Figure 1

Consensus sequences of the vif gene of HIV-1. The consensus was obtained from an alignment of 71 sequences containing only subtype B viruses. Open and filled diamonds indicate sites under positive selection. The figure shows positively selected codons detected in non-recombinant (filled diamonds) sequences and detected in hypermutated viruses (open diamonds). The regions linked to Vif protein functions are highlighted in dark grey with white letters within. The BC-Box and the Cullin5-Box are also highlighted (yellow). Dashed grey lines mark regions where cytotoxic T lymphocytes (CTL) epitopes were previously identified in the Vif protein (http://www.hiv.lanl.gov/content/immunology/maps/maps.html). Orange ovals linked by dashed lines indicate epistatic sites associated with CD4+ cell counts detected by permutation test. Blue circles linked by dashed lines indicate co-evolving sites detected by BGM analysis.