title: Molecular characteristics of human immunodeficiency virus type 1 subtype C viruses from KwaZulu-Natal, South Africa: implications for vaccine and antiretroviral control strategies.
abstract: The KwaZulu-Natal region of South Africa is experiencing an explosive outbreak of human immunodeficiency virus type 1 (HIV-1) subtype C infections. Understanding the genetic diversity of C viruses and the biological consequences of this diversity is important for the design of effective control strategies. We analyzed the protease gene, the first 935 nucleotides of reverse transcriptase, and the C2V5 envelope region of a representative set of 72 treatment-naïve patients from KwaZulu-Natal and correlated the results with amino acid signature and resistance patterns. Phylogenetic analysis revealed multiple clusters or "lineages" of HIV-1 subtype C that segregated with other C viruses from southern Africa. The same pattern was observed for both black and Indian subgroups and for retrospective specimens collected prior to 1990, indicating that multiple sublineages of HIV-1 C have been present in KwaZulu-Natal since the early stages of the epidemic. With the exception of three nonnucleoside reverse transcriptase inhibitor mutations, no primary resistance mutations were identified. Numerous accessory polymorphisms were present in the protease, but none were located at drug-binding or active sites of the enzyme. One frequent polymorphism, I93L, was located near the protease/reverse transcriptase cleavage site. In the envelope, disruption of the glycosylation motif at the beginning of V3 was associated with the presence of an extra protein kinase C phosphorylation site at codon 11. Many polymorphisms were embedded within cytotoxic T lymphocyte or overlapping cytotoxic T-lymphocyte/T-helper epitopes, as defined for subtype B. This work forms a baseline for future studies aimed at understanding the impact of genetic diversity on vaccine efficacy and on natural susceptibility to antiretroviral drugs.
authors.affiliation: HIV-1 Molecular Virology and Bioinformatics Laboratories, Africa Centre for Health and Population Studies and the Nelson R. Mandela School of Medicine, University of Natal, Congella 4013, Durban, South Africa.
authors.forename: M
authors.initials: M
authors.lastname: Gordon
authors.forename: T
authors.initials: T
authors.lastname: De Oliveira
authors.forename: K
authors.initials: K
authors.lastname: Bishop
authors.forename: H M
authors.initials: HM
authors.lastname: Coovadia
authors.forename: L
authors.initials: L
authors.lastname: Madurai
authors.forename: S
authors.initials: S
authors.lastname: Engelbrecht
authors.forename: E
authors.initials: E
authors.lastname: Janse van Rensburg
authors.forename: A
authors.initials: A
authors.lastname: Mosam
authors.forename: A
authors.initials: A
authors.lastname: Smith
authors.forename: S
authors.initials: S
authors.lastname: Cassol
mesh_terms: D016915:AIDS Vaccines; D000328:Adult; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D019380:Anti-HIV Agents / Q000494:pharmacology; D024882:Drug Resistance, Viral / Q000235:genetics; D005260:Female; D015752:Genes, env / Q000235:genetics; D014644:Genetic Variation; D015658:HIV Infections / Q000188:drug therapy / Q000517:prevention & control / Q000821:virology*; D016333:HIV Protease / Q000737:chemistry / Q000235:genetics; D054303:HIV Reverse Transcriptase / Q000737:chemistry / Q000235:genetics; D015497:HIV-1 / Q000145:classification* / Q000187:drug effects / Q000235:genetics*; D006801:Humans; D007223:Infant; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013019:South Africa
chemical_list: D016915:AIDS Vaccines; D019380:Anti-HIV Agents; D054303:HIV Reverse Transcriptase; D016333:HIV Protease