PUBLICATIONS SPOTLIGHT


Nature Reviews Genetics


Science


Cell

PUBLICATIONS

Epidemiology and evolution of Zika virus in Minas Gerais, Southeast Brazil

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


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:


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:


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:


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:


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:


Dengue Virus Serotype 2 Intrahost Diversity in Patients with Different Clinical Outcomes

Torres MC, Lima de Mendonça MC, Damasceno dos Santos Rodrigues C, Fonseca V, Ribeiro MS, Brandão AP, Venâncio da Cunha R, Dias AI, Santos Vilas Boas L, Felix AC, Alves Pereira M, de Oliveira Pinto LM, Sakuntabhai A, Bispo de Filippis AM, on behalf of ZikAction Consortium., Viruses (2021), 13(2), 349:


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:


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:


Appropriate names for COVID-19 variants

Karim SSA, de Oliveira T, Loots G, Science (2021), http://science.sciencemag.org/content/371/6535/1215:


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), :


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:


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:


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.:


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:


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.:


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:


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:


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:


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:


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.:


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:


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:


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.:


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.:


Genomic Evidence of SARS-CoV-2 Reinfection Involving E484K Spike Mutation, Brazil

Nonaka CV, Franco M, Gräf T, Lorenzo BC, Avila MR, Sousa K, Neiva LMC, Fonseca V, Mendes AVA, Aguiar RS, Giovanetti M, Freitas BS., Emerg Infect Dis (2021), 2021;27(5):1522-1524.:


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:


Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS-CoV-2 mitigation strategies

Lopes EN, Fonseca V, Frias D, Tosta S, Salgado A, Vialle RA, Toscano PES, Barreto FK, Azevedo VA, Guarino M, Angeletti S, Ciccozzi M, Alcantara LCJ, Giovanetti M, J Med Virol (2021), 2021; 1- 5. DOI: 10.1002/jmv.27056:


Promoting Responsible Research and Innovation (RRI) During Brazilian Activities of Genomic and Epidemiological Surveillance of Arboviruses

Giovanetti M, Alcantara LCJ, Dorea AS, Ferreira QR, Marques WA, Barros JJF, Adelino TER, Tosta S, Fritsch H, Iani FCM, Mares-Guia MA, Salgado A, Fonseca V, Xavier J, Lopes EN, Soares GC, Amarante MFC, Azevedo V, Kruger A, Matta GC, Paineiras-Domingos LL, Colonnello C, Filippis AMB, Montesano C, Colizzi V, Barreto FK, Front. Public Health (2021), v. 9, p. 1, 2021.:


Molecular surveillance of the on-going SARS-COV-2 epidemic in Ribeirao Preto City, Brazil

Slavov SN, Giovanetti M, Bezerra RS, Fonseca V, Santos EV, Rodrigues ES, Adelino T, Xavier J, Borges JS, Evaristo M, Pereira GC, Yamamoto AY, Clé DV, Calado RT, Covas DT, Alcantara LCJ, Kashima S, Infect Genet Evol (2021), 2021; Volume 93, September 2021, 104976:


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 (2021), 29(7):1093-1110. doi: 10.1016/j.chom.2021.05.012:


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:


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:


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:


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:


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:


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:


A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Wilkinson E, Giovanetti M, Tegally H, San EJ, Lessells R, Abdoul K. Sangare, Abdoul-Salam Ouedraogo, Abdul K. Sesay, Abechi Priscilla, Adedotun-Sulaiman Kemi, Adewunmi M. Olubusuyi, Adeyemi O.O. Oluwapelumi, Adnène Hammami, Adrienne A. Amuri, Ahmad Sayed, Ahmed E.O. Ouma, Aida Elargoubi, Ajayi N. Anthony, Ajogbasile F. Victoria, Akano Kazeem, Akpede George, Alexander J. Trotter, Ali A. Yahaya, Alpha K. Keita, Amadou Diallo, Amadou Kone, Amal Souissi, Amel Chtourou, Ana V. Gutierrez, Andrew J. Page, Anika Vinze, Arash Iranzadeh, Arnold Lambisia, Arshad Ismail, Audu Rosemary, Augustina Sylverken, Ayoade Femi, Azeddine Ibrahimi, Baba Marycelin, Bamidele S. Oderinde, Bankole Bolajoko, Beatrice Dhaala, Belinda L. Herring, Berthe-Marie Njanpop-Lafourcade, Bronwyn Kleinhans, Bronwyn McInnis, Bryan Tegomoh, Cara Brook, Catherine B. Pratt, Cathrine Scheepers, Chantal G. Akoua-Koffi, Charles N. Agoti, Christophe Peyrefitte, Claudia Daubenberger, Collins M. Morang’a, D. James Nokes, Daniel G. Amoako, Daniel L. Bugembe, Danny Park, David Baker, Deelan Doolabh, Deogratius Ssemwanga, Derek Tshiabuila, Diarra Bassirou, Dominic S.Y. Amuzu, Dominique Goedhals, Donwilliams O. Omuoyo, Dorcas Maruapula, Ebenezer Foster-Nyarko, Eddy K. Lusamaki, Edgar Simulundu, Edidah M. Ong'era, Edith N. Ngabana, Edwin Shumba, Elmostafa El Fahime, Emmanuel Lokilo, Enatha Mukantwari, Eromon Philomena, Essia Belarbi, Etienne Simon-Loriere, Etilé A. Anoh, Fabian Leendertz, Faida Ajili, Fakayode O. Enoch, Fares Wasfi, Fatma Abdelmoula, Fausta S. Mosha, Faustinos T. Takawira, Fawzi Derrar, Feriel Bouzid, Folarin Onikepe, Fowotade Adeola, Francisca M. Muyembe, Frank Tanser, Fred A. Dratibi, Gabriel K. Mbunsu, Gaetan Thilliez, Gemma L. Kay, George Githinji, Gert van Zyl, Gordon A. Awandare, Grit Schubert, Gugu P. Maphalala, Hafaliana C. Ranaivoson, Hajar Lemriss, Happi Anise, Haruka Abe, Hela H. Karray, Hellen Nansumba, Hesham A. Elgahzaly, Hlanai Gumbo, Ibtihel Smeti, Ikhlas B. 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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:


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:


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:


Co-Circulation of Two Independent Clades and Persistence of CHIKV-ECSA Genotype during Epidemic Waves in Rio de Janeiro, Southeast Brazil.

Fabri AA, Rodrigues CDS, Santos CC, Chalhoub FLL, Sampaio AS, Faria NRC, Torres MC, Fonseca V, Brasil P, Calvet G, Alcantara LCJ, Filippis AMB, Giovanetti M, Bruycker-Nogueira F., Pathogens (2020), 2020, 9(12), 984:


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:


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:


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


Spatial structure of depression in South Africa: A longitudinal panel survey of a nationally representative sample of households

Cuadros DF, Tomita A, Vandormael A, Slotow R, Burns JK, Tanser F, Scientific Reports (2019), 9(1):979:doi.org/10.1038/s41598-018-37791-1


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 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


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:


The Pharmaceutical Industry in 2018. An Analysis of FDA Drug Approvals from the Perspective of Molecules.

de la Torre B, Albericio F, Molecules (2019), 24(4): pii: E809. doi: 10.3390/molecules24040809.


Estimating trends in the incidence rate with interval censored data and time-dependent covariates

Vandormael A, Tanser F, Cuadros D, Dobra A, Stat Methods Med Res (2019), 962280219829892. doi: 10.1177/0962280219829892:


Effects of genetic variability on rifampicin and isoniazid pharmacokinetics in South African patients with recurrent tuberculosis

Naidoo A, Chirehwa M, Ramsuran V, McIlleron H, Naidoo K, Yende-Zuma N, Singh R, Ncgapu S, Adamson J, Govender K, Denti P, Padayatchi N, Pharmacogenomics (2019), doi: 10.2217/pgs-2018-0166:


Major depression and household food insecurity among individuals with multidrug-resistant tuberculosis (MDR-TB) in South Africa.

Tomita A, Ramlall S, Naidu T, Mthembu SS, Padayatchi N, Burns JK, Soc Psychiatry Psychiatr Epidemiol. (2019), doi: 10.1007/s00127-019-01669-y:


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:


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


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


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:


High rate of occult hepatitis B virus infection in hemodialysis units of KwaZulu-Natal, South Africa

Msomi N, Ndlovu K, Giandhari J, Wilkinson E, Parboosing R, Zungu S, Mlisana K, J Med Virol. (2019), doi: 10.1002/jmv.25510:


Bypassing Osmotic Shock Dilemma in a Polystyrene Resin Using the Green Solvent Cyclopentyl methyl Ether (CPME): A Morphological Perspective.

Al Musaimi O, El-Faham A, Almarhoon Z, Basso A, de la Torre BG, Albericio F, Polymers (Basel) (2019), 11(5). pii: E874. doi: 10.3390/polym11050874.:


Predictors of quality of life among community psychiatric patients in a peri-urban district of Gauteng Province, South Africa.

Mapatwana D, Tomita A, Burns JK, Robertson LJ, Int J Soc Psychiatry (2019), 65(4):322-332. doi: 10.1177/0020764019842291


Phylodynamic analyses of Brazilian antigenic variants of infectious bursal disease virus

de Fraga AP, Graf T, Coltro VP, Ikuta N, Fonseca ASK, Majó N, Lunge VR, Infect Genet Evol. (2019), 73:159-166. doi: 10.1016/j.meegid.2019.04.020:


The clinical presentation caused by truncating CHD8 variants.

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


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:


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:


The Role of Adverse Childhood Experiences on Perinatal Substance Use Behaviour in KwaZulu-Natal Province, South Africa.

Bhengu BS, Tomita A, Mashaphu S, Paruk S, AIDS Behav. (2019), doi: 10.1007/s10461-019-02661-y:


Investigating Triorthogonal Chemoselectivity. Effect of Azide Substitution on the Triazine Core.

Sharma A, Sheyi R, Kumar A, El-Faham A, de la Torre BG, Albericio F., Org Lett. (2019), doi: 10.1021/acs.orglett.9b02878:


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:


Recent levels and trends in HIV incidence rates among adolescent girls and young women in ten high-prevalence African countries: a systematic review and meta-analysis

Birdthistle I, Tanton C, Tomita A, de Graaf K, Schaffnit SB, Tanser F, Slaymaker E, Lancet Global Health (2019), 7: e1521–40:


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:


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:


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:


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:


The pharmacokinetic properties of HIV-1 protease inhibitors: A computational perspective on herbal phytochemicals.

Kehinde I, Ramharack P, Nlooto M, Gordon M, Heliyon (2019), 5(10):e02565. doi: 10.1016/j.heliyon.2019.e02565:


Emtricitabine-induced pure red cell aplasia

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


Synthesis and Antimicrobial Activity of a New Series of Thiazolidine-2,4-diones Carboxamide and Amino Acid Derivatives

Abd Alhameed R, Almarhoon Z, Bukhari SI, El-Faham A, de la Torre BG, Albericio F, Molecules (2019), 25(1). pii: E105. doi: 10.3390/molecules25010105:


Depression, anxiety and stress symptoms in patients presenting with dyspepsia at a regional hospital in KwaZulu-Natal province

Tshabalala SJ, Tomita A, Ramlall S , South African Journal of Psychiatry (2019), 2019;25(0), a1382. https://doi.org/10.4102/ sajpsychiatry.v25i0.1382:25(0), a1382. https://doi.org/10.4102/ sajpsychiatry.v25i0.1382


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


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


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


Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1

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


Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells

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


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:


Impact of the scale-up of piped water on urogenital schistosomiasis infection in rural South Africa

Tanser F, Azongo DK, Vandormael A, Barnighausen T, Appleton C, eLIFE (2018), 7:e33065:


N-methylation in amino acids and peptides: Scope and limitations

Sharma A, Kumar A, Abdel Monaim SAH, Jad YE, El-Faham A, de la Torre BG, Albericio F, Biopolymers (2018), doi: 10.1002/bip.23110:


Solid-Phase Synthesis of Pyrrole Derivatives through a Multicomponent Reaction Involving Lys-Containing Peptides

Jad YE, Gudimella SK, Govender T, de la Torre BG, Albericio F, ACS Comb Sci. (2018), doi: 10.1021/acscombsci.8b00006:


1,3,5-Triazino Peptide Derivatives: Synthesis, Characterization, and Preliminary Antileishmanial Activity

Khattab SN, Khalil HH, Bekhit AA, Abd El-Rahman MM, de la Torre BG, El-Faham A, Albericio F, ChemMedChem. (2018), doi: 10.1002/cmdc.201700770:


Application of Decafluorobiphenyl (DFBP) Moiety as a Linker in Bioconjugation

Alapour S, de la Torre BG, Ramjugernath D, Koorbanally NA, Albericio F, Bioconjug Chem (2018), 29(2):225-233. doi: 10.1021/acs.bioconjchem.7b00800:


Epidemiological patterns of mental disorders and stigma in a community household survey in urban slum and rural settings in Kenya

Mutiso VN, Musyimi CW, Tomita A, Loeffen L, Burns JK, Ndetei DM, Int J Soc Psychiatry (2018), 64(2):120-129. doi: 10.1177/0020764017748180:


Case report: mechanisms of HIV elite control in two African women

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


Effect of genetic variation in UGT1A and ABCB1 on moxifloxacin pharmacokinetics in South African patients with tuberculosis

Naidoo A, Ramsuran V, Chirehwa M, Denti P, McIlleron H, Naidoo K, Yende-Zuma N, Singh R, Ngcapu S, Chaudhry M, Pepper MS, Padayatchi N, Pharmacogenomics (2018), 19(1):17-29. doi: 10.2217/pgs-2017-0144:


Spatial clustering of drug-resistant tuberculosis in Hlabisa subdistrict, KwaZulu-Natal, 2011-2015

Smith CM, Lessells R, Grant AD, Herbst K, Tanser F, Int J Tuberc Lung Dis. (2018), 1;22(3):287-293. doi: 10.5588/ijtld.17.0457:


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


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:


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:


Sexual trauma and post-traumatic stress among African female refugees and migrants in South Africa

Mhlongo MD, Tomita A, Thela L, Maharaj V, Burns JK, S Afr J Psychiatr (2018), 24:1208:10.4102/sajpsychiatry.v24.i0.1208


Recurrent tuberculosis among HIV-coinfected patients: a case series from KwaZulu-Natal

Naidoo K, Dookie N, Naidoo K, Yende-Zuma N, Chimukangara B, Bhushan A, Govender D, Gengiah S, Padayatchi N, Infect Drug Resist (2018), 11:1413-1421


Pre-eclampsia: the role of highly active antiretroviral therapy and immune markers

Phoswa WN, Naicker T, Ramsuran V, Moodley J, Inflamm Res. (2018), doi: 10.1007/s00011-018-1190-3:


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:


In Vitro Antibacterial Activity of Teixobactin Derivatives on Clinically Relevant Bacterial Isolates

Ramchuran EJ, Somboro AM, Abdel Monaim SAH, Amoako DG, Parboosing R, Kumalo HM, Agrawal N, Albericio F, Torre BG, Bester LA, Front Microbiol. (2018), 9:1535


Intimate partner violence among HIV-serodiscordant couples in Durban, South Africa

Mashaphu S, Wyatt GE, Gomo E, Tomita A, SAMJ (2018), 108(11):960-964


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


HIV drug resistance in sub-Saharan Africa: public health questions and the potential role of real-world data and mathematical modelling

de waal R, Lessells R, Hauser A, Kouyos R, Davies M-A, Egger M, Wandeler G, for ieDeA-Southern Africa, Journal of Virus Eradication (2018), 4(Supplement 2): :55–58


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


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:


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:


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


Perfluorophenyl Derivatives as Unsymmetrical Linkers for Solid Phase Conjugation

Alapour S, Sharma A, de la Torre BG, Ramjugernath D, Koorbanally NA, Albericio F, Front Chem (2018), 6:589: doi: 10.3389/fchem.2018.00589


Crystal structure, spectroscopic studies and theoretical studies of thiobarbituric acid derivatives: understanding the hydrogen-bonding patterns.

Sharma A, Zamisa SJ, Noki S, Almarhoon Z, El-Faham A, de la Torre BG, Albericio F., Acta Crystallogr C Struct Chem (2018), 74(Pt 12)::1703-1714


Exploring the Orthogonal Chemoselectivity of 2,4,6-Trichloro-1,3,5-Triazine (TCT) as a Trifunctional Linker With Different Nucleophiles: Rules of the Game.

Sharma A, El-Faham A, de la Torre BG, Albericio F, Front Chem. (2018), 6:516:doi: 10.3389/fchem.2018.00516


Identification of patients with recent-onset psychosis in KwaZulu Natal, South Africa: a pilot study with traditional health practitioners and diagnostic instruments

Veling W, Burns JK, Makhathini EM, Mtshemla S, Nene S, Shabalala S, Mbatha N, Tomita A, Baumgartner J, Susser I, Hoek HW, Susser E, Soc Psychiatry Psychiatr Epidemiol (2018), doi: 10.1007/s00127-018-1623-x:


Bacteria Hunt Bacteria through an Intriguing Cyclic Peptide

Abdel Monaim SAH, Somboro AM, El-Faham A, de la Torre BG, Albericio F, ChemMedChem (2018), 14(1):24-51


Formation of N?-terminal 2-dialkyl amino oxazoles from guanidinated derivatives under mild conditions

Abdel Monaim SAH, Mhlongo JT, Kumar A, El-Faham A, Albericio F, de la Torre BG, Org Biomol Chem (2018), 16(31):5661-5666


Exploiting the Thiobarbituric Acid Scaffold for Antibacterial Activity

Sharma A, Noki S, Zamisa SJ, Hazzah HA, Almarhoon ZM, El-Faham A, de la Torre BG, Albericio F, ChemMedChem (2018), 13(18):1923-1930


Inferring population dynamics of HIV-1 subtype C epidemics in Eastern Africa and Southern Brazil applying different Bayesian phylodynamics approaches

Mir D, Graf T, Esteves de Matos Almeida S, Pinto AR, Delatorre E, Bello G, Scientific Reports (2018), 8(1):877:doi: 10.1038/s41598-018-26824-4


2017 FDA Peptide Harvest

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


Spatiotemporal and demographic history of the HIV-1 circulating recombinant form CRF31_BC in Brazil

Fritsch HM, Almeida SEM, Pinto AR, Graf T, Infect Genet Evol. (2018), 61:113-118


Phylodynamic analysis and molecular diversity of the avian infectious bronchitis virus of chickens in Brazil

Fraga AP, Graf T, Pereira CS, Ikuta N, Fonseca ASK, Lunge VR, Infect Genet Evol. (2018), 61:77-83


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


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


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:


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


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:


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


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


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


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]


Sequence and Phylogenetic Analysis of the Untranslated Promoter Regions for HLA Class I Genes

Ramsuran V, Hernandez-Sanchez PG, O'hUigin C, Sharma G, Spence N, Augusto DG, Gao X, Garcia-Sepulveda CA, Kaur G, Mehra NK, Carrington M,, J Immunol (2017), pii: 1601679:


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


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


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


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


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


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


Sexual partnership age pairings and risk of HIV acquisition in rural South Africa

Akulliana A, Bershteyna A, Kleina D, Vandormael A, Barnighausen T, Tanser F, AIDS (2017), :DOI:10.1097/QAD.0000000000001553


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


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


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


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


Hyperbilirubinemia in atazanavir-treated human immunodeficiency virus-infected patients: the impact of the UGT1A1*28 allele

Naidoo A, Naidoo K, Ramsuran V, Reddy M, Padayatchi N, Pharmacogenomics and Personalized Medicine (2017), :doi: 10.2147/PGPM.S146787


Impact of point-of-care Xpert MTB/RIF on tuberculosis treatment initiation: a cluster randomised trial

Lessells RJ, Cooke GS, McGrath N, Nicol MP, Newell ML, Godfrey-Faussett P, Am J Respir Crit Care Med (2017), :doi: 10.1164/rccm.201702-0278OC


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


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


Highlights of the second ISCB Student Council Symposium in Africa, 2017

Rafael CN, Ashano E, Moosa Y, Shome S, DeBlasio D, F1000 Research (2017), 6(ISCB Comm J):2183 (doi: 10.12688/f1000research.13463.1)


Green environment and incident depression in South Africa: a geospatial analysis and mental health implications in a resource-limited setting

Tomita A, Vandormael AM, Cuadros D, Di Minin E, Heikinheimo V, Tanser F, Slotow R, Burns JK, Lancet Planetary Health (2017), 1:152?62


HIV assessment and testing for hospital in-patients: still a weak link in the cascade

Iwuji CC, Lessells RJ, Public Health Action (2017), 21;7(4):243. doi: 10.5588/pha.17.0111:


Tuberculosis mortality and the male survival deficit in rural South Africa: An observational community cohort study

Reniers G, Blom S, Lieber J, Herbst AJ, Calvert C, Bor J, Barnighausen T, Zaba B, Li ZR, Clark SJ, Grant AD, Lessells R, Eaton JW, Hosegood V, PLoS ONE (2017), 12(10):e0185692. doi: 10.1371/journal.pone.0185692:


Investigation of the N-Terminus Amino Function of Arg10-Teixobactin

Monaim SAHA, Noki S, Ramchuran EJ, El-Faham A, Albericio F, Torre BG, Molecules (2017), 22(10):doi: 10.3390/molecules22101632


Converting Teixobactin into a Cationic Antimicrobial Peptide (AMP)

Abdel Monaim SAH, Ramchuran EJ, El-Faham A, Albericio F, de la Torre BG, J Med Chem. (2017), 60(17):7476-7482


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


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


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


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


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


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


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


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


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


Substance use and duration of untreated psychosis in KwaZulu-Natal, South Africa

Davis GP, Tomita A, Baumgartner JN, Mtshemla S, Nene S, King H, Susser E and Burns JK, South African Journal of Psychiatry (2016), 22(1):p. 7


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


Comprehensive Characterization of HIV-1 Molecular Epidemiology and Demographic History in the Brazilian Region Most Heavily Affected by AIDS

Graf T, Fritsch HM, de Medeiros RM, Junqueira DM, Almeida SEM, Pinto AR , Journal of Virology (2016), 90(18):8160-8168


Contribution of Gag and Protease to HIV-1 Phenotypic Drug Resistance in Pediatric Patients Failing Protease Inhibitor-Based Therapy

Giandhari J, Basson AE, Sutherland K, Parry CM, Cane PA, Coovadia A, Kuhn L, Hunt G, Morris L, Antimicrob Agents Chemother. (2016), 60(4):2248-56


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


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


HIV drug resistance testing among patients failing second line antiretroviral therapy-Comparison of in-house and commercial sequencing

Chimukangara B, Varyani B, Shamu T, Mutsvangwa J, Manasa J, White E, Chimbetete C, Luethy R, Katzenstein D, J Virol Methods (2016), pii: S0166-0934(16)30289-0: doi: 10.1016/j.jviromet.2016.11.010


HLA-C Level Is Regulated by a Polymorphic Oct1 Binding Site in the HLA-C Promoter Region

Vince N, Li H, Ramsuran V, Naranbhai V, Duh FM, Fairfax BP, Saleh B, Knight JC, Anderson SK, Carrington M, Am J Hum Genet (2016), 99(6):1353-1358


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


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


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:


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


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


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


Long-range HIV genotyping using viral RNA and proviral DNA for analysis of HIV drug-resistance and HIV clustering

Novitsky V, Zahralban-Steele M, McLane MF, Moyo S, Widenfelt E, Gaseitsiwe S, Makhema J, Essex M, Journal of Clinical Microbiology (2015), in press:in press


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 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


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


Clinical, Virologic, Immunologic Outcomes and Emerging HIV Drug Resistance Patterns in Children and Adolescents in Public ART Care in Zimbabwe

Makadzange AT, Higgins-Biddle M, Chimukangara B, Birri R, Gordon M, Mahlanza T, McHugh G, van Dijk JH, Bwakura-Dangarembizi M, Ndung'u T, Masimirembwa C, Phelps B, Amzel A, Ojikutu BO, Walker BD, Ndhlovu CE, PLoS One (2015), 10(12):DOI: 10.1371/journal.pone.0144057


Genetic Changes in HIV-1 Gag-Protease Associated with Protease Inhibitor-Based Therapy Failure in Pediatric Patients

Giandhari J, Basson AE, Coovadia A, Kuhn L, Abrams AJ, Strehlau R, Morris L, Hunt GM, AIDS Res Hum Retroviruses (2015), 31(8):776-82


Epigenetic mechanisms, T-cell activation, and CCR5 genetics interact to regulate T-cell expression of CCR5, the major HIV-1 coreceptor

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


Epigenetic regulation of differential HLA-A allelic expression levels

Ramsuran V, Kulkarni S, O'huigin C, Yuki Y, Augusto DG, Gao X, Carrington M, Hum Mol Genet (2015), 24(15):4268-75


HIV treatment cascade in tuberculosis patients

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


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


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


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


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


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


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


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 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


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 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


Drug resistance mutations from whole blood proviral DNA among patients on antiretroviral drugs in Zimbabwe

Chimukangara B, Gwanzura G, Mitchell R, Katzenstein D, Masimirembwa C , Curr HIV Res (2014), 12(5):309-16


Effect of female genital schistosomiasis and anti-schistosomal treatment on monocytes, CD4+ T-cells and CCR5 expression in the female genital tract

Kleppa E, Ramsuran V, Zulu S, Karlsen GH, Bere A, Passmore JA, Ndhlovu P, Lillebo K, Holmen SD, Onsrud M, Gundersen SG, Taylor M, Kjetland EF, Ndung'u T, PLoS One (2014), 9(6):e98593


Expression of the CCR5 HIV co-receptor in women with genital schistosomiasis

Kleppa E, Ramsuran V, Zulu S, Karlsen GH, Bere A, Passmore JA, Ndhlovu P, Lillebo K, Holmen SD, Onsrud M, Gundersen SG, Taylor M, Kjetland EF, Ndung'u T, 16th ICID Abstracts / International Journal of Inf (2014), 21S:1-460


Searching for Virus Phylotypes

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


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:


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


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


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 :


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


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


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


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


Pili contribute to biofilm formation in vitro in Mycobacterium tuberculosis

Ramsugit S, Guma S, Pillay B, Jain P, Larsen MH, Danaviah S, Pillay M., Antonie Van Leeuwenhoek (2013), 104(2):DOI 10.1007/s10482-013-9981-6


A qualitative and quantitative histopathological analysis of the host immune response to TB of the spine in HIV-positive and negative patients

Danaviah S, Sacks J, Taylor L, Govender S, Fallows D, Kumar KPS, Ndung'u T, Kaplan G. , Tuberculosis (2013), 93(4):432-41


High coverage of ART associated with decline in risk of HIV acquisition in rural KwaZulu-Natal, South Africa

Tanser F, Barnighausen T, Grapsa E, Zaidi J, Newell M-L., Science (2013), 339(6122):966-971


A Pragmatic Approach to HIV-1 Drug Resistance Determination in Resource-Limited Settings by Use of a Novel Genotyping Assay Targeting the Reverse Transcriptase-Encoding Region Only

Aitken SC, Bronze M, Wallis CL, Stuyver L, Steegen K, Balinda S, Kityo C, Stevens W, Rinke De Wit TF & Schuurman R., J Clin Microbiol (2013), 51:1757-1761


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


Genetic interplay between HLA-C and MIR148A in HIV control and Crohn disease

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


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


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


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:


The tainted milk of human kindness

Goedhals D, Rossouw I, Hallbauer U, Mamabolo M, de Oliveira T, Lancet (2012), 380:702


Gender Differences in Survival among Adult Patients Starting Antiretroviral Therapy in South Africa: A Multicentre Cohort Study

Cornell M, Schomaker M, Garone DB, Giddy J, Hoffmann CJ, Lessells R, Maskew M, Prozesky H, Wood R, Johnson LF, Egger M, Boulle A, Myer L For IeDEA-SA, PLoS Medicine (2012), 9(9):e1001304


Are subtype differences important in HIV drug resistance?

Lessells RJ, Katzenstein DK, de Oliveira T, Current Opinion Virology (2012), 2(5):636-43


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


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


Universal Amplification, Next-Generation Sequencing, and Assembly of HIV-1 Genomes

Gall A, Ferns B, Morris C, Watson S, Cotten M, Robinson M, Berry N, Pillay D, Kellam P, Journal of Clinical Microbiology (2012), 50(12):doi:10.1128/JCM.01516-12


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


Evaluation of tuberculosis diagnostics: establishing an evidence base around the public health impact

Lessells RJ, Cooke GS, Newell ML, Godfrey-Faussett P, J Infect Dis (2011), 204:S1187-95


International spread of multidrug-resistant tuberculosis from Tugela Ferry, South Africa

Cooke GS, Beaton RK, Lessells RJ, John L, Ashworth S, Kon OM, Williams OM, Supply P, Moodley P, Pym AS, Emerg Infect Dis (2011), 17:2035-2037


Poor long-term outcomes for cryptococcal meningitis in rural South Africa

Lessells RJ, Mutevedzi PC, Heller T, Newell ML, S Afr Med (2011), 101:251-2


Retention in HIV care for individuals not yet eligible for antiretroviral therapy: rural KwaZulu-Natal, South Africa

Lessells RJ, Mutevedzi PC, Cooke GS, Newell ML., J Acquir Immune Defic Syndr (2011), 56(3):e79-86


Cohort profile: Hlabisa HIV Treatment and Care Programme

Houlihan C, Bland R, Mutevedzi P, Lessells R, Ndirangu J, Thulare H, Newell ML, Int J Epidemiol (2011), 40:318-26


Surveillance of transmitted antiretroviral drug resistance among HIV-1 infected women attending antenatal clinics in Chitungwiza, Zimbabwe.

Tshabalala M, Manasa J, Zijenah LS, Rusakaniko S, Kadzirange G, Mucheche M, Kassaye S, Johnston E, Katzenstein D, PLoS ONE (2011), 6(6):e21241


Use of dried blood spots for the determination of genetic variation of IL-10, Killer Immunoglobulin-like Receptor and HLA Class I genes

Ndlovu BG, Danaviah S, Moodley E, Ghebremichael M, Bland R, Viljoen J, Newell M-L, Ndung'u T, and Carr WH, Tissue Antigens (2011), 79(2):114-22


Cumulative exposure to cell-free HIV in breast milk, rather than feeding pattern per se, identifies postnatally infected infants

Neveu D, Viljoen J, Bland RM, Nagot N, Danaviah S, Coutsoudis A, Rollins NC, Coovadia HM, Van de Perre P, Newell ML. , Clin Infect Dis (2011), 52(6):819-25


Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings.

Zhou Z, Wagar N, Devos JR, Rottinghaus E, Diallo K, Nguyen DB, Bassey O, Ugbena R, Wadonda-Kabondo N, Mcconnell MS, Zulu I, Chilima B, Nkengasong J, Yang C , PLoS One (2011), 6:e28184


Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women

Ramsuran V, Kulkarni H, He W, Mlisana K, Wright EJ, Werner L, Castiblanco J, Dhanda R, Le T, Dolan MJ, Guan W, Weiss RA, Clark RA, Karim SS, Ahuja SK, Ndung'u T, Clin Infect Dis. (2011), 52(10):1248-56


Influence of variations in CCL3L1 and CCR5 on tuberculosis in a northwestern Colombian population

Mamtani M, Mummidi S, Ramsuran V, Pham MH, Maldonado R, Begum K, Valera MS, Sanchez R, Castiblanco J, Kulkarni H, Ndung'u T, He W, Anaya JM, Ahuja SK, J Infect Dis (2011), 203(11):1590-4


Public Database for HIV Drug Resistance in southern Africa

de Oliveira T, Shafer WR, Seebregts C, for SATuRN, Nature (2010), 464(7289):673


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


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


Scale-up of a decentralised HIV treatment programme in rural KwaZulu- Natal, South Africa: does rapid expansion affect patient outcomes?

Mutevedzi P, Lessells RJ, Heller T, Barnighausen T, Cooke G, Newell ML, Bull WHO (2010), 88:593-600


The TB challenge in a rural South African HIV programme

Houlihan C, Mutevedzi P, Lessells R, Cooke G, Tanser F, Newell ML, BMC Infect Dis (2010), 10:23


Community-based treatment for multidrug-resistant tuberculosis in rural KwaZulu-Natal, South Africa

Heller T, Lessells RJ, Wallrauch C, Barnighausen T, Cooke GS, Mhlongo L, Master I, Newell ML, Int J TB Lung Dis (2010), 14:420-426


Dried Blood Spot HIV-1 RNA Quantification Using Open Real-Time Systems in South Africa and Burkina Faso

Viljoen J, Gampini S, Danaviah S, Valea D, Pillay S, Kania D, Meda N, Newell ML, Van de Perre P, Rouet F; for the World Health Organization/ANRS 1289 Kesho Bora Study Group, Acquir Immune Defic Syndr (2010), 55(3):290-8


Comparison of the Generic HIV Viral Load assay with the Amplicor HIV-1 monitor v1.5 and Nuclisens HIV-1 EasyQ v1.2 techniques for plasma HIV-1 RNA quantitation of non-B subtypes: the Kesho Bora preparatory study.

Rouet F, Foulongne V, Viljoen J, Steegen K, Becquart P, Valea D, Danaviah S, Segondy M, Verhofstede C, Van de Perre P; WHO/ANRS 1289 Kesho Bora Study Group, Virol Methods (2010), 163(2):253-7


Affordable in-house antiretroviral drug resistance assay with good performance in non-subtype B HIV-1

Wallis CL, Papathanasopoulos MA, Lakhi S, Karita E, Kamali A, Kaleebu P, Sanders E, Anzala O, Bekker LG, Stevens G, De Wit TF, Stevens W , J Virol Methods (2010), 163:505-508


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


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


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


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


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


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


The RNA virus database

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


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


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


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


Effect of the HIV epidemic on liver cancer in Africa

Lessells RJ, Cooke GS, Lancet (2008), 371:1504


HIV and hepatitis B co-infection in Africa

Lessells RJ, Main J, Cooke GS, Lancet Infectious Diseases (2008), 8:210-11


In-house HIV-1 RNA real-time reverse transcription PCR assays: principle, available tests and usefulness in developing countries

Rouet F, Menan H, Viljoen J, Ngo Giang Huong N, Mandaliya K, Valea D, Xuan L, Danaviah S, Rousset D, Ganon A and Nerrienet E, Expert Review of Molecular Diagnostics (2008), 8(5):635-650


Antiretroviral drug resistance surveillance among drug-naive HIV-1-infected individuals in Gauteng Province, South Africa in 2002 and 2004

Pillay V, Ledwaba J, Hunt G, Rakgotho M, Singh B, Makubalo L, Bennett D E, Puren A, Morris L , Antivir Ther (2008), 13 Suppl 2:101-107


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


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


Libya should stop denying scientific evidence on HIV

Colizzi V, de Oliveira T, Roberts RJ, Nature (2007), 448(7157):992


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


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


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


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


Cervical spine tuberculosis in children

Govender S, Ramnarain A, Danaviah S, Clin Orthop Relat Res. (2007), 460:50-5


Atypical mycobacterial spondylitis in HIV-negative patients identified by 16S rDNA genotyping

Danaviah S, Govender S, Gordon ML, Cassol S. , J Bone Joint Surg Br. (2007), 89(3) :346-348


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


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


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


Out of Africa: The BioAfrica website

de Oliveira T, BioTechniques (2006), 41:129


A report of 3 unusual opportunistic bacterial infections of the spine

Danaviah S, Govender S, Gordon M, Cassol S, SAOJ (2006), 5(3):12-16


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


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


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


Scourge of a Continent: The BioAfrica Website

de Oliveira T, Cassol S (edited by M. Leslie), Science (2005), 310:1877


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


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


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


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


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


Prevalence, incidence and mother-to-child transmission of HIV-1 in rural South Africa

Rollins NC, Dedicoat M, Danaviah S, Page T, Bishop K, Kleinschmidt I, Coovadia HM, Cassol SA, Lancet (2002), 360(9330):389


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



Ranked by Impact Factor (top 20)

The tainted milk of human kindness. Lancet (2012), I.F.:47.831

Microbial genome-wide association studies: lessons from human GWAS. Nature Reviews Genetics (2017), I.F.:40.282

Scourge of a Continent: The BioAfrica Website. Science (2005), I.F.:37.205

PANGEA-HIV: phylogenetics for generalised epidemics in Africa. Lancet Infect Dis. (2015), I.F.:19.864

HIV and hepatitis B co-infection in Africa. Lancet Infectious Diseases (2008), I.F.:19.864


Ranked by Citation (top 20)


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