PMID: 8959243Dec 10, 1996Paper

Human immunodeficiency virus type 1 molecular evolution and the measure of selection

AIDS Research and Human Retroviruses
A G Rodrigo, J I Mullins

Abstract

Human immunodeficiency virus (HIV) envelope genes are highly variable between and often within individuals. Part of this variability is thought to be the result of immune-mediated positive selection for sequence diversity. To measure positive selection it has become customary in HIV research to calculate the ratio of the proportions of synonymous (ds) and nonsynonymous (dn) substitutions per potential synonymous or nonsynonymous site, respectively. However, another measure that can be used is the difference between ds and dn, delta d. We show, by example, that using the ratio, ds/dn, or the difference, delta d, may lead us to different conclusions regarding the existence of positive selection pressure. We conclude by noting that until we understand the processes that mediate nucleotide variation in a host selective environment, inferences based on summary statistics characterizing types of nucleotide substitutions should be made with caution.

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Citations

Aug 3, 2001·Journal of Colloid and Interface Science·M. L. González-MartínC. M. González-García
Jul 27, 2001·Current Infectious Disease Reports·Jaime Deville, Yvonne Bryson
Aug 1, 2000·Colloids and Surfaces. B, Biointerfaces·M Morra, C Cassinelli
Nov 25, 2000·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·A L Halpern
Sep 15, 1999·Proceedings of the National Academy of Sciences of the United States of America·A G Rodrigo
Nov 21, 1998·AIDS Research and Human Retroviruses·J GoudsmitM Cornelissen
Jul 22, 2014·Journal of Basic and Clinical Physiology and Pharmacology·Kesava Rao V KurapatiMadhavan P N Nair
Jan 30, 1999·Antimicrobial Agents and Chemotherapy·A TanuriM A Rayfield

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