PUBLICATIONS SPOTLIGHT

PUBLICATIONS

HIV-1 Subtypes B and C Unique Recombinant Forms (URFs) and Transmitted Drug Resistance Identified in the Western Cape Province, South Africa

Jacobs GB, Wilkinson E, Isaacs S, Spies G, de Oliveira T, Seedat S, Engelbrecht S , PLoS One (2014), 9(3):e90845. doi:10.1371/journal.pone.0090845

Implementing antiretroviral resistance testing in a primary health care HIV treatment programme in rural KwaZulu-Natal, South Africa: early experiences, achievements and challenges

Lessells RJ, Stott KE, Manasa J, Naidu KK, Skingsley A, Rossouw T, de Oliveira T, BMC Health Services Research (2014), 14:116:doi:10.1186/1472-6963-14-116

Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa

Manasa J, Lessells R, Rossouw T, Naidu K, Van Vuuren C, Goedhals D, Van Zyl G, Bester A, Skingsley A, Stott K, Danaviah S, Chetty T, Singh L, Moodley P, Iwuji C, McGrath N, Seebregts CJ, de Oliveira T, Database (Oxford) (2014), Vol. 2014 :bat082. doi: 10.1093/database/bat082

Drug resistance in children at virological failure in a rural KwaZulu-Natal, South Africa, cohort

Pillay S, Bland RM, Lessells RJ, Manasa J, de Oliveira T, Danaviah S., AIDS Res Ther. (2014), 11(1):3. doi: 10.1186/1742-6405-11-3

Concentrated HIV subepidemics in generalized epidemic settings

Tanser F, de Oliveira T, Maheu-Giroux M, Barnighausen T, Curr Opin HIV AIDS (2014), 9(2):115-125

An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings

Manasa J, Danaviah S, Pillay S, Padayachee P, Mthiyane H, Seebregts C, Rinke De Wit TF, Viljoen J, Katzenstein D, De Oliveira T , Journal of Visualized Experiments (JoVE) (2014), (85):e51242, doi:10.3791/51242

Public engagement with HIV in a rural South African context: an analysis of a small-media, taxi-based edutainment model applied in Jiving with Science

Treffry-Goatley A, Mahlinza M, Imrie J, Critical Arts (2013), 27:112-126

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

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

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

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

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

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 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

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

Combined antiretroviral and antituberculosis drug resistance following incarceration

Stott KE, de Oliveira T, Lessells RJ, S Afr J HIV Med (2013), 14(3):135-137

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

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

High-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

High Level of HIV-2 False Positivity in KwaZulu-Natal Province: A Region of South Africa With a Very High HIV-1 Subtype C Prevalence

Singh L, Parboosing R, Manasa J, Moodley P, de Oliveira T, Journal of Medical Virology (2013), Advanced Access:doi: 10.1002/jmv.23716

Trends in Genotypic HIV-1 Antiretroviral Resistance between 2006 and 2012 in South African Patients Receiving First- and Second-Line Antiretroviral Treatment Regimens

Van Zyl GU, Liu TF, Claassen M, Engelbrecht S, de Oliveira T, Preiser W, Wood NT, Travers S, Shafer RW, PLoS One (2013), 8(6):e67188

Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools

Pena ACP, Faria NR, Imbrechts S, Libin P, Abecasis AB, Deforche K, Gomez A, Camacho RJ, de Oliveira T, Vandamme A-M, Infectious Genetics and Evolution (2013), in press :

Development and evaluation of an affordable real-time qualitative assay for determining HIV-1 virological failure in plasma and dried blood spots.

Aitken SC, Kliphuis A, Bronze M, Wallis CL, Kityo C, Balinda S, Stevens WS, Spieker N, de Oliveira T, Rinke de Wit TF, Schuurman R., J Clin Microbiol (2013), 29 (11):JCM.03305-12

RegaDB: Community-driven data management and analysis for infectious diseases

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

HIV & TB Drug Resistance & Clinical Management Case Book

Rossouw T, Lessells RJ, de Oliveira T, South African Medical Research Council Press (2013), ISBN 978-1-920014-91-9:

Searching for Virus Phylotypes

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

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

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

Principles of HIV drug resistance for clinical management in South Africa

Stott K, Michel J, de Oliveira T, HIV Nursing Matters (2012), 3(4):46-51

The 2012 southern African ARV drug resistance testing guidelines

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

Are subtype differences important in HIV drug resistance?

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