Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1

Molecular Biology and Evolution

Volumn 27, Issue 4, 2010, Pages 819-832

  Poon, Art F Y ^a   Swenson, Luke C ^a   Dong, Winnie W Y ^a   Deng, Wenjie ^b   Pond, Sergei L Kosakovsky ^c   Brumme, Zabrina L ^d   Mullins, James I ^b   Richman, Douglas D ^e,f   Harrigan, P Richard ^a   Frost, Simon D W ^g  

^a BRITISH COLUMBIA CENTRE FOR EXCELLENCE IN HIV AIDS   (Canada)

^b UNIVERSITY OF WASHINGTON   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d SIMON FRASER UNIVERSITY   (Canada)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f VA SAN DIEGO HEALTHCARE SYSTEM   (United States)

^g UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Ancestral reconstruction; Coevolution; Epistasis; HIV 1; Next generation sequencing; Sequencing error

Indexed keywords

NEF PROTEIN; VIRUS RNA;

ARTICLE; CANADA; COHORT ANALYSIS; CONTROLLED STUDY; EPISTASIS; EVOLUTION; GENE SEQUENCE; GENETIC LINKAGE; GENETIC POLYMORPHISM; HOST; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; MAJOR CLINICAL STUDY; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; PHYLOGENY; PLASMA; POPULATION RESEARCH; PYROSEQUENCING; QUANTITATIVE ANALYSIS; AMINO ACID SEQUENCE; CHEMISTRY; GENETICS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; VIROLOGY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

AMINO ACID SEQUENCE; BRITISH COLUMBIA; COHORT STUDIES; EVOLUTION, MOLECULAR; HIV INFECTIONS; HIV-1; HUMANS; MOLECULAR SEQUENCE DATA; NEF GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

EID: 77952299935     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp289     Document Type: Article

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