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. 2002 Jan;76(2):851–864. doi: 10.1128/JVI.76.2.851-864.2002

FIG. 1.

FIG. 1.

Amino acid alignment of 29 genetic populations identified in the HIV-1/JC499-P0 stock. The consensus sequence at the top of the alignment was generated from the 104 sequences of all populations defined by specific V4-plus-V5 combinations. For seven populations for which there were multiple clones, consensus sequences were used in the alignment and are indicated by the number of clones shown in parentheses. Consensus sequences with open circles to the left were generated from sequences in both the HIV-1/JC499-P1 stock and cultured PBMC. Individual sequences, for which clone numbers are given, are shown for the remaining populations in the alignment. Solid circles to the left of population designations identify previously reported sequences (52). Dots denote identity with the consensus sequence, while dashes represent deletions or gaps introduced to optimize alignments. Question marks in the consensus sequence indicate sites at which fewer than 50% of the sequences share the same amino acid residue. Asterisks denote in-frame stop codons. The hypervariable V3, V4, and V5 regions of the HIV-1 envelope are underlined.