. doi: 10.3201/eid3103.240996.
2025
Infectious diseases in a warming world: A call for action

Moir M, Baxter C, Tegally H, de Oliveira T

South African Journal of Science
121(3/4):. doi: 10.17159/sajs.2025/20722.
2025
Travel-associated international spread of Oropouche virus beyond the Amazon

de Melo Iani F, Pereira F, de Oliveira E, Rodrigues J, Machado M, Fonseca V, Adelino T, Guimarães N, Tomé L, Gómez M, Nardy V, Ribeiro A, Rosewell A, Ferreira, Silva de Mello A, Fernandes B, de Albuquerque C, dos Santos Pereira D, Pimentel E, Lima F, Silva F, de Carvalho Pereira G, Tegally H, Almeida J, Moreno K, Vasconcelos K, Santos L, Silva L, Frutuoso L, Lamounier L, Costa M, de Oliveira M, dos Anjos M, Ciccozzi M, Lima M, Pereira M, Rocha M, de Souza da Silva P, Rabinowitz P, de Almeida P, Lessells R, Gazzinelli R, da Cunha R, Gonçalves S, dos Santos S, de Alcântara Belettini S, Pedroso S, Araújo S, da Silva S, Croda J, Maciel E, Van Voorhis W, Martin D, Holmes E, de Oliveira T, Lourenço J, Alcantara L, Giovanetti M

Journal of Travel Medicine
doi: 10.1093/jtm/taaf018.
2025
Craft: A Machine Learning Approach to Dengue Subtyping

van Zyl D, Dunaiski M, Tegally H, Baxter C, de Oliveira T, Xavier J

doi: 10.1101/2025.02.10.637410.
2025
Identifying genomic surveillance gaps in Africa for the global public health response to West Nile Virus

Moir M, Sitharam N, Hofstra M, Dor G, Mwanyika G, Ramphal Y, Reichmuth M, James S, Gifford R, Wilkinson E, Tshiabuila D, Preiser W, Konou A, Bitew M, Onoja B, Paganotti G, Abera A, Maror J, Kayiwa J, Abuelmaali S, Lusamaki E, , Venter M, Burt F, Baxter C, Lessells R, de Oliveira T, Tegally H

doi: 10.1101/2024.12.18.629123.
2025
Hybrid versus vaccine immunity of mRNA-1273 among people living with HIV in East and Southern Africa: a prospective cohort analysis from the multicentre CoVPN 3008 (Ubuntu) study

Garrett N, Tapley A, Hudson A, Dadabhai S, Zhang B, Mgodi N, Andriesen J, Takalani A, Fisher L, Kee J, Magaret C, Villaran M, Hural J, Andersen-Nissen E, Ferarri G, Miner M, Le Roux B, Wilkinson E, Lessells R, de Oliveira T, Odhiambo J, Shah P, Polakowski L, Yacovone M, Samandari T, Chirenje Z, Elyanu P, Makhema J, Kamuti E, Nuwagaba-Biribonwoha H, Badal-Faesen S, Brumskine W, Coetzer S, Dawson R, Delany-Moretlwe S, Diacon A, Fry S, Gill K, Ebrahim Hoosain Z, Hosseinipour M, Inambao M, Innes C, Innes S, Kalonji D, Kasaro M, Kassim P, Kayange N, Kilembe W, Laher F, Malahleha M, Maluleke V, Mboya G, McHarry K, Mitha E, Mngadi K, Mda P, Moloantoa T, Mutuluuza C, Naicker N, Naicker V, Nana A, Nanvubya A, Nchabeleng M, Otieno W, Potgieter E, Potloane D, Punt Z, Said J, Singh Y, Tayob M, Vahed Y, Wabwire D, McElrath M, Kublin J, Bekker L, Gilbert P, Corey L, Gray G, Huang Y, Kotze P, Badal-Faesen S, Baepanye K, Bailey V, Baloyi-Oseh K, Booley M, Botha J, Brown Y, Brown V, Bunts L, Coetzer S, Cohen M, Collie S, Dawson R, Deb P, El Sahly H, El-Khorazaty J, Engelbrecht A, Gildea M, Govender D, Hanke J, Harris J, Hendricks S, Hopkinson N, Howell H, Ketter N, Khuto K, Laher Omar F, Katsidzira L, Linton K, Ludwig J, Mabilane B, Malefo M, Mamushiana N, Margineantu D, May J, Mayat F, Molitor C, Naidoo Y, Nebergall M, Nguyen A, Nikles S, Noronha B, Peda M, Phiri T, Pillay S, Pillay S, Proulx-Burns L, Rinn L, Sanders L, Sopher C, Sripathy S, Stirewalt M, Tegally H, Thiebaud S, Toledano A, Van Wyk S, Whitby S, Wilcox S, Wilkinson E, Wilvich H, Wiysonge C, Xaba N, Xulu N

eClinicalMedicine
80():103054. doi: 10.1016/j.eclinm.2024.103054.
2024
Doing just sustainability transitions: Facing thelegitimation crisis in the Anthropocene today

van Breda J, Treffry-Goatley A

South African Journal of Science
120:19223
2024
Dynamics and ecology of a multi-stage expansion of Oropouche virus in Brazil

Tegally H, Dellicour S, Poongavanan J, Mavian C, Dor G, Fonseca V, Tagliamonte M, Dunaiski M, Moir M, Wilkinson E, de Albuquerque C, Frutuoso L, , Holmes E, Baxter C, Lessells R, Kraemer M, Lourenço J, Alcantara L, de Oliveira T, Giovanetti M

doi: 10.1101/2024.10.29.24316328.
2024
Dengue virus importation risks in Africa: a modelling study

Poongavanan J, Lourenço J, Tsui J, Colizza V, Ramphal Y, Baxter C, Kraemer M, Dunaiski M, de Oliveira T, Tegally H

The Lancet Planetary Health
8(12):e1043-e1054. doi: 10.1016/s2542-5196(24)00272-9.
2024
Using HIV and Hepatitis C Molecular Epidemiology to Investigate Assisted Partner Services Recruitment Among People Who Inject Drugs in Kenya

Kingston H, Chohan B, Mbogo L, Bukusi D, Monroe-Wise A, Sambai B, Omballa V, Tram K, Guthrie B, Giandhari J, Masyuko S, Bosire R, Sinkele W, de Oliveira T, Scott J, Farquhar C, Herbeck J

AIDS Research and Human Retroviruses
doi: 10.1089/aid.2024.0036.
2024
SARS-CoV-2 Infections in a Triad of Primary School Learners (Grades 1-7), Their Parents, and Teachers in KwaZulu-Natal, South Africa: Protocol for a Cross-Sectional and Nested Case-Cohort Study

Dassaye R, Chetty T, Daniels B, Gaffoor Z, Spooner E, Ramraj T, Mthethwa N, Nsibande D, Pillay S, Bhana A, Magasana V, Reddy T, Mohlabi K, Moore P, Burgers W, de Oliveira T, Msomi N, Goga A

JMIR Research Protocols
13():e52713. doi: 10.2196/52713.
2024
“The COVID-19 pandemic in BRICS: Milestones, interventions, and molecular epidemiology”

van Wyk S, Moir M, Banerjee A, Bazykin G, Biswas N, Sitharam N, Das S, Ma W, Maitra A, Mazumder A, Karim W, Lamarca A, Li M, Nabieva E, Tegally H, San J, Vasconcelos A, Xavier J, Wilkinson E, de Oliveira T

PLOS Global Public Health
4(12):e0003023. doi: 10.1371/journal.pgph.0003023.
2024
Alignment-Free Viral Sequence Classification at Scale

van Zyl D, Dunaiski M, Tegally H, Baxter C, , de Oliveira T, Xavier J

doi: 10.1101/2024.12.10.627186.
2024
Emergence of Omicron FN.1 a descendent of BQ.1.1 in Botswana

Choga W, Gustani-Buss E, Tegally H, Maruapula D, Yu X, Moir M, Zuze B, James S, Ndlovu N, Seru K, Motshosi P, Blenkinsop A, Gobe I, Baxter C, Manasa J, Lockman S, Shapiro R, Makhema J, Wilkinson E, Blackard J, Lemey P, Lessells R, Martin D, de Oliveira T, Gaseitsiwe S, Moyo S

Virus Evolution
10(1):. doi: 10.1093/ve/veae095.
2024
North–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic

Miguel I, Feliz E, Agramonte R, Martinez P, Vergara C, Imbert Y, De la Cruz L, de Castro N, Cedano O, De la Paz Y, Fonseca V, Santiago G, Muñoz-Jordán J, Peguero A, Paulino-Ramírez R, Grubaugh N, de Filippis A, Alcantara L, Rico J, Lourenço J, Franco L, Giovanetti M

BMC Infectious Diseases
24(1):. doi: 10.1186/s12879-024-09658-6.
2024
Genomics-based timely detection of dengue virus type I genotypes I and V in Uruguay

Morel N, Giovanetti M, Fonseca V, Burgueño A, Lima M, Castro E, Guimarães N, Iani F, Bormida V, Cortinas M, Ramas V, Coppola L, Bento A, Rosewell A, Franco L, Mendez Rico J, Lourenço J, Junior Alcantara L, Chiparelli H

Heliyon
10(22):e39246. doi: 10.1016/j.heliyon.2024.e39246.
2024
Unraveling the Complexity of Chikungunya Virus Infection Immunological and Genetic Insights in Acute and Chronic Patients

Fritsch H, Giovanetti M, Clemente L, da Rocha Fernandes G, Fonseca V, de Lima M, Falcão M, de Jesus N, de Cerqueira E, Venâncio da Cunha R, de Oliveira Francisco M, de Siqueira I, de Oliveira C, Xavier J, Ferreira J, Queiroz F, Smith E, Tisoncik-Go J, Van Voorhis W, Rabinowitz P, Wasserheit J, Gale M, de Filippis A, Alcantara L

Genes
15(11):1365. doi: 10.3390/genes15111365.
2024
Integrated analyses of the transmission history of SARS-CoV-2 and its association with molecular evolution of the virus underlining the pandemic outbreaks in Italy, 2019-2023

Cella E, Fonseca V, Branda F, Tosta S, Moreno K, Schuab G, Ali S, Slavov S, Scarpa F, Santos L, Kashima S, Wilkinson E, Tegally H, Mavian C, Borsetti A, Caccuri F, Salemi M, de Oliveira T, Azarian T, de Filippis A, Alcantara L, Ceccarelli G, Caruso A, Colizzi V, Marcello A, Lourenço J, Ciccozzi M, Giovanetti M

International Journal of Infectious Diseases
():107262. doi: 10.1016/j.ijid.2024.107262.
2024
Fatal Oropouche Virus Infections in Nonendemic Region, Brazil, 2024

Bandeira A, Pereira F, Leal A, Santos S, Barbosa A, Souza M, de Souza D, Guimaraes N, Fonseca V, Giovanetti M, Alcantara L, Lessa A, Saavedra R, Tomé L, Iani F, Barros R, Purificação S, de Jesus J, Fonseca R, Araújo M

Emerging Infectious Diseases
30(11):. doi: 10.3201/eid3011.241132.
2024
North–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic

Miguel I, Feliz E, Agramonte R, Martinez P, Vergara C, Imbert Y, De la Cruz L, de Castro N, Cedano O, De la Paz Y, Fonseca V, Santiago G, Muñoz-Jordán J, Peguero A, Paulino-Ramírez R, Grubaugh N, de Filippis A, Alcantara L, Rico J, Lourenço J, Franco L, Giovanetti M

BMC Infectious Diseases
24(1):. doi: 10.1186/s12879-024-09658-6.
2024
Detection of Multiple Human Viruses, including Mpox, Using a Wastewater Surveillance Approach in Brazil

Calabria de Araujo J, Carvalho A, Leal C, Natividade M, Borin M, Guerra A, Carobin N, Sabino A, Almada M, Costa M, Saia F, Frutuoso L, Iani F, Adelino T, Fonseca V, Giovanetti M, Alcantara L

Pathogens
13(7):589. doi: 10.3390/pathogens13070589.
2024
Insights into SARS-CoV-2 Surveillance among Prison Populations in Mato Grosso do Sul, Brazil, in 2022

Ferreira da Silva L, Alcantara L, Fonseca V, Frias D, Umaki Zardin M, de Castro Lichs G, Esposito A, Xavier J, Fritsch H, Lima M, de Oliveira C, Castilho de Arruda L, Maziero L, Rodrigues Barretos E, Tsuha Oshiro P, Gimenes Mendes Menezes E, de Freitas Cardoso L, Ferreira Lemos E, Lourenço J, de Albuquerque C, do Carmo Said R, Rosewell A, Ferraz Demarchi L, Croda J, Giovanetti M, Maymone Gonçalves C

Viruses
16(7):1143. doi: 10.3390/v16071143.
2024
Exploring Microorganisms Associated to Acute Febrile Illness and Severe Neurological Disorders of Unknown Origin: A Nanopore Metagenomics Approach

Moreno K, de Andrade V, de Melo Iani F, Fonseca V, Lima M, de Castro Barbosa E, Tomé L, Guimarães N, Fritsch H, Adelino T, Oliveira Fereguetti T, Aspahan M, Gamarano Barros T, Alcantara L, Giovanetti M

Genes
15(7):922. doi: 10.3390/genes15070922.
2024
Tracing the evolution of the chikungunya virus in Argentina, 2016-2023: independent introductions and prominence of Latin American lineages

Fabbri C, Giovanetti M, Luppo V, Fonseca V, Garcia J, Barulli C, Feroci M, Perrone S, Casoni D, Giamperetti S, Alvarez Lopez M, Foussal M, Figueredo M, Salvatierra K, Lejona S, Ruiz Diaz N, Castro G, Bravo G, Jackel N, Sen C, Poklepovich Caride T, Franco L, Giovachini C, Mendez Rico J, Alcantara L, Morales M

Emerging Microbes & Infections
13(1):. doi: 10.1080/22221751.2024.2362941.
2024
Exploring the urban arbovirus landscape in Rio de Janeiro, Brazil: transmission dynamics and patterns of disease spread

Schuab G, Tosta S, Moreno K, Fonseca V, Santos L, Slavov S, Kashima S, Ciccozzi M, Lourenço J, Cella E, de Oliveira C, Cavalcanti A, Junior Alcantara L, de Bruycker-Nogueira F, Bispo de Filippis A, Giovanetti M

The Lancet Regional Health - Americas
35():100786. doi: 10.1016/j.lana.2024.100786.
2024
Detection of encephalitis-causing viruses reveals predominance of chikungunya virus in the state of Bahia, Brazil

Sampaio M, do Rosário M, Martins L, Trindade L, Francisco M, Costa B, Vasconcelos G, Lima I, Macêdo Y, Carvalho F, de Santana M, Khouri R, Fritsch H, Xavier J, Fonseca V, Giovanetti M, de Mello A, Pereira F, Campos G, de Jesus P, Farias D, de Souza M, Galvão A, Costa F, Bessa M, Chagas J, Silvany C, Teles J, de Lima M, Farias T, Gräf T, de Siqueira I

International Journal of Infectious Diseases
145():107090. doi: 10.1016/j.ijid.2024.107090.
2024
Exploring the Chikungunya virus landscape in a dengue-endemic Brazilian area

de La Roque D, Santos E, Policastro L, da Costa P, Evaristo M, Yamamoto A, Giomo D, Torres P, Gentil D, Minto E, Slavov S, Fonseca V, dos Santos Barros C, Martins A, Calado R, Passos L, Elias M, Sampaio S, Giovanetti M, Covas D, Alcântara L, Kashima S

Journal of Infection and Public Health
17(7):102442. doi: 10.1016/j.jiph.2024.04.026.
2024
Genomic and eco-epidemiological investigations in Uruguay reveal local Chikungunya virus transmission dynamics during its expansion across the Americas in 2023

Burgueño A, Giovanetti M, Fonseca V, Morel N, Lima M, Castro E, Guimarães N, Iani F, Bormida V, Cortinas M, Ramas V, Coppola L, Bento A, Franco L, Rico J, Lourenço J, Junior Alcantara L, Chiparelli H

Emerging Microbes & Infections
13(1):. doi: 10.1080/22221751.2024.2332672.
2024
Mapping the Dynamics of Dengue Serotypes in the 2023 Epidemic: Insights from Spatial-Temporal Analysis and Emergence of the Cosmopolitan DENV-2 Genotype in Ribeirão Preto, São Paulo, Brazil

Carmo S, Torres P, Roque D, Santos E, Elias M, Sampaio S, Giovanetti M, Fonseca V, Alcantara L, Gentil D, Giomo D, Kashima S, Passos L

International Journal of Health Science
4(28):2-9. doi: 10.22533/at.ed.1594282419035.
2024
DENV-1 genotype V circulation during the nonepidemic period in the Northeast of São Paulo State endemic area

de La-Roque D, Santos E, Oliveira R, Slavov S, Rodrigues E, Fonseca V, Martins A, Giomo D, Torres P, Gentil D, Catoia E, Chiquito N, Medeiros A, Yamamoto A, Passos L, Calado R, Barros C, Elias M, Sampaio S, Giovanetti M, Junior Alcantara L, Covas D, Kashima S

Journal of Medical Virology
96(3):. doi: 10.1002/jmv.29526.
2024
Resurgence of Dengue Virus Serotype 3 in Minas Gerais, Brazil: A Case Report

Adelino T, Lima M, Guimarães N, Xavier J, Fonseca V, Tomé L, Pereira M, Machado V, Alcantara L, Iani F, Giovanetti M

Pathogens
13(3):202. doi: 10.3390/pathogens13030202.
2024
Epidemiology of the SARS-CoV-2 Omicron Variant Emergence in the Southeast Brazilian Population

Rodrigues E, Slavov S, de La Roque D, Santos E, Borges J, Evaristo M, da Costa P, de Matos Maçonetto J, Marques A, Baccarin A, Oliveira R, Junior W, Benincasa B, de Andrade da Cruz L, Lima A, Ribeiro G, Viala V, de Lima L, Martins A, dos Santos Barros C, Marqueze E, de Souza Todao Bernardino J, Grotto R, Souza-Neto J, Fonseca V, Nogueira M, Fukumasu H, Coutinho L, Calado R, Covas D, Giovanetti M, Alcantara L, Sampaio S, Elias M, Kashima S

Microorganisms
12(3):449. doi: 10.3390/microorganisms12030449.
2024
Evidence of Zika Virus Reinfection by Genome Diversity and Antibody Response Analysis, Brazil

da Costa Castilho M, de Filippis A, Machado L, de Lima Calvanti T, Lima M, Fonseca V, Giovanetti M, Docena C, Neto A, Bôtto-Menezes C, Kara E, de La Barrera R, Modjarrad K, Giozza S, Pereira G, Alcantara L, Broutet N, Calvet G, Wallau G, Franca R

Emerging Infectious Diseases
30(2):. doi: 10.3201/eid3002.230122.
2024
Exploring the Genomic Dynamics of the Monkeypox Epidemic in Paraguay

Vazquez C, Fonseca V, de la Fuente A, Gonzalez S, Fleitas F, Lima M, Guimarães N, Iani F, Rojas A, Alfonso T, Cantero C, Barrios J, Villalba S, Ortega M, Torales J, Gamarra M, Aquino C, Franco L, Rico J, Alcantara L, Giovanetti M

Viruses
16(1):83. doi: 10.3390/v16010083.
2024
The third era of genomics is at risk of being dismantled across the Global South

de Oliveira T

Science
386(6718):eadt4843. doi: 10.1126/science.adt4843.
2024
A new lineage nomenclature to aid genomic surveillance of dengue virus

Hill V, Cleemput S, Pereira JS, Gifford RJ, Fonseca V, Tegally H, Brito AF, Ribeiro G, de Souza VC, Brcko IC, Ribeiro IS, De Lima ITT, Slavov SN, Sampaio SC, Elias MC, Tran VT, Kien DTH, Huynh T, Yacoub S, Dieng I, Salvato R, Wallau GL, Gregianini TS, Godinho FMS, Vogels CBF, Breban MI, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara LCJ, Faria NR, Carrington CVF, Hanley KA, Holmes EC, Dumon W, Lima ARJ, de Oliveira T, Grubaugh ND.

PLoS Biology
22(9):e3002834. doi: 10.1371/journal.pbio.3002834.
2024
Impacts of climate change-related human migration on infectious diseases

Tsui JLH, Pena RE, Moir M, Inward RPD, Wilkinson E, San JE, Poongavanan J, Bajaj S, Gutierrez B, Dasgupta A, de Oliveira T, Kraemer MUG, Tegally H, Sambaturu P

Nature Climate Change
14, 793–802 (2024). https://doi.org/10.1038/s41558-024-02078-z
2024
Phylogenetic evidence of extensive spatial mixing of diverse HIV-1 group M lineages within Cameroon but not between its neighbours

Godwe C, Goni OH, San JE, Sonela N, Tchakoute M, Nanfack A, Koro FK, Butel C, Vidal N, Duerr R, Martin DP, de Oliveira T, Peeters M, Altfeld M, Ayouba A, Ndung'u T, Tongo M

Virus Evolution
10(1):veae070. doi: 10.1093/ve/veae070
2024
SARS-CoV-2 Genomic Epidemiology Dashboards: A Review of Functionality and Technological Frameworks for the Public Health Response

Sitharam N, Tegally H, Silva DC, Baxter C, de Oliveira T, Xavier JS

Genes
15(7):876. doi: 10.3390/genes15070876
2024
Understanding the Transmission Dynamics of the Chikungunya Virus in Africa

Ramphal Y, Tegally H, San JE, Reichmuth ML, Hofstra M, Wilkinson E, Baxter C, Climade Consortium, de Oliveira T, Moir M

Pathogens
13(7):605. doi: 10.3390/pathogens13070605
2024
Sustained Human Outbreak of a New MPXV Clade I Lineage in the Eastern Democratic Republic of the Congo

Vakaniaki EH, Kacita C, Kinganda-Lusamaki E, O'Toole Á, Wawina-Bokalanga T, Mukadi-Bamuleka D, Amuri-Aziza A, Malyamungu-Bubala N, Mweshi-Kumbana F, Mutimbwa-Mambo L, Belesi-Siangoli F, Mujula Y, Parker E, Muswamba-Kayembe PC, Nundu SS, Lushima RS, Makangara-Cigolo JC, Mulopo-Mukanya N, Pukuta-Simbu E, Akil-Bandali P, Kavunga H, Abdramane O, Brosius I, Bangwen E, Vercauteren K, Sam-Agudu NA, Mills EJ, Tshiani-Mbaya O, Hoff NA, Rimoin AW, Hensley LE, Kindrachuk J, Baxter C, de Oliveira T, Ayouba A, Peeters M, Delaporte E, Ahuka-Mundeke S, Mohr EL, Sullivan NJ, Muyembe-Tamfum JJ, Nachega JB, Rambaut A, Liesenborghs L, Mbala-Kingebeni P

Nature Medicine
doi: 10.1038/s41591-024-03130-3
2024
Associations of inter-annual rainfall decreases with subsequent HIV outcomes for persons with HIV on antiretroviral therapy in Southern Africa: a collaborative analysis of cohort studies

Trickey A, Johnson LF, Fung F, Bonifacio R, Iwuji C, Biraro S, Bosomprah S, Chirimuta L, Euvrard J, Fatti G, Fox MP, Von Groote P, Gumulira J, Howard G, Jennings L, Kiragga A, Muula G, Tanser F, Wagener T, Low A, Vickerman P

BMC Infect Dis
doi: 10.1186/s12879-023-08902-9
2024
Convergence of HIV and non-communicable disease epidemics: geospatial mapping of the unmet health needs in an HIV hyperendemic community in South Africa

Cuadros DF, Devi C, Singh U, Olivier S, Castle AC, Moosa Y, Edwards JA, Kim HY, Siedner MJ, Wong EB, Tanser F

BMJ Glob Health
9(1):e012730. doi: 10.1136/bmjgh-2023-012730
2024
Effect of a male-targeted digital decision support application aimed at increasing linkage to HIV care among men: Findings from the HITS cluster randomized clinical trial in rural South Africa

Kim HY, Inghels M, Mathenjwa T, Shahmanesh M, Seeley J, Matthews P, Wyke S, McGrath N, Adeagbo O, Gareta D, Yapa HM, Zuma T, Dobra A, Blandford A, Bärnighausen T, Tanser F

medRxiv [Preprint]
2024.03.15.24304373. doi: 10.1101/2024.03.15.24304373
2024
The impact of a conditional financial incentive on linkage to HIV care: Findings from the HITS cluster randomized clinical trial in rural South Africa

Kim HY, Inghels M, Mathenjwa T, Shahmanesh M, Seeley J, Matthews P, McGrath N, Adeagbo O, Gareta D, Yapa HM, Zuma T, Dobra A, Bärnighausen T, Tanser F

medRxiv [Preprint]
2024.03.15.24304278. doi: 10.1101/2024.03.15.24304278
2024
HIV transmission dynamics and population-wide drug resistance in rural South Africa

Kemp SA, Kamelian K, Cuadros DF; PANGEA Consortium; Vukuzazi Team; Cheng MTK, Okango E, Hanekom W, Ndung'u T, Pillay D, Bonsall D, Wong EB, Tanser F, Siedner MJ, Gupta RK

Nat Commun.
15(1):3644. doi: 10.1038/s41467-024-47254-z
2024
Population impacts of conditional financial incentives and a male-targeted digital decision support application on the HIV treatment cascade in rural KwaZulu Natal: findings from the HITS cluster randomized clinical trial

Inghels M, Kim HY, Mathenjwa T, Shahmanesh M, Seeley J, Wyke S, Matthews P, Adeagbo O, Gareta D, McGrath N, Yapa HM, Blandford A, Zuma T, Dobra A, Bärnighausen T, Tanser F

J Int AIDS Soc.
27(5):e26248. doi: 10.1002/jia2.26248
2024
Geospatial and temporal mapping of detectable HIV-1 viral loads amid dolutegravir rollout in KwaZulu-Natal, South Africa. PLOS Glob Public Health

Gounder L, Tomita A, Lessells R, Moodley S, Francois KL, Khan A, Pillay M, Manyana SC, Govender S, Govender K, Moodley P, Parboosing R, Msomi N, Tanser F, Naidoo K, Chimukangara B

PLOS Glob Public Health
4(5):e0003224. doi: 10.1371/journal.pgph.0003224
2024
HIV escape and resistance in the central nervous system in treatment experienced South Africans

Collier D, Derache A, Karim F, Smit T, Adamson J, Khan K, Naidoo T, Perumal N, Brijkumar J, Giandhari J, De Oliveira T, Sigal A, Kemp S, Gupta RK

medRxiv [Preprint]
2024
Disentangling seasonal introduction and establishment risk of dengue in Africa

Poongavanan J, Lourenço J, Tsui JHL, Colizza V, Ramphal Y, Baxter C, Kraemer MOG, Dunaiski M, de Oliveira T, Tegally H

medRxiv [Preprint]
https://doi.org/10.1101/2024.05.07.24306997
2024
A new lineage nomenclature to aid genomic surveillance of dengue virus

Hill V, Cleemput S, Fonseca V, Tegally H, Brito AF, Gifford R, Tran VT, Kien DTH, Huynh T, Yacoub S, Dieng I, Ndiaye M, Balde D, Diagne MM, Faye O, Salvato R, Wallau GL, Gregianini TS, Godinho FMS, Vogels CBF, Breban MI, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara LCJ, Faria NR, Carrington CVF, Hanley KA, Holmes EC, Dumon W, de Oliveira T, Grubaugh ND

medRxiv [Preprint]
2024.05.16.24307504. doi: 10.1101/2024.05.16.24307504
2024
Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation

Karim F, Riou C, Bernstein M, Jule Z, Lustig G, van Graan S, Keeton RS, Upton JL, Ganga Y, Khan K, Reedoy K, Mazibuko M, Govender K, Thambu K, Ngcobo N, Venter E, Makhado Z, Hanekom W, von Gottberg A, Hoque M, Karim QA, Abdool Karim SS, Manickchund N, Magula N, Gosnell BI, Lessells RJ, Moore PL, Burgers WA, de Oliveira T, Moosa MS, Sigal A

Nature Communications
15;15(1):2360
2024
Managing and assembling population-scale data streams, tools and workflows to plan for future pandemics within the INFORM-Africa Consortium

Poongavanan J, Xavier J, Dunaiski M, Tegally H, Oladejo S, Ayorinde O, Wilkinson E, Baxter C, de Oliveira T

S Afr J Sci.
119(5-6):14569. doi: 10.17159/sajs.2023/14659
2024
An updated framework for SARS-CoV-2 variants reflects the unpredictability of viral evolution

Subissi L, Otieno JR, Worp N, Attar Cohen H, Oude Munnink BB, Abu-Raddad LJ, Alm E, Barakat A, Barclay WS, Bhiman JN, Caly L, Chand M, Chen M, Cullinane A, de Oliveira T, Drosten C, Druce J, Effler P, El Masry I, Faye A, Ghedin E, Grant R, Haagmans BL, Happi C, Herring BL, Hodcroft EB, Ikejezie J, Katawera V, Kassamali ZA, Leo YS, Leung GM, Kondor RJ, Marklewitz M, Mendez-Rico J, Melhem NM, Munster V, Nahapetyan K, Naindoo D, Oh DY, Peacock TP, Peiris M, Peng Z, Poon LLM, Rambaut A, Saha S, Shen Y, Siqueira MM, Volz E, Tessema SK, Thiel V, Triki H, van der Werf S, von Eije K, Cunningham J, Koopmans MPG, von Gottberg A, Agrawal A, Van Kerkhove MD

Nature Medicine
doi: 10.1038/s41591-024-02949-0
2024
Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

Hunt M, Hinrichs AS, Anderson D, Karim L, Dearlove BL, Knaggs J, Constantinides B, Fowler PW, Rodger G, Street T, Lumley S, Webster H, Sanderson T, Ruis C, de Maio N, Amenga-Etego LN, Amuzu DSY, Avaro M, Awandare GA, Ayivor-Djanie R, Bashton M, Batty EM, Bediako Y, Belder D, Benedetti E, Bergthaler A, Boers SA, Campos J, Ampomah Carr RA, Cuba F, Dattero ME, Dejnirattisai W, Dilthey A, Duedu KO, Endler L, Engelmann I, Francisco NM, Fuchs J, Gnimpieba EZ, Groc S, Gyamfi J, Heemskerk D, Houwaart T, Hsiao NY, Huska M, Hölzer M, Iranzadeh A, Jarva H, Jeewandara C, Jolly B, Joseph R, Kant R, Ki KKK, Kurkela S, Lappalainen M, Lataretu M, Liu C, Malavige GN, Mashe T, Mongkolsapaya J, Montes B, Molina Mora JA, Morang'a CM, Mvula B, Nagarajan N, Nelson A, Ngoi JM, da Paixão JP, Panning M, Poklepovich T, Quashie PK, Ranasinghe D, Russo M, San JE, Sanderson ND, Scaria V, Screaton G, Sironen T, Sisay A, Smith D, Smura T, Supasa P, Suphavilai C, Swann J, Tegally H, Tegomoh B, Vapalahti O, Walker A, Wilkinson RJ, Williamson C; IMSSC2 Laboratory Network Consortium; de Oliveira T, Peto TE, Crook D, Corbett-Detig R, Iqbal Z.

bioRxiv [Preprint]
2024.04.29.591666. doi: 10.1101/2024.04.29.59166
2024
Save lives in the next pandemic: ensure vaccine equity now

Carlson C, Becker D, Happi C, O'Donoghue Z, de Oliveira T, Oyola SO, Poisot T, Seifert S, Phelan A

Nature
626(8001):952-953. doi: 10.1038/d41586-024-00545-3
2024
SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations

Lustig G, Ganga Y, Rodel HE, Tegally H, Khairallah A, Jackson L, Cele S, Khan K, Jule Z, Reedoy K, Karim F, Bernstein M, Ndung'u T, Moosa MS, Archary D, de Oliveira T, Lessells R, Neher RA, Abdool Karim SS, Sigal A

Virus Evolution
10(1):vead075. doi: 10.1093/ve/vead075
2024
Investing in Africa's scientific future

de Oliveira T, Baxter C

Science
;383(6678):eadn4168. doi: 10.1126/science.adn4168
2023
Global SARS-CoV-2 genomic surveillance: What we have learned (so far)

Tosta S, Moreno K, Schuab G, Fonseca V, Segovia F, Kashima S, Elias M, Sampaio S, Ciccozzi M, Alcantara L, Slavov S, Lourenço J, Cella E, Giovanetti M

Infection, Genetics and Evolution
108():105405. doi: 10.1016/j.meegid.2023.105405.
2023
SARS-CoV-2 Spillback to Wild Coatis in Sylvatic–Urban Hotspot, Brazil

Stoffella-Dutra A, de Campos B, Bastos e Silva P, Dias K, da Silva Domingos I, Hemetrio N, Xavier J, Iani F, Fonseca V, Giovanetti M, de Oliveira L, Teixeira M, Lobato Z, Ferreira H, Arns C, Durigon E, Drumond B, Alcantara L, de Carvalho M, de Souza Trindade G

Emerging Infectious Diseases
29(3):664-667. doi: 10.3201/eid2903.221339.
2023
Phylogenetic Reconstructions Reveal the Circulation of a Novel Dengue Virus-1V Clade and the Persistence of a Dengue Virus-2 III Genotype in Northeast Brazil

Fritsch H, Moreno K, Lima I, Santos C, Costa B, de Almeida B, dos Santos R, Francisco M, Sampaio M, de Lima M, Pereira F, Fonseca V, Tosta S, Xavier J, de Oliveira C, Adelino T, de Mello A, Gräf T, Alcantara L, Giovanetti M, de Siqueira I

Viruses
15(5):1073. doi: 10.3390/v15051073.
2023
Genomic Surveillance of Monkeypox Virus, Minas Gerais, Brazil, 2022

Guimarães N, Tomé L, Lamounier L, Silva M, Lima M, da Costa A, Luiz K, de Jesus R, Trindade G, Oliveira D, da Fonseca F, Fernandes A, de Oliveira J, Moura J, Kroon E, Giovanetti M, Fonseca V, Alcantara L, Adelino T, de Milo Iani F

Emerging Infectious Diseases
29(6):. doi: 10.3201/eid2906.230113.
2023
Retrospective Spatio-Temporal Dynamics of Dengue Virus 1, 2 and 4 in Paraguay

Vazquez C, Alcantara L, Fonseca V, Lima M, Xavier J, Adelino T, Fritsch H, Castro E, de Oliveira C, Schuab G, Lima A, Villalba S, Gomez de la Fuente A, Rojas A, Cantero C, Fleitas F, Aquino C, Ojeda A, Sequera G, Torales J, Barrios J, Elias M, Iani F, Ortega M, Gamarra M, Montoya R, Rodrigues E, Kashima S, Sampaio S, Coluchi N, Leite J, Gresh L, Franco L, Lourenço J, Rico J, Bispo de Filippis A, Giovanetti M

Viruses
15(6):1275. doi: 10.3390/v15061275.
2023
Potential use of high-resolution melting analyses for SARS-CoV-2 genomic surveillance

de Souza Andrade A, Freitas E, de Castro Barbosa E, Guimarães N, de Melo Iani F, da Costa A, Bernardes A, Adelino T, Ataide A, Gregianini T, Nunes J, Stringari L, Riediger I, Fernandes S, de Jesus R, Fonseca V, Caldas S

Journal of Virological Methods
317():114742. doi: 10.1016/j.jviromet.2023.114742.
2023
The Importance of Entomo-Virological Investigation of Yellow Fever Virus to Strengthen Surveillance in Brazil

Cruz A, Hernández L, Aragão C, da Paz T, da Silva S, da Silva F, de Aquino A, Cereja G, Nascimento B, Rosa Junior J, Elias C, Nogueira C, Ramos D, Fonseca V, Giovanetti M, Alcantara L, Nunes B, Vasconcelos P, Martins L, Nunes-Neto J

Tropical Medicine and Infectious Disease
8(6):329. doi: 10.3390/tropicalmed8060329.
2023
Molecular Characterization of Salmonella Phage Wara Isolated from River Water in Brazil

Romero-Calle D, Pedrosa-Silva F, Ribeiro Tomé L, Fonseca V, Guimarães Benevides R, de Oliveira Santos L, de Oliveira T, da Costa M, Alcantara L, de Carvalho Azevedo V, Brenig B, Venancio T, Billington C, Góes-Neto A

Microorganisms
11(7):1837. doi: 10.3390/microorganisms11071837.
2023
Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil

Xavier J, Alcantara L, Fonseca V, Lima M, Castro E, Fritsch H, Oliveira C, Guimarães N, Adelino T, Evaristo M, Rodrigues E, Santos E, de La-Roque D, de Moraes L, Tosta S, Neto A, Rosewell A, Mendonça A, Leite A, Vasconcelos A, Silva de Mello A, Vasconcelos B, Montalbano C, Zanluca C, Freitas C, de Albuquerque C, Duarte dos Santos C, Santos C, dos Santos C, Gonçalves C, Teixeira D, Neto D, Cabral D, de Oliveira E, Noia Maciel E, Pereira F, Iani F, de Carvalho F, Andrade G, Bezerra G, de Castro Lichs G, Pereira G, Barroso H, Franz H, Ferreira H, Gomes I, Riediger I, Rodrigues I, de Siqueira I, Silva J, Rico J, Lima J, Abrantes J, do Nascimento J, Wasserheit J, Pastor J, de Magalhães J, Luz K, Lima Neto L, Frutuoso L, da Silva L, Sena L, de Sousa L, Pereira L, Demarchi L, Câmara M, Astete M, Almiron M, Lima M, Umaki Zardin M, Presibella M, Falcão M, Gale M, Freire N, Marques N, de Moura N, Almeida Da Silva P, Rabinowitz P, da Cunha R, Trinta K, do Carmo Said R, Kato R, Stabeli R, de Jesus R, Hans Santos R, Kashima S, Slavov S, Andrade T, Rocha T, Carneiro T, Nardy V, da Silva V, Carvalho W, Van Voorhis W, Araujo W, de Filippis A, Giovanetti M

Nature Communications
14(1):. doi: 10.1038/s41467-023-40099-y.
2023
Unveiling the Impact of the Omicron Variant: Insights from Genomic Surveillance in Mato Grosso do Sul, Midwest Brazil

de Mello Almeida Maziero L, Giovanetti M, Fonseca V, Zardin M, de Castro Lichs G, de Rezende Romera G, Tsuha D, Frias D, Escandolhero V, Demarchi L, Domingues Castilho L, Barbosa K, Tebet D, Xavier J, Fritsch H, Lima M, de Oliveira C, Santos E, Kashima S, Said R, Rosewell A, Croda J, Alcantara L, Cavalheiro Maymone Gonçalves C

Viruses
15(7):1604. doi: 10.3390/v15071604.
2023
Case report: Urbanized non-human primates as sentinels for human zoonotic diseases: a case of acute fatal toxoplasmosis in a free-ranging marmoset in coinfection with yellow fever virus

Sousa D, Wilson T, Macêdo I, Romano A, Ramos D, Passos P, Costa G, Fonseca V, Mares-Guia M, Giovanetti M, Alcantara L, de Filippis A, Paludo G, Melo C, Castro M

Frontiers in Public Health
11():. doi: 10.3389/fpubh.2023.1236384.
2023
Rapid Epidemic Expansion of Chikungunya Virus East/Central/South African Lineage, Paraguay

Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, Gomez de la Fuente A, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega M, Gamarra M, Villalba S, Alfonzo T, Xavier J, Adelino T, Fritsch H, Iani F, Pereira G, de Oliveira C, Schuab G, Rodrigues E, Kashima S, Leite J, Gresh L, Franco L, Tegally H, Van Voorhis W, Lessels R, de Filippis A, Ojeda A, Sequera G, Montoya R, Holmes E, de Oliveira T, Rico J, Lourenço J, Fonseca V, Alcantara L

Emerging Infectious Diseases
29(9):. doi: 10.3201/eid2909.230523.
2023
Dengue Fever Surveillance in Mato Grosso do Sul: Insights from Genomic Analysis and Implications for Public Health Strategies

Castilho de Arruda L, Giovanetti M, Fonseca V, Zardin M, Lichs G, Asato S, Esposito A, Tokeshi Müller M, Xavier J, Fritsch H, Lima M, de Oliveira C, Santos E, Maziero L, Frias D, Ahad das Neves D, Ferreira da Silva L, Rodrigues Barretos E, Tsuha Oshiro P, Modafari Goday B, Lemos dos Santos J, Kashima S, Albuquerque C, Said R, Rosewell A, Demarchi L, Croda J, Alcantara L, Cavalheiro Maymone Gonçalves C

Viruses
15(9):1790. doi: 10.3390/v15091790.
2023
Technology transfer during the COVID-19 pandemic: report on the first face-to-face practical training course in Brazil

Barreto F, Santos L, Giovanetti M, Fonseca V, Aburjaile F, Silva J, Freitas C, Peterka C, Rico J, Almiron M, Melo C, Alcântara L

Epidemiologia e Serviços de Saúde
32(2):. doi: 10.1590/s2237-96222023000200017.
2023
Genomic Epidemiology and Lineage Dynamics of SARS-CoV-2 in Bulgaria: Insights from a Three-Year Pandemic Analysis

Giovanetti M, Cella E, Ivanov I, Grigorova L, Stoikov I, Donchev D, Dimitrova R, Slavov S, Mavian C, Fonseca V, Scarpa F, Borsetti A, Korsun N, Trifonova I, Dobrinov V, Kantardjiev T, Christova I, Ciccozzi M, Alexiev I

Viruses
15(9):1924. doi: 10.3390/v15091924.
2023
Genomic characterization of SARS-CoV-2 from an indigenous reserve in Mato Grosso do Sul, Brazil

de Oliveira L, de Rezende I, Navarini V, Marchioro S, Torres A, Croda J, Croda M, Gonçalves C, Xavier J, de Castro E, Lima M, Iani F, Adelino T, Aburjaile F, Ferraz Demarchi L, Taira D, Zardin M, Fonseca V, Giovanetti M, Andrews J, Alcantara L, Simionatto S

Frontiers in Public Health
11():. doi: 10.3389/fpubh.2023.1195779.
2023
Strengthening Genomic Surveillance Capacity for Epidemic-Prone Pathogens by Training Personnel From Public Health Laboratories in Brazil and Paraguay

Giovanetti M, Fonseca V, Navegantes W, Abreu AL, Stabeli R, Vazquez CC, Albuquerque CFC, Rico JM, Galiano SG, Almiron M, Alcantara LCJ

Weekly Epidemiological Record
v. 98, p. 63-68
2023
A Multiplex Nanopore Sequencing Approach for the Detection of Multiple Arboviral Species

Xavier J, Fonseca V, Adelino T, Iani F, Pereira G, Duarte M, Lima M, Castro E, Oliveira C, Fritsch H, Guimarães N, Lamounier L, Barreto F, Braga de Oliveira C, Maymone Gonçalves C, Malta Lima D, de Oliveira E, de Castro Lichs G, Gomes I, Mazaro J, Rodrigues J, Abrantes J, Colares J, Luz K, Barbosa da Silva L, Demarchi L, Câmara M, Umaki Zardin M, Sabatini Mello Pinheiro R, Barbosa Souza R, Haddad S, Figueiredo da Silva S, Slavov S, Rocha T, Morel N, Chiparelli H, Burgueño A, Bórmida V, Cortinas M, Martín R, Pereira A, dos Santos M, André Júnior W, Mendez Rico J, Franco L, Rosewell A, do Carmo Said R, de Albuquerque C, Noia Maciel E, Santini de Oliveira M, Venâncio da Cunha R, Vinhal Frutuoso L, de Filippis A, Giovanetti M, Carlos Junior Alcantara L

Viruses
16(1):23. doi: 10.3390/v16010023.
2023
Climate Change and Epidemics 2023 Synthesis Report

de Oliveira T, Baxter C, for the CLIMADE consortium

CLIMADE, Stellenbosch, South Africa. pp1-23, doi 10.25413/sun.24599043
2023
NEJM Case 40-2023: A 70-Year-Old Woman with Cough and Shortness of Breath

Gandhi RT, Castle AC, de Oliveira T, Lessells RJ

New England Journal of Medicine
389(26):2468-2476. doi: 10.1056/NEJMcpc2300910
2023
Evolution and neutralization escape of the SARS-CoV-2 BA.2.86 subvariant

Khan K, Lustig G, Römer C, Reedoy K, Jule Z, Karim F, Ganga Y, Bernstein M, Baig Z, Jackson L, Mahlangu B, Mnguni A, Nzimande A, Stock N, Kekana D, Ntozini B, van Deventer C, Marshall T, Manickchund N, Gosnell BI, Lessells RJ, Karim QA, Abdool Karim SS, Moosa MS, de Oliveira T, von Gottberg A, Wolter N, Neher RA, Sigal A.

Nature Communications
14(1):8078. doi: 10.1038/s41467-023-43703-3
2023
Rapid dynamic changes of FL.2 variant: A case report of COVID-19 breakthrough infection.

Choga WT, Kurusa Gasenna GK, San JE, Ookame T, Gobe I, Chand M, Phafane B, Seru K, Matshosi P, Zuze B, Ndlovu N, Matsuru T, Maruapula D, Bareng OT, Macheke K, Kuate-Lere L, Tlale L, Lesetedi O, Tau M, Mbulawa MB, Smith-Lawrence P, Matshaba M, Shapiro R, Makhema J, Martin DP, de Oliveira T, Lessells RJ, Lockman S, Gaseitsiwe S, Moyo S

Int J Infect Dis.
138:91-96. doi: 10.1016/j.ijid.2023.11.011
2023
An emerging clade of Chikungunya West African genotype discovered in real-time during 2023 outbreak in Senegal

Padane A, Tegally H, Ramphal Y, Ndiaye S, Sarr M, Diop M, Diedhiou CK, Mboup A, Diouf N, Souare A, Diagne ND, Aza-Gnandji M, Dabo NA, Dia YA, Diaw NA, Leye N, Diaw PA, Ambroise A, Cisse B, Diallo AS, Diop O, Diallo AA, Ndoye S, Sanko TJ, Baxter C, Wilkinson E, James SE, Tshiabuila D, Naidoo Y, Pillay S, Lessells R, Cisse K, Leye A, Mbaye A, Kania D, Traore I, Kagone ST, Tinto B, Ouedraogo A, Lourenco J, Giovanetti M, Giandhari J, de Oliveira T, Mboup S

medrxiv
MEDRXIV-2023-298527v1
2023
Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil

Giovanetti M, Pinotti F, Zanluca C, Fonseca V, Nakase T, Koishi AC, Tscha M, Soares G, Dorl GG, Marques AEML, Sousa R, Adelino TER, Xavier J, de Oliveira C, Patroca S, Guimaraes NR, Fritsch H, Mares-Guia MA, Levy F, Passos PH, da Silva VL, Pereira LA, Mendonça AF, de Macêdo IL, Ribeiro de Sousa DE, Rodrigues de Toledo Costa G, Botelho de Castro M, de Souza Andrade M, de Abreu FVS, Campos FS, Iani FCM, Pereira MA, Cavalcante KRLJ, de Freitas ARR, Campelo de Albuquerque CF, Macário EM, Dos Anjos MPD, Ramos RC, Campos AAS, Pinter A, Chame M, Abdalla L, Riediger IN, Ribeiro SP, Bento AI, de Oliveira T, Freitas C, Oliveira de Moura NF, Fabri A, Dos Santos Rodrigues CD, Dos Santos CC, Barreto de Almeida MA, Dos Santos E, Cardoso J, Augusto DA, Krempser E, Mucci LF, Gatti RR, Cardoso SF, Fuck JAB, Lopes MGD, Belmonte IL, Mayoral Pedroso da Silva G, Soares MRF, de Castilhos MMS, de Souza E Silva JC, Bisetto Junior A, Pouzato EG, Tanabe LS, Arita DA, Matsuo R, Dos Santos Raymundo J, Silva PCL, Santana Araújo Ferreira Silva A, Samila S, Carvalho G, Stabeli R, Navegantes W, Moreira LA, Ferreira AGA, Pinheiro GG, Nunes BTD, de Almeida Medeiros DB, Cruz ACR, Venâncio da Cunha R, Van Voorhis W, Bispo de Filippis AM, Almiron M, Holmes EC, Ramos DG, Romano A, Lourenço J, Alcantara LCJ, Duarte Dos Santos CN

Science Advances
9(35):eadg9204. doi: 10.1126/sciadv.adg9204
2023
Will climate change amplify epidemics and give rise to pandemics?

de Oliveira T, Tegally H

Science
381,6660, DOI: 10.1126/science.adk4500
2023
Genomic epidemiology of the cholera outbreak in Malawi 2022-2023

Chabuka L, Choga WT, Mavian CN, Moir M, Tegally H, Wilkinson E, Naidoo Y, Inward R, Morgenstern C, Bhatt S, Wint WGR, Khan K, Bogoch II, Kraemer MUG, Baxter C, Tagliamonte M, Salemi M, Lessells RJ, Mitambo C, Chitatanga R, Bango JB, Chiwaula M, Chavula Y, Bukhu M, Manda H, Chitenje M, Malolo I, Mwanyongo A, Mvula B, Nyenje M, de Oliveira T, Kagoli M

medRxiv
https://doi.org/10.1101/2023.08.22.23294324
2023
Dispersal patterns and influence of air travel during the global expansion of SARS-CoV-2 variants of concern

Tegally H, Wilkinson E, Tsui JL, Moir M, Martin D, Brito AF, Giovanetti M, Khan K, Huber C, Bogoch II, San JE, Poongavanan J, Xavier JS, Candido DDS, Romero F, Baxter C, Pybus OG, Lessells RJ, Faria NR, Kraemer MUG, de Oliveira T

Cell
S0092-8674(23)00641-4. doi: 10.1016/j.cell.2023.06.001
2023
Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Tsui JL, McCrone JT, Lambert B, Bajaj S, Inward RPD, Bosetti P, Pena RE, Tegally H, Hill V, Zarebski AE, Peacock TP, Liu L, Wu N, Davis M, Bogoch II, Khan K, Kall M, Abdul Aziz NIB, Colquhoun R, O'Toole Á, Jackson B, Dasgupta A, Wilkinson E, de Oliveira T, COVID-19 Genomics UK (COG-UK) consortium¶, Connor TR, Loman NJ, Colizza V, Fraser C, Volz E, Ji X, Gutierrez B, Chand M, Dellicour S, Cauchemez S, Raghwani J, Suchard MA, Lemey P, Rambaut A, Pybus OG, Kraemer MUG

Science
381(6655):336-343. doi: 10.1126/science.adg6605.
2023
Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages

Subramoney K, Mtileni N, Giandhari J, Naidoo Y, Ramphal Y, Pillay S, Ramphal U, Maharaj A, Tshiabuila D, Tegally H, Wilkinson E, de Oliveira T, Fielding BC, Treurnicht FK

Viruses
15(5):1194. doi: 10.3390/v15051194
2023
SARS-CoV-2 spike protein diversity at an intra-host level, among SARS-CoV-2 infected individuals in South Africa, 2020 to 2022

Subramoney K, Mtileni N, Davis A, Giandhari J, Tegally H, Wilkinson E, Naidoo Y, Ramphal Y, Pillay S, Ramphal U, Simane A, Reddy B, Mashishi B, Mbenenge N, de Oliveira T, Fielding BC, Treurnicht FK

PLoS One
18(5):e0286373. doi: 10.1371/journal.pone.0286373
2023
High prevalence of self-reported sexually transmitted diseases among older adults in Tanzania: results from the list experiment

Kim HY, Rohr J, Leyna GH, Killewo J, Tomita A, Tanser F, Bärnighausen T

Ann Epidemiol.
S1047-2797(23)00086-8. doi: 10.1016/j.annepidem.2023.05.001
2023
International epidemiology Databases to Evaluate AIDS (IeDEA) Southern Africa. Abacavir safety and effectiveness in young infants with HIV in South African observational cohorts

de Waal R, Rabie H, Technau KG, Eley B, Sipambo N, Cotton M, Boulle A, Wood R, Tanser F, Fatti G, Egger M, Davies MA

Antivir Ther.
28(2):13596535231168480. doi: 10.1177/13596535231168480
2023
Convergence of HIV and non-communicable disease epidemics: Geospatial mapping of the unmet health needs in a HIV Hyperendemic South African community.

Cuadros DF, Devi C, Singh U, Olivier S, Castle A, Moosa Y, Edwards JA, Kim HY, Siedner MJ, Wong EB, Tanser F

medRxiv
2023.03.27.23287807. doi: 10.1101/2023.03.27.23287807
2023
Spatial variations in STIs among women enrolled in HIV prevention clinical trials in Durban, KwaZulu-Natal

Dassaye R, Wand H, Reddy T, Tanser F, Sartorius B, Morris N, Ramjee G

SAHARA J.
(1):2193238. doi: 10.1080/17290376.2023.2193238
2023
HIV-1 drug resistance in people on dolutegravir-based ART: Collaborative analysis of cohort studies

Loosli T, Hossmann S, Ingle SM, Okhai H, Kusejko K, Mouton J, Bellecave P, van Sighem A, Stecher M, Monforte AD, Gill MJ, Sabin CA, Maartens G, Günthard HF, Sterne JAC, Lessells R, Egger M, Kouyos R

medRxiv
5:2023.04.05.23288183. doi: 10.1101/2023.04.05.23288183
2023
Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing

Pillay S, San JE, Tshiabuila D, Naidoo Y, Pillay Y, Maharaj A, Anyaneji UJ, Wilkinson E, Tegally H, Lessells RJ, Baxter C, de Oliveira T, Giandhari J

PLoS ONE
18(4):e0283219. doi: 10.1371/journal.pone.0283219
2023
Genomic epidemiology sheds light on the recent spatio-temporal dynamics of Yellow Fever virus and the spatial corridor that fueled its ongoing emergence in southern Brazil

Giovanetti M, Pinotti F, Zanluca C, Fonseca V, Nakase T, Koishi A, Tscha M, Soares G, Dorl G, Marques AE, Sousa RS, Adelino TER, Xavier J, Oliveira C, Patroca S, Guimaraes NR, Fritsch H, Mares-Guia MA, Levy F, Passos PH, da Silva VL, Pereira LA, Mendonca AF, de Macedo IL, de Souze DER , Costa GRT, de Castro MB, Iani FCM, Pereira MA, Cavalcante KRLJ, Freitas ARR, de Albuquerque CFC, Macario EM, dos Anjos MPD, Ramos RC, Campos AAS, Pinter A, Chame M, Abdalla L, Riediger IN, Ribeiro SP, Bento AI, de Oliveira T, Freitas C, de Moura NFB, Fabri A, Rodrigues CDS, dos Santos CC, de Almeida MAB, dos Santos E, Cardoso J, Augusto DA, Krempser E, Mucci LF, Gatti RR, Cardoso SF, Fuck JAB, Lopes MGD, Belmonte IL, da Silva GMP, Soares MRF, de Castilhos MMS, Silva JCS, Junior AB, Pouzato EG, Tanabe LS, Arita DA, Matsuo RM, Raymundo JS, Silva PCL, Silva ASAF, Samila S, Pereira GC, Stabeli R, Navegantes W, Moreira LA, Ferreira AGA, Pinheiro GG, Nunes BTD, Medeiros DBA, Cruz ACR, Cunha RV, Voorhis WV, de Filippis AMB, Almiron MA, Holmes EC, Ramos DG, Martins AP, Lourenco JL, Alcantara LCJ, dos Santos CND

medRxiv
2023.01.13.23284525v1
2023
Rapid epidemic expansion of chikungunya virus-ECSA lineage in Paraguay

Giovanetti M, Vazquez C, Lima M, Castro E, Rojas A, de la Fuente AG, Aquino C, Cantero C, Fleitas F, Torales J, Barrios J, Ortega MJ, Gamarra ML, Villalba S, Alfonzo T, Xavier J, Adelino T, Fritsch H, Iani FCM, Pereira GC, de Oliveira C, Schuab G, Rodrigues ES, Kashima S, Leite J, Gresh L, Franco L, Tegally H, Van Voorhis WC, Lessels R, de Filippis AMB, Ojeda A, Sequera G, Montoya R, Holmes EC, de Oliveira T, Rico JM, Lourenço J, Fonseca V, Junior Alcantara LC

medRXiV
doi:10.1101/2023.04.16.23288635
2023
SARS-CoV-2 Africa dashboard for real-time COVID-19 information

Xavier JS, Moir M, Tegally H, Sitharam N, Abdool Karim W, San JE, Linhares J, Wilkinson E, Ascher DB, Baxter C, Pires DEV, de Oliveira T

Nature Microbiology
8(1):1-4. doi: 10.1038/s41564-022-01276-9
2023
Advancing detection and response capacities for emerging and re-emerging pathogens in Africa

achega JB, Nsanzimana S, Rawat A, Wilson LA, Rosenthal PJ, Siedner MJ, Varma JK, Kilmarx PH, Mutesa L, Tanner M, Binagwaho A, Forrest J, Mbala-Kingebeni P, Muyembe-Tamfum JJ, Ntoumi F, Zumla A, de Oliveira T, Mills EJ

Lancet Infect Dis.
S1473-3099(22)00723-X. doi: 10.1016/S1473-3099(22)00723-X
2023
New nomenclature for mpox (monkeypox) and monkeypox virus clades

Ulaeto D, Agafonov A, Burchfield J, Carter L, Happi C, Jakob R, Krpelanova E, Kuppalli K, Lefkowitz EJ, Mauldin MR, de Oliveira T, Onoja B, Otieno J, Rambaut A, Subissi L, Yinka-Ogunleye A, Lewis RF

Lancet Infect Dis.
23(3):273-275. doi: 10.1016/S1473-3099(23)00055-5
2023
Consequences of rpoB mutations missed by the GenoType MTBDRplus assay in a programmatic setting in South Africa

Mvelase NR, Cele LP, Singh R, Naidoo Y, Giandhari J, Wilkinson E, de Oliveira T, Swe-Han KS, Mlisana KP

Afr J Lab Med.
12(1):1975. doi: 10.4102/ajlm.v12i1.1975
2023
Genomic epidemiology of SARS-CoV-2 during the first four waves in Mozambique

Ismael N, van Wyk S, Tegally H, Giandhari J, San JE, Moir M, Pillay S, Utpatel C, Singh L, Naidoo Y, Ramphal U, Mabunda N, Abílio N, Arnaldo P, Xavier J, Amoako DG, Everatt J, Ramphal Y, Maharaj A, de Araujo L, Anyaneji UJ, Tshiabuila D, Viegas S, Lessells R, Engelbrecht S, Gudo E, Jani I, Niemann S, Wilkinson E, de Oliveira T

PLOS Glob Public Health
6;3(3):e0001593. doi: 10.1371/journal.pgph.0001593
2023
Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia 2020-2022

Sisay A, Tshiabuila D, van Wyk S, Tesfaye A, Mboowa G, Oyola SO, Tesema SK, Baxter C, Martin D, Lessells R, Tegally H, Moir M, Giandhari J, Pillay S, Singh L, Ramphal Y, Maharaj A, Pillay Y, Maharaj A, Naidoo Y, Ramphal U, Chabuka L, Wilkinson E, de Oliveira T, Desta AF, San JE

Genes
13;14(3):705. doi: 10.3390/genes14030705
2022
Fast surveillance response reveals the introduction of a new yellow fever virus sub-lineage in 2021, in Minas Gerais, Brazil

Andrade M, Campos F, Oliveira C, Oliveira R, Campos A, Almeida M, Fonseca V, Simonini-Teixeira D, Seva A, Temponi A, Magalhaes F, Chaves D, Pereira M, Lamounier L, Menezes G, Aquino-Teixeira S, Goncalves-dos-Santos M, Bernal-Valle S, Muller N, Cardoso J, Santos E, Mares-Guia M, Albuquerque G, Romano A, Franco A, Ribeiro B, Roehe P, Abreu F

Memórias do Instituto Oswaldo Cruz
117():. doi: 10.1590/0074-02760220127.
2022
Retrospective Analysis of the SARS-CoV-2 Infection Profile in COVID-19 Positive Patients in Vitoria da Conquista, Northeast Brazil

Dantas A, Oliveira H, Gomes C, Alves D, Infante P, Caitite R, Fritsch H, Cucco M, Silva L, Oliveira C, Bittencourt R, Amorim A, Nascimento A, Marinho F, de Medeiros D, de Oliveira M, Mistro S, de Melo F, Pereira T, Guimaraes A, Timenetsky J, Moreira P, de Oliveira S, Alcantara L, Giovanetti M, Santos L, Fonseca V, Barreto F, Campos G, Marques L

Viruses
14(11):2424. doi: 10.3390/v14112424.
2022
Emergence of Dengue Virus Serotype 2 Cosmopolitan Genotype, Brazil

Giovanetti M, Pereira L, Santiago G, Fonseca V, Mendoza M, de Oliveira C, de Moraes L, Xavier J, Tosta S, Fristch H, de Castro Barbosa E, Rodrigues E, Figueroa-Romero D, Padilla-Rojas C, Cáceres-Rey O, Mendonça A, de Bruycker Nogueira F, Venancio da Cunha R, de Filippis A, Freitas C, Peterka C, de Albuquerque C, Franco L, Méndez Rico J, Muñoz-Jordán J, Lemes da Silva V, Alcantara L

Emerging Infectious Diseases
28(8):1725-1727. doi: 10.3201/eid2808.220550.
2022
Dynamics of SARS-CoV-2 Variants of Concern in Vaccination Model City in the State of Sao Paulo, Brazil

Slavov S, de La-Roque D, da Costa P, Rodrigues E, Santos E, Borges J, Evaristo M, de Matos Maçonetto J, Marques A, Milhomens J, Rós F, Fonseca V, Lima A, Ribeiro G, Lima L, Garibaldi P, Ferreira N, Moraes G, Marqueze E, Barros C, Martins A, Coutinho L, Calado R, Borges M, Elias M, Sampaio S, Giovanetti M, Alcantara L, Covas D, Kashima S

Viruses
14(10):2148. doi: 10.3390/v14102148.
2022
Retrospective Genomic Surveillance of Chikungunya Transmission in Minas Gerais State, Southeast Brazil

Fritsch H, Giovanetti M, Xavier J, Adelino T, Fonseca V, de Jesus J, de Jesus R, Freitas C, Peterka C, Campelo de Albuquerque C, Bispo de Filippis A, da Cunha R, Silva E, Alcantara L, Iani F

Microbiology Spectrum
10(5):. doi: 10.1128/spectrum.01285-22.
2022
Molecular dynamics simulations of the SARS-CoV-2 Spike protein and variants of concern: structural evidence for convergent adaptive evolution

Neto D, Fonseca V, Jesus R, Dutra L, Portela L, Freitas C, Fillizola E, Soares B, Abreu A, Twiari S, Azevedo V, Goes-Neto A, de Medeiros A, Lopes N, Zanotto P, Kato R

Journal of Biomolecular Structure and Dynamics
41(12):5789-5801. doi: 10.1080/07391102.2022.2097955.
2022
Retrospective Investigation in Horses with Encephalitis Reveals Unnoticed Circulation of West Nile Virus in Brazil

Fritsch H, Pereira F, Costa E, Fonseca V, Tosta S, Xavier J, Levy F, Oliveira C, Menezes G, Lima J, Santos L, Silva L, Nardy V, Astete M, Santos B, Aguiar N, Guedes M, Faria G, Furtini R, Drumond S, Cunha G, Souza M, Jesus R, Guimarães S, Nuno I, Santana I, J, Santos G, Silva W, Guedes T, Araújo E, Said R, Albuquerque C, Peterka C, Romano A, Cunha R, Filippis A, Leal e Silva de Mello A, Giovanetti M, Alcantara L

Viruses
14(7):1540. doi: 10.3390/v14071540.
2022
SARS-CoV-2 epidemic in Brazil: how the displacement of variants has driven distinct epidemic waves

Alcantara L, Nogueira E, Shuab G, Tosta S, Fristch H, Pimentel V, Souza-Neto J, Coutinho L, Fukumasu H, Sampaio S, Elias M, Kashima S, Slavov S, Ciccozzi M, Cella E, Lourenco J, Fonseca V, Giovanetti M

Virus Research
315():198785. doi: 10.1016/j.virusres.2022.198785.
2022
Global disparities in SARS-CoV-2 genomic surveillance.

Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C; Bulgarian SARS-CoV-2 sequencing group; Communicable Diseases Genomics Network (Australia and New Zealand); COVID-19 Impact Project; Danish Covid-19 Genome Consortium; Fiocruz COVID-19 Genomic Surveillance Network; GISAID core curation team; Network for Genomic Surveillance in South Africa (NGS-SA); Swiss SARS-CoV-2 Sequencing Consortium, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, Carrington CVF, Sahadeo NSD, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND, Baele G, Faria NR.

Nature Communications
16;13(1):7003. doi: 10.1038/s41467-022-33713-y.
2022
Ethics and governance challenges related to genomic data sharing in southern Africa: the case of SARS-CoV-2

Moodley K, Cengiz N, Domingo A, Nair G, Obasa AE, Lessells RJ, de Oliveira T

Lancet Global Health
https://doi.org/10.1016/ S2214-109X(22)00417-X
2022
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

Tegally H, San JE, Cotten M, Moir M, Tegomoh B, Mboowa G, Martin DP, Baxter C, Lambisia AW, Diallo A, Amoako DG, Diagne MM, Sisay A, Zekri AN, Gueye AS, Sangare AK, Ouedraogo AS, Sow A, Musa AO, Sesay AK, Abias AG, Elzagheid AI, Lagare A, Kemi AS, Abar AE, Johnson AA, Fowotade A, Oluwapelumi AO, Amuri AA, Juru A, Kandeil A, Mostafa A, Rebai A, Sayed A, Kazeem A, Balde A, Christoffels A, Trotter AJ, Campbell A, Keita AK, Kone A, Bouzid A, Souissi A, Agweyu A, Naguib A, Gutierrez AV, Nkeshimana A, Page AJ, Yadouleton A, Vinze A, Happi AN, Chouikha A, Iranzadeh A, Maharaj A, Batchi-Bouyou AL, Ismail A, Sylverken AA, Goba A, Femi A, Sijuwola AE, Marycelin B, Salako BL, Oderinde BS, Bolajoko B, Diarra B, Herring BL, Tsofa B, Lekana-Douki B, Mvula B, Njanpop-Lafourcade BM, Marondera BT, Khaireh BA, Kouriba B, Adu B, Pool B, McInnis B, Brook C, Williamson C, Nduwimana C, Anscombe C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Mapanguy CM, Loucoubar C, Onwuamah CK, Ihekweazu C, Malaka CN, Peyrefitte C, Grace C, Omoruyi CE, Rafaï CD, Morang'a CM, Erameh C, Lule DB, Bridges DJ, Mukadi-Bamuleka D, Park D, Rasmussen DA, Baker D, Nokes DJ, Ssemwanga D, Tshiabuila D, Amuzu DSY, Goedhals D, Grant DS, Omuoyo DO, Maruapula D, Wanjohi DW, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong'era EM, Ngabana EN, Abworo EO, Otieno E, Shumba E, Barasa E, Ahmed EB, Ahmed EA, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Manuel E, Leendertz F, Taweh FM, Wasfi F, Abdelmoula F, Takawira FT, Derrar F, Ajogbasile FV, Treurnicht F, Onikepe F, Ntoumi F, Muyembe FM, Ragomzingba FEZ, Dratibi FA, Iyanu FA, Mbunsu GK, Thilliez G, Kay GL, Akpede GO, van Zyl GU, Awandare GA, Kpeli GS, Schubert G, Maphalala GP, Ranaivoson HC, Omunakwe HE, Onywera H, Abe H, Karray H, Nansumba H, Triki H, Kadjo HAA, Elgahzaly H, Gumbo H, Mathieu H, Kavunga-Membo H, Smeti I, Olawoye IB, Adetifa IMO, Odia I, Ben Boubaker IB, Mohammad IA, Ssewanyana I, Wurie I, Konstantinus IS, Halatoko JWA, Ayei J, Sonoo J, Makangara JC, Tamfum JM, Heraud JM, Shaffer JG, Giandhari J, Musyoki J, Nkurunziza J, Uwanibe JN, Bhiman JN, Yasuda J, Morais J, Kiconco J, Sandi JD, Huddleston J, Odoom JK, Morobe JM, Gyapong JO, Kayiwa JT, Okolie JC, Xavier JS, Gyamfi J, Wamala JF, Bonney JHK, Nyandwi J, Everatt J, Nakaseegu J, Ngoi JM, Namulondo J, Oguzie JU, Andeko JC, Lutwama JJ, Mogga JJH, O'Grady J, Siddle KJ, Victoir K, Adeyemi KT, Tumedi KA, Carvalho KS, Mohammed KS, Dellagi K, Musonda KG, Duedu KO, Fki-Berrajah L, Singh L, Kepler LM, Biscornet L, de Oliveira Martins L, Chabuka L, Olubayo L, Ojok LD, Deng LL, Ochola-Oyier LI, Tyers L, Mine M, Ramuth M, Mastouri M, ElHefnawi M, Mbanne M, Matsheka MI, Kebabonye M, Diop M, Momoh M, Lima Mendonça MDL, Venter M, Paye MF, Faye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina MG, Owusu M, Wiley MR, Tatfeng MY, Ayekaba MO, Abouelhoda M, Beloufa MA, Seadawy MG, Khalifa MK, Matobo MM, Kane M, Salou M, Mbulawa MB, Mwenda M, Allam M, Phan MVT, Abid N, Rujeni N, Abuzaid N, Ismael N, Elguindy N, Top NM, Dia N, Mabunda N, Hsiao NY, Silochi NB, Francisco NM, Saasa N, Bbosa N, Murunga N, Gumede N, Wolter N, Sitharam N, Ndodo N, Ajayi NA, Tordo N, Mbhele N, Razanajatovo NH, Iguosadolo N, Mba N, Kingsley OC, Sylvanus O, Femi O, Adewumi OM, Testimony O, Ogunsanya OA, Fakayode O, Ogah OE, Oludayo OE, Faye O, Smith-Lawrence P, Ondoa P, Combe P, Nabisubi P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Okokhere PO, Bejon P, Dussart P, Bester PA, Mbala PK, Kaleebu P, Abechi P, El-Shesheny R, Joseph R, Aziz RK, Essomba RG, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Neto Rodrigues RMDESA, Audu RA, Carr RAA, Gargouri S, Masmoudi S, Bootsma S, Sankhe S, Mohamed SI, Femi S, Mhalla S, Hosch S, Kassim SK, Metha S, Trabelsi S, Agwa SH, Mwangi SW, Doumbia S, Makiala-Mandanda S, Aryeetey S, Ahmed SS, Ahmed SM, Elhamoumi S, Moyo S, Lutucuta S, Gaseitsiwe S, Jalloh S, Andriamandimby SF, Oguntope S, Grayo S, Lekana-Douki S, Prosolek S, Ouangraoua S, van Wyk S, Schaffner SF, Kanyerezi S, Ahuka-Mundeke S, Rudder S, Pillay S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Mohale T, Le-Viet T, Velavan TP, Schindler T, Maponga TG, Bedford T, Anyaneji UJ, Chinedu U, Ramphal U, George UE, Enouf V, Nene V, Gorova V, Roshdy WH, Karim WA, Ampofo WK, Preiser W, Choga WT, Ahmed YA, Ramphal Y, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR; Africa Pathogen Genomics Initiative (Africa PGI), Ouma AEO, von Gottberg A, Githinji G, Moeti M, Tomori O, Sabeti PC, Sall AA, Oyola SO, Tebeje YK, Tessema SK, de Oliveira T, Happi C, Lessells R, Nkengasong J, Wilkinson E

Science
eabq5358. doi: 10.1126/science.abq5358
2022
Molecular Epidemiology and Trends in HIV-1 Transmitted Drug Resistance in Mozambique 1999-2018

Ismael N, Wilkinson E, Mahumane I, Gemusse H, Giandhari J, Bauhofer A, Vubil A, Mambo P, Singh L, Mabunda N, Bila D, Engelbrecht S, Gudo E, Lessells R, de Oliveira T

Viruses
14(9):1992. doi: 10.3390/v14091992
2022
Clinical evaluation of SARS-CoV-2 rapid antigen tests during the Omicron wave in South Africa

Samsunder N, de Vos M, Ngcapu S, Giandhari J, Lewis L, Kharsany AB, Carwood C, de Oliveira T, Karim QA, Karim SA, Naidoo K, Escadafal C, Sivro A

J Infect Dis.
jiac333. doi: 10.1093/infdis/jiac333
2022
Impact of intra-host immune adaptations on the evolution of SARS-CoV-2 S protein among individuals with SARS-CoV-2 infections in South Africa, 2020 to 2022.

Subramoney K, Mtileni N, Davis A, Giandhari J, Naidoo Y, Ramphal Y, Pillay S, Ramphal U, Tegally H, Wilkinson E, Simane A, Reddy B, Mashishi B, Mbenenge N, de Oliveira T, Fielding B, Treurnicht F

Authorea Preprints
DOI: 10.22541/au.166305249.90395426/v1
2022
Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus

Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, Ndodo N, Ayansola O, Mboowa G, Bedford T, Neher RA, Roemer C, Hodcroft E, Tegally H, O'Toole Á, Rambaut A, Pybus O, Kraemer MUG, Wilkinson E, Isidro J, Borges V, Pinto M, Gomes JP, Freitas L, Resende PC, Lee RTC, Maurer-Stroh S, Baxter C, Lessells R, Ogwell AE, Kebede Y, Tessema SK, de Oliveira T

PLoS Biology
doi: 10.1371/journal.pbio.3001769.
2022
Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San EJ, Rodrigues ES, Santos EV, Aburjaile F, Xavier J, Fritsch H, Adelino TER, Pereira F, Leal A, Iani FCM, de Carvalho Pereira G, Vazquez C, Sanabria GME, Oliveira EC, Demarchi L, Croda J, Dos Santos Bezerra R, Paola Oliveira de Lima L, Martins AJ, Renata Dos Santos Barros C, Marqueze EC, de Souza Todao Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Mariani PDSC, Kitajima JP, Santos B, Proto-Siqueira R, Cantarelli VV, Tosta S, Nardy VB, Reboredo de Oliveira da Silva L, Gómez MKA, Lima JG, Ribeiro AA, Guimarães NR, Watanabe LT, Barbosa Da Silva L, da Silva Ferreira R, da Penha MPF, Ortega MJ, de la Fuente AG, Villalba S, Torales J, Gamarra ML, Aquino C, Figueredo GPM, Fava WS, Motta-Castro ARC, Venturini J, do Vale Leone de Oliveira SM, Gonçalves CCM, do Carmo Debur Rossa M, Becker GN, Giacomini MP, Marques NQ, Riediger IN, Raboni S, Mattoso G, Cataneo AD, Zanluca C, Duarte Dos Santos CN, Assato PA, Allan da Silva da Costa F, Poleti MD, Lesbon JCC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Grotto RMT, Souza-Neto JA, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, Bispo de Filippis AM, Venancio da Cunha R, Freitas C, Peterka CRL, de Fátima Rangel Fernandes C, Navegantes W, do Carmo Said RF, Campelo de A E Melo CF, Almiron M, Lourenço J, de Oliveira T, Holmes EC, Haddad R, Sampaio SC, Elias MC, Kashima S, Junior de Alcantara LC, Covas DT

Nature Microbiology
doi: 10.1038/s41564-022-01191-z
2022
SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic

Roshdy WH, Khalifa MK, San JE, Tegally H, Wilkinson E, Showky SM, Darren P, Moir M, Naguib AEN, Gomaa MR, Fahim MAEH, Mohsen AGR, Hassany M, Lessells R, Al-Karmalawy AA, EL-Shesheny R, Kandeil AM, Ali MA, de Oliveira T

Viruses
https://www.mdpi.com/1999-4915/14/9/1878
2022
Building genomic sequencing capacity in Africa to respond to the SARS-CoV-2 pandemic

de Oliveira T, Wilkinson E, Baxter C, Tegally H, Giandhari J, Naidoo Y, Pillay S

Science
https://www.science.org/content/resource/pandemic-preparedness-changing-world-fostering-global-collaboration, 2022
2022
Omicron BA.4/BA.5 escape neutralizing immunity elicited by BA.1 infection.

Khan K, Karim F, Ganga Y, Bernstein M, Jule Z, Reedoy K, Cele S, Lustig G, Amoako D, Wolter N, Samsunder N, Sivro A, San JE, Giandhari J, Tegally H, Pillay S, Naidoo Y, Mazibuko M, Miya Y, Ngcobo N, Manickchund N, Magula N, Karim QA, von Gottberg A, Abdool Karim SS, Hanekom W, Gosnell BI; COMMIT-KZN Team, Lessells RJ, de Oliveira T, Moosa MS, Sigal A

Nature Communications
doi: 10.1038/s41467-022-32396-9
2022
Genomic surveillance of Rift Valley fever virus: from sequencing to lineage assignment

Juma J, Fonseca V, Konongoi SL, van Heusden P, Roesel K, Sang R, Bett B, Christoffels A, de Oliveira T, Oyola SO

BMC Genomics
23(1):520. doi: 10.1186/s12864-022-08764-6
2022
HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy

Kemp SA, Charles OJ, Derache A, Smidt W, Martin DP, Iwuji C, Adamson J, Govender K, de Oliveira T, Dabis F, Pillay D, Goldstein RA, Gupta RK

mBio
13(3):e0026922. doi: 10.1128/mbio.00269-22
2022
Adherence measured using electronic dose monitoring is associated with emergent antiretroviral resistance and poor outcomes in patients co-infected with HIV/AIDS and multidrug-resistant tuberculosis

Bateman M, Wolf A, Chimukangara B, Brust JCM, Lessells R, Amico R, Boodhram R, Singh N, Orrell C, Friedland G, Naidoo K, Padayatchi N, O'Donnell MR

Clin Infect Dis.
ciac232. doi: 10.1093/cid/ciac232
2022
Low-frequency HIV-1 drug resistance mutations in antiretroviral naive individuals in Botswana

Maruapula D, Seatla KK, Morerinyane O, Molebatsi K, Giandhari J, de Oliveira T, Musonda RM, Leteane M, Mpoloka SW, Rowley CF, Moyo S, Gaseitsiwe S

Medicine (Baltimore)
101(28):e29577. doi: 10.1097/MD.0000000000029577
2022
Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021

Subramoney K, Mtileni N, Bharuthram A, Davis A, Kalenga B, Rikhotso M, Maphahlele M, Giandhari J, Naidoo Y, Pillay S, Ramphal U, Ramphal Y, Tegally H, Wilkinson E, Mohale T, Ismail A, Mashishi B, Mbenenge N, de Oliveira T, Makatini Z, Fielding BC, Treurnicht FK

J Med Virol.
4(8):3676-3684. doi: 10.1002/jmv.27797
2022
Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa.

Davies MA, Kassanjee R, Rousseau P, Morden E, Johnson L, Solomon W, Hsiao NY, Hussey H, Meintjes G, Paleker M, Jacobs T, Raubenheimer P, Heekes A, Dane P, Bam JL, Smith M, Preiser W, Pienaar D, Mendelson M, Naude J, Schrueder N, Mnguni A, Le Roux S, Murie K, Prozesky H, Mahomed H, Rossouw L, Wasserman S, Maughan D, Boloko L, Smith B, Taljaard J, Symons G, Ntusi NAB, Parker A, Wolter N, Jassat W, Cohen C, Lessells R, Wilkinson RJ, Arendse J, Kariem S, Moodley M, Wolmarans M, Cloete K, Boulle A

Trop Med Int Health
27(6):564-573. doi: 10.1111/tmi.13752
2022
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

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

Nature Medicine
https://doi.org/10.1038/s41591-022-01911-2
2022
Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus

Happi C, Adetifa I, Mbala P, Njouom R, Nakoune E, Happi A, Ndodo N, Ayansola O, Mboowa G, Bedford T, Neher RA, Roemer C, Hodcroft E, Tegally H, ’Toole A, Rambaut A, Pybus O, Kraemer MUG, Wilkinson E, Isidro J, Borges V, Pinto M, Gomes JP, Baxter C, Lessells R, Ogwell AE, Kebede Y, Tessema SK, de Oliveira T

Virological
https://virological.org/t/urgent-need-for-a-non-discriminatory-and-non-stigmatizing-nomenclature-for-monkeypox-virus/853
2022
Tracking the 2022 monkeypox outbreak with epidemiological data in real-time

Kraemer MUG, Tegally H, Pigott DM, Dasgupta A, Sheldon J, Wilkinson E, Schultheiss M, Han A, Oglia M, Marks S, Kanner J, O’Brien K, Dandamudi S, Rader B, Sewalk K, Bento AI, Scarpino SV, de Oliveira T, Bogoch II, Katz R, Brownstein JS,

The Lancet Infectious Diseases
DOI:https://doi.org/10.1016/S1473-3099(22)00359-0
2022
An early warning system for emerging SARS-CoV-2 variants

Subissi L, von Gottberg A, Thukral L, Worp N, Oude Munnink BB, Rathore S, Abu-Raddad LJ, Aguilera X, Alm E, Archer BN, Attar Cohen H, Barakat A, Barclay WS, Bhiman JN, Caly L, Chand M, Chen M, Cullinane A, de Oliveira T, Drosten C, Druce J, Effler P, El Masry I, Faye A, Gaseitsiwe S, Ghedin E, Grant R, Haagmans BL, Herring BL, Iyer SS, Kassamali Z, Kakkar M, Kondor RJ, Leite JA, Leo Y, Leung GM, Marklewitz M, Moyo S, Mendez-Rico J, Melhem NM, Munster V, Nahapetyan K, Oh D, Pavlin BI, Peacock TP, Peiris M, Peng Z, Poon LLM, Rambaut A, Sacks J, Shen Y, Siqueira MM, Tessema SK, Volz EM, Thiel V, van der Werf S, Briand S, Perkins MD, Van Kerkhove MD, Koopmans MPG, Agrawal A

Nature Medicine
https://doi.org/10.1038/s41591-022-01836-w
2022
Infectious diseases science in Africa takes a leading place in the world

de Oliveira T

The Lancet
https://doi.org/10.1016/S0140-6736(22)00977-1I
2022
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
https://doi.org/10.1038/s41586-022-04830-x
2022
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
399(10330):1141-1153. doi: 10.1016/S0140-6736(22)00007-1
2022
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
https://doi.org/10.1371/journal.pgph.0000055
2022
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
13(1):1976. doi: 10.1038/s41467-022-29579-9
2022
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]
28:2021.10.07.21264644. doi: 10.1101/2021.10.07.21264644
2022
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
doi: 10.1093/ve/veac024
2022
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.
doi: 10.1093/molbev/msac061
2022
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
doi: 10.3201/eid2805.220121
2022
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.
doi: 10.1099/mgen.0.000774
2022
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.
e0015522. doi: 10.1128/spectrum.00155-22
2022
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
https://doi.org/10.1371/journal.pgph.0000105
2022
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
https://doi.org/10.21203/rs.3.rs-1249711/v1
2022
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

Clin Infect Dis.
ciac548. doi: 10.1093/cid/ciac548
2022
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
2022.01.14.476382. doi: 10.1101/2022.01.14.476382
2022
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
2021.12.27.21268439. doi: 10.1101/2021.12.27.21268439
2022
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
doi: 10.1038/s41586-022-04460-3
2022
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.
105080. doi: 10.1016/j.jcv.2022.105080
2022
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
302:114471. doi: 10.1016/j.jviromet.2022.114471
2022
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
doi: 10.1038/s41586-022-04411-y
2022
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
29(7):1093-1110. doi: 10.1016/j.chom.2021.05.012
2021
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.
S2213-7165(21)00249-6. doi: 10.1016/j.jgar.2021.10.023.
2021
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.
18(1):74. doi: 10.1186/s12981-021-00393-5
2021
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.
12:730986. doi: 10.3389/fimmu.2021.730986.
2021
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.
10:ciab1008. doi: 10.1093/cid/ciab1008
2021
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
DOI: 10.1126/scitranslmed.abj6824
2021
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
https://doi.org/10.1016/ S0140-6736(21)02752-5
2021
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
DOI: 10.1126/science.abn4543
2021
Africa: tackle HIV and COVID-19 together

Msomi N, Lessells RJ, Mlisana K, de Oliveira T

Nature
600, 33-36, doi: https://doi.org/10.1038/d41586-021-03546-8
2021
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
doi: 10.1038/s41586-021-04387-1.
2021
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
MEDRXIV-2021-264018v1
2021
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
https://doi.org/10.1038/s41576-021-00408- x
2021
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
DOI: 10.1126/science.abj4336
2021
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
https://doi.org/10.1016/j.cell.2021.09.003
2021
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
11(1):17793. doi: 10.1038/s41598-021-96934-z
2021
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
https://doi.org/10.1038/s41467-021-25167-5
2021
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
10(7):896. doi: 10.3390/pathogens10070896
2021
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
10:e69317. doi: 10.7554/eLife.69317
2021
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.
15(7):e0009591. doi: 10.1371/journal.pntd.0009591
2021
Molecular surveillance of the on-going SARS-COV-2 epidemic in Ribeirao Preto City, Brazil

Slavov SN, Giovanetti M, Bezerra RS, Fonseca V, Santos EV, Rodrigues ES, Adelino T, Xavier J, Borges JS, Evaristo M, Pereira GC, Yamamoto AY, Clé DV, Calado RT, Covas DT, Alcantara LCJ, Kashima S

Infect Genet Evol
2021; Volume 93, September 2021, 104976
2021
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
v. 9, p. 1, 2021.
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; 1- 5. DOI: 10.1002/jmv.27056
2021
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; 15(4): e0009290. https://doi.org/10.1371/journal.pntd.0009290
2021
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;27(5):1522-1524.
2021
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
12(1):2296. doi: 10.1038/s41467-021-22607-0.
2021
SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy

Giovanetti M, Cella E, Benedetti F, Rife Magalis B, Fonseca V, Fabris S, Campisi G, Ciccozzi A, Angeletti S, Borsetti A, Tambone V, Sagnelli C, Pascarella S, Riva A, Ceccarelli G, Marcello A, Azarian T, Wilkinson E, de Oliveira T, Alcantara LCJ, Cauda R, Caruso A, Dean NE, Browne C, Lourenco J, Salemi M, Zella D, Ciccozzi M

Communications Biology
4(1):489. doi: 10.1038/s42003-021-02025-0.
2021
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
11(4):e041083. doi: 10.1136/bmjopen-2020-041083
2021
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
27(5):1393-1404. doi: 10.3201/eid2705.204244
2021
Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant

Shinde V, Bhikha S, Hoosain Z, Archary M, Bhorat Q, Fairlie L, Lalloo U, Masilela MSL, Moodley D, Hanley S, Fouche L, Louw C, Tameris M, Singh N, Goga A, Dheda K, Grobbelaar C, Kruger G, Carrim-Ganey N, Baillie V, de Oliveira T, Lombard Koen A, Lombaard JJ, Mngqibisa R, Bhorat AE, Benade G, Lalloo N, Pitsi A, Vollgraaff PL, Luabeya A, Esmail A, Petrick FG, Oommen-Jose A, Foulkes S, Ahmed K, Thombrayil A, Fries L, Cloney-Clark S, Zhu M, Bennett C, Albert G, Faust E, Plested JS, Robertson A, Neal S, Cho I, Glenn GM, Dubovsky F, Madhi SA; 2019nCoV-501 Study Group.

NEJM
384(20):1899-1909. doi: 10.1056/NEJMoa2103055.
2021
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
DOI: 10.1371/journal.pbio.3001236
2021
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
doi: 10.1002/jmv.27086
2021
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
DOI:https://doi.org/10.1016/j.jinf.2021.05.014
2021
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
7(1):veab041. doi: 10.1093/ve/veab041. eCollection 2021 Jan
2021
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
6:121. doi: 10.12688/wellcomeopenres.16661.1. eCollection 2021.
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
https://doi.org/10.1038/s41564-021-00932-w
2021
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
submitted, available on KRISP website.
2021
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
DOI: 10.1056/NEJMc2104192
2021
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
22;13(3):526. doi: 10.3390/v13030526
2021
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
DOI: 10.1038/s41586-021-03471-w
2021
A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa

de Oliveira T, Lutucuta S, Nkengasong J, Morais J, Paixao JP, Neto Z, Afonso P, Miranda J, David K, Ingles L, Amilton P A P R R C, Freitas H R, Mufinda F, Tessema K S , Tegally H, San E J, Wilkinson E, Giandhari J, Pillay S, Giovanetti M, Naidoo Y, Katzourakis A, Ghafari M, Singh L, Tshiabuila D, Martin D, Lessells R

medRxiv
2021
New SARS-CoV-2 Variants — Clinical, Public Health, and Vaccine Implications

Karim SSA, de Oliveira T

NEJM
DOI: 10.1056/NEJMc2100362
2021
Appropriate names for COVID-19 variants

Karim SSA, de Oliveira T, Loots G

Science
http://science.sciencemag.org/content/371/6535/1215
2021
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
https://doi.org/10.1056/NEJMoa2102214
2021
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
https://doi.org/10.1038/s41587-021-00847-1
2021
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
https://doi.org/10.1038/s41586-021-03402-9
2021
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
S1567-1348(21)00082-4
2021
SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma

Wibmer CK, Ayres F, Hermanus T, Madzivhandila M, Kgagudi P, Oosthuysen B, Lambson BE, de Oliveira T, Vermeulen M, van der Berg K, Rossouw T, Boswell M, Ueckermann V, Meiring S, von Gottberg A, Cohen C, Morris L, Bhiman JN, Moore PL

Nature Medicine
https://doi.org/10.1038/s41591-021-01285-x
2021
Dengue Virus Serotype 2 Intrahost Diversity in Patients with Different Clinical Outcomes

Torres MC, Lima de Mendonça MC, Damasceno dos Santos Rodrigues C, Fonseca V, Ribeiro MS, Brandão AP, Venâncio da Cunha R, Dias AI, Santos Vilas Boas L, Felix AC, Alves Pereira M, de Oliveira Pinto LM, Sakuntabhai A, Bispo de Filippis AM, on behalf of ZikAction Consortium.

Viruses
13(2), 349
2021
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
S1201-9712(21)00037-0
2021
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
https://doi.org/10.1038/s41591-021-01255-3
2021
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
250224v1-Sigal
2020
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, 9(12), 984
2020
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; Pages 237-250
2020
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
https://doi.org/10.1101/2020.12.21.20248640
2020
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
https://doi.org/10.1038/s41467-020-19801-x
2020
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
doi: https://doi.org/10.1101/2020.11.23.20236828
2020
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
https://doi.org/10.1101/2020.11.15.20231993
2020
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
https://doi.org/10.1016/S2214-109X(20)30452-6
2020
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
https://doi.org/10.1101/2020.09.01.20183301
2020
Adding a Voice to the Unique Ethical Considerations in Molecular HIV Surveillance

Mutenherwa F, Wassenaar D, de Oliveira T

The American Journal of Bioethics
https://doi.org/10.1080/15265161.2020.1806399
2020
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
doi: 10.1089/AID.2020.0097
2020
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
11: 1250, https://doi.org/10.3389/fgene.2020.544162
2020
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
75, 11:3319–3326, https://doi.org/10.1093/jac/dkaa343
2020
Unlocking the efficiency of genomics laboratories with robotic liquid-handling

Tegally H, San JE, Giandhari J, de Oliveira T

BMC Genomics
729:https://doi.org/10.1186/s12864-020-07137-1
2020
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
ciaa1038 DOI: https://doi.org/10.1093/cid/ciaa1038
2020
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
14(8): e0008405. https://doi.org/10.1371/journal.pntd.0008405:14(8): e0008405
2020
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
https://doi.org/10.1016/S2666-5247(20)30117-8
2020
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
https://doi.org/10.1016/S2666-5247(20)30116-6
2020
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
25 (8), 919–927
2020
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
17:97–108 https://doi.org/10.1007/s11904-020-00487-1
2020
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) 10:13771. https://doi.org/10.1038/s41598-020-70647-1
2020
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
20:1205 https://doi.org/10.1186/s12889-020-09193-4
2020
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
6(0), a1509. https://doi.org/ 10.4102/sajpsychiatry. v26i0.1509
2020
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
doi: https://doi.org/10.3390/genes11080949:11(8), 949
2020
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
doi: https://doi.org/10.1016/j.ijid.2020.11.128
2020
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
5:109
2020
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
vol 9
2020
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
veaa004, https://doi.org/10.1093/ve/veaa004
2020
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)
doi:10.1073/pnas.2007295117
2020
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
24(4):396-402. doi: 10.5588/ijtld.18.0740
2020
Naturally Occurring Oxazole-Containing Peptides

Mhlongo JT, Brasil E, de la Torre BG, Albericio F

Mar Drugs
18(4). pii: E203. doi: 10.3390/md18040203
2020
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
doi: 10.1089/AID.2020.0031
2020
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.
24(3):295-302. doi: 10.5588/ijtld.19.0214
2020
Breaking a Couple: Disulfide Reducing Agents

Mthembu SN, Sharma A, Albericio F, de la Torre BG

Chembiochem.
doi: 10.1002/cbic.202000092
2020
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
7:100825. doi: 10.1016/j.mex.2020.100825
2020
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.
doi: 10.1007/s10096-020-03862-3.
2020
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
9. pii: e54012. doi: 10.7554/eLife.54012
2020
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.
182(5):1021-1031. doi: 10.1002/ajmg.a.61515
2020
The Pharmaceutical Industry in 2019. An Analysis of FDA Drug Approvals from the Perspective of Molecules

de la Torre BG, Albericio F

Molecules
25(3). pii: E745. doi: 10.3390/molecules25030745
2020
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.
246:129-133. doi: 10.1016/j.ejogrb.2020.01.034
2020
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.
106(2):264-271. doi: 10.1016/j.ajhg.2020.01.004
2020
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
https://doi.org/10.1016/j.celrep.2020.01.085
2020
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
btaa145, https://doi.org/10.1093/bioinformatics/btaa145
2020
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.
pii: S0002-9297(20)30004-5. doi: 10.1016/j.ajhg.2020.01.004
2020
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.
https://doi.org/10.3389/fmicb.2019.03119
2020
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
https://doi.org/10.1016/ S2352-3018(19)30378-9
2020
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.
pii: dyz269. doi: 10.1093/ije/dyz269
2020
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.
23(1):e25432. doi: 10.1002/jia2.25432
2020
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
15(1):e0226098. doi: 10.1371/journal.pone.0226098
2020
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.
9(1):53-57. doi: 10.1080/22221751.2019.1701954
2020
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
144168. doi: 10.1016/j.gene.2019.144168.
2019
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;25(0), a1382. https://doi.org/10.4102/ sajpsychiatry.v25i0.1382:25(0), a1382. https://doi.org/10.4102/ sajpsychiatry.v25i0.1382
2019
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
25(1). pii: E105. doi: 10.3390/molecules25010105
2019
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
20(1):983. doi: 10.4102/sajhivmed.v20i1.983
2019
The pharmacokinetic properties of HIV-1 protease inhibitors: A computational perspective on herbal phytochemicals.

Kehinde I, Ramharack P, Nlooto M, Gordon M

Heliyon
5(10):e02565. doi: 10.1016/j.heliyon.2019.e02565
2019
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
10(1):5482. doi: 10.1038/s41467-019-13473-y
2019
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)
98(47):e18014. doi: 10.1097/MD.0000000000018014
2019
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
2(11):e1914378. doi:10.1001/jamanetworkopen.2019.14378
2019
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
JVI.01623-19. doi: 10.1128/JVI.01623-19
2019
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
7: e1521–40
2019
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
20:67, https://doi.org/10.1186/s12910-019-0403-9
2019
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
DOI: 10.5772/intechopen.88769
2019
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.
doi: 10.1021/acs.orglett.9b02878
2019
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.
doi: 10.1007/s10461-019-02661-y
2019
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
https://doi.org/10.1038/s41598-019-46455-7
2019
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
https://doi.org/10.1016/j.jctube.2019.100115
2019
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.
96(1):72-84. doi: 10.1111/cge.13554
2019
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.
73:159-166. doi: 10.1016/j.meegid.2019.04.020
2019
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
65(4):322-332. doi: 10.1177/0020764019842291
2019
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)
11(5). pii: E874. doi: 10.3390/polym11050874.
2019
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.
doi: 10.1002/jmv.25510
2019
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
14(6):e0217871
2019
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
13(5):e0007231: doi: 10.1371/journal.pntd.0007231
2019
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
10:1411:https://doi.org/10.1038/s41467-019-09139-4
2019
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)
DOI:https://doi.org/10.1016/j.eclinm.2019.03.006
2019
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.
doi: 10.1007/s00127-019-01669-y
2019
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
19(1):196:doi: 10.1186/s12889-019-6494-x
2019
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
doi: 10.2217/pgs-2018-0166
2019
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
962280219829892. doi: 10.1177/0962280219829892
2019
The Pharmaceutical Industry in 2018. An Analysis of FDA Drug Approvals from the Perspective of Molecules.

de la Torre B, Albericio F

Molecules
24(4): pii: E809. doi: 10.3390/molecules24040809.
2019
Factors influencing HIV-1 phylogenetic clustering

Junqueira DM, Sibisi Z, Wilkinson E, de Oliveira T

Curr Opin HIV AIDS
doi: 10.1097/COH.0000000000000540
2019
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.
25(4):784-787
2019
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
9:2640:https://doi.org/10.1038/s41598-018-37749-3
2019
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
33(3):559–569
2019
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
9(1):979:doi.org/10.1038/s41598-018-37791-1
2019
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.
pii: AAC.01834-18.:doi: 10.1128/AAC.01834-18
2019
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
1556264618809608. doi: 10.1177/1556264618809608
2019
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
https://doi.org/10.1089/AID.2018.0202
2019
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
doi: 10.1093/bioinformatics/bty695
2018
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.
61:77-83
2018
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.
61:113-118
2018
2017 FDA Peptide Harvest

Al Musaimi O, Al Shaer D, de la Torre BG, Albericio F

Pharmaceuticals (Basel)
11(2):doi: 10.3390/ph11020042
2018
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
8(1):877:doi: 10.1038/s41598-018-26824-4
2018
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
13(18):1923-1930
2018
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
16(31):5661-5666
2018
Bacteria Hunt Bacteria through an Intriguing Cyclic Peptide

Abdel Monaim SAH, Somboro AM, El-Faham A, de la Torre BG, Albericio F

ChemMedChem
14(1):24-51
2018
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
doi: 10.1007/s00127-018-1623-x
2018
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
74(Pt 12)::1703-1714
2018
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
6:589: doi: 10.3389/fchem.2018.00589
2018
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
4(2): vey037
2018
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
https://doi.org/10.1155/2018/1298542
2018
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.
https://doi.org/10.3389/fmicb.2018.02799
2018
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
73(8):2186–2196
2018
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
44:239–246
2018
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
4(Supplement 2): :55–58
2018
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.
doi: 10.1093/jac/dky428:doi:10.1093/jac/dky428
2018
Intimate partner violence among HIV-serodiscordant couples in Durban, South Africa

Mashaphu S, Wyatt GE, Gomo E, Tomita A

SAMJ
108(11):960-964
2018
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.
9:1535
2018
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
doi: 10.1093/cid/ciy881
2018
Pre-eclampsia: the role of highly active antiretroviral therapy and immune markers

Phoswa WN, Naicker T, Ramsuran V, Moodley J

Inflamm Res.
doi: 10.1007/s00011-018-1190-3
2018
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
11:1413-1421
2018
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
24:1208:10.4102/sajpsychiatry.v24.i0.1208
2018
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
DOI: 10.1126/science.aat7115
2018
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
https://doi.org/10.1016/S2352-3018(18)30093-6
2018
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
doi:10.1038/s41586-018-0043-0
2018
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
https://doi.org/10.1111/dewb.12191
2018
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.
1;22(3):287-293. doi: 10.5588/ijtld.17.0457
2018
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
19(1):17-29. doi: 10.2217/pgs-2017-0144
2018
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
18(1):54. doi: 10.1186/s12879-018-2961-8
2018
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
64(2):120-129. doi: 10.1177/0020764017748180
2018
Application of Decafluorobiphenyl (DFBP) Moiety as a Linker in Bioconjugation

Alapour S, de la Torre BG, Ramjugernath D, Koorbanally NA, Albericio F

Bioconjug Chem
29(2):225-233. doi: 10.1021/acs.bioconjchem.7b00800
2018
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.
doi: 10.1002/cmdc.201700770
2018
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.
doi: 10.1021/acscombsci.8b00006
2018
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
doi: 10.1002/bip.23110
2018
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
7:e33065
2018
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
4(1) doi:vey003/4877091
2018
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
359:86-90
2018
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.
pii: 98463. doi: 10.1172/JCI98463
2018
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
http://dx.doi.org/10.1016/S1473-3099(17)30702-8
2018
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
http://dx.doi.org/10.1016/S2352-3018(17)30205-9
2018
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
doi: 10.1136/jech-2017-209713
2017
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.
60(17):7476-7482
2017
Investigation of the N-Terminus Amino Function of Arg10-Teixobactin

Monaim SAHA, Noki S, Ramchuran EJ, El-Faham A, Albericio F, Torre BG

Molecules
22(10):doi: 10.3390/molecules22101632
2017
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
12(10):e0185692. doi: 10.1371/journal.pone.0185692
2017
HIV assessment and testing for hospital in-patients: still a weak link in the cascade

Iwuji CC, Lessells RJ

Public Health Action
21;7(4):243. doi: 10.5588/pha.17.0111
2017
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
1:152?62
2017
Highlights of the second ISCB Student Council Symposium in Africa, 2017

Rafael CN, Ashano E, Moosa Y, Shome S, DeBlasio D

F1000 Research
6(ISCB Comm J):2183 (doi: 10.12688/f1000research.13463.1)
2017
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
9:eaam8012
2017
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.
doi: 10.1093/cid/cix976
2017
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
doi: 10.1164/rccm.201702-0278OC
2017
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
doi: 10.2147/PGPM.S146787
2017
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
https://doi.org/10.1093/jac/dkx252
2017
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
doi: 10.1093/ve/vew036.033
2017
Persistent circulation of highly divergent HIV-1M lineages in the Congo Basin Region

Tongo M, Dorfman JR, de Oliveira T, Martin DP

Virus Evolution
doi: 10.1093/ve/vew036.039
2017
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
doi: 10.1093/ve/vew036.018
2017
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
DOI:10.1097/QAD.0000000000001553
2017
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
doi.org/10.1093/ije/dyx134
2017
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
doi: 10.1016/j.ebiom.2017.03.024
2017
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
doi: 10.1093/cid/cix056
2017
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
doi: 10.1093/cid/cix015
2017
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
doi: 10.2174/1570162X15666170216114917
2017
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.
10.1097/QAI.0000000000001349
2017
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
pii: 1601679
2017
Primary HIV-1 Drug Resistant Minority Variants

Chimukangara B, Samuel R, Naidoo K, de Oliveira T

AIDS Reviews
19(2):[Epub ahead of print]
2017
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)
96:doi: 10.1097/MD.0000000000006041
2017
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
JVI.01841-16:doi: 10.1128/JVI.01841-16
2017
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
10.1089/AID.2016.0321
2017
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
http://dx.doi.org/10.1016/S1473-3099(16)30513-8
2017
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
pii: S1473-3099(16)30469-8:http://dx.doi.org/10.1016/S1473-3099(16)30447-9
2017
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
http://dx.doi.org/10.1016/S2352-3018(16)30186-2
2017
Microbial genome-wide association studies: lessons from human GWAS

Power RA, Parkhill J, de Oliveira T

Nature Reviews Genetics
nrg.2016.132:doi:10.1038/nrg.2016.132
2017
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.
2016 :doi: 10.1111/hiv.12400
2016
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, Bärnighausen T, de Oliveira T, Moletsane R, Seeley J

PLOS ONE
11:e0148801
2016
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
6:39489. doi: 10.1038/srep39489
2016
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
99(6):1353-1358
2016
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
pii: S0166-0934(16)30289-0: doi: 10.1016/j.jviromet.2016.11.010
2016
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
48:doi: 10.1016/j.meegid.2016.12.005
2016
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
11(9):e0163746
2016
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.
60(4):2248-56
2016
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
90(18):8160-8168
2016
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
11(8):DOI:10.1371/journal.pone.0160649
2016
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
22(1):p. 7
2016
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
S1567-1348(16)30298-2:doi: 10.1016/j.meegid.2016.07.008
2016
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
41:142-145
2016
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:doi:10.1093/database/baw045
2016
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
32(8):763-769
2016
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.
15:http://dx.doi.org/10.1016/S1473-3099(15)00536-8
2016
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
12(2):e1004395
2016
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
11(2):doi: 10.1371/journal.pone.0148801
2016
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
doi:10.1089/aid.2015.0189
2016
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.
71(4):462?466
2015
HIV treatment cascade in tuberculosis patients

Lessells RJ, Swaminathan S, Godfrey-Faussett P

Curr Opin HIV AIDS
10(6):439-46. doi: 10.1097/COH.0000000000000197
2015
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
24(15):4268-75
2015
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
112(34):E4762-71
2015
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
31(8):776-82
2015
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
10(12):DOI: 10.1371/journal.pone.0144057
2015
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
5:16897. doi: 10.1038/srep16897
2015
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
10(12):e0145772. doi: 10.1371/journal.pone.0145772
2015
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
6: 525. doi:10.4172/2155-6113.1000525
2015
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
7:5508-5524; doi:10.3390/v7102887
2015
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
in press:in press
2015
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
dx.doi.org/10.1016/j.virep.2015.05.002
2015
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.
15(3):259-61
2015
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
10(3):e0120389
2015
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
in press
2015
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
pii: AAC.04215-14:pii: AAC.04215-14
2014
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
21S:1-460
2014
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
9(6):e98593
2014
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
12(5):309-16
2014
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
9(10):doi:10.1371/journal.pone.0109296
2014
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
5:doi: 10.4172/2155-6113.1000299
2014
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.
in press
2014
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
7:doi: 10.1016/j.celrep.2014.03.031
2014
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.
2014:198413:doi: 10.1155/2014/198413
2014
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
9(3):e90845. doi:10.1371/journal.pone.0090845
2014
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
14:116:doi:10.1186/1472-6963-14-116
2014
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)
Vol. 2014 :bat082. doi: 10.1093/database/bat082
2014
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.
11(1):3. doi: 10.1186/1742-6405-11-3
2014
Concentrated HIV subepidemics in generalized epidemic settings

Tanser F, de Oliveira T, Maheu-Giroux M, Barnighausen T

Curr Opin HIV AIDS
9(2):115-125
2014
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)
(85):e51242, doi:10.3791/51242
2013
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
110(51):20705-10
2013
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)
8315:236-253
2013
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
51:1757-1761
2013
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
339(6122):966-971
2013
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
93(4):432-41
2013
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
104(2):DOI 10.1007/s10482-013-9981-6
2013
Combined antiretroviral and antituberculosis drug resistance following incarceration

Stott KE, de Oliveira T, Lessells RJ

S Afr J HIV Med
14(3):135-137
2013
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
7:1-11
2013
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
Advanced Access:doi: 10.1002/jmv.23716
2013
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
8(6):e67188
2013
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
in press
2013
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
29 (11):JCM.03305-12
2013
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
29 (11):1477-1480, doi: 10.1093/bioinformatics/btst162
2013
HIV & TB Drug Resistance & Clinical Management Case Book

Rossouw T, Lessells RJ, de Oliveira T

South African Medical Research Council Press
ISBN 978-1-920014-91-9
2013
Searching for Virus Phylotypes

Chevenet F, Jung M, Peeters M, de Oliveira T, Gascuel O

Bioinformatics
29 (5):561-570
2012
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
50(12):doi:10.1128/JCM.01516-12
2012
Principles of HIV drug resistance for clinical management in South Africa

Stott K, Michel J, de Oliveira T

HIV Nursing Matters
3(4):46-51
2012
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
13(4):162-167
2012
Are subtype differences important in HIV drug resistance?

Lessells RJ, Katzenstein DK, de Oliveira T

Current Opinion Virology
2(5):636-43
2012
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
9(9):e1001304
2012
The tainted milk of human kindness

Goedhals D, Rossouw I, Hallbauer U, Mamabolo M, de Oliveira T

Lancet
380:702
2012
WHO HIV drug resistance report 2012

WHO ResNet, including - Jordan MR, Barcarolo J, Parkin N, de Oliveira T (analysis support), Bertagnolio S

WHO report
ISBN 978 92 4 150393 8
2012
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
8(5):e1002507
2012
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
28(6):558-565
2011
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
203(11):1590-4
2011
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.
52(10):1248-56
2011
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
6:e28184
2011
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
52(6):819-25
2011
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
79(2):114-22
2011
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
6(6):e21241
2011
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
40:318-26
2011
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
56(3):e79-86
2011
Poor long-term outcomes for cryptococcal meningitis in rural South Africa

Lessells RJ, Mutevedzi PC, Heller T, Newell ML

S Afr Med
101:251-2
2011
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
17:2035-2037
2011
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
204:S1187-95
2011
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
6(3):e17865
2010
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
163:505-508
2010
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
163(2):253-7
2010
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
55(3):290-8
2010
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
14:420-426
2010
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
10:23
2010
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
88:593-600
2010
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.
10(3):380-5
2010
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
19;5(2):e9311
2010
Public Database for HIV Drug Resistance in southern Africa

de Oliveira T, Shafer WR, Seebregts C, for SATuRN

Nature
464(7289):673
2009
Molecular characterization of non-subtype C and recombinant HIV-1 viruses from Cape Town, South Africa

Wilkinson E, Engelbrecht S

Infectious Genetics and Evolution
9:840-846
2009
The RNA virus database

Belshaw R, de Oliveira T, Markowitz S, Rambaut A

Nucleic Acids Res
37(Database issue):D431-5
2009
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
81(3):391-9
2009
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
4(3):e5065
2009
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
23(9):1047-57
2009
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
37(Web Server issue):W634-42
2009
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.
14(7):975-84
2009
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
23(18):2523-32
2008
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
13 Suppl 2, DOI: 10.1177/135965350801302S09:101-107
2008
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
8(5):635-650
2008
HIV and hepatitis B co-infection in Africa

Lessells RJ, Main J, Cooke GS

Lancet Infectious Diseases
8:210-11
2008
Effect of the HIV epidemic on liver cancer in Africa

Lessells RJ, Cooke GS

Lancet
371:1504
2008
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
3(1):e1390
2008
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
24(6):771-9
2008
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
82(17):8743-61
2007
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.
89(3) :346-348
2007
Cervical spine tuberculosis in children

Govender S, Ramnarain A, Danaviah S

Clin Orthop Relat Res.
460:50-5
2007
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
2(2):e225
2007
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
88(Pt 6):1733-7
2007
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
21(9):1213-5
2007
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
81(16):8543-51
2007
Libya should stop denying scientific evidence on HIV

Colizzi V, de Oliveira T, Roberts RJ

Nature
448(7157):992
2007
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
81(23):13050-6
2007
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
102(6):741-9
2006
A report of 3 unusual opportunistic bacterial infections of the spine

Danaviah S, Govender S, Gordon M, Cassol S

SAOJ
5(3):12-16
2006
Out of Africa: The BioAfrica website

de Oliveira T

BioTechniques
41:129
2006
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
20(5):780-2
2006
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
20(11):1521-9
2006
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
444(7121):836-7
2005
Scourge of a Continent: The BioAfrica Website

de Oliveira T, Cassol S (edited by M. Leslie)

Science
310:1877
2005
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
2:18
2005
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
60(5):598-605
2005
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
21(19):3797-800
2003
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
17(1):11-21
2003
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
77(4):2587-99
2003
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
77(13):7202-13
2003
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
77(17):9422-30
2002
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
360(9330):389
2002
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
18(17):1327-32
1999
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
15(13):1229-33
Antiretroviral therapy adherence patterns, virological suppression, and emergence of drug resistance: A nested case-control study from Uganda and South Africa.

Tyagi A, Tong Y, Rabideau DJ, Reynolds Z, De Oliveira T, Lessells R, Amanyire G, Orrell C, Asiimwe S, Chimukangara B, Giandhari J, Pillay S, Haberer JE, Siedner MJ; META Study Investigators.

Antivir Ther.
27(5):13596535221114822. doi: 10.1177/13596535221114822