HTLV-1 Genetic Diversity of 52 Complete Sequences from 14 African Countries Reveals Novel Variants and Lack of Typical P12/P8 and P30 Accessory Proteins in HTLV-1b, d and f Genotypes. > Cassar et al, 2026

texts : complete sequences generated in the manuscript + alignment of complete PTLV genomesHigh-resolution figuresFigure 2 – Phylogenetic tree based on the alignment of concatenated gag-pro-pol+env+tax genesPhylogenetic analysis is based on a 6,915-bp alignment of concatenated gag-pro-pol+env+tax genes, using PhyML in SeaView, with the Tam-Nei model (TN93+I+G). Rearrangements using NNI and SPR are used.Figure 3 – Phylogenetic tree of PTLV-1 based on the alignment of complete LTR sequencesPhylogenetic analysis is based on a 774-bp alignment of complete LTR, using PhyML in SeaView, with the GTR+I+G model. Rearrangements using NNI and SPR are used.Figure 5 – Phylogenetic tree of PTLV-1 based on the alignment of partial LTR sequencesPhylogenetic analysis is based on a 544-bp alignment of partial LTR, using PhyML in SeaView, with the GTR+I+G model. Rearrangements using NNI and SPR are used.