About Prof. Tulio de Oliveira

deoliveira@ukzn.ac.za and tuliodna@uw.edu +27 (0) 31 260 4898


Prof. Tulio de Oliveira is the director of KRISP. 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 an Associate Professor on Global Health at the University of Washington, Seattle, USA. 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 150 publications, with many of them in, the top scientific journals, Nature, Science and Lancet.

KRISP boasts state-of-the-art laboratory facilities and scientific expertise and capacity not commonly found in Africa. This places our multidisciplinary team in the ideal position of being able to play a critical role in supporting the public health response to the COVID-19 pandemic. Our scientific activities are receiving extensive media coverage in the national and international media.

Current Affiliations:

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

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).


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:.

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 , medRxiv (2021), https://doi.org/10.1101/2021.02.10.21251247:.

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:.

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:.

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:.

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:.

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

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

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

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

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

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.

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.

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

News Section from Bioafrica and SATuRN websites


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


Chapter 2: The resistant variant - YouTube - 2021-01-22

Blogs from Bioafrica and SATuRN websites


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