Estimating selection pressures on HIV-1 using phylogenetic likelihood models

被引：15

作者：

Pond, S. L. Kosakovsky

Poon, A. F. Y.

Zarate, S. ^{[7
]}

Smith, D. M. ^{[2
,3
]}

Little, S. J. ^{[2
]}

Pillai, S. K. ^{[4
,5
]}

Ellis, R. J. ^{[2
]}

Wong, J. K. ^{[4
,5
]}

Brown, A. J. Leigh ^{[6
]}

Richman, D. D. ^{[2
,3
]}

Frost, S. D. W. ^{[1
]}

机构：

[1] Univ Calif San Diego, Antiviral Res Ctr, Dept Pathol, San Diego, CA 92103 USA

[2] Univ Calif San Diego, Sch Med, San Diego, CA 92103 USA

[3] Vet Affairs San Diego Healthcare Syst, San Diego, CA USA

[4] Univ Calif San Francisco, Sch Med, San Francisco, CA USA

[5] Vet Affairs Med Ctr, San Francisco, CA 94121 USA

[6] Univ Edinburgh, Inst Evolutionary Biol, Edinburgh, Midlothian, Scotland

[7] Univ Autonoma Ciudad Mexico, Mexico City, DF, Mexico

来源：

STATISTICS IN MEDICINE | 2008年 / 27卷 / 23期

关键词：

D O I：

10.1002/sim.3192

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Human immunodeficiency virus (HIV-1) can rapidly evolve due to selection pressures exerted by HIV-specific immune responses, antiviral agents, and to allow the virus to establish infection in different compartments in the body. Statistical models applied to HIV-1 sequence data can help to elucidate the nature of these selection pressures through comparisons of non-synonymous (or amino acid changing) and synonymous (or amino acid preserving) substitution rates. These models also need to take into account the non-independence of sequences due to their shared evolutionary history. We review how we have developed these methods and have applied them to characterize the evolution of HIV-1 in vivo. To illustrate our methods, we present an analysis of compartment-specific evolution of HIV-1 em) in blood and cerebrospinal fluid and of site-to-site variation in the gag gene of subtype C HIV-1. Copyright (C) 2008 John Wiley & Sons, Ltd.

引用

页码：4779 / 4789

页数：11

共 47 条

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