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Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.
Mol Biol Evol. 2010 Apr;27(4):819-32
Publication Type
Art F Y Poon
Luke C Swenson
Winnie W Y Dong
Wenjie Deng
Sergei L Kosakovsky Pond
Zabrina L Brumme
James I Mullins
Douglas D Richman
P Richard Harrigan
Simon D W Frost
Author Affiliation
British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.
Mol Biol Evol. 2010 Apr;27(4):819-32
Publication Type
Amino Acid Sequence
British Columbia
Cohort Studies
Evolution, Molecular
HIV Infections - virology
HIV-1 - genetics
Molecular Sequence Data
Sequence Alignment
Sequence Analysis, RNA - methods
nef Gene Products, Human Immunodeficiency Virus - chemistry - genetics
Rapidly evolving viruses such as HIV-1 display extensive sequence variation in response to host-specific selection, while simultaneously maintaining functions that are critical to replication and infectivity. This apparent conflict between diversifying and purifying selection may be resolved by an abundance of epistatic interactions such that the same functional requirements can be met by highly divergent sequences. We investigate this hypothesis by conducting an extensive characterization of sequence variation in the HIV-1 nef gene that encodes a highly variable multifunctional protein. Population-based sequences were obtained from 686 patients enrolled in the HOMER cohort in British Columbia, Canada, from which the distribution of nonsynonymous substitutions in the phylogeny was reconstructed by maximum likelihood. We used a phylogenetic comparative method on these data to identify putative epistatic interactions between residues. Two interactions (Y120/Q125 and N157/S169) were chosen to further investigate within-host evolution using HIV-1 RNA extractions from plasma samples from eight patients. Clonal sequencing confirmed strong linkage between polymorphisms at these sites in every case. We used massively parallel pyrosequencing (MPP) to reconstruct within-host evolution in these patients. Experimental error associated with MPP was quantified by performing replicates at two different stages of the protocol, which were pooled prior to analysis to reduce this source of variation. Phylogenetic reconstruction from these data revealed correlated substitutions at Y120/Q125 or N157/S169 repeated across multiple lineages in every host, indicating convergent within-host evolution shaped by epistatic interactions.
Cites: Genome Res. 2007 Aug;17(8):1195-20117600086
Cites: J Virol. 2006 Feb;80(3):1311-2016415008
Cites: PLoS Comput Biol. 2007 Nov;3(11):e23118039027
Cites: Genome Biol. 2007;8(7):R14317659080
Cites: Mol Biol Evol. 2008 Jan;25(1):199-20617981928
Cites: Science. 2008 Jan 25;319(5862):473-618218900
Cites: Nat Protoc. 2008;3(2):267-7818274529
Cites: Genome Res. 2008 May;18(5):763-7018212088
Cites: J Immunol. 2008 Jun 15;180(12):7878-8618523251
Cites: Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):13081-618723673
Cites: PLoS Comput Biol. 2008 Nov;4(11):e100022519023406
Cites: Retrovirology. 2009;6:1519216757
Cites: Clin Chem. 2009 Apr;55(4):641-5819246620
Cites: PLoS Pathog. 2009 Apr;5(4):e100036519343217
Cites: Virol J. 2008;5:16019105834
Cites: PLoS One. 2009;4(5):e568319479085
Cites: Nature. 2009 Aug 6;460(7256):711-619661910
Cites: J Virol. 2002 Sep;76(17):8757-6812163596
Cites: J Virol. 2002 Nov;76(22):11273-8212388687
Cites: Science. 2003 Mar 7;299(5612):1515-8; author reply 1515-812624248
Cites: J Clin Microbiol. 2003 Jul;41(7):2900-712843019
Cites: AIDS Rev. 2003 Jan-Mar;5(1):52-6112875108
Cites: Virology. 2003 Sep 30;314(2):536-4814554082
Cites: J Virol. 2004 Jun;78(11):5745-5515140972
Cites: AIDS. 2004 Jul 2;18(10):1383-9215199314
Cites: Comput Appl Biosci. 1988 Mar;4(1):11-73382986
Cites: J Immunol. 1991 Mar 1;146(5):1560-51704397
Cites: Oncogene. 1991 Mar;6(3):491-31707154
Cites: Mol Biol Evol. 1993 May;10(3):512-268336541
Cites: Proc Natl Acad Sci U S A. 1993 Aug 1;90(15):7176-808346232
Cites: J Gen Virol. 1994 Feb;75 ( Pt 2):341-517509370
Cites: Mol Biol Evol. 1994 Sep;11(5):715-247968485
Cites: Immunity. 1994 Aug;1(5):373-847882168
Cites: Biophys J. 1996 Jul;71(1):101-88804593
Cites: Comput Appl Biosci. 1996 Dec;12(6):543-89021275
Cites: J Virol. 1998 May;72(5):3646-579557645
Cites: J Virol. 1999 Jul;73(7):5497-50810364298
Cites: Mol Biol Evol. 2005 Feb;22(2):223-3415483327
Cites: Bioinformatics. 2005 Mar 1;21(5):676-915509596
Cites: Mol Biol Evol. 2005 May;22(5):1208-2215703242
Cites: Syst Biol. 2005 Jun;54(3):401-1816012107
Cites: Evolution. 2005 Jun;59(6):1165-7416050094
Cites: Genetics. 2005 Jul;170(3):1323-3215879511
Cites: Genetics. 2005 Jul;170(3):989-9915911582
Cites: Genetics. 1999 Nov;153(3):1077-8910545443
Cites: Mol Biol Evol. 2000 Jun;17(6):890-610833195
Cites: AIDS. 2001 Mar 30;15(5):601-711316997
Cites: JAMA. 2001 Nov 28;286(20):2568-7711722271
Cites: J Mol Evol. 2002 Feb;54(2):156-6511821909
Cites: J Mol Evol. 2002 Mar;54(3):396-40211847565
Cites: Curr Opin Infect Dis. 2001 Feb;14(1):23-811979111
Cites: Microbiol Mol Biol Rev. 2006 Jun;70(2):548-6316760313
Cites: Mol Biol Evol. 2006 Sep;23(9):1724-3016774976
Cites: AIDS Rev. 2006 Jul-Sep;8(3):125-4017078483
Cites: Biophys Chem. 2007 Mar;126(1-3):36-4216730880
Cites: J Virol. 2007 May;81(9):4776-8617329339
Cites: PLoS Comput Biol. 2007 May;3(5):e8717500586
Cites: PLoS One. 2007;2(7):e59117611623
Cites: J Virol. 2007 Aug;81(15):8346-5117507468
Cites: Nucleic Acids Res. 2007;35(13):e9117576693
Cites: Genome Res. 2007 Aug;17(8):1186-9417545577
Cites: Nature. 2005 Sep 15;437(7057):376-8016056220
Cites: AIDS Res Hum Retroviruses. 2005 Dec;21(12):1016-3016379605
Cites: J Virol. 2007 Dec;81(24):13852-6417928336
PubMed ID
19955476 View in PubMed
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