Nef and Env sequences in SIV_mac239_AAA-infected animals.

Viral RNA was extracted from plasma and subjected to full-length sequencing using an Illumina MiSeq instrument as previously described [64]. The predicted amino acid sequences for Nef (A) and Env (B) at weeks 22 (r12024) and 24 (r12062, r12085 & r11092) post-infection are aligned to the wild-type Nef and Env sequences of SIV_mac239. Positions of amino acid identity are indicated with a period, differences are identified by their single-letter amino acid code, and deletions are indicated with a dash.

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