43 Ghaffari G, Tuttle D L, Briggs D, et al. Complex determinants in human immunodeficiency virus type 1 envelope gp120 mediateCXCR4-dependent infection of macrophages. J Virol, 2005, 79: 13250–13261??
[2]
44 Cho M W, Lee M K, Carney M C, et al. Identification of determinants on a dualtropic human immunodeficiency virus type 1 envelopeglycoprotein that confer usage of CXCR4. J Virol, 1998, 72: 2509–2515
[3]
45 Bunnik E M, Pisas L, van Nuenen A C, et al. Autologous neutralizing humoral immunity and evolution of the viral envelope in the course ofsubtype B human immunodeficiency virus type 1 infection. J Virol, 2008, 82: 7932–7941??
[4]
46 Chambers P, Pringle C R, Easton A J. Heptad repeat sequences are located adjacent to hydrophobic regions in several types of virus fusionglycoproteins. J Gen Virol, 1990, 71: 3075–3080??
[5]
47 Zhang C Y, Wei J F, He S H. Adaptive evolution of the spike gene of SARS coronavirus: changes in positively selected sites in differentepidemic groups. BMC Microbiol, 2006, 6: 88??
[6]
1 Berger E A, Murphy P M, Farber J M. Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease. Annu RevImmunol, 1999, 17: 657–700
[7]
2 Berger E A, Doms R W, Fenyo E M, et al. A new classification for HIV-1. Nature, 1998, 391: 240??
[8]
3 Bjorndal A, Deng H, Jansson M, et al. Coreceptor usage of primary human immunodeficiency virus type 1 isolates varies according tobiological phenotype. J Virol, 1997, 71: 7478–7487
[9]
4 Regoes R R, Bonhoeffer S. The HIV coreceptor switch: a population dynamical perspective. Trends Microbiol, 2005, 13: 269–277??
[10]
5 Moore J P, Kitchen S G, Pugach P, et al. The CCR5 and CXCR4 coreceptors– central to understanding the transmission and pathogenesis ofhuman immunodeficiency virus type 1 infection. AIDS Res Hum Retroviruses, 2004, 20: 111–126??
[11]
6 Connor R I, Sheridan K E, Ceradini D, et al. Change in coreceptor use correlates with disease progression in HIV-1--infected individuals. JExp Med, 1997, 185: 621–628
[12]
7 Ross H A, Rodrigo A G. Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predictsdisease duration. J Virol, 2002, 76: 11715–11720??
[13]
8 Choisy M, Woelk C H, Guegan J F, et al. Comparative study of adaptive molecular evolution in different human immunodeficiency virusgroups and subtypes. J Virol, 2004, 78: 1962–1970??
[14]
9 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
[15]
10 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??
[16]
11 Travers S A, O''Connell M J, McCormack G P, et al. Evidence for heterogeneous selective pressures in the evolution of the env gene indifferent human immunodeficiency virus type 1 subtypes. J Virol, 2005, 79: 1836–1841??
[17]
12 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
[18]
13 de Oliveira T, Salemi M, Gordon M, et al. Mapping sites of positive selection and amino acid diversification in the HIV genome: analternative approach to vaccine design? Genetics, 2004, 167: 1047–1058
[19]
14 Soares A E, Soares M A, Schrago C G. Positive selection on HIV accessory proteins and the analysis of molecular adaptation afterinterspecies transmission. J Mol Evol, 2008, 66: 598–604??
[20]
15 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??
[21]
16 Leal E, Janini M, Diaz R S. Selective pressures of human immunodeficiency virus type 1 (HIV-1) during pediatric infection. Infect GenetEvol, 2007, 7: 694–707
[22]
17 Williamson S. Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol Biol Evol, 2003, 20: 1318–1325??
[23]
18 Yamaguchi Y, Gojobori T. Evolutionary mechanisms and population dynamics of the third variable envelope region of HIV within singlehosts. Proc Natl Acad Sci USA, 1997, 94: 1264–1269??
[24]
19 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 motifanalysis of human immunodeficiency virus type 1 env V3 loop sequences. J Virol, 2003, 77: 13376–13388??
[25]
20 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: 1097–106
[26]
21 Xu S, Huang X, Xu H, et al. Improved prediction of coreceptor usage and phenotype of HIV-1 based on combined features of V3 loopsequence using random forest. J Microbiol, 2007, 45: 441–446
[27]
22 Nozawa M, Suzuki Y, Nei M. Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc NatlAcad Sci USA, 2009, 106: 6700–6705??
[28]
23 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
[29]
24 Guindon S, Lethiec F, Duroux P, et al. PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference. NucleicAcids Res, 2005, 33: W557–559
[30]
25 Yang Z, Nielsen R, Goldman N, et al. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics, 2000,155: 431–449
[31]
26 Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol, 2007, 24: 1586–1591??
[32]
27 Anisimova M, Bielawski J P, Yang Z. Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol BiolEvol, 2001, 18: 1585–1592
[33]
28 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
[34]
29 Pond S L, Frost S D. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics, 2005, 21:2531–2533??
[35]
30 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??
[36]
31 Javaherian K, Langlois A J, LaRosa G J, et al. Broadly neutralizing antibodies elicited by the hypervariable neutralizing determinant ofHIV-1. Science, 1990, 250: 1590–1593??
[37]
32 Wain L V, Bailes E, Bibollet-Ruche F, et al. Adaptation of HIV-1 to its human host. Mol Biol Evol, 2007, 24: 1853–1860??
[38]
33 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??
[39]
34 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: S137–S162
[40]
35 Klenerman P, Wu Y, Phillips R. HIV: current opinion in escapology. Curr Opin Microbiol, 2002, 5: 408–413??
[41]
36 Fouchier R A, Groenink M, Kootstra N A, et al. Phenotype-associated sequence variation in the third variable domain of the humanimmunodeficiency virus type 1 gp120 molecule. J Virol, 1992, 66: 3183–3187
[42]
37 Xiao L, Owen S M, Goldman I, et al. CCR5 coreceptor usage of non-syncytium-inducing primary HIV-1 is independent of phylogeneticallydistinct global HIV-1 isolates: delineation of consensus motif in the V3 domain that predicts CCR-5 usage. Virology, 1998, 240: 83–92??
[43]
38 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 gp120alters cellular tropism. J Virol, 1993, 67: 3649–3652
[44]
39 Smyth R J, Yi Y, Singh A, et al. Determinants of entry cofactor utilization and tropism in a dualtropic human immunodeficiency virus type1 primary isolate. J Virol, 1998, 72: 4478–4484
[45]
40 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??
[46]
41 Pastore C, Nedellec R, Ramos A, et al. Human immunodeficiency virus type 1 coreceptor switching: V1/V2 gain-of-fitness mutationscompensate for V3 loss-of-fitness mutations. J Virol, 2006, 80: 750–758??
[47]
42 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 gp120glycoprotein on subunit association, syncytium formation, and recognition by a neutralizing antibody. J Virol, 1993, 67: 3674–3679