Viral Diversity and Diversification of Major Non-Structural Genes vif,

To assess the level of intra-patient diversity and evolution of HIV-1C non-structural genes in primary infection, viral quasispecies obtained by single genome amplification (SGA) at multiple sampling timepoints up to 500 days postseroconversion (p/s) were analyzed. The mean intra-patient diversity was 0.11% (95% CI; 0.02 to 0.20) for vif, 0.23% (95% CI; 0.08 to 0.38) for vpr, 0.35% (95% CI;20.05 to 0.75) for vpu, 0.18% (95% CI; 0.01 to 0.35) for tat exon 1 and 0.30% (95% CI; 0.02 to 0.58) for rev exon 1 during the time period 0 to 90 days p/s. The intra-patient diversity increased gradually in all nonstructural genes over the first year of HIV-1 infection, which was evident from the vif mean intra-patient diversity of 0.46% (95% CI; 0.28 to 0.64), vpr 0.44% (95% CI; 0.24 to 0.64), vpu 0.84% (95% CI; 0.55 to 1.13), tat exon 1 0.35% (95% CI; 0.14 to 0.56 ) and rev exon 1 0.42% (95% CI; 0.18 to 0.66) during the time period of 181 to 500 days p/s. There was a statistically significant increase in viral diversity for vif (p = 0.013) and vpu (p = 0.002). No associations between levels of viral diversity within the non-structural genes and HIV-1 RNA load during primary infection were found. The study details the dynamics of the non-structural viral genes during the early stages of HIV-1C infection. Citation: Rossenkhan R, Novitsky V, Sebunya TK, Musonda R, Gashe BA, et al. (2012) Viral Diversity and Diversification of Major Non-Structural Genes vif, vpr, vpu, tat exon 1 and rev exon 1 during Primary HIV-1 Subtype C Infection. PLoS ONE 7(5): e35491. doi:10.1371/journal.pone.0035491 Editor: Sylvie Le Gall, Massachusetts General Hospital, United States of America Received January 4, 2012; Accepted March 16, 2012; Published May 9, 2012 Copyright: 2012 Rossenkhan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The primary HIV-1 subtype C infection study in Botswana, the Tshedimoso study, was supported by NIH grant R01 AI057027. This work was supported in part by a Research Grant from the Office of Research and Development (ORD), University of Botswana (TKS). This work was also supported in part by the AAMC FIC (Association of American Medical Colleges Fogarty International Centre)/Ellison Overseas Fellowships in Global Health and Clinical Research (RR) and by the NIH grant D43 TW000004 (RR). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected]