About Prof. Tulio de Oliveira

tulio@sun.ac.za and deoliveira@ukzn.ac.za +27 (0) 31 260 4898

Background:

Prof. Tulio de Oliveira is the director of the Centre for Epidemic Response and Innovation (CERI) and the KwaZulu-Natal Research Innovation and Sequencing Plaform (KRISP). Prof. de Oliveira is a Professor of Bioinformatics at the School for Data Science and Computational Thinking, Stellenbosch University and at the Collegue of Health Sciences at University of KwaZulu-Natal.

He has received his BSc at the Federal University of Rio Grande do Sul (UFRGS), Brazil and MSc/PhD at the Nelson R Mandela School of Medicine, UKZN, South Africa. He was a Marie Curie Research Fellow at the University of Oxford, U.K. from 2004 to 2006 and a Newton Advanced Fellow at the Wellcome Trust Sanger Institute (WTSI) and at the University of Edinburgh from 2015-2019. In 2015, he became a Professor at UKZN and in 2018, Associate Professor on Global Health at the University of Washington, Seattle, USA and in 2021, he became a Professor at Stellenbosch University.

Prof. de Oliveira has worked for over 20 years with viral outbreaks, including HIV, Hepatitis B and C, Chikungunya, Dengue, SARS-CoV-2, Zika, and Yellow Fever Virus. Prof. de Oliveira has more than 250 publications, with many of them in, the top scientific journals, Nature, Science and Lancet.

Prof. de Oliveira was included in a list of ten scientists with important roles in scientific developments in 2021 compiled by the scientific journal Nature. De Oliveira was also included in a list of the MIT Technology Review as one of the leaders of the ten breakthrough technologies in 2022. In 2022, he received the Gold Medal Award from the South African Medical Research Council (SAMRC). In the same year, for his contributions to society, he received the Batho Pele Award from the Government of South Africa.


Current Affiliations:

Professor on Bioinformatics: School for Data Science and Computational Thinking, Faculty of Science and Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa.

Director: KRISP - KwaZulu-Natal Research and Innovation Sequencing Platform, UKZN, Durban, South Africa.

Fractional Professor - College of Health Sciences, University of KwaZulu-Natal (UKZN), Durban, South Africa.

Affiliate Professor, Department of Global Health, University of Washington, Seattle, US.

Senior Research Associate, Centre for the Aids Programme of Research in South Africa (CAPRISA), Durban, South Africa.

Vice-President: South African Society for Bioinformatics (SASBi).


PUBLICATIONS


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 (2022), 16;13(1):7003. doi: 10.1038/s41467-022-33713-y.:.


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:.


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 (2022), https://doi.org/10.1016/ S2214-109X(22)00417-X:.


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 (2022), eabq5358. doi: 10.1126/science.abq5358:.


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 (2022), 14(9):1992. doi: 10.3390/v14091992:.


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. (2022), jiac333. doi: 10.1093/infdis/jiac333:.


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 (2022), DOI: 10.22541/au.166305249.90395426/v1 :.


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 (2022), doi: 10.1371/journal.pbio.3001769.:.


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 (2022), doi: 10.1038/s41564-022-01191-z:.


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 (2022), https://www.mdpi.com/1999-4915/14/9/1878:.


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 (2022), https://www.science.org/content/resource/pandemic-preparedness-changing-world-fostering-global-collaboration, 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 (2022), doi: 10.1038/s41467-022-32396-9:.


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 (2022), 23(1):520. doi: 10.1186/s12864-022-08764-6:.


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 (2022), 13(3):e0026922. doi: 10.1128/mbio.00269-22:.


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) (2022), 101(28):e29577. doi: 10.1097/MD.0000000000029577:.


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. (2022), 4(8):3676-3684. doi: 10.1002/jmv.27797:.


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 (2022), https://doi.org/10.1038/s41591-022-01911-2:.


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 (2022), https://virological.org/t/urgent-need-for-a-non-discriminatory-and-non-stigmatizing-nomenclature-for-monkeypox-virus/853:.


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 (2022), DOI:https://doi.org/10.1016/S1473-3099(22)00359-0:.


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 (2022), https://doi.org/10.1038/s41591-022-01836-w:.


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


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


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


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


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


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


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


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


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


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


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


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. (2022), ciac548. doi: 10.1093/cid/ciac548:.


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy.
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 (2021), 4(1):489. doi: 10.1038/s42003-021-02025-0.:.


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


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


Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant.
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 (2021), 384(20):1899-1909. doi: 10.1056/NEJMoa2103055.:.


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


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


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


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


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


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


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


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


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


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


A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa.
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), :.


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


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


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


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


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 (2021), https://doi.org/10.1038/s41591-021-01285-x:.


Chikungunya virus ECSA lineage reintroduction in the northeasternmost region of Brazil.
Xavier J, Fonseca V, Bezerra JF, Do Monte Alves M, Mares-Guia NA, Claro IM, De Jesus R, Adelino T, Araujo E, Cavalcante KRLJ, Tosta S, De Souza TR, Moreira Da Cruz FE, De Araujo Fabri A, de Oliveira EC, De Moura NFO, Do Carmo Said RF, De Albuquerque CFC, Azevedo V, de Oliveira T, De Filippis AMB, Venancio Da Cunha R, Luz KG, Giovanetti M, Alcantara L, IJID (2021), S1201-9712(21)00037-0:.


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


News Section from Bioafrica and SATuRN websites

NEWS


Monkeypox Has a New Name: Mpox - NY Times - 2022-12-02


Why Experts Want to Rename Monkeypox - New York Times - 2022-08-23


No Real-World Evidence BA.2 Is More Severe - MedPage Today - 2022-02-26


Africa’s first mRNA hub in Cape Town a potential ‘game changer’, says WHO boss - https://www.news24.com/health24/medical/infectious-diseases/coronavirus/pics-africas-first-mrna-hub- - 2022-02-10


A Virus Variant by Any Other Name - Please - The New York Times - 2021-03-03


South African scientists on pandemic’s frontline - Financial Times - 2021-02-15


KRISP produces over 1000 HIV-1 genomes in record time - SAMRC Press Release - 2020-12-03


SA's first Covid-19 vaccine trial brings hope - Sunday Tribune - 2020-07-12


Human trials for vaccine begins - Independent on Saturday - 2020-04-25


The Pros and Cons of high-speed science - Daily Maverick - 2020-04-24


SA scientists on breaking the Covid-19 code - Saturday Independent - 2020-04-21


Testing to be ramped up and new tests in pipeline for COVID-19 - Spotlight and Daily Maverick - 2020-03-31


KRISP scientists quick action lauded by Nature - Saturday Independent - 2020-02-25


Social media helped scientists with coronavirus - Independent on Saturday - 2020-02-15


Science Through the Lens of Photography - KRISP News - 2019-12-12


Swiss South African Symposium on Pathogen Genomics - Swiss National Science Foundation & SA NRF - 2017-02-23


PhD Fellowship I: Genomics, Bioinformatics & Drug Resistance - CAPRISA, UKZN & MRC Flagship - 2016-08-23


Social cycle aids HIV spread - Nature - 2016-07-21


South Africa's bid to end AIDS - Science - 2016-06-29


21st International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME) - Rega Institute & Korea University College of Medicine - 2016-03-15


Postdoctoral Research Fellows in HIV - WT Africa Centre, UCL & LSHTM - 2014-07-17


SA Medical Research Council Scientific Awards - Mail & Guardian - 2013-12-08


Heroes in the battle for health - Sunday Times - 2013-12-01


BOOK REVIEW - HIV & TB Drug Resistance & Clinical Management Case Book - Southern African Journal of HIV Medicine - 2013-06-20


Bioinformatics in the tropics workshop series 2013-2014 - Bioinformatics in the Tropics - 2013-05-30


The Network Marker - International Innovation - 2013-04-22


Case book tackles HIV and TB drug resistance - Zululand Observer - 2013-04-15


University of Pretoria and partners launch a book - University of Pretoria - 2013-03-19


Casebook aims to curb drug resistance - PretoriaNews - 2013-03-19


'Tainted milk' from wet nurse HIV risk - Cape Argus - 2012-08-26


Local centre proves 'surrogate' HIV infection - Zululand Observer - 2012-08-24


Breastfeeding in the spotlight - SABC - 2012-08-16


BioAfrica Art & Science section is open! - BioAfrica - 2012-05-10


Believe in ART, get tested please - Die Burger - 2008-09-10


High noon in Libya - Nature - 2007-07-19


New evidence in Libyan HIV trial - New Scientist - 2006-12-20


Libya sentences medics to death - BBC - 2006-12-19


New scientific evidence in Libya HIV death penalty case - University of Oxford - BluePrint News - 2006-12-07



VIDEOS


Blogs from Bioafrica and SATuRN websites

BLOGS


Genetic study indicates two novel resistance loci for severe malaria in Africa - by Zakia Jeewa and Tulio de Oliveira - 2014-08-01

Data Curation and its tenets - by Lungani Ndwandwe, Tulio de Oliveira - 2013-08-15

SATuRN on the Chair of African Dreams - by Lungani Ndwandwe, Justen Manasa, Xolile Kineri, Zakhona Gumede, Astrid Treffry-Goatley, Eduan Wilkinson, Tulio de Oliveira - 2013-04-06

The Southern African Treatment Resistance Network (SATuRN) at the KZNSA Gallery - by Lungani Ndwandwe, Tulio de Oliveira - 2012-12-01

Zooming in on home-based health care givers in rural South Africa - by Lungani Ndwandwe, Tulio de Oliveira - 2012-09-13

Shortage of doctors in rural South Africa? - by Lungani Ndwandwe, Tulio de Oliveira - 2012-03-29

Social Worker perspective: Adolescents on Antiretroviral (ARV) therapy - a VideoBlog - by Pretty Nkosi, Nokuthula Skhosana, Lungani Ndwandwe and Tulio de Oliveira - 2012-02-10

Botswana hosted a successful HIV and TB workshop - by Tulio de Oliveira, Lungani Ndwandwe - 2011-12-01


KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).


Location: K-RITH Tower Building
Nelson R Mandela School of Medicine, UKZN
719 Umbilo Road, Durban, South Africa.
Director: Prof. Tulio de Oliveira