FIG 6.
Nucleotide repeats are associated with variation in V1 loop of TP1 during early infection. The frequency of haplotypes based on 90-nucleotide windows were determined from deep sequence reads of each sample that spanned the V1 loop region from position 115 to 144 and assembled to the SIVmac239 reference sequence. Haplotypes contained unique amino acid sequences, with inoculum haplotypes being found in the source inoculum and novel haplotypes being found in the viral population of posttransmission longitudinal samples. Haplotypes that contained novel N-linked glycosylation motifs are labeled with a green tree icon.