A1 Pairwise diversity and tMRCA as potential markers of HIV infection recency

Intra-host HIV-1 diversity increases linearly over time. We assessed the extent to which mean pairwise distances and the time to the most recent common ancestor (tMRCA) inferred from intra-host HIV-1 C env sequences were associated with the estimated time of HIV infection. Data from a primary HIV-1 C infection study in Botswana were used for this analysis (N = 42). A total of 2,540 HIV-1 C env gp120 V1C5 viral sequences were generated by single genome amplification and sequencing, with an average of sixty-one viral sequences per participant and eleven sequences per time point per participant. Raw pairwise distances were calculated for each time point and participant using the ape package in R software. The tMRCA was estimated using phylogenetic inference implemented in BEAST v1.8.2. Pairwise distances and tMRCA were significantly associated with the estimated time since HIV infection (both P < 0.001). Taking into account multiplicity of HIV infection strengthened these associations. HIV-1 C env-based pairwise distances and tMRCA can be used as potential markers for HIV recency. However, the tMRCA estimates demonstrated no advantage over the pairwise distances estimates.