Extended Data Table 1 The genetic distance measured between the haplotypes in the Gag or Pol regions of HIV-1

From: Persistent HIV-1 replication maintains the tissue reservoir during therapy

  1. We used sequence data from the Gag or Pol regions (protease (Pol1) and reverse transcriptase (Pol2)) of HIV-1 (range, 315–487 bp) to perform a genetic distance analysis. We masked the guanosines in APOBEC3 trinucleotide contexts of the edited sites from the alignments. We compared the proportion of substitutions per site (p-distance) for haplotypes within lymph node (LN) or peripheral blood (PB) from each subject at 6 months to the most common haplotype present at day 0. Most comparisons were statistically significant (Mann–Whitney U test, P-values <0.1), indicating ongoing diversification of the viral populations.
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