TEAM
Prof. Cheryl Baxter
CERI Team

Prof. Cheryl
Baxter

Head: Scientific Support and Training
// Affiliations
Primary
CERI - Stellenbosch University
Also at
Centre for the AIDS Programme of Research in South Africa
// Education
PhD in Medical Virology
UKZN, 2014
MSc in Conservation Biology
University of Natal, 2000
BSc (Hons) in Biology
University of Natal, 1997
BSc in Biology
University of Natal, 1996

Cheryl Baxter, PhD, is Head of Scientific Research Support and Training at the Centre for Epidemic Response and Innovation (CERI) and Associate Professor in Medical Virology at Stellenbosch University. She is also a Research Associate at the Centre for the AIDS Programme of Research in South Africa (CAPRISA). She has extensive experience in research and clinical trial operations, including ethics and regulatory compliance. Prior to joining CERI, her research focused on clinical trials for HIV prevention, specifically strategies to reduce HIV acquisition among young women, issues related to sexual and reproductive health and tuberculosis treatment in people living with HIV. She is currently project manager for several projects, including the Genomic Surveillance to Control Pathogen Infections in Africa (GenPath Africa) project that aims to apply genomic epidemiology to guide the public health response, the DSI Africa project that uses big data to elucidate the clinical and epidemiological interactions between COVID-19 and HIV, the GIZ-funded project that aims to advance genomic surveillance for pandemic preparedness in Africa and is part of the steering committee of the Climate Amplified Diseases and Epidemics (CLIMADE) Consortium that is assessing the impact of climate change on epidemics.

 

// Research Output

Publications

2026
Evolutionary dynamics and molecular adaptation of Rift Valley fever virus across human and non-human outbreaks in Africa

Omara I, Juma J, Tshiabuila D, Dor G, Wilkinson E, Baxter C, Tegally H, Moir M, Oyola S, de Oliveira T

Neurosurgical focus: Video
2:V1
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:btaf665
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
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
Alignment-free viral sequence classification at scale

van Zyl D, Dunaiski M, Tegally H, Baxter C, de Oliveira T, Xavier J, Riley C, Winters A, Naranbhai V, Made F, Karim S, Otwombe K, Abimiku A, Osawe S, Onyemata J, Dakum P, Murtala-Ibrahim F, Andrew N, Musa A, Adenekan T, Ewerem K, Etuk V, de Oliveira T, Baxter C, Wilkinson E, Tegally H, Poongavanan J, Parker M, Silva D, Xavier J, Stafford K, Charurat M, Blanco N, O’Connor T, Fitzpatrick M, Sajadi M, Lawal O, Xiong C, Luo W, Wu X

BMC Genomics
26:389
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
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
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
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
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
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.
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
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
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
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
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
Investing in Africa's scientific future

de Oliveira T, Baxter C

Science
;383(6678):eadn4168. doi: 10.1126/science.adn4168
2023
Insights into SARS?CoV?2 in Angola during the COVID?19 peak: Molecular epidemiology and genome surveillance

Francisco N, van Wyk S, Moir M, San J, Sebastião C, Tegally H, Xavier J, Maharaj A, Neto Z, Afonso P, Jandondo D, Paixão J, Miranda J, David K, Inglês L, Pereira A, Paulo A, Carralero R, Freitas H, Mufinda F, Lutucuta S, Ghafari M, Giovanetti M, Giandhari J, Pillay S, Naidoo Y, Singh L, Tshiabuila D, Martin D, Chabuka L, Choga W, Wanjohi D, Mwangi S, Pillay Y, Kebede Y, Shumba E, Ondoa P, Baxter C, Wilkinson E, Tessema S, Katzourakis A, Lessells R, de Oliveira T, Morais J

Influenza and Other Respiratory Viruses
17:e13198
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
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 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
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
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
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
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
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
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
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
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
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