Prof. Tulio de Oliveira

My research interests concentrates on viral evolution under selection pressure created in the transmission, acquisition and drug escape processes. A particular point of interest is on the study of virus' origins and the effect of network of transmissions in the spread of epidemics in Africa and other continents. I also enjoy developing bioinformatics software applications and running a next generation sequencing (NGS) laboratory.

Contact Details:

Email: tuliodna@gmail.com & deoliveira@ukzn.ac.za

Telephone: +27 (0) 31 260 4898

Background:

Prof. Tulio de Oliveira is a bioinformatician that has been working with HIV research since 1997. He has received his PhD at the Nelson R Mandela School of Medicine, UKZN, South Africa. He was a Marie Curie research fellow at the University of Oxford, U.K. from 2004 to 2006, where he received in depth training on virus genetic analysis and molecular evolution. He is recognized as an expert on HIV genetic data and bioinformatics and has published some high-impact articles including the one that presents the Rega Subtyping tools (de Oliveira et al. Bioinformatics 2005), one that proof the innocence of the six foreign medical personnel condemned to death for infecting with HIV 438 children in a hospital in Libya (de Oliveira et al. Nature 2006), open access and public HIV drug resistance databases in Africa (de Oliveira et al. Nature 2010) and the first case of proven HIV surrogate transmission in South Africa (Goedhals et al. Lancet 2012).


Current Affiliations:

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

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

Director: Southern African Treatment Research Network (SATuRN).

President: South African Society for Bioinformatics (SASBi).

Royal Society Newton Fellow at Wellcome Trust Sanger Institute, U.K.


Videos Videos Descriptions

YouTube Video

Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa: a community-wide phylogenetic study - Keynote presentation at AIDS 2016.

Author: Anthony Fauci, Quarraisha Abdool Karim, David Khanyile, Tulio de Oliveira, Salim Abdool Karim - Date: 2016-06-20

This is a short video of our keynote presentation at the AIDS 2016 conference in Durban.


YouTube Video

Completion of a world-class genomics lab at Africa Centre/UKZN, Durban, South Africa - Part III

Author: Prevashinee Padayachee and Tulio de Oliveira - Date: 2014-08-06

This short video diary is the third in a series that traced the creation of a world class DNA genomic facility in the African continent that focuses on research on diseases that affect human health. This video shows the completion of genomics centre. It shows Illumina Miseq and Life Technologies Next Generation (NextGen) sequencing Facilities used in HIV & TB research.


YouTube Video

WTAC & UKZN Genomics Laboratory Construction - Video Diary Part II

Author: Prevashinee Padayachee and Tulio de Oliveira - Date: 2014-04-05

This short video diary is the second in a series of movies that will trace the transformation of our existing laboratory into a world class DNA genomic facility. The second video provides an introduction to the robotics system and present our new bioinformatics facility. The genomics facility is based at the College of Health Sciences, University of KwaZulu-Natal and funded by the Wellcome Trust Africa Centre, South Africa MRC, UKZN, NRF and BMGF. This will be one of the first facilities in the African continent that focuses on research on diseases that affect human health.


YouTube Video

WTAC & UKZN Genomics Laboratory Construction - Video Diary Part I

Author: Prevashinee Padayachee and Tulio de Oliveira - Date: 2014-03-13

This short video diary is the first in a series of four weekly movies that will trace the transformation of our existing laboratory into a world class DNA genomic facility. This will be one of the first facilities in the African continent that focuses on research on diseases that affect human health. The first video provides an introduction to the series, a pictorial tour of the current facilities and outlines the exciting renovation plans that are under way. The genomics facility is based at the College of Health Sciences, University of KwaZulu-Natal and funded by the Wellcome Trust Africa Centre, South Africa MRC, UKZN, NRF and BMGF


YouTube Video

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

Author: Manasa J, Danaviah S, Pillay S, Padayachee P, Mthiyane H, Seebregts C, Rinke De Wit TF, Viljoen J, Katzenstein D, De Oliveira T - Date: 2013-10-18

SATuRN/Life Technologies open access and affordable drug resistance genotyping system. This is a video that accompain a peer-reviewed manuscript that provides detailed information on how to our affordable drug resistance testing. The paper and video are open accessible!


YouTube Video

Are subtype differences important in HIV drug resistance?

Author: Tulio de Oliveira - Date: 2013-10-10

Short interview about a review paper on HIV-1 subtypes and drug resistance


YouTube Video

HIV & TB Drug Resistance & Clinical Management Case Book

Author: Tulio de Oliveira - Date: 2013-10-06

Short interview about our HIV & TB Drug Resistance & Clinical Management Case Book


YouTube Video

Intro to BioAfrica/SATuRN Videos - Prof. Tulio de Oliveira

Author: Tulio de Oliveira - Date: 2013-09-29

In this interview, Prof. Tulio de Oliveira highlights theirs plans to use new media and videos in their research.


YouTube Video

African Dream - Dr Tulio de Oliveira for Southern African Treatment Resistance Network (SATuRN)

Author: Tulio de Oliveira - Date: 2013-08-01

Prof Tulio de Oliveira tell about his passion of the usage of open source bioinformatics applications and open access information to curb HIV & TB drug resistance in Africa.


YouTube Video

SABC 2 - HIV & TB Drug Resistance and Clinical Management Book Launch

Author: Tulio de Oliveira - Date: 2013-04-02

This is the TV coverage of the HIV & TB Drug Resistance and Clinical Management Book Launch. SABC broadcast in many official languages, this is the Venda version.


Open access pdf Publications

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

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

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

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

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

Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015-16: a modelling study.
Kraemer MUG, Faria NR, Reiner Jr RC, Golding N, Nikolay B, Stasse S, Johansson MA, Salje H, Faye O, Wint GRW, Niedrig M, Shearer FM, Hill SC, Thompson RN, Bisanzio D, Taveira N, Nax HH, Pradelski BSR, Nsoesie EO, Murphy NR, Bogoch II, Khan K, Brownstein JS, Tatem AJ, de Oliveira T, Smith DL, Sall AA, Pybus OG, Hay SI, Cauchemez S, Lancet Infectious Diseases (2016), http://dx.doi.org/10.1016/S1473-3099(16)30513-8:.

Occult HIV-1 drug resistance to thymidine analogues following failure of first-line tenofovir combined with a cytosine analogue and nevirapine or efavirenz in sub Saharan Africa: a retrospective multi-centre cohort study.
Gregson J, Kaleebu P, Marconi VC, van Vuuren C, Ndembi N, Hamers RL, Kanki P, Hoffmann CJ, Lockman S, Pillay D, de Oliveira T, Clumeck N, Hunt G, Kerschberger B, Shafer RW, Yang C, Raizes E, Kantor R, Gupta RK, Lancet Infectious Diseases (2016), pii: S1473-3099(16)30469-8:http://dx.doi.org/10.1016/S1473-3099(16)30447-9.

Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa: a community-wide phylogenetic study.
de Oliveira T, Kharsany ABM, Graf T, Cawood C, Khanyile D, Grobler A, Puren A, Madurai S, Baxter C, Karim QA, Karim SSA, Lancet HIV (2016), http://dx.doi.org/10.1016/S2352-3018(16)30186-2:.

Microbial genome-wide association studies: lessons from human GWAS.
Power RA, Parkhill J, de Oliveira T, Nature Reviews Genetics (2016), nrg.2016.132:doi:10.1038/nrg.2016.132.

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

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

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

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

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

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

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.

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

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

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

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

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.

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.

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

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

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

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

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

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

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

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

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.

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

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

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

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

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.

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, 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.

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.

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 VS, 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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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.

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.

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

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

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

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

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.

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.

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Blogs Blogs Description & Link

bioafrica - Blogs from Bioafrica and SATuRN websites

Genetic study indicates two novel resistance loci for severe malaria in Africa

Author: Zakia Jeewa and Tulio de Oliveira - 2014-08-01

Wellcome Trust Africa Centre Seminar & Twitter Q&A on HIV drug resistance in Africa, 15-Jan-2014

Author: Tulio de Oliveira - 2014-01-16

Data Curation and its tenets

Author: Lungani Ndwandwe, Tulio de Oliveira - 2013-08-15

South African scientific excellence: South African AIDS scientist to lead UNAIDS Expert Panel

Author: Tulio de Oliveira - 2013-07-01

Pirate Science - an interesting website on open-access phylogenetic publications

Author: Tulio de Oliveira - 2013-04-28

SATuRN on the Chair of African Dreams

Author: Lungani Ndwandwe, Justen Manasa, Xolile Kineri, Zakhona Gumede, Astrid Treffry-Goatley, Eduan Wilkinson, Tulio de Oliveira - 2013-04-06

Internet Freedom Activist Commit Suicide due to Criminal Charges for Distributing Academic Publications. We Increase the Open Distribution of our Publications!

Author: Tulio de Oliveira - 2013-01-15

The Southern African Treatment Resistance Network (SATuRN) at the KZNSA Gallery

Author: Lungani Ndwandwe, Tulio de Oliveira - 2012-12-01

Zooming in on home-based health care givers in rural South Africa

Author: Lungani Ndwandwe, Tulio de Oliveira - 2012-09-13

ACiLT Practical Course on Quality Assurance of HIV-1 Drug Resistance Interpretation in Sequence Editing and Data Management Process, 7-11 May 2012

Author: Justen Manasa, Tulio de Oliveira - 2012-06-01

National Strategic Plan 2012-2016: Integrating research and all sectors of society to fight HIV, STIs and TB in South Africa

Author: Lungani Ndwandwe, Tulio de Oliveira - 2012-04-20

Shortage of doctors in rural South Africa?

Author: Lungani Ndwandwe, Tulio de Oliveira - 2012-03-29

Social Worker perspective: Adolescents on Antiretroviral (ARV) therapy - a VideoBlog

Author: Pretty Nkosi, Nokuthula Skhosana, Lungani Ndwandwe and Tulio de Oliveira - 2012-02-10

Scientific Community Engagement Activities in rural KwaZulu-Natal, South Africa

Author: Tulio de Oliveira - 2012-01-22

Botswana hosted a successful HIV and TB workshop

Author: Tulio de Oliveira, Lungani Ndwandwe - 2011-12-01

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News News Description and Link

bioafrica - News Section from Bioafrica and SATuRN websites

BioAfrica & SATuRN

Newsletter, Dec 2016: Ethics & phylogenetics, HIV transmission cycle, UNAIDS Report, Drug resistance increases in Africa

BioAfrica & SATuRN - 2016-12-15

The concept behind this newsletter is that anyone with 15 minutes to spare can learn about our research work. In this December 2016 issue of our newsletter, we have included interesting news, blogs, reports, tweets, publications and training information produced by our group.


Mercury

Unrelenting spread of HIV amongst Adolescent girls and young women in rural and urban KwaZulu-Natal

Mercury - 2016-12-01

By Professor Ayesha Kharsany, December 1, 2016, Durban - Globally, over 1.6 billion people are in the age group 12-24 years, the largest generation of adolescents and young people. However, almost 42% of new HIV infections occur in this age group, nearly 80% of these live in sub-Saharan Africa and more than 70% of these infections occur in adolescent girls and young women. Not only do these adolescent girls and young women have higher rates of HIV, they also acquire infection 5-7 years earlier than their male peers.


The Lancet

Two manuscripts featured in the Lancet website front webpage on AIDS day.

The Lancet - 2016-12-01

Two of our recently published manuscripts (de Oliveira et al. Lancet HIV 2016 & Gregson et al Lancet Infectious Diseases 2016) are highlighed in the Lancet website front webpage...


UNAIDS

UNAIDS Report 2016 - Get on the Fast-Track - The life-cycle approach to HIV

UNAIDS - 2016-11-22

In this report, UNAIDS is announcing that 18.2 million people now have access to HIV treatment. The Fast-Track response is working. Increasing treatment coverage is reducing AIDS-related deaths among adults and children. But the life-cycle approach, which highlight our phylogenetics manuscript (de Oliveira et al. Lancet HIV 2016), has to include more than just treatment.


Reuters

More than 18 million on HIV treatment, a million more than 2015: UNAIDS 2016 Report

Reuters - 2016-11-22

More than 18 million people now have access to life-saving AIDS treatment, 1.2 million more than at the end of last year, the United Nations said on Monday. With detailed data showing some of the many complexities of the HIV epidemic, the report found that people are particularly vulnerable to HIV at certain points in their lives (de Oliveira et al. Lancet HIV 2016). It called for 'life-cycle; approach to offer help and prevention measures for everyone at every stage of life.


AWACC

10th Annual Workshop on Advanced Clinical Care - AIDS (AWACC)

AWACC - 2016-10-06

This AWACC annual workshop is in the 10th edition and it is organized as a joint effort of the Centre for AIDS research (CFAR) of Harvard Medical School, SATuRN, CAPRISA, UKZN and the KwaZulu-Natal Department of Health. AWACC objecitve is to translate the latest evidence-based research and apply best practice models of care into good clinical practice, specifically for resource constrained areas.


SASBi & SAGS

4th Joint Congress of the South African Society for Bioinformatics (SASBi) and the South African Genetics Society (SAGS)

SASBi & SAGS - 2016-09-23

The biennial SASBi and SAGS congresses are the premier national scientific meetings on bioinformatics and genetics in South Africa. In total, 187 participats delivered 40 oral presentations and 65 posters in SASBi-SAGS-2016. This congress provided an exciting opportunity to learn about cutting-edge research in both disciplines, and to network with members of the two societies and with leading international scientists.


CAPRISA, UKZN & MRC Flagship

PhD Fellowship I: Genomics, Bioinformatics & Drug Resistance

CAPRISA, UKZN & MRC Flagship - 2016-08-23

The Professional Development Programme (PDP) at CAPRISA aims to develop and retain South African scientists and professionals of the highest calibre. The genomics and bioinformatics project in HIV-1 drug resistance is inter-disciplinary in nature and involves collaboration between the CAPRISA's MRC HIV-TB Pathogenesis and Treatment Research Unit and the Flagship Program of the MRC, which are two of the most prestigious research programs in South Africa.


CAPRISA, UKZN & MRC Flagship

PhD Fellowship II: Genomics, Bioinformatics, Epidemioloy and Phylogenetics

CAPRISA, UKZN & MRC Flagship - 2016-08-23

The Professional Development Programme (PDP) at CAPRISA aims to develop and retain South African scientists and professionals of the highest calibre. The genomics and bioinformatics project in HIV-1 phylogenetics and molecular epidemiology is inter-disciplinary in nature and involves collaboration between the CAPRISA's MRC HIV-TB Pathogenesis and Treatment Research Unit and the Flagship Program of the MRC, which are two of the most prestigious research programs in South Africa.


Nature

Social cycle aids HIV spread

Nature - 2016-07-21

Nature (Vol. 535, pp. 335, 2016) report our recent results on the use of genetic sequences to uncover HIV-1 transmission patterns in young woman in South Africa (de Oliveira et al. Lancet HIV 2016). The paper was presented as a Keynote at AIDS 2016 conference.


Wall Street Journal

Studies Offer Fresh Hope in Fight Against HIV/AIDS in South Africa.

Wall Street Journal - 2016-07-18

Researchers with the Centre for the AIDS Programme of Research in South Africa, or CAPRISA, a consortium of South African and North American scientists, analyzed genetic codes (de Oliveira et al. Lancet HIV 2016) from study subjects in South Africa to try to pinpoint biological factors that may contribute, along with behavioral factors, to the large number of infections.


Science

South Africa's bid to end AIDS

Science - 2016-06-29

Science magazine (Vol. 353, Issue 6294, pp. 18-21, 2016). This issue was published before the AIDS conference in Durban 2016 and highlights some of our research, including our treatment as prevention trial (TasP) as well our phylogenetic analysis (de Oliveira et al. Lancet HIV 2016).


Rega Institute & Korea University College of Medicine

21st International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME)

Rega Institute & Korea University College of Medicine - 2016-03-15

The 21st International Workshop on Virus Evolution and Molecular Epidemiology (VEME2016) will be hosted by the Korea University College of Medicine, 14-19 August, Seoul, Republic of Korea. Abstract deadline: 15 March 2016


WTAC & MRC Flagship UKZN

Research travel grants: Doctoral or post-doctoral students to Wellcome Trust Africa Centre, South Africa

WTAC & MRC Flagship UKZN - 2015-08-15

Introduction: This is an excellent opportunity for outstanding and motivated individuals to access one of the most comprehensive population-based HIV surveillance and genomics datasets in the world at the Wellcome Trust Africa Centre for Health and Population Studies based in KwaZulu-Natal, South Africa.


Science

MOLECULAR EPIDEMIOLOGY: HIV family trees reveal viral spread.

Science - 2015-06-12

By John Cohen, Science, 12 June 2015. New studies could aid public health efforts. Last week at the New York Academy of Sciences in New York City, researchers, public health specialists, and HIV/AIDS advocates discussed how to exploit the potential of the technique, called phylogenetic analysis - and the thorny ethical and legal issues it raises...


UNAIDS

Feature story: Understanding HIV through phylogenetic research

UNAIDS - 2015-06-08

Phylogenetic research 'the analysis of molecular sequencing data to study evolutionary relationships among groups and organisms' needs to be scaled up to end the AIDS epidemic, according to the participants at a symposium held on 4 June at the New York Academy of Sciences called HIV 2015: Using Phylogenetics to Enhance the HIV Response.


New York Academy of Sciences

HIV 2015: Using Phylogenetics to Enhance the HIV Response, New York, June 4, 2015

New York Academy of Sciences - 2015-06-04

A discussion meeting presented by the Joint United Nations Programme on HIV/AIDS (UNAIDS) and the Microbiology & Infectious Diseases Discussion Group at the New York Academy of Sciences on the use of phylogenetics to enhance HIV response.


WTAC & MRC Flagship UKZN

Seminar: Near Full Length Sequencing to Understand HIV & TB Epidemics In Africa In Real Time

WTAC & MRC Flagship UKZN - 2015-04-30

The Wellcome Trust Africa Centre Genomics & Bioinformatics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Prof. Tulio de Oliveira, 30 April 2015, K-RITH building, Nelson R Mandela School of Medicine, Durban, South Africa


UKZN

Ground-breaking PhD Study helps Rural Doctors monitor HIV Drug Resistance

UKZN - 2015-04-17

Dr Justen Manasa graduated with a PhD after completing ground-breaking research in the Hlabisa District of KwaZulu-Natal that resulted in a low cost genotyping method envisaged to help doctors monitor and evaluate drug resistance among HIV-infected patients in resource-limited settings.


Illumina User Meeting

Our genomics and bioinformatics research program was selected as a keynote presentation in the 1st South African Illumina User Group Meeting, 2015

Illumina User Meeting - 2015-03-31

By: Tulio de Oliveira, Franschoek, South Africa, 31 March 2015 - Continuing advances in next generation genomic analysis are rapidly changing the way we approach our research. The setup of our high-throughput genomics facility at the Nelson R Mandela School of Medicine, in collaboration with Africa Centre and Health and Population Studies allowed our research group to produce HIV-1 complete genomes at an unprecedented scale.


SATuRN & Harvard

Doris Duke Annual Seminar for Medical Students from Harvard and UKZN

SATuRN & Harvard - 2014-10-09

Each year during AWAAC, the Doris Duke International Research Fellowship at Harvard Medical School sponsors a special seminar for medical students who will be attending the conference. During the seminar, invited faculty members discuss journals article that they select with a group of medical students from the US who are engaging in research in sub-Saharan Africa and a group of South African medical students from UKZN. This year 20-25 students will attend the seminar.


WTAC, UCL, LSHTM & UKZN

Postdoc Fellowship available - HIV Genomics & Bioinformatics I

WTAC, UCL, LSHTM & UKZN - 2014-07-26

We invite applications from ambitious post doctoral scientists, to undertake research in a Flagship programme of the Wellcome Trust & MRC in South Africa.This Fellowship aims to apply and develop bioinformatics software applications to analyze large datasets of complete HIV-1 genomes.


WTAC, UCL, LSHTM & UKZN

Postdoc Fellowship available - HIV Bioinformatics & Phylogenetics II

WTAC, UCL, LSHTM & UKZN - 2014-07-26

We invite applications from ambitious post doctoral scientists, to undertake research in a Flagship programme of the Wellcome Trust & MRC in South Africa.This Fellowship aims to develop and/or apply phylogenetic software applications to create a framework to identify epidemiologically important HIV strains.


WTAC, UKZN, FioCruz, CNPQ

Postdoc Fellowship available - HIV & HTLV Bioinformatics & Phylogenetics III

WTAC, UKZN, FioCruz, CNPQ - 2014-07-26

We invite applications from ambitious post doctoral scientists, to undertake research in a collaborative programme of the the Wellcome Trust Africa Centre and the FioCruz Foundation in South Africa and Brazil.This fellowship aims to apply and develop bioinformatics software applications to analyze large datasets of HIV-1 and HTLV-1 complete genomes


SATuRN

SATuRN Newsletter, Jul 2014: Annual HIVDR Workshop, News, Publications & Blogs

SATuRN - 2014-07-24

The newsletter idea is that anyone with 15 minutes to spare can learn about our work and its application in everyday life. In our second issue of 2014 (Vol. 3 Num. 2), we advertise our annual workshop, which will be presented as part of the Annual Workshop on Advanced Clinical Care - AIDS (AWACC), Durban, 8-9 Oct 2014. We also included interesting news, blogs and publications produced by our network and partners.


WT Africa Centre, UCL & LSHTM

Postdoctoral Research Fellows in HIV

WT Africa Centre, UCL & LSHTM - 2014-07-17

We invite applications from ambitious clinical or non-clinical postdoctoral scientists, to undertake research in a Flagship programme of the Wellcome Trust & MRC in South Africa


UKZN

Inaugural Lecture: Bioinformatics, Genomics and HIV Research in Africa: A Brief Personal History

UKZN - 2014-07-14

The Vice-Chancellor and Principal Professor Malegapuru Makgoba cordially invites you and your spouse/partner to attend an inaugural lecture presented by Professor Tulio de Oliveira, 30 July 2014, K-RITH, Durban


WTAC & MRC Flagship UKZN

Seminar: Genomics & Bioinformatics: The need to engage biologists, mathematicians & computer scientists.

WTAC & MRC Flagship UKZN - 2014-06-25

The Wellcome Trust Africa Centre Genomics Programme, the UKZN MRC Flagship project and School of Mathematics, Statistics and Computer Science, UKZN, cordially invites you to a seminar presented by Prof. Tulio de Oliveira, 7 July 2014, UKZN, Pietermaritzburg, South Africa


WTAC & MRC Flagship UKZN

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

WTAC & MRC Flagship UKZN - 2014-01-15

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Prof. Tulio de Oliveira, 15 January 2014, Africa Centre headquarters, Mtubatuba


UVRI

Bioinformatics in the Tropics Uganda 2014, UVRI, Entebbe, Uganda, 7th to 10th April 2014

UVRI - 2014-01-06

This is a series of four workshops, which will be presented in Brazil (2013 & 2014), South Africa (2013) and Uganda (2014) as part of a south to south capacity building programme to develop the next generation of bioinformaticians in Africa and Latin America. The objective is to train post-doctoral researchers to become trainers and post-graduate students to use bioinformatics and phylogenetic software applications needed for their research.


Mail & Guardian

SA Medical Research Council Scientific Awards

Mail & Guardian - 2013-12-08

In his address to MRC award and grant winners at a prestigious ceremony in Cape Town, outgoing MRC Chairperson Professor Lizo Mazwai described the South African Medical Research Council (MRC) as 'richer, more focused, more efficient and better placed to deliver a healthy nation through research.'


Sunday Times

Heroes in the battle for health

Sunday Times - 2013-12-01

There have been major successes in the fight agains the disease since it was first identified in 1983. Bianca Capazorio speaks to some young South Africans at the forefront of work in the field.


UKZN

Putting the I into HIV - World Aids Day UKZN

UKZN - 2013-11-30

Leading scientists in HIV/AIDS research discussed the diversity of the HIV epidemic, new scientific evidence and the promising interventions on the horizon to tackle it.


K-RITH

'An HIV-1 vaccine is possible' says Prof Thumbi Ndung'u at UKZN AIDS Day 2013

K-RITH - 2013-11-29

Ahead of World AIDS Day 2013, leading HIV/AIDS researchers in Durban have urged society to focus on insights, innovation and integrity in the journey into an HIV-free future and to put people at the centre of health services.


UFS Press Release

International Workshop in Bloemfontein to Translate Research and Clinical Knowledge into Clinical Practice to Fight HIV & TB Drug Resistance in Africa

UFS Press Release - 2013-11-19

BLOEMFONTEIN, 21 November 2013. Today, a large intentional workshop on HIV & TB drug resistance starts, which will bring some of the top international researchers, clinicians and policy makers to the University of the Free State in order to discuss strategies to manage and prevent drug resistance in Africa.


UKZN, CAPRISA & HEARD

A UKZN panel discussion: Bringing the 'I' into HIV - New approaches in developing person-centred interventions to fight the HIV epidemic

UKZN, CAPRISA & HEARD - 2013-11-08

A UKZN panel discussion on 26 November 2013: 'Bringing the 'I' into HIV - New approaches in developing person-centred interventions to fight the HIV epidemic' as part of World AIDS Day 2013 activities.


SAFM

SAFM Radio Interview with Prof. Tulio de Oliveira on their HIV Drug Resistance and Transmission Research and Award

SAFM - 2013-11-03

Radio interview by Sisanda Jonas at SAfm weekend pmlive show 3 Nov 2013


MRC

The SA Medical Research Council announces funding of R190 million for high impact research projects

MRC - 2013-11-01

The MRC has established a new high-profile R190 million funding opportunity for Medical Schools and Universities to undertake 'Flagship Projects' aimed at addressing South Africa's key health problems. The winning projects, led by some of South Africa's most accomplished scientists, were announced at a media briefing at the MRC in Cape Town on Wednesday evening.


Africa Centre & UKZN DVC

16.5 million rand to convert cutting-edge HIV research in rural South Africa into national policy

Africa Centre & UKZN DVC - 2013-10-31

Professor Salim Abdool Karim and Health Minister, Dr Aaron Motsoaledi, awarded a R16.5 million grant to fight HIV drug resistance and transmission in rural KwaZulu-Natal.


UKZN

Multi-million rand award to UKZN scientists for Cutting-Edge HIV Research

UKZN - 2013-10-30

Professor Frank Tanser and Professor Tulio de Oliveira from UKZN's Africa Centre for health and Population studies were recently awarded a large grant to fight HIV drug resistance and transmission in rural KwaZulu-Natal. The grant, funded by the Medical Research Council (MRC) Flagship Projects is part of the MRC's strategy to sustain vibrant medical research in South Africa.


K-RITH

BioMedical research is undergoing a revolution

K-RITH - 2013-10-25

'Intensive', 'Comprehensive', 'Fulfilling' and 'Exciting' were just some of the words used by students to describe the first Bioinformatics course hosted by the KwaZulu-Natal Research Institute for TB and HIV (K-RITH) in partnership with the US-based Broad Institute and the NIH recently.


SATuRN

Newsletter, Oct 2013: News, blogs, manuscripts & Youtube videos!

SATuRN - 2013-10-01

The concept behind this newsletter is that anyone with 15 minutes to spare can learn about the work of SATuRN. In this third issue of 2013 our newsletter we focus on our digital videos activities. We have also included interesting news, blogs, reports, tweets, publications and training information produced by our network.


Southern African Journal of HIV Medicine

BOOK REVIEW - HIV & TB Drug Resistance & Clinical Management Case Book

Southern African Journal of HIV Medicine - 2013-06-20

by Sigaloff & Hamers, The Southern African Journal of HIV Medicine, Book Review on the HIV & TB Drug Resistance & Clinical Management Case Book by Rossouw, Lessells and de Oliveira


Africa Centre/SATuRN

Bioinformatics in the tropics II: Large data sets analysis workshop: HIV phylogenetics and drug resistance, Durban, South Africa, 23-26 Sept 2013

Africa Centre/SATuRN - 2013-06-02

This is the second workshop of the bioinformatics in the tropics series, which will be presented by the Wellcome Trust Africa Centre for Health and Population Studies at K-RITH at the University of KwaZulu-Natal, Durban, South Africa, 23 to 27 September 2013. The bioinformatics in the tropics series is part of a south to south capacity building programme to develop the next generation of bioinformaticians in Africa and Latin America.


FioCruz

Bioinformatics in the tropics I: 1st International Bioinformatics & Molecular Viral Evolution Workshop, Salvador, Bahia, Brazil, 22-26 July 2013

FioCruz - 2013-06-01

This is the first workshop of the bioinformatics in the tropics series, which will be presented at the Oswaldo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil, 22 to 26 July 2013.


Bioinformatics in the Tropics

Bioinformatics in the tropics workshop series 2013-2014

Bioinformatics in the Tropics - 2013-05-30

This is a series of four workshops, which will be presented in Brazil (2013 & 2014), South Africa (2013) and Uganda (2014) as part of a south to south capacity building programme to develop the next generation of bioinformaticians in Africa and Latin America.


Wellcome Trust

Infectious Disease Genomics and Global Health Wellcome Trust Conference

Wellcome Trust - 2013-05-24

We are pleased to announce that we are presenting at the Sixth Infectious Disease Genomics and Global Health conference, Cambridge, U.K, 16-18 October 2013. The focus of this meeting is the application of genomic technologies to the problems of infectious disease in a global health context.


International Innovation

The Network Marker

International Innovation - 2013-04-22

Drug resistance poses significant potential problems in the fight against HIV and TB, but little is known about how best to tackle it. Dr Tulio de Oliveira heads a network that aims to fill this knowledge gap.


Zululand Observer

Case book tackles HIV and TB drug resistance

Zululand Observer - 2013-04-15

By Jonathan Davis, 15 April 2013 - Researchers from the Africa Centre for Health and Population Research near Mtubatuba have published a important book to help rural doctors, nurses and pharmacists working on the frontline of the country's interlinked HIV and tuberculosis (TB) pandemics manage increasing levels of resistance to the drugs needed to fight the diseases.


University of Pretoria

University of Pretoria and partners launch a book

University of Pretoria - 2013-03-19

By Sanku Tsunke, Pretoria, 19 March 2013. Drug resistance is one of the main challenges confronting HIV and TB programmes in Africa. Facing these challenges requires an understanding of how drug resistance develops, as well as up-to-date knowledge of how to diagnose and manage drug resistance in HIV and TB patients.


PretoriaNews

Casebook aims to curb drug resistance

PretoriaNews - 2013-03-19

Pretoria News - 19 March 2013, DOCTORS from the University of Pretoria (UP) and University of KwaZulu-Natal (UKZN) have stepped up to the challenge of providing a clinical management casebook for health care workers treating patients with HIV and TB drug resistance.


UKZNonline

BOOK ON MANAGEMENT OF HIV AND TB DRUG RESISTANCE LAUNCHED

UKZNonline - 2013-03-16

HIV and TB: Drug Resistance and Clinical Management Case Book - a book co-authored by two academics from the Africa Centre for Health and Population Studies - has been presented to frontline health workers at a workshop in northern KwaZulu-Natal.


UKZN

Transferring Critical Knowledge and Skills to Frontline Medical Personnel Fighting the HIV & TB epidemics in rural South Africa

UKZN - 2013-03-15

UKZN's Africa Centre for Health and Population Studies, based in the College of health Sciences, has once again made huge strides in HIV management. Recently, the Centre's, Dr Richard Lessells and Dr Tulio de Oliveira together with the University of Pretoria's, Dr. Theresa Rossouw; launched a book entitled, 'HIV and TB: Drug Resistance and Clinical Management Case Book'.


Universiteit van Pretoria

Universiteit van Pretoria en vennote stel boek vry oor weerstand teen middels wat gebruik word om MIV en tuberkulose te bekamp

Universiteit van Pretoria - 2013-03-15

Weerstand teen medikasie is een van die belangrikste struikelblokke wat programme om MIV en tuberkulose in Afrika te bestry te bowe moet kom. Om hierdie uitdagings die hoof te bied, word 'n begrip vereis van hoe weerstand teen die middels tot stand kom, sowel as vertroudheid met die jongste metodes om weerstand teen die medikasie in MIV- en tuberkulosepasiente te diagnoseer en bestuur.


Africa Centre

PRESS RELEASE: Book Launch: HIV and TB Drug Resistance & Clinical Management Case Book

Africa Centre - 2013-03-06

Prof Eric Buch, Dean of the Faculty of Health Sciences at the University of Pretoria, in partnership with European Delegation to South Africa, MRC Inflammation and Immunity Unit and the Africa Centre for Health and Population Studies, UKZN, invite members of the media to attend the launch of the 'HIV and TB Resistance & Clinical Management Case Book' that is authored by Dr Theresa Rossouw of UP and Drs Richard Lessells and Tulio de Oliveira of the Africa Centre for Health and Population Studies. The details are as follows:


University of Pretoria

Invitation to the launch of the HIV and TB drug resistance & clinical management case book

University of Pretoria - 2013-03-05

University of Pretoria invites you to attend the launch of the publication HIV and TB resistance & clinical management case book. The invitation is writen in three official South African languages: Afrikaans, English and Sepedi.


Leuven & Univ. Florida

18th International Bioinformatics Workshop on Virus Evolution & Molecular Epidemiology, USA, 25-30 Aug 2013

Leuven & Univ. Florida - 2013-02-27

We are announcing the organization of the international workshop on Virus Evolution and Molecular Epidemiology (VEME) in 2013, hosted by the Emerging Pathogens Institute in the warm city of Gainsville and sponsored by several local partners.


SATuRN

HIV/TB Drug Resistance and Clinical Management Workshop & Book Launch, Ghost Mountain Inn, Mkuze, South Africa, 7-8 Mar 2013

SATuRN - 2013-02-18

Organised by the Africa Centre for Health and Population Studies and Southern African Treatment and Resistance Network (SATuRN) in collaboration with the uMkhanyakude District Health Office. This workshop is aimed at developing knowledge and skills around the prevention and management of drug resistance and treatment failure in both HIV and TB.


The Communication Initiative Network

Comminit News: Scientific Community Engagement Activities in Rural KwaZulu-Natal, South Africa

The Communication Initiative Network - 2012-11-30

BioAfrica, Southern African Treatment and Resistance Network (SATuRN), and the Africa Centre Bioinformatics Unit use art to present scientific facts in Rural KwaZulu-Natal, South Africa. They are involved in many community engagement activities, presenting to African communities about the origin of HIV, the causes and consequences of drug resistance development, and how to successfully manage HIV and tuberculosis (TB) treatment.


SATuRN

HIV and TB bioinformatics presentation and tweet coverage at K-RITH opening, 9-11 October 2012

SATuRN - 2012-10-04

SATuRN is presenting a talk at the KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH) opening. This symposium has a fantastic scientific program, with some of the leading researchers and funders in the world! Please follow our tweeter coverage!


Cape Argus

'Tainted milk' from wet nurse HIV risk

Cape Argus - 2012-08-26

By BIANCA CAPAZORIO - A BABY girl who contracted HIV after being breast-fed by a well-meaning aunt has become the first proven case in SA to have contracted HIV from a surrogate feeder or 'wet nurse'.


Zululand Observer

Local centre proves 'surrogate' HIV infection

Zululand Observer - 2012-08-24

The Africa Centre for Health and Population Studies, Zululand's HIV-AIDS research hub based near Mtubatuba, has revealed the first proven HIV surrogate transmission case in South Africa.


Wellcome Trust

DNA sequencing confirms HIV transmission through surrogate breastfeeding

Wellcome Trust - 2012-08-23

DNA sequencing has provided evidence of HIV-1 transmission from an infected woman breastfeeding her niece in South Africa, drawing attention to infant feeding practices and the need for HIV testing of all breastfeeding surrogates as well as mothers.


SABC

Breastfeeding in the spotlight

SABC - 2012-08-16

A case where an aunt infected her niece with HIV through breastfeeding has drawn attention to feeding practices in South Africa. The case was published in the medical journal Lancet and highlighted the risk of HIV transmission from a surrogate carer, the Africa Centre for Health and Population Studies said today.


LabMedica

Collaboration to Undertake HIV Resistance Testing in Africa

LabMedica - 2012-08-06

Sequencing-based diagnostics for human immunodeficiency virus (HIV)-infected individuals will be carried out in Africa in order to determine resistance to antiretroviral drugs.


CAPRISA

Creating access to HIV/TB drug resistance testing

CAPRISA - 2012-08-01

During July, the acclaimed researcher, Dr Tulio de Oliveira from the Southern African Treatment Research Network (SATuRN), was invited to CAPRISA to visit CAPRISA's eThekwini Clinical Research Site. He also presented latest developments on affordable HIV and TB drug resistance testing and open access, public, drug resistance databases to CAPRISA's management team, followed by discussions on possible opportunities for collaboration.


GenomeWeb

Life Tech, SATuRN Collaborate on Dx for Antiretroviral Resistance in HIV in Africa

GenomeWeb - 2012-07-26

NEW YORK (GenomeWeb News) - Life Technologies today announced a collaboration with the Southern African Treatment and Resistance Network (SATuRN) covering sequencing-based diagnostics for HIV patients in Africa.


The Wall Street Journal

Life Technologies and SATuRN Collaborate to Increase Access to HIV Testing in Africa

The Wall Street Journal - 2012-07-24

Life and Southern African Treatment and Resistance Network (SATuRN) Partner in Sequencing-Based Surveillance of Drug Resistance


BioAfrica

BioAfrica Art & Science section is open!

BioAfrica - 2012-05-10

In this exciting new section of bioafrica.net art we feature creative projects that celebrate, investigate and/or communicate biomedical science. Here, we share blogs, news articles, tweets, audio and audiovisual media to increase public awareness of innovative collaborations between art and science.


BioAfrica

SATuRN Newsletter Vol. 1 Number 1, Jan-Mar 2012

BioAfrica - 2012-04-15

The newsletter idea is that anyone with 15 minutes to spare can learn about our work and its application in everyday life.


IAS

Transmitted Drug Resistance Rate Remains Below 5% in South Africa

IAS - 2012-03-05

by Mark Mascolini - Analysis of South Africans with newly diagnosed, untreated HIV infection indicates low levels of transmitted antiretroviral-resistant HIV across the country through 2010 and no evidence of transmitted drug-resistant HIV in rural KwaZulu Natal


UKZN

Highly Specialized Team to Tackle HIV Drug Resistance Problem in Southern Africa

UKZN - 2012-02-22

DURBAN, SOUTH AFRICA, 24-26 FEB 2012 - A small, highly specialized multidisciplinary team of doctors and statisticians from South Africa, Botswana, the USA and the UK will meet in Durban this weekend with the express purpose of pooling their resources, knowledge and expertise in an attempt to improve understanding the problem of HIV drug resistance in southern Africa.


CDC - South Africa

Meeting to Discuss the Growing Threat of HIV & TB Drug Resistance in South Africa and Botswana

CDC - South Africa - 2011-11-04

JOHANNESBURG - A group of renowned HIV and TB scientists, public health officials and physicians will meet at the University of Botswana in Gaborone, this coming Monday and Tuesday (7th & 8th of November) to discuss the growing problem of HIV and TB drug resistance in southern Africa.


Die Burger

Believe in ART, get tested please

Die Burger - 2008-09-10

CAPE TOWN - Believe that anti-retroviral treatment (ART) medication works and get yourself tested. People who are infected with the virus are able to live longer, healthier lives, provided they use their medication and seek treatment early enough. This was the key message Dr. Tulio de Oliveira, a bio-informatics researcher from SATuRN wanted to be convey to the general public.


Nature

High noon in Libya

Nature - 2007-07-19

This week sees yet another crisis point in the Libyan case of six foreign health professionals sentenced to death on charges of injecting hundreds of children with HIV. Declan Butler traces the efforts of scientists to help establish the truth.


Cape Times

World-class scientist due to join UWC team tackling HIV/Aids treatment in SA.

Cape Times - 2007-01-14

CAPE TOWN - A world-class molecular biologist whose research on HIV and anti-retrovirals (ARVs) could dramatically improve the treatment of HIV/Aids in South Africa. Doctor Tulio de Oliveira, an expert in bioinformatics at Oxford University, will join the SA National Bioinformatics Institute at UWC.


Science

Genetic Analysis Clears Accused Medics

Science - 2006-12-20

A new molecular study provides the strongest scientific evidence yet that six foreign medics held in Libya are innocent of charges that they deliberately infected more than 400 children with HIV. Accumulated mutations in the virus genomes reveal that the outbreak began well before the medics arrived in the country. The Libyan supreme court is set to decide on 19 December whether to execute the medics. It is unclear whether the new study will influence its verdict.


New Scientist

New evidence in Libyan HIV trial

New Scientist - 2006-12-20

New and compelling scientific evidence has emerged in support of five Bulgarian nurses and a Palestinian doctor accused of deliberately spreading HIV to 426 Libyan children in 1998.


BBC

Libya sentences medics to death

BBC - 2006-12-19

A Libyan court has sentenced five Bulgarian nurses and a Palestinian doctor to death for knowingly infecting hundreds of Libyan children with HIV.


The Guardian

Medics face death while Libya uses HIV children as diplomatic pawns

The Guardian - 2006-12-17

Alex Duval Smith The Observer, Sunday 17 December 2006 13.12 GMT - The death in Libya six weeks ago of nine-year-old Marwa Annouiji from Aids was much more than just another developing world statistic. In her short, life, dominated by illness, the frail child was a pawn in a high-level game of international relations. Marwa, from al-Bayda on the Mediterranean coast, was the 52nd Libyan child to die as a result, Libya claims, of a deliberate operation by foreign medical workers to pump HIV-infected blood into 426 girls and boys at the al-Fatah Hospital in Benghazi.


University of Oxford - BluePrint News

New scientific evidence in Libya HIV death penalty case

University of Oxford - BluePrint News - 2006-12-07

OXFORD - New molecular evidence from Oxford Zoology Department casts significant doubt on charges against six medical workers who are facing execution in Libya. The medical workers are charged with deliberately contaminating more than 400 children with HIV in 1998.However, new evidence published online in Nature from the Evolutionary Biology Group at Oxford, in collaboration with several European universities, shows that the subtype of HIV involved began infecting patients well before the medical workers arrived in Libya.


NY Times

New Evidence Disputes Libya Case in H.I.V. Trial

NY Times - 2006-12-07

LONDON, Dec. 6 (Reuters) - Scientists have produced new evidence that casts doubt on charges against five Bulgarian nurses and a Palestinian doctor accused by Libya of deliberately infecting 426 children with the virus that causes AIDS in 1998.


BBC

Study backs Libya HIV case medics

BBC - 2006-12-06

LONDON - Scientists have cast doubt on charges that five Bulgarian nurses and a Palestinian doctor deliberately infected Libyan children with HIV. The medics could face the death penalty if found guilty by a court in Tripoli later this month.


Nature

Molecular HIV evidence backs accused medics

Nature - 2006-12-06

International experts in DNA forensics say that a paper published online by Nature this week provides a firm alibi for the six medical workers facing the death penalty in Libya. The workers have been charged with deliberately infecting more than 400 children with HIV in 1998.



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