HIV-1 envelope sequence comparison and coreceptor usage. HIV-1 envelope gene was amplified from infected individuals and subjected to sequencing as described in the text. Only the V3 loop region sequences with short flanking constant regions are shown with their accession numbers, their subtype assignment and possible co-receptor usage. Dots in the sequence indicate identity with consensus C, B, 02_AG and A sequences; asterisk indicates identical amino acids; single dot at the bottom of four groups of samples represents semi-conserved substitution of amino acids and double dots represent conserved substitution. Subtypes were determined using Viral Genotyping Tool, REGA Subtyping Tool and RIP 3.0 with maximum blast identity.