HIV type 1 subtype C gag and nef diversity in Southern Africa

AIDS Research and Human Retroviruses

Volumn 23, Issue 3, 2007, Pages 477-481

  Bredell, Helba ^a   Martin, Darren P ^a   Van Harmelen, Joanne ^a   Varsanii, Arvind ^a   Sheppard, Haynes W ^b   Donovan, Richard ^b   Gray, Clive M ^c   Williamson, Carolyn ^a  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

^b CALIFORNIA DEPARTMENT OF PUBLIC HEALTH   (United States)

^c NATIONAL INSTITUTE FOR COMMUNICABLE DISEASES   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

GAG PROTEIN; NEF PROTEIN;

AFRICA; ARTICLE; EPIDEMIC; FOUNDER EFFECT; GENE CLUSTER; GENE SEQUENCE; GENETIC RECOMBINATION; GENETIC VARIABILITY; GROUP SPECIFIC ANTIGEN GENE; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MALAWI; NEF GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; TREATMENT FAILURE; VIRUS GENE; ZAMBIA; ZIMBABWE;

AFRICA, SOUTHERN; GENES, GAG; GENES, NEF; HIV INFECTIONS; HIV-1; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; VARIATION (GENETICS);

EID: 34247238154     PISSN: 08892229     EISSN: None     Source Type: Journal    
DOI: 10.1089/aid.2006.0232     Document Type: Article

References (17)

1. Bredell H, Williamson C, Sonnenberg P, Martin DJ, and Morris L: Genetic characterization of HIV type 1 from migrant workers in three South African gold mines. AIDS Res Hum Retroviruses 1998;14:677-684.
2. Novitsky V, Smith UR, Gilbert P, et al.: Human immunodeficiency virus type 1 subtype C molecular phylogeny: Consensus sequence for an AIDS vaccine design? J Virol 2002;76:5435-5451.
3. Mansky LM and Temin HM: Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J Virol 1995;69:5087-5094.
4. Perelson AS, Neumann AU, Markowitz M, Leonard JM, and Ho DD: HIV-1 dynamics in vivo: Virion clearance rate, infected cell life-span, and viral generation time. Science 1996;271:1582-1586.
5. Kelleher AD, Long C, Holmes EC, et al.: Clustered mutations in HIV-1 gag are consistently required for escape from HLA-B27-restricted cytotoxic T lymphocyte responses. J Exp Med 2001;193: 375-386.
6. Wagner R, Leschonsky B, Harrer E, et al.: Molecular and functional analysis of a conserved CTL epitope in HIV-1 p24 recognized from a long-term non-progressor: Constraints on immune escape associated with targeting a sequence essential for viral replication. J Immunol 1999;162:3727-3734.
7. Mashishi T, Loubser S, Hide W, et al.: Conserved domains of subtype C nef from South African HIV type 1-infected individuals include cytotoxic T lymphocyte epitope-rich regions. AIDS Res Hum Retroviruses 2001;17:1681-1687.
8. Addo MM, Yu XG, Rathod A, et al.: Comprehensive epitope analysis of human immunodeficiency virus type 1 (HIV-1)-specific T-cell responses directed against the entire expressed HIV-I genome demonstrate broadly directed responses, but no correlation to viral load. J Virol 2003;77:2081-2092.
9. + T cells: Correlation with viral load. J Virol 2004;78:3233-3243.
10. Edwards BH, Bansal A, Sabbaj S, Bakari J, Mulligan MJ, and Goepfert PA: Magnitude of functional CD8+ T-cell responses to the gag protein of human immunodeficiency virus type 1 correlates inversely with viral load in plasma. J Virol 2002;76:2298-2305.
11. Novitsky V, Gilbert P, Peter T, et al.: Association between virus-specific T-cell responses and plasma viral load in human immunodeficiency virus type 1 subtype C infection. J Virol 2003;77:882-890.
12. Grasso C and Lee C: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics 2004;20:546-1556.
13. Felsenstein J: PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1988;5:164-166.
14. Martin DP, Williamson C, and Posada D: RDP2: Recombination detection and analysis from sequence alignments. Bioinformatics 2005;21:260-262.
15. Schierup MH and Hein J: Consequences of recombination on traditional phylogenetic analysis. Genetics 2000;156:879-891.
16. Posada D and Crandall KA: The effect of recombination on the accuracy of phylogeny estimation. J Mol Evol 2002;54:396-402.
17. Kumar S, Tamura K, and Nei M: MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinf 2004;5:150-163.