Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1.

Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. Research Abstract Details 

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Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. Abstract Text:

Selene ,Sergei L Kosakovsky Pond,Paul Shapshak,Simon D W Frost,

Human immunodeficiency virus (HIV) infects different organs and tissues. During these infection events, subpopulations of HIV type 1 (HIV-1) develop and, if viral trafficking is restricted between subpopulations, the viruses can follow independent evolutionary histories, i.e., become compartmentalized. This phenomenon is usually detected via comparative sequence analysis and has been reported for viruses isolated from the central nervous system (CNS) and the genital tract. Several approaches have been proposed to study the compartmentalization of HIV sequences, but to date, no rigorous comparison of the most commonly employed methods has been made. In this study, we systematically compared inferences made by six different methods for detecting compartmentalization based on three data sets: (i) a sample of 45 patients with sequences gathered from the CNS, (ii) sequences from the female genital tract of 18 patients, and (iii) a set of simulated sequences. We found that different methods often reached contradictory conclusions. Methods based on the topology of a phylogenetic tree derived from clonal sequences were generally more sensitive in detecting compartmentalization than those that relied solely upon pairwise genetic distances between sequences. However, as the branching structure in a phylogenetic tree is often uncertain, especially for short, low-diversity, or recombinant sequences, tree-based approaches may need to be modified to take phylogenetic uncertainty into account. Given the frequently discordant predictions of different methods and the strengths and weaknesses of each particular methodology, we recommend that a suite of several approaches be used for reliable inference of compartmentalized population structure.

Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. Publishing Authors By Initials

S ,SL Pond,P Shapshak,SD Frost,

For similar genetic processes: recombination, genetic research abstracts see: genetic processes: recombination, genetic research

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Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: Journal of virology

VOLUME: 81

Page Numbers: 6643-51

Journal Abbreviation: J. Virol.

ISSN: 0022-538X

DAY: 11

MONTH: 04

YEAR: 2007

Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. Information

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LANGUAGE: eng

NlmUniqueID: 113724

Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. Keywords Mesh Terms:

KEYWORDS: Recombination, Genetic

MESH TERMS: metabolism

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Grant and Affiliation Information for Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1.

AFFILIATION: Antiviral Research Center, 150 W Washington St., Ste. 100, San Diego, CA 92103, USA. cszarate@ucsd.edu

Country: United States

AGENCY: United States NIGMS

GRANT: GM056529

ACRONYM: GM

MEDLINETA: J Virol

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