Table 1.
Primers used for HTLV-1 LTR and p24 PCR and sequencing.
Table 2.
Characteristics of subjects of whom HTLV-1 LTR and/or p24 sequences were obtained from Caió, Guinea-Bissau, 2003–2007.
Figure 1.
ML tree of 630-bp LTR sequences from 48 Caio infected subjects (Caio sequences in red).
Also included are 66 STLV/HTLV-1 reference sequences (in black); Mel5 was used as an outgroup. The names of the countries of origin are denoted in brackets (CAR, Central African Republic). The phylogenetic tree was inferred under a Tamura-Nei evolutionary model with a gamma model of among-site substitution rate heterogeneity. Bootstrap values using 1000 replicates of ≥60 are indicated on the branches. The asterisks indicate significant branch length on ML testing (* p-value≤0.001; ** p-value≤0.05). The scale bar represents the number of nucleotide substitutions per site. The scale of the MarB43 is not on scale because it did not fit in the figure. Sequences identical to Caio4676 are Caio4126, Caio4142, Caio4315, Caio4768, Caio5324, Caio5801, Caio6460, Caio6936 and Caio7120. Sequence identical to Caio4647 is Caio4650. Sequence identical to Caio4799 is Caio4801. Sequences identical to Caio5620 are Caio4743, Caio4745 and Caio5883. Sequences identical to Caio5187 are Caio5846, Caio5884 and Caio5931. Sequences identical to Caio4634 are Caio4635 and Caio5448. Sequences identical to Caio4758 are: Caio4658, Caio4659 and Caio4757. Sequence identical to Caio4671 is Caio4702. Sequences identical to 7580 are 7421 and 7661. Only one example of each set of identical sequences was included in the analysis.
Figure 2.
ML tree of 647-bp p24 sequences from 36 Caio infected subjects (Caio sequences in red).
Also included are 15 STLV/HTLV-1 reference sequences (in black); Mel5 was used as an outgroup. The countries of origin are denoted in brackets (CAR, Central African Republic; NA, not available). The phylogenetic tree was inferred under a Tamura-Nei evolutionary model with a gamma model of among-site substitution rate heterogeneity. Bootstrap values using 1000 replicates of ≥60 are indicated on the branches. The asterisks indicate significant branch length on ML testing (* p-value≤0.001; ** p-value≤0.05). The scale bar represents the number of nucleotide substitutions per site. Sequences identical to Caio4009 are Caio4072, Caio4106, Caio4112, Caio4211, Caio4315, Caio4328, Caio4358, Caio4383, Caio4417, Caio4418, Caio5801, Caio6473, Caio6590, Caio65396 and Caio65407. Sequence identical to Caio65363 is Caio65571. Sequence identical to Caio4258 is Caio65325. Only one example of each set of identical sequences was included in the analysis.