PUBLICATIONS SPOTLIGHT

PUBLICATIONS

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

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, DOI: 10.1177/135965350801302S09:101-107

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

HIV and hepatitis B co-infection in Africa

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

Effect of the HIV epidemic on liver cancer in Africa

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

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

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

Cervical spine tuberculosis in children

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

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

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

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

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