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Volumn 53, Issue 10, 2010, Pages 1204-1214

Complex positive selection pressures drive the evolution of HIV-1 with different co-receptor tropisms

Author keywords

adaptive evolution; epitopes; Gp120; HIV 1 co receptor tropism; positively selected site; R5 and X4

Indexed keywords

GLYCOPROTEIN GP 120; GLYCOPROTEIN GP 41; GP120 PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS 1; GP41 PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS 1; VIRUS RECEPTOR;

EID: 77958459054     PISSN: 16747305     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11427-010-4066-5     Document Type: Article
Times cited : (3)

References (47)
  • 1
    • 0033012398 scopus 로고    scopus 로고
    • Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease
    • Berger E A, Murphy P M, Farber J M. Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease. Annu Rev Immunol, 1999, 17: 657-700.
    • (1999) Annu Rev Immunol , vol.17 , pp. 657-700
    • Berger, E.A.1    Murphy, P.M.2    Farber, J.M.3
  • 2
    • 20344399376 scopus 로고    scopus 로고
    • The HIV coreceptor switch: a population dynamical perspective
    • Regoes R R, Bonhoeffer S. The HIV coreceptor switch: a population dynamical perspective. Trends Microbiol, 2005, 13: 269-277.
    • (2005) Trends Microbiol , vol.13 , pp. 269-277
    • Regoes, R.R.1    Bonhoeffer, S.2
  • 3
    • 0742325043 scopus 로고    scopus 로고
    • The CCR5 and CXCR4 coreceptors-central to understanding the transmission and pathogenesis of human immunodeficiency virus type 1 infection
    • Moore J P, Kitchen S G, Pugach P, et al. The CCR5 and CXCR4 coreceptors-central to understanding the transmission and pathogenesis of human immunodeficiency virus type 1 infection. AIDS Res Hum Retroviruses, 2004, 20: 111-126.
    • (2004) AIDS Res Hum Retroviruses , vol.20 , pp. 111-126
    • Moore, J.P.1    Kitchen, S.G.2    Pugach, P.3
  • 4
    • 0042376485 scopus 로고    scopus 로고
    • A new classification for HIV-1
    • Berger E A, Doms R W, Fenyo E M, et al. A new classification for HIV-1. Nature, 1998, 391: 240.
    • (1998) Nature , vol.391 , pp. 240
    • Berger, E.A.1    Doms, R.W.2    Fenyo, E.M.3
  • 5
    • 1842415431 scopus 로고    scopus 로고
    • Coreceptor usage of primary human immunodeficiency virus type 1 isolates varies according to biological phenotype
    • Bjorndal A, Deng H, Jansson M, et al. Coreceptor usage of primary human immunodeficiency virus type 1 isolates varies according to biological phenotype. J Virol, 1997, 71: 7478-7487.
    • (1997) J Virol , vol.71 , pp. 7478-7487
    • Bjorndal, A.1    Deng, H.2    Jansson, M.3
  • 6
    • 0031575431 scopus 로고    scopus 로고
    • Change in coreceptor use correlates with disease progression in HIV-1-infected individuals
    • Connor R I, Sheridan K E, Ceradini D, et al. Change in coreceptor use correlates with disease progression in HIV-1-infected individuals. J Exp Med, 1997, 185: 621-628.
    • (1997) J Exp Med , vol.185 , pp. 621-628
    • Connor, R.I.1    Sheridan, K.E.2    Ceradini, D.3
  • 7
    • 0036828069 scopus 로고    scopus 로고
    • Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration
    • Ross H A, Rodrigo A G. Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J Virol, 2002, 76: 11715-11720.
    • (2002) J Virol , vol.76 , pp. 11715-11720
    • Ross, H.A.1    Rodrigo, A.G.2
  • 8
    • 0842326022 scopus 로고    scopus 로고
    • Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes
    • Choisy M, Woelk C H, Guegan J F, et al. Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J Virol, 2004, 78: 1962-1970.
    • (2004) J Virol , vol.78 , pp. 1962-1970
    • Choisy, M.1    Woelk, C.H.2    Guegan, J.F.3
  • 9
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R, Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 1998, 148: 929-936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 10
    • 0041884768 scopus 로고    scopus 로고
    • Widespread adaptive evolution in the human immunodeficiency virus type 1 genome
    • Yang W, Bielawski J P, Yang Z. Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J Mol Evol, 2003, 57: 212-221.
    • (2003) J Mol Evol , vol.57 , pp. 212-221
    • Yang, W.1    Bielawski, J.P.2    Yang, Z.3
  • 11
    • 13744254693 scopus 로고    scopus 로고
    • Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes
    • Travers S A, O'Connell M J, McCormack G P, et al. Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes. J Virol, 2005, 79: 1836-1841.
    • (2005) J Virol , vol.79 , pp. 1836-1841
    • Travers, S.A.1    O'Connell, M.J.2    McCormack, G.P.3
  • 12
    • 0032737463 scopus 로고    scopus 로고
    • Genealogical evidence for positive selection in the nef gene of HIV-1
    • Zanotto P M, Kallas E G, de Souza R F, et al. Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics, 1999, 153: 1077-1089.
    • (1999) Genetics , vol.153 , pp. 1077-1089
    • Zanotto, P.M.1    Kallas, E.G.2    de Souza, R.F.3
  • 13
    • 3843062475 scopus 로고    scopus 로고
    • Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design?
    • de Oliveira T, Salemi M, Gordon M, et al. Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design? Genetics, 2004, 167: 1047-1058.
    • (2004) Genetics , vol.167 , pp. 1047-1058
    • de Oliveira, T.1    Salemi, M.2    Gordon, M.3
  • 14
    • 46649087123 scopus 로고    scopus 로고
    • Positive selection on HIV accessory proteins and the analysis of molecular adaptation after interspecies transmission
    • Soares A E, Soares M A, Schrago C G. Positive selection on HIV accessory proteins and the analysis of molecular adaptation after interspecies transmission. J Mol Evol, 2008, 66: 598-604.
    • (2008) J Mol Evol , vol.66 , pp. 598-604
    • Soares, A.E.1    Soares, M.A.2    Schrago, C.G.3
  • 15
    • 39649118635 scopus 로고    scopus 로고
    • Disease progression and evolution of the HIV-1 env gene in 24 infected infants
    • Carvajal-Rodriguez A, Posada D, Perez-Losada M, et al. Disease progression and evolution of the HIV-1 env gene in 24 infected infants. Infect Genet Evol, 2008, 8: 110-120.
    • (2008) Infect Genet Evol , vol.8 , pp. 110-120
    • Carvajal-Rodriguez, A.1    Posada, D.2    Perez-Losada, M.3
  • 16
    • 35448977610 scopus 로고    scopus 로고
    • Selective pressures of human immunodeficiency virus type 1 (HIV-1) during pediatric infection
    • Leal E, Janini M, Diaz R S. Selective pressures of human immunodeficiency virus type 1 (HIV-1) during pediatric infection. Infect Genet Evol, 2007, 7: 694-707.
    • (2007) Infect Genet Evol , vol.7 , pp. 694-707
    • Leal, E.1    Janini, M.2    Diaz, R.S.3
  • 17
    • 0041571679 scopus 로고    scopus 로고
    • Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression
    • Williamson S. Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol Biol Evol, 2003, 20: 1318-1325.
    • (2003) Mol Biol Evol , vol.20 , pp. 1318-1325
    • Williamson, S.1
  • 18
    • 0031029083 scopus 로고    scopus 로고
    • Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts
    • Yamaguchi Y, Gojobori T. Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within single hosts. Proc Natl Acad Sci USA, 1997, 94: 1264-1269.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 1264-1269
    • Yamaguchi, Y.1    Gojobori, T.2
  • 19
    • 10744231634 scopus 로고    scopus 로고
    • Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences
    • Jensen M A, Li F S, van't Wout A B, et al. Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences. J Virol, 2003, 77: 13376-13388.
    • (2003) J Virol , vol.77 , pp. 13376-13388
    • Jensen, M.A.1    Li, F.S.2    van't Wout, A.B.3
  • 20
    • 36148931769 scopus 로고    scopus 로고
    • Predicting HIV coreceptor usage on the basis of genetic and clinical covariates
    • Sing T, Low A J, Beerenwinkel N, et al. Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir Ther, 2007, 12: 1097-1106.
    • (2007) Antivir Ther , vol.12 , pp. 1097-1106
    • Sing, T.1    Low, A.J.2    Beerenwinkel, N.3
  • 21
    • 35648983524 scopus 로고    scopus 로고
    • Improved prediction of coreceptor usage and phenotype of HIV-1 based on combined features of V3 loop sequence using random forest
    • Xu S, Huang X, Xu H, et al. Improved prediction of coreceptor usage and phenotype of HIV-1 based on combined features of V3 loop sequence using random forest. J Microbiol, 2007, 45: 441-446.
    • (2007) J Microbiol , vol.45 , pp. 441-446
    • Xu, S.1    Huang, X.2    Xu, H.3
  • 22
    • 66149086564 scopus 로고    scopus 로고
    • Reliabilities of identifying positive selection by the branch-site and the site-prediction methods
    • Nozawa M, Suzuki Y, Nei M. Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci USA, 2009, 106: 6700-6705.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 6700-6705
    • Nozawa, M.1    Suzuki, Y.2    Nei, M.3
  • 23
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4
    • Tamura K, Dudley J, Nei M, et al. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol Biol Evol, 2007, 24: 1596-1599.
    • (2007) 0. Mol Biol Evol , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3
  • 24
    • 23144433822 scopus 로고    scopus 로고
    • PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference
    • Guindon S, Lethiec F, Duroux P, et al. PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res, 2005, 33: W557-W559.
    • (2005) Nucleic Acids Res , vol.33
    • Guindon, S.1    Lethiec, F.2    Duroux, P.3
  • 25
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: phylogenetic analysis by maximum likelihood
    • Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol, 2007, 24: 1586-1591.
    • (2007) Mol Biol Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 26
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang Z, Nielsen R, Goldman N, et al. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics, 2000, 155: 431-449.
    • (2000) Genetics , vol.155 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3
  • 27
    • 0034897709 scopus 로고    scopus 로고
    • Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
    • Anisimova M, Bielawski J P, Yang Z. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol, 2001, 18: 1585-92.
    • (2001) Mol Biol Evol , vol.18 , pp. 1585-1592
    • Anisimova, M.1    Bielawski, J.P.2    Yang, Z.3
  • 28
    • 0036272936 scopus 로고    scopus 로고
    • Accuracy and power of bayes prediction of amino acid sites under positive selection
    • Anisimova M, Bielawski J P, Yang Z. Accuracy and power of bayes prediction of amino acid sites under positive selection. Mol Biol Evol, 2002, 19: 950-958.
    • (2002) Mol Biol Evol , vol.19 , pp. 950-958
    • Anisimova, M.1    Bielawski, J.P.2    Yang, Z.3
  • 29
    • 17744395033 scopus 로고    scopus 로고
    • Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
    • Pond S L, Frost S D. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics, 2005, 21: 2531-2533.
    • (2005) Bioinformatics , vol.21 , pp. 2531-2533
    • Pond, S.L.1    Frost, S.D.2
  • 30
    • 0025783669 scopus 로고
    • Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1
    • Hwang S S, Boyle T J, Lyerly H K, et al. Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science, 1991, 253: 71-74.
    • (1991) Science , vol.253 , pp. 71-74
    • Hwang, S.S.1    Boyle, T.J.2    Lyerly, H.K.3
  • 31
    • 0025696633 scopus 로고
    • Broadly neutralizing antibodies elicited by the hypervariable neutralizing determinant of HIV-1
    • Javaherian K, Langlois A J, LaRosa G J, et al. Broadly neutralizing antibodies elicited by the hypervariable neutralizing determinant of HIV-1. Science, 1990, 250: 1590-1593.
    • (1990) Science , vol.250 , pp. 1590-1593
    • Javaherian, K.1    Langlois, A.J.2    Larosa, G.J.3
  • 32
  • 33
    • 0035868713 scopus 로고    scopus 로고
    • Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA
    • Sarafianos S G, Das K, Tantillo C, et al. Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA: DNA. EMBO J, 2001, 20: 1449-1461.
    • (2001) EMBO J , vol.20 , pp. 1449-1461
    • Sarafianos, S.G.1    Das, K.2    Tantillo, C.3
  • 34
    • 0000604395 scopus 로고    scopus 로고
    • The neutralizing antibody response to HIV-1: viral evasion and escape from humoral immunity
    • Parren P W, Moore J P, Burton D R, et al. The neutralizing antibody response to HIV-1: viral evasion and escape from humoral immunity. AIDS, 1999, 13 Suppl A: S137-S162.
    • (1999) Aids , vol.13 SupplA
    • Parren, P.W.1    Moore, J.P.2    Burton, D.R.3
  • 36
    • 0026606727 scopus 로고
    • Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule
    • Fouchier R A, Groenink M, Kootstra N A, et al. Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. J Virol, 1992, 66: 3183-3187.
    • (1992) J Virol , vol.66 , pp. 3183-3187
    • Fouchier, R.A.1    Groenink, M.2    Kootstra, N.A.3
  • 37
    • 0032484486 scopus 로고    scopus 로고
    • CCR5 coreceptor usage of non-syncytium-inducing primary HIV-1 is independent of phylogenetically distinct global HIV-1 isolates: delineation of consensus motif in the V3 domain that predicts CCR-5 usage
    • Xiao L, Owen S M, Goldman I, et al. CCR5 coreceptor usage of non-syncytium-inducing primary HIV-1 is independent of phylogenetically distinct global HIV-1 isolates: delineation of consensus motif in the V3 domain that predicts CCR-5 usage. Virology, 1998, 240: 83-92.
    • (1998) Virology , vol.240 , pp. 83-92
    • Xiao, L.1    Owen, S.M.2    Goldman, I.3
  • 38
    • 0027154014 scopus 로고
    • A single amino acid substitution in the V1 loop of human immunodeficiency virus type 1 gp120 alters cellular tropism
    • Boyd M T, Simpson G R, Cann A J, et al. A single amino acid substitution in the V1 loop of human immunodeficiency virus type 1 gp120 alters cellular tropism. J Virol, 1993, 67: 3649-3652.
    • (1993) J Virol , vol.67 , pp. 3649-3652
    • Boyd, M.T.1    Simpson, G.R.2    Cann, A.J.3
  • 39
    • 0031978550 scopus 로고    scopus 로고
    • Determinants of entry cofactor utilization and tropism in a dualtropic human immunodeficiency virus type 1 primary isolate
    • Smyth R J, Yi Y, Singh A, et al. Determinants of entry cofactor utilization and tropism in a dualtropic human immunodeficiency virus type 1 primary isolate. J Virol, 1998, 72: 4478-4484.
    • (1998) J Virol , vol.72 , pp. 4478-4484
    • Smyth, R.J.1    Yi, Y.2    Singh, A.3
  • 40
    • 0027205624 scopus 로고
    • Relation of phenotype evolution of HIV-1 to envelope V2 configuration
    • Groenink M, Fouchier R A, Broersen S, et al. Relation of phenotype evolution of HIV-1 to envelope V2 configuration. Science, 1993, 260: 1513-1516.
    • (1993) Science , vol.260 , pp. 1513-1516
    • Groenink, M.1    Fouchier, R.A.2    Broersen, S.3
  • 41
    • 30344443665 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 coreceptor switching: V1/V2 gain-of-fitness mutations compensate for V3 loss-of-fitness mutations
    • Pastore C, Nedellec R, Ramos A, et al. Human immunodeficiency virus type 1 coreceptor switching: V1/V2 gain-of-fitness mutations compensate for V3 loss-of-fitness mutations. J Virol, 2006, 80: 750-758.
    • (2006) J Virol , vol.80 , pp. 750-758
    • Pastore, C.1    Nedellec, R.2    Ramos, A.3
  • 42
    • 0027204667 scopus 로고
    • Effect of amino acid changes in the V1/V2 region of the human immunodeficiency virus type 1 gp120 glycoprotein on subunit association, syncytium formation, and recognition by a neutralizing antibody
    • Sullivan N, Thali M, Furman C, et al. Effect of amino acid changes in the V1/V2 region of the human immunodeficiency virus type 1 gp120 glycoprotein on subunit association, syncytium formation, and recognition by a neutralizing antibody. J Virol, 1993, 67: 3674-3679.
    • (1993) J Virol , vol.67 , pp. 3674-3679
    • Sullivan, N.1    Thali, M.2    Furman, C.3
  • 43
    • 27144478617 scopus 로고    scopus 로고
    • Complex determinants in human immunodeficiency virus type 1 envelope gp120 mediate CXCR4-dependent infection of macrophages
    • Ghaffari G, Tuttle D L, Briggs D, et al. Complex determinants in human immunodeficiency virus type 1 envelope gp120 mediate CXCR4-dependent infection of macrophages. J Virol, 2005, 79: 13250-13261.
    • (2005) J Virol , vol.79 , pp. 13250-13261
    • Ghaffari, G.1    Tuttle, D.L.2    Briggs, D.3
  • 44
    • 0031935146 scopus 로고    scopus 로고
    • Identification of determinants on a dualtropic human immunodeficiency virus type 1 envelope glycoprotein that confer usage of CXCR4
    • Cho M W, Lee M K, Carney M C, et al. Identification of determinants on a dualtropic human immunodeficiency virus type 1 envelope glycoprotein that confer usage of CXCR4. J Virol, 1998, 72: 2509-2515.
    • (1998) J Virol , vol.72 , pp. 2509-2515
    • Cho, M.W.1    Lee, M.K.2    Carney, M.C.3
  • 45
    • 49149118421 scopus 로고    scopus 로고
    • Autologous neutralizing humoral immunity and evolution of the viral envelope in the course of subtype B human immunodeficiency virus type 1 infection
    • Bunnik E M, Pisas L, van Nuenen A C, et al. Autologous neutralizing humoral immunity and evolution of the viral envelope in the course of subtype B human immunodeficiency virus type 1 infection. J Virol, 2008, 82: 7932-7941.
    • (2008) J Virol , vol.82 , pp. 7932-7941
    • Bunnik, E.M.1    Pisas, L.2    van Nuenen, A.C.3
  • 46
    • 0025678671 scopus 로고
    • Heptad repeat sequences are located adjacent to hydrophobic regions in several types of virus fusion glycoproteins
    • Chambers P, Pringle C R, Easton A J. Heptad repeat sequences are located adjacent to hydrophobic regions in several types of virus fusion glycoproteins. J Gen Virol, 1990, 71: 3075-3080.
    • (1990) J Gen Virol , vol.71 , pp. 3075-3080
    • Chambers, P.1    Pringle, C.R.2    Easton, A.J.3
  • 47
    • 33750164592 scopus 로고    scopus 로고
    • Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups
    • Zhang C Y, Wei J F, He S H. Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in different epidemic groups. BMC Microbiol, 2006, 6: 88.
    • (2006) BMC Microbiol , vol.6 , pp. 88
    • Zhang, C.Y.1    Wei, J.F.2    He, S.H.3


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