Evolution of nef variants in gut associated lymphoid tissue of rhesus macaques during primary simian immunodeficiency virus infection

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• 作者：Thomas Ndolo ; Michael Syvanen ; Thomas Ellison and Satya Dandekar
• 关键词：SIV-Nef ; Evolution ; Positive selection ; Neutral model ; Adaptive ; GALT ; Synonymous and nonsynonymous
• 刊名：Virology
• 出版年：2005
• 出版时间：5 December 2005
• 年：2005
• 卷：343
• 期：1
• 页码：1-11
• 全文大小：301 K

文摘

We utilized the simian immunodeficiency virus model of AIDS to examine evolution of nef gene in gut-associated lymphoid tissue (GALT) during primary and early asymptomatic stages of infection. Macaques were infected with a cloned virus, SIVmac239/nef-stop harboring a premature stop codon in the nef gene. Restoration of the nef open reading frame occurred in GALT early at 3 days post-infection. Analysis of nef sequences by phylogenetic tools showed that evolution of nef was neutral thereafter, as evidenced by the ratio of synonymous to nonsynonymous substitutions, a star pattern in unrooted trees and distribution of amino acid replacements fitting a simple Poisson process. Two regions encoding for a nuclear localization signal and a CTL epitope were conserved. Thus, GALT was a site for strong positive selection of functional nef during initial stages of infection. However, evolution of the nef gene thereafter was neutral during early asymptomatic stage of infection.