High prevalence of genetically similar HIV-1 recombinants among infected sex workers in Nairobi, Kenya

• Published in: AIDS research and human retroviruses Vol. 24; no. 11; p. 1455
• Main Authors: Land, Allison M, Luo, Ma, Pilon, Richard, Sandstrom, Paul, Embree, Joanne, Wachihi, Charles, Kimani, Joshua, Plummer, Francis A, Ball, T Blake
• Format: Journal Article
• Language: English
• Published: United States 01.11.2008
• Subjects: Adult; DNA, Viral - chemistry; DNA, Viral - genetics; env Gene Products, Human Immunodeficiency Virus - genetics; Female; Genotype; HIV Infections - epidemiology; HIV Infections - virology; HIV-1 - classification; HIV-1 - genetics; HIV-1 - isolation & purification; Human Immunodeficiency Virus Proteins - genetics; Humans; Kenya - epidemiology; Male; Molecular Sequence Data; Proviruses - classification; Proviruses - genetics; Proviruses - isolation & purification; Recombination, Genetic; Sequence Analysis, DNA; Sex Work; Viral Regulatory and Accessory Proteins - genetics
• ISSN: 1931-8405
• DOI: 10.1089/aid.2008.0179

HIV-1, a highly diverse infectious agent, shows the greatest sequence diversity in highly exposed individuals, including greater levels of recombination. HIV-1 diversity in Nairobi, Kenya was examined in 240 individuals, including both those with high and low exposure to HIV. Sequence analysis of a 590 nucleotide proviral region encompassing vpu and part of env revealed that most viruses were clade A1 (70%), while both clade D (9%) and clade C (6%) virus were also observed, as was recombinant virus (15%). Participation in sex work was significantly associated with clade: these subjects had a lower likelihood of infection with clade C virus and a higher likelihood of infection with a recombinant isolate (p = 0.038). Interestingly, most of the recombinants formed distinct groups based on shared recombination breakpoints between common clades (n = 33/37). This study shows the value of continued HIV sequence analysis to examine and monitor viral genetic variability.