PUBLICATIONS SPOTLIGHT

Clinical Infectious Diseases

Nature Reviews Genetics

Lancet HIV



PUBLICATIONS

2017
EBioMedicine

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


2017
Clinical Infectious Diseases

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


2017
Clinical Infectious Diseases

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


2017
Current HIV Research

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


2017
J Acquir Immune Defic Syndr.

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


2017
J Immunol

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:


2017
AIDS Reviews

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]


2017
Medicine (Baltimore)

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


2017
Journal of Virology

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


2017
AIDS Res Hum Retroviruses

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


2016
Scientific Reports

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; PANGEA_HIV Consortium de Oliveira T; ICONIC Project., Scientific Reports (2016), 6:39489. doi: 10.1038/srep39489


2016
Am J Hum Genet

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


2016
J Virol Methods

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


2016
Infection, Genetics and Evolution

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


2016
Lancet Infectious Diseases

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 (2016), http://dx.doi.org/10.1016/S1473-3099(16)30513-8:


2016
Lancet Infectious Diseases

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 (2016), pii: S1473-3099(16)30469-8:http://dx.doi.org/10.1016/S1473-3099(16)30447-9


2016
Lancet HIV

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 (2016), http://dx.doi.org/10.1016/S2352-3018(16)30186-2:


2016
Nature Reviews Genetics

Microbial genome-wide association studies: lessons from human GWAS

Power RA, Parkhill J, de Oliveira T, Nature Reviews Genetics (2016), nrg.2016.132:doi:10.1038/nrg.2016.132


2016
PLoS One

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


2016
Antimicrob Agents Chemother.

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


2016
Journal of Virology

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


2016
PLoS One

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


2016
Southern African Journal of Infectious Diseases

Relationship between HIV serostatus, CD4 count and rehospitalisation: Potential implications for health systems strengthening in South Africa

Moodley Y, Tomita A, Southern African Journal of Infectious Diseases (2016), 1(1):1-6


2016
South African Journal of Psychiatry

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


2016
Infection, Genetics and Evolution

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


2016
HIV Med.

HIV drug resistance levels in adults failing first-line antiretroviral therapy in an urban and a rural setting in South Africa

Rossouw TM, Nieuwoudt M, Manasa J, Malherbe G, Lessells RJ, Pillay S, Danaviah S, Mahasha P, van Dyk G, de Oliveira T, HIV Med. (2016), 2016 :doi: 10.1111/hiv.12400


2016
Infection, Genetics and Evolution

Zika virus complete genome from Salvador, Bahia, Brazil

surname=de OliveiraGiovanetti 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


2016
Database

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


2016
Lancet Infect Dis.

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


2016
AIDS Res Hum Retroviruses

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


2016
PLoS Comput Biol

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


2016
PLoS One

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


2016
AIDS Research and Human Retroviruses

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


2016
J Acquir Immune Defic Syndr.

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


2016
AIDS Research and Human Retroviruses

Deep Sequencing Analysis of Human T Cell Lymphotropic Virus Type 1 Long Terminal Repeat 5' Region from Patients with Tropical Spastic Paraparesis/Human T Cell Lymphotropic Virus Type 1-Associated Myelopathy and Asymptomatic Carriers.

Rego FF, de Oliveira T, Giovanetti M, Galvao-Castro B, Goncalves MS, Alcantara LC., AIDS Research and Human Retroviruses (2016), 32(3):279-83


2015
Hum Mol Genet

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


2015
Proc Natl Acad Sci U S A

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


2015
AIDS Res Hum Retroviruses

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


2015
PLoS One

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


2015
Scientific Reports

History and origin of the HIV-1 subtype C epidemic in South Africa and the greater southern African region

Wilkinson E, Engelbrecht S, de Oliveira T, Scientific Reports (2015), 5:16897. doi: 10.1038/srep16897


2015
PLoS One

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


2015
AIDS & Clinical Research

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


2015
Viruses

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


2015
Journal of Clinical Microbiology

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


2015
Virology Reports

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


2015
Lancet Infect Dis.

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


2015
PLoS One

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


2015
AIDS Research and Human Retroviruses

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:


2015
Antimicrob Agents Chemother

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


2014
16th ICID Abstracts / International Journal of Inf

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


2014
PLoS One

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


2014
Lancet Global Health

Use of antiretroviral therapy in households and risk of HIV acquisition in rural KwaZulu-Natal, South Africa, 2004-12: a prospective cohort study

Vandormael A, Newell ML, Barnighausen T, Tanser F, Lancet Global Health (2014), 2:e209-215


2014
Curr HIV Res

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


2014
PLoS One

Detection of Transmission Clusters of HIV-1 Subtype C over a 21-Year Period in Cape Town, South Africa

Wilkinson E, Engelbrecht S, de Oliveira T, PLoS One (2014), 9(10):doi:10.1371/journal.pone.0109296


2014
J AIDS Clin Res

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


2014
J Acquir Immune Defic Syndr.

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:


2014
Cell Reports

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


2014
Mediators Inflamm.

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


2014
Journal of Visualized Experiments (JoVE)

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


2014
PLoS One

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


2014
BMC Health Services Research

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


2014
Database (Oxford)

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, de Oliveira T, Database (Oxford) (2014), Vol. 2014 :bat082. doi: 10.1093/database/bat082


2014
AIDS Res Ther.

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


2014
Curr Opin HIV AIDS

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


2013
Proc Natl Acad Sci U S A

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


2013
AIDS Reviews

Implementing HIV-1 Genotypic Resistance Testing in Antiretroviral Therapy Programs in Africa: Needs, Opportunities, and Challenges

Lessells RJ, Avalos A, de Oliveira T, AIDS Reviews (2013), 15:221-229


2013
Lecture Notes in Computer Science (LNCS)

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


2013
J Clin Microbiol

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


2013
AIDS

Dramatic increases in HIV prevalence after scale-up of antiretroviral treatment: a longitudinal population-based HIV surveillance study in rural Kwazulu-Natal

Zaidi J, Grapsa E, Tanser F, Newell M-L, Barnighausen T, AIDS (2013), 27(14):2301-2305


2013
Science

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


2013
Tuberculosis

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


2013
Antonie Van Leeuwenhoek

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


2013
S Afr J HIV Med

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


2013
Bioinformatics and Biology Insights

Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights

Frias D, Monteiro-Cunha JP, Mota-Miranda AC, Fonseca VS, de Oliveira T, Galvao-Castro B Alcantara LCJ, Bioinformatics and Biology Insights (2013), 7:1-11


2013
PLoS One

High-Levels of Acquired Drug Resistance in Adult Patients Failing First-Line Antiretroviral Therapy in a Rural HIV Treatment Programme in KwaZulu-Natal, South Africa

Manasa J, Lessells RJ, Skingsley A, Naidu KK, Newell M-L, McGrath N, de Oliveira T, PLoS One (2013), 8(8):e72152


2013
Journal of Medical Virology

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


2013
PLoS One

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


2013
Infectious Genetics and Evolution

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 :


2013
J Clin Microbiol

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


2013
Bioinformatics

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


2013
South African Medical Research Council Press

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:


2013
Bioinformatics

Searching for Virus Phylotypes

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


2012
Journal of Clinical Microbiology

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


2012
Hong Kong Med J

In-house human immunodeficiency virus-1 genotype resistance testing to determine highly active antiretroviral therapy resistance mutations in Hong Kong

Chen JH, Wong KH, Li PC, Chan KK, Lee MP, To SW, Yam WC , Hong Kong Med J (2012), 18:20-24


2012
HIV Nursing Matters

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


2012
S Afr J HIV Med

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


2012
Current Opinion Virology

Are subtype differences important in HIV drug resistance?

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


2012
PLoS Medicine

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


2012
Lancet

The tainted milk of human kindness

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


2012
WHO report

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:


2012
PLoS Comput Biol

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


2012
AIDS Res Hum Retroviruses

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


2011
J Infect Dis

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


2011
Clin Infect Dis.

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


2011
PLoS One

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


2011
Clin Infect Dis

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


2011
Tissue Antigens

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


2011
PLoS ONE

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


2011
Int J Epidemiol

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


2011
J Acquir Immune Defic Syndr

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


2011
PLoS ONE

Association of age with mortality and virological and immunological response to antiretroviral therapy in rural South African adults

Mutevedzi PC, Lessells RJ, Rodger AJ, Newell ML, PLoS ONE (2011), 6(7):e21795


2011
S Afr Med

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


2011
Emerg Infect Dis

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


2011
J Infect Dis

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


2011
PLoS One

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


2010
J Virol Methods

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


2010
Virol Methods

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


2010
Acquir Immune Defic Syndr

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


2010
Int J TB Lung Dis

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


2010
BMC Infect Dis

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


2010
Bull WHO

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


2010
Infect Genet Evol.

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


2010
PLoS One

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


2010
Nature

Public Database for HIV Drug Resistance in southern Africa

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


2009
Infectious Genetics and Evolution

Molecular characterization of non-subtype C and recombinant HIV-1 viruses from Cape Town, South Africa

Wilkinson E, Engelbrecht S, Infectious Genetics and Evolution (2009), 9:840-846


2009
Nucleic Acids Res

The RNA virus database

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


2009
J Med Virol

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


2009
PLoS One

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


2009
AIDS

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


2009
Nucleic Acids Res

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


2009
Antivir Ther.

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


2009
AIDS

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


2008
Antivir Ther

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


2008
Expert Review of Molecular Diagnostics

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


2008
Lancet Infectious Diseases

HIV and hepatitis B co-infection in Africa

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


2008
Lancet

Effect of the HIV epidemic on liver cancer in Africa

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


2008
PLoS One

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


2008
AIDS Res Hum Retroviruses

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


2008
J Virol

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


2007
J Bone Joint Surg Br.

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


2007
Clin Orthop Relat Res.

Cervical spine tuberculosis in children

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


2007
Clin Vaccine Immunol

Evaluation of the Partec flow cytometer against the BD FACSCalibur system for monitoring immune responses of human immunodeficiency virus-infected patients in Zimbabwe

Manasa J, Musabaike H, Masimirembwa C, Burke E, Luthy R, Mudzori J, Clin Vaccine Immunol (2007), 14(3):293-8


2007
PLos One

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


2007
Mem Inst Oswaldo Cruz

Re-mapping the molecular features of the human immunodeficiency virus type 1 and human T-cell lymphotropic virus type 1 Brazilian sequences using a bioinformatics unit established in Salvador, Bahia, Brazil, to give support to the viral epidemiology studies

de Queiroz AT, Mota-Miranda AC, de Oliveira T, Moreau DR, Urpia Cde C, Carvalho CM, Galvao-Castro B, Alcantara LC, Mem Inst Oswaldo Cruz (2007), 102(2):133-9


2007
J Gen Virol

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


2007
AIDS

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


2007
J Virol

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


2007
Nature

Libya should stop denying scientific evidence on HIV

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


2007
J Virol

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


2007
Mem Inst Oswaldo Cruz

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


2006
SAOJ

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


2006
BioTechniques

Out of Africa: The BioAfrica website

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


2006
AIDS

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


2006
AIDS

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


2006
Nature

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


2005
Science

Scourge of a Continent: The BioAfrica Website

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


2005
Retrovirology

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


2005
J Mol Evol

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


2005
Bioinformatics

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


2005
J Virol

Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS

Salemi M, Lamers SL, Yu S, de Oliveira T, Fitch WM, McGrath MS, J Virol (2005), 79(17):11343-52


2004
Eur J Clin Micro ID

Management of hepatitis B co-infection in human immunodeficiency virus infected subjects

Lessells R, Leen CLS, Eur J Clin Micro ID (2004), 23(5):366-374


2003
AIDS

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


2003
Bioinformatics

An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences

De Oliveira T, Miller R, Tarin M, Cassol S, Bioinformatics (2003), 19(1):153-4


2003
J Virol

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


2003
J Virol

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


2003
J Virol

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


2002
Lancet

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


2002
AIDS Res Hum Retroviruses

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


2000
J Virol

Molecular cloning and functional analysis of three type D endogenous retroviruses of sheep reveal a different cell tropism from that of the highly related exogenous jaagsiekte sheep retrovirus

Palmarini M, Hallwirth C, York D, Murgia C, de Oliveira T, Spencer T, Fan H, J Virol (2000), 74(17):8065-76


1999
AIDS Res Hum Retroviruses

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)

Microbial genome-wide association studies: lessons from human GWAS. Nature Reviews Genetics (2016), I.F.:35.989

Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature (2006), I.F.:34.48

Libya should stop denying scientific evidence on HIV. Nature (2007), I.F.:34.48

Public Database for HIV Drug Resistance in southern Africa. Nature (2010), I.F.:34.48

Prevalence, incidence and mother-to-child transmission of HIV-1 in rural South Africa. Lancet (2002), I.F.:33.633

Effect of the HIV epidemic on liver cancer in Africa. Lancet (2008), I.F.:33.633

The tainted milk of human kindness. Lancet (2012), I.F.:33.633

Scourge of a Continent: The BioAfrica Website. Science (2005), I.F.:29.747

High coverage of ART associated with decline in risk of HIV acquisition in rural KwaZulu-Natal, South Africa. Science (2013), I.F.:29.747

HIV and hepatitis B co-infection in Africa. Lancet Infectious Diseases (2008), I.F.:16.144

PANGEA-HIV: phylogenetics for generalised epidemics in Africa. Lancet Infect Dis. (2015), I.F.:16.144

Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study. Lancet Infect Dis. (2016), I.F.:16.144

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. Lancet Infectious Diseases (2016), I.F.:16.144

Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study. Lancet Infectious Diseases (2016), I.F.:16.144

Gender Differences in Survival among Adult Patients Starting Antiretroviral Therapy in South Africa: A Multicentre Cohort Study. PLoS Medicine (2012), I.F.:13.05

Use of antiretroviral therapy in households and risk of HIV acquisition in rural KwaZulu-Natal, South Africa, 2004-12: a prospective cohort study. Lancet Global Health (2014), I.F.:12

HLA-C Level Is Regulated by a Polymorphic Oct1 Binding Site in the HLA-C Promoter Region. Am J Hum Genet (2016), I.F.:11.202

Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa: a community-wide phylogenetic study. Lancet HIV (2016), I.F.:11

HIV-1 adaptation to antigen processing results in population-level immune evasion and affects subtype diversification. Cell Reports (2014), I.F.:10.5

Genetic interplay between HLA-C and MIR148A in HIV control and Crohn disease. Proc Natl Acad Sci U S A (2013), I.F.:9.423

Ranked by Citation (top 20)

An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics (2005), Citations:435

Molecular cloning and functional analysis of three type D endogenous retroviruses of sheep reveal a different cell tropism from that of the highly related exogenous jaagsiekte sheep retrovirus. J Virol (2000), Citations:131

A specific subtype C of human immunodeficiency virus type 1 circulates in Brazil. AIDS (2003), Citations:121

Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature (2006), Citations:114

Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form. J Virol (2007), Citations:101

A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Res (2009), Citations:92

Different epidemic potentials of the HIV-1B and C subtypes. J Mol Evol (2005), Citations:89

Molecular characteristics of human immunodeficiency virus type 1 subtype C viruses from KwaZulu-Natal, South Africa: implications for vaccine and antiretroviral control strategies. J Virol (2003), Citations:78

Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. J Virol (2007), Citations:74

Phylodynamic analysis of human immunodeficiency virus type 1 in distinct brain compartments provides a model for the neuropathogenesis of AIDS. J Virol (2005), Citations:72

Antiretroviral drug resistance surveillance among drug-naive HIV-1-infected individuals in Gauteng Province, South Africa in 2002 and 2004. Antivir Ther (2008), Citations:72

Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences. J Virol (2008), Citations:69

Sequential broadening of CTL responses in early HIV-1 infection is associated with viral escape. PLos One (2007), Citations:68

High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania. PLoS One (2008), Citations:66

Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools. Infectious Genetics and Evolution (2013), Citations:65

Variability at human immunodeficiency virus type 1 subtype C protease cleavage sites: an indication of viral fitness?. J Virol (2003), Citations:62

Evidence for recombination in natural populations of porcine circovirus type 2 in Hong Kong and mainland China. J Gen Virol (2007), Citations:59

High coverage of ART associated with decline in risk of HIV acquisition in rural KwaZulu-Natal, South Africa. Science (2013), Citations:49

Prevalence, incidence and mother-to-child transmission of HIV-1 in rural South Africa. Lancet (2002), Citations:48

The HIV-1 Subtype C Epidemic in South America is Linked to the United Kingdom. PLoS One (2010), Citations:47


KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), K-RITH Tower Building, Nelson R Mandela School of Medicine, UKZN

Contact: Prof. Tulio de Oliveira, Tel: +27 31 260 4898, Email: tuliodna@gmail.com & deoliveira@ukzn.ac.za

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