Kiwelu, Ireen E.Novitsky, VladimirMargolin, LaurenBaca, JeannieManongi, RachelSam, NoelShao, JohnMcLane, MaryKapiga, Saidi H.Essex, M.2014-03-012013Kiwelu, Ireen E., Vladimir Novitsky, Lauren Margolin, Jeannie Baca, Rachel Manongi, Noel Sam, John Shao, Mary F. McLane, Saidi H. Kapiga, and M. Essex. 2013. “Frequent Intra-Subtype Recombination among HIV-1 Circulating in Tanzania.” PLoS ONE 8 (8): e71131. doi:10.1371/journal.pone.0071131. http://dx.doi.org/10.1371/journal.pone.0071131.1932-6203http://nrs.harvard.edu/urn-3:HUL.InstRepos:11855755The 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.en-USBiologyPopulation BiologyEpidemiologyInfectious Disease EpidemiologyMedicineClinical Research DesignCohort StudiesProspective StudiesInfectious DiseasesViral DiseasesHIVHIV epidemiologyRetrovirology and HIV immunopathogenesisObstetrics and GynecologyGenitourinary InfectionsUrologyJournal Article2014-03-0110.1371/journal.pone.0071131