Table 1.
Samples Information.
Table 2.
The genetic distances to M130805 within three genes regions.
Fig 1.
Neighbor-joining phylogenetic tree of consensus sequences from the man, the woman and local controls.
A, Neighbor-joining phylogenetic tree for consensus gag sequences and reference sequences. The scale bar indicates 5% nucleotide sequence divergence. B, Neighbor-joining phylogenetic tree for consensus pol sequences and relative reference sequences. The scale bar indicates 5% nucleotide sequence divergence. C, Neighbor-joining phylogenetic tree for consensus env sequences and relative reference sequences. The scale bar indicates 10% nucleotide sequence divergence. Values on the branches represent the percentage of 1000 bootstrap replicates and bootstrap values over 70% are shown in the tree. Red triangle: the sequence from the male source; Green triangle: the sequences from the female recipient.
Fig 2.
Bootscanning analysis of possible intertype mosaicism.
Window: 80 bp, step: 10 bp, GapStrip: on, reps: 100, Kinura (2-parameter), T/t: 2.0. The reference sequences are shown at the bottom right of the figure.
Table 3.
The genetic distances of env quasispecies.
Fig 3.
Maximum clade credibility (MCC) tree for env quasispecies from the subjects.
The MCC trees were obtained by Bayesian MCMC analysis based on partial env gene (HXB2: 7002–7541) implemented in BEAST. The uncorrelated exponential relaxed molecular clock method was used in combination with the Bayesian Skyline coalescent tree prior under GTR+I+G4 nucleotide substitution model. Red taxon: the viral quasispecies from the man; Green taxon: the viral quasispecies from the woman. The posterior probabilities of the key nodes are indicated. The most recent common ancestor of sequences from the man is shown by a filled circle. The scale bar indicates 5% nucleotide sequence divergence.