HIV-1 Subtypes and Recombinants in Northern Tanzania: Distribution of Viral Quasispecies

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HIV-1 Subtypes and Recombinants in Northern Tanzania: Distribution of Viral Quasispecies

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Title: HIV-1 Subtypes and Recombinants in Northern Tanzania: Distribution of Viral Quasispecies
Author: Kiwelu, Ireen E.; Novitsky, Vladimir A.; Margolin, Lauren; Baca, Jeannie; Manongi, Rachel; Sam, Noel; Shao, John; McLane, Mary Frances; Kapiga, Saidi Hussein; Essex, Myron Elmer

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Citation: Kiwelu, Ireen E., Vladimir Novitsky, Lauren Margolin, Jeannie Baca, Rachel Manongi, Noel Sam, John Shao, Mary F. McLane, Saidi H. Kapiga, and M. Essex. 2012. HIV-1 subtypes and recombinants in Northern Tanzania: distribution of viral quasispecies. PLoS ONE 7(10): e47605.
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Abstract: This study analyzed the distribution and prevalence of HIV-1 subtypes, multiplicity of HIV-1 infection, and frequency of inter-subtype recombination among HIV-1-infected female bar and hotel workers in Moshi, Kilimanjaro Region, Tanzania, from 2004 to 2007. The HIV-1 viral sequences spanning the V1-C5 region of HIV-1 env gp120 were analyzed from 50 subjects by single genome amplification and sequencing (SGA/S) technique. A total of 1740 sequences were amplified and sequenced from the HIV-1 proviral DNA template. The median env sequences analyzed per subject per two time points was 38 (IQR 28–50) over one year of HIV infection. In a subset of 14 subjects, a total of 239 sequences were obtained from HIV-1 RNA template at the baseline visit. The most prevalent HIV-1 subtypes were A1 (56%) and C (30%), while HIV-1 subtype D and inter-subtype recombinant viruses were found in 6% and 8% of subjects respectively. Transmission of multiple HIV-1 variants was evident in 27% of the subjects infected with pure HIV-1 subtypes A1, C, or D. The HIV-1 inter-subtype recombinants were found in 8% including HIV-1 C/A, D/A, and complex mosaic recombinants. Multiple viral variants were found in two subjects infected with inter-subtype recombinants. One subject harbored quasispecies of both pure HIV-1 A1 and C/A recombinant. The other subject was infected with two complex mosaic inter-subtype recombinant variants belonging to subtype D. HIV-1 multiple infections and ongoing recombination contribute significantly to the genetic diversity of circulating HIV-1 in Tanzania and have important implications for vaccine design and the development of therapeutic strategies.
Published Version: doi:10.1371/journal.pone.0047605
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