Phylogenetic reconstructions for the assignment of HIV-1 subtypes, including the newly sequenced strain, in Gabon, central Africa. (A) Phylogenetic tree of the partial pol gene constructed with a > 1000-bp fragment (n = 95; range, 1004-1073 bp); (B) phylogenetic tree of reverse transcriptase coding region (n = 2; 785 bp); (C) phylogenetic tree of protease coding region (n = 10; range, 467-479 bp). Dataset of sequences was compiled by combining reference sequences representative of groups M (each pure subtype and commonest CRFs), N and O. The CPZ.US.85.CPZUS (AF103818) strain was used as outgroup to root the trees. The neighbor-joining method was used for the partial pol gene, reverse transcriptase and protease coding regions. Confidence levels were estimated for 1000 replicates, and only bootstrapping values higher than 60% were considered significant.
Caron et al. BMC Infectious Diseases 2012 12:64 doi:10.1186/1471-2334-12-64