Figure 2

Phylogenetic analysis of CASE1 HIV-1 gag and env sequences. Viral genome templates corresponding to the near full length gag gene (HXB2 nucleotides 818–2276) and the gp120 coding region of env (HXB2 nucleotides 6229–7786) were PCR amplified from blood plasma and PBMC DNA collected in June and November of 2009, and from PBMC from June 2011, as described in Additional data. PCR products derived from individual viral templates were sequenced directly and analyzed as described in Additional data. PBMC- and plasma (PL)-derived sequences are labeled by date (YYMMDD). Mutations at specific tree branches are tallied as either non-synonymous (NS) or synonymous (S). Two epitopes changed over time in gag (A). The B*57 associated AA substitution I147L in the immunodominant B*57 epitope IW9 was a reversion mutation, resulting in a susceptible, consensus form of the epitope - hence the branch extends from the CASE1 sequences earlier in infection towards the consensus. The TW10 mutation, by contrast, was an escape mutation, with the consensus of all of the Group M viruses being the susceptible form of the epitope - hence the branch extends from the CASE1 sequences earlier in infection away from the consensus. These 2 NS mutations are bolded and noted by a thick arrow between the sequences. NS mutations resulting in two potential N-linked glycosylation sites (PNLGS) were found in env (B). The scale bar below each dendrogram illustrates the branch length formed by mutations corresponding to a 1% change. Amino acid alignments are provided in Additional data.