Viral Diversity and Diversification of Major Non-Structural Genes <em>vif, vpr, vpu, tat</em> exon 1 and <em>rev</em> exon 1 during Primary HIV-1 Subtype C Infection

<div><p>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 post-seroconversion (p/s) were analyzed. The mean intra-patient diversity was 0.11% (95% CI; 0.02 to 0.20) for <em>vif</em>, 0.23% (95% CI; 0.08 to 0.38) for <em>vpr</em>, 0.35% (95% CI; −0.05 to 0.75) for <em>vpu</em>, 0.18% (95% CI; 0.01 to 0.35) for <em>tat</em> exon 1 and 0.30% (95% CI; 0.02 to 0.58) for <em>rev</em> exon 1 during the time period 0 to 90 days p/s. The intra-patient diversity increased gradually in all non-structural genes over the first year of HIV-1 infection, which was evident from the <em>vif</em> mean intra-patient diversity of 0.46% (95% CI; 0.28 to 0.64), <em>vpr</em> 0.44% (95% CI; 0.24 to 0.64), <em>vpu</em> 0.84% (95% CI; 0.55 to 1.13), <em>tat</em> exon 1 0.35% (95% CI; 0.14 to 0.56 ) and <em>rev</em> 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 <em>vif</em> (p = 0.013) and <em>vpu</em> (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.</p> </div>