Phylogenetic tree from 362 nucleotides of CA gag alignment. The tree was inferred using the neighbor-joining distance method and Kimura's two-parameter model. Shown are bootstrap values of 1,000 replicates. Bootstrap values greater than 70% are shown. Circles represent isolates from location A (black circles represent cats undergoing treatment), pentagons represent isolates from location B, triangles represent isolates from location C, lozenges represent isolates from location D, and squares represent isolates from location E. The horizontal bar indicates the nucleotide substitution scale.

Phylogenetic tree from 487 nucleotides of V3-V4 env alignment. The tree was inferred as described in the legend to Fig. 1. The symbols used in this figure represent different regions and treatment statuses as depicted in Fig. 1.

Alignment of RT pol by position related to TM2 genome. Shown are positions 2415 to 2968 (554 bp; amino acids 26 to 209). For the HXB2 HIV-1 isolate shown at the top, positions K65R and K70R of HIV-1 are highlighted in italics and boxed with their FIV RT counterparts. Amino acids are represented by the IUPAC one-letter code. Dots in the alignment represent similar amino acids to the TM2 sequence at each position. Dashes represent sequence gaps (related to the HIV-1 HXB2 sequence). Numbers over the sequences represent the actual position of the amino acid in the original RT sequence. Ambiguities at certain positions of a single sequence are shown by two amino acids separated by a dash.

Phylogenetic tree from 554 nucleotides of RT pol alignment. The tree was inferred as described in the legend to Fig. 1. The symbols used in this figure represent different regions and treatment statuses as depicted in Fig. 1.

Box plot representation of genetic distances found within each subtype group analyzed. Values above the bars represent the overall mean of genetic distance found in each group. Dashed lines indicate 2.0% genetic distance. The sequence isolates used are shown in each box plot. (A) CA region. The following samples were used: subtype A (Sub A), Petaluma, PPR, and Sendai1; subtype B from Japan (Sub B JP), Sendai2, TM2, Yokohama, Aomori1, and Aomori2; subtype B from Japan and from the United States (Sub B JP/US), Sendai2, TM2, Yokohama, Aomori1, Aomori2, and USIL2489_7B; subtype B from Brazil (Sub B BR), RJ01, RJ02, RJ03, RJ04, RJ05, RJ06, RJ07, RJ08, RJ09, RJ10, RJ11, RJ12, RJ13, RJ14, RJ15, RJ16, RJ17, RJ18, RJ19, RJ20, RJ21, RJ22, RJ23, RJ24, RJ34, and RJ35; subtype C from Canada (Sub C CA), C and C36; subtype C from Taiwan (Sub C Ti), Ti1 and Ti3; subtype C from Canada and Taiwan (Sub C all), C, C36, Ti1, and Ti4; subtype D (Sub D), Shizuoka and Fukuoka; and subtype E (Sub E), LP20E, LP24E, and LP3E. (B) RT region. The following samples were used: Sub A, Petaluma and PPR; Sub B JP/US, TM2 and USIL2489_7B; Sub B BR, RJ01, RJ02, RJ03, RJ04, RJ05, RJ06, RJ07, RJ08, RJ09, RJ10, RJ11, RJ12, RJ13, RJ14, RJ15, RJ16, RJ17, RJ18, RJ19, RJ20, RJ21, RJ22, RJ23, RJ24, RJ34, and RJ35; subtype C from Canada (Sub C), C and C36. (C) V3-V4 region. The following samples were used: Sub A, Petaluma, PPR, and Sendai1; Sub B JP, Sendai2, TM2, Yokohama, Aomori1, and Aomori2; subtype B from the United States and Italy (Sub B US/IT), M2, M3, and USIL2489_7B; Sub B BR, RJ01, RJ02, RJ03, RJ04, RJ05, RJ06, RJ07, RJ08, RJ09, RJ10, RJ11, RJ12, RJ13, RJ14, RJ15, RJ16, RJ17, RJ18, RJ19, RJ20, RJ21, RJ22, RJ23, RJ24, RJ34, and RJ35; subtype C from Canada (Sub C), C and C36; Sub D, Shizuoka and Fukuoka; and Sub E, LP20E, LP24E, and LP3E.