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Sequencing of individually cloned viral cDNA amplicons. At least 10 individual nef amplicons derived from chronic-phase vRNA of each animal were cloned and sequenced as described in the text. No wild-type sequences were detected within the Nef159-167 YY9 epitope, whereas there was relatively little variation outside the epitope sequence (see Table 2). The sequence of the clonal SIVmac239 inoculum is indicated at the top; the epitope is indicated by a yellow box.
