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Nucleotide insertions and deletions in the V1 loop arise after 18 weeks in TP2. The frequency of haplotypes was determined from deep sequence reads of each sample spanning Env amino acid residues 115 to 144 and assembled to the SIVmac239 reference sequence. Inoculum haplotypes were observed in the source inoculum and/or during infection, in contrast to haplotypes only observed during infection of individual animals.
