Fig. 1

Phylogenetic analysis of the intra- and inter-patient relationship between clinical C-HIV Envs. The phylogenetic tree was generated with 52 env nucleotide sequences of the Acc65I–BamHI region (corresponding to amino acid positions 6348–8478 of HXB2). This tree confirms that there was no inter-subject mixing of env sequences and that all sequences were subtype C as they clustered with an unrelated C-HIV isolate (C.ET.86.ETH2220.U46016) instead of the out-group sequence HXB2. Red font labels indicate sequences isolated at enrolment (acute infection), blue labels indicate sequences isolated at 1-year post-infection, green labels indicate sequences isolated at 3-years post-infection and black labels indicate control sequences. The scale represents number of nucleotide substitutions per site and numbers on branches indicate bootstrap values