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

Abstract

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.

Authors:
 [1];  [1];  [1];  [2]
  1. Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616 (United States)
  2. Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616 (United States). E-mail: sdandekar@ucdavis.edu
Publication Date:
OSTI Identifier:
20779435
Resource Type:
Journal Article
Resource Relation:
Journal Name: Virology; Journal Volume: 343; Journal Issue: 1; Other Information: DOI: 10.1016/j.virol.2005.08.013; PII: S0042-6822(05)00508-8; Copyright (c) 2005 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; AIDS; AMINO ACIDS; BIOLOGICAL RECOVERY; EVOLUTION; GENES; TREES; VIRUSES

Citation Formats

Ndolo, Thomas, Syvanen, Michael, Ellison, Thomas, and Dandekar, Satya. Evolution of nef variants in gut associated lymphoid tissue of rhesus macaques during primary simian immunodeficiency virus infection. United States: N. p., 2005. Web. doi:10.1016/J.VIROL.2005.0.
Ndolo, Thomas, Syvanen, Michael, Ellison, Thomas, & Dandekar, Satya. Evolution of nef variants in gut associated lymphoid tissue of rhesus macaques during primary simian immunodeficiency virus infection. United States. doi:10.1016/J.VIROL.2005.0.
Ndolo, Thomas, Syvanen, Michael, Ellison, Thomas, and Dandekar, Satya. Mon . "Evolution of nef variants in gut associated lymphoid tissue of rhesus macaques during primary simian immunodeficiency virus infection". United States. doi:10.1016/J.VIROL.2005.0.
@article{osti_20779435,
title = {Evolution of nef variants in gut associated lymphoid tissue of rhesus macaques during primary simian immunodeficiency virus infection},
author = {Ndolo, Thomas and Syvanen, Michael and Ellison, Thomas and Dandekar, Satya},
abstractNote = {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.},
doi = {10.1016/J.VIROL.2005.0},
journal = {Virology},
number = 1,
volume = 343,
place = {United States},
year = {Mon Dec 05 00:00:00 EST 2005},
month = {Mon Dec 05 00:00:00 EST 2005}
}
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