Fig. 1

Phylogenetic trees of STLV-1 isolates from JMs. Single-nucleotide variants (SNVs) of STLV-1 were analyzed by RAxML, an algorithm that uses the maximum-likelihood method. The trees were drawn using the GTRGAMMA model. Bootstrap values are shown above and to the left of the major nodes. Scale bars indicate the number of SNVs per site. A Phylogenetic tree of STLV-1 and other PTLV sequences. All STLV-1 strains are shown in red. B Phylogenetic tree showing the relationship among STLV-1 strains from different geographical regions. Representative strains of each STLV-1 subcluster are underlined. The accession numbers of the STLV-1 sequences used to construct the trees are A1671 (LC490306), A2213 (LC490307), A2312 (LC490308), A2365 (LC490309), A2437 (LC490310), A2594 (LC490311), A2601 (LC490312), H0168 (LC490313), H0175 (LC490314), H0188 (LC490315), H0548 (LC490316), H0734 (LC490317), M0275 (LC490318), M0279 (LC490319), M0304 (LC490320), M0315 (LC490321), M0317 (LC490322), M0656 (LC490323), M0689 (LC490324), M0725 (LC490325), M0726 (LC490326), M0776 (LC490327), T2297 (LC490328), T2497 (LC490329), T2571 (LC490330), T2589 (LC490331), T2625 (LC490332), T2626 (LC490333), T2635 (LC490334), W1971 (LC490335), W2045 (LC490336), W2171 (LC490337), W2291 (LC490338), W2321 (LC490339), W2478 (LC490340), W2514 (LC490341), W2559 (LC490342), W2566 (LC490343), W2567 (LC490344), W2621 (LC490345), A1916 (LC490346), M0589 (LC490347), M0280 (LC490348), M0309 (LC490349), W1779 (LC490350), HTLV-1A (AB513134), HTLV-1B (JX507077), HTLV-1C (KF242505), baboon STLV-1 (MF621979), Macaca tonkeana STLV-1 (Mto STLV-1: Z46900), Macaca arctoides STLV-1 (Mar STLV-1: AY590142), STLV-2 (NC_001815), STLV-3 (NC_003323), and bovine leukemia virus (BLV) (AF033818)