Fig. 1

Maximum likelihood phylogenetic tree of 898 pol sequences of HIV-1 in a city in southern Sichuan. 331 HIV-1 sequences were branched with the CRF01_AE reference sequence (depicted in green), 368 HIV-1 sequences were branched with the CRF07_BC reference sequence (depicted in pink), 173 HIV-1 sequences were clustered with the CRF08_BC reference sequence (depicted in purple), and 21 HIV-1 CRF85_BC sequences were identified (depicted in yellow), 3 CRF57_BC sequences (depicted in light blue), 1 CRF64_BC sequence (depicted in dark blue), and 1 CRF55_01B (depicted in dark brown) were also identified—the reference sequences from the Los Alamos HIV sequence database. On the upper edge of the CRF01_AE group, a number of seemingly ambiguous sequences were typed as well as verified and confirmed by the HIV BLAST and RIP functions in the HIV database page, all of which were CRF01_AE.