FIG 1.

Phylogenetic ancestral reconstruction of HIV-1 in North America. (A) Time-scaled maximum-likelihood phylogenetic tree inferred from historic and modern PRRT sequences. The MRCA, representing the epidemic founder virus, is indicated by the black dot at the root. (B) Amino acid alignments of the inferred PRRT (PR, red; RT, blue) MRCA sequence at the root of the tree (ANC), the global HIV-1 subtype B consensus (Los Alamos database; GLOBAL_CONSB), the North American HIV-1 subtype B consensus (Los Alamos database; N.AM_CONSB), the consensus of our historic cohort (HIS_CONS), and the consensus of our modern cohort (MOD_CONS). Note that PRRT codon numbering in the alignment begins from PR and continues through RT; as such, RT 207 is PRRT codon 306.