Frequent intra-subtype recombination among HIV-1 circulating in Tanzania

• Published in: PloS one 2013-08, Vol.8 (8), p.e71131-e71131
• Main Authors: Kiwelu, Ireen E, Novitsky, Vladimir, Margolin, Lauren, Baca, Jeannie, Manongi, Rachel, Sam, Noel, Shao, John, McLane, Mary F, Kapiga, Saidi H, Essex, M
• Format: Article
• Language: English
• Subjects: Acquired immune deficiency syndrome; Adult; AIDS; Analysis; Bioinformatics; Biology; Breakpoints; Cohort Studies; Deoxyribonucleic acid; DNA; Epidemics; Female; Gene Frequency; Gene sequencing; Genes, env; Genetic Variation - physiology; Genomes; Genomics; Glycoprotein gp120; Health aspects; HIV; HIV Envelope Protein gp120 - genetics; HIV infections; HIV Infections - epidemiology; HIV Infections - virology; HIV-1 - genetics; Human immunodeficiency virus; Humans; Identification; Immunology; Infectious diseases; Medicine; Phylogenetics; Public health; Recombination; Recombination, Genetic; Reproductive health; Studies; Tanzania - epidemiology; Viral Load; Virology; Viruses; Womens health; Workers
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0071131

The study estimated the prevalence of HIV-1 intra-subtype recombinant variants among female bar and hotel workers in Tanzania. While intra-subtype recombination occurs in HIV-1, it is generally underestimated. HIV-1 env gp120 V1-C5 quasispecies from 45 subjects were generated by single-genome amplification and sequencing (median (IQR) of 38 (28-50) sequences per subject). Recombination analysis was performed using seven methods implemented within the recombination detection program version 3, RDP3. HIV-1 sequences were considered recombinant if recombination signals were detected by at least three methods with p-values of ≤0.05 after Bonferroni correction for multiple comparisons. HIV-1 in 38 (84%) subjects showed evidence for intra-subtype recombination including 22 with HIV-1 subtype A1, 13 with HIV-1 subtype C, and 3 with HIV-1 subtype D. The distribution of intra-patient recombination breakpoints suggested ongoing recombination and showed selective enrichment of recombinant variants in 23 (60%) subjects. The number of subjects with evidence of intra-subtype recombination increased from 29 (69%) to 36 (82%) over one year of follow-up, although the increase did not reach statistical significance. Adjustment for intra-subtype recombination is important for the analysis of multiplicity of HIV infection. This is the first report of high prevalence of intra-subtype recombination in the HIV/AIDS epidemic in Tanzania, a region where multiple HIV-1 subtypes co-circulate. HIV-1 intra-subtype recombination increases viral diversity and presents additional challenges for HIV-1 vaccine design.