Holland JJ, de la Torre JC, Steinhauer DA: RNA virus populations as quasispecies. Curr Top Microbiol Immunol 1992, 176: 1–20.
CAS
PubMed
Google Scholar
Smith DB, McAllister J, Casino C, Simmonds P: Virus 'quasispecies': making a mountain out of a molehill? J Gen Virol 1997, 78: 1511–1519.
Article
CAS
PubMed
Google Scholar
Domingo E, Martinez-Salas E, Sobrino F, de la Torre JC, Portela A, Ortin J, Lopez-Galindez C, Perez-Brena P, Villanueva N, Najera R, VandePol S, DePolo N, Holland J: The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance-a review. Gene 1985, 40: 1–8.
Article
CAS
PubMed
Google Scholar
Domingo E, Holland J, Biebricher C, Eigen M: Quasi-species: the concept and the word. In: Molecular Basis of Virus Evolution Edited by Gibbs AJ, Calisher C, García-Arenal F. pp. Cambridge: Cambridge University Press; 1995, 181–191.
Google Scholar
Duarte EA, Novella IS, Weaver SC, Domingo E, Wain-Hobson S, Clarke DK, Moya A, Elena SF, de la Torre JC, Holland JJ: RNA virus quasispecies: significance for viral disease and epidemiology. Infect Agents Dis 1994, 3: 201–214.
CAS
PubMed
Google Scholar
Wilson IA, Cox NJ: Structural basis of immune recognition of influenza virus hemagglutinin. Annu Rev Immunol 1990, 8: 737–771.
Article
CAS
PubMed
Google Scholar
Taboga O, Tami C, Carrillo E, Nunez JI, Rodriguez A, Saiz JC, Blanco E, Valero ML, Roig X, Camarero JA, Andreu D, Mateu MG, Giralt E, Domingo E, Sobrino F, Palma EL: A large-scale evaluation of peptide vaccines against foot-and-mouth disease: lack of solid protection in cattle and isolation of escape mutants. J Virol 1997, 71: 2606–2614.
PubMed Central
CAS
PubMed
Google Scholar
Berman PW, Gray AM, Wrin T, Vennari JC, Eastman DJ, Nakamura GR, Francis DP, Gorse G, Schwartz DH: Genetic and Immunologic Characterization of Viruses Infecting MN-rgp120-Vaccinated Volunteers. J Inf Dis 1997, 176: 384–397.
Article
CAS
Google Scholar
Webster RG, Laver WG, Air GM, Schild GC: Molecular mechanisms of variation in influenza viruses. Nature 1982, 296: 115–121.
Article
CAS
PubMed
Google Scholar
Yewdell JW, Caton AJ, Gerhard W: Selection of influenza A virus adsorptive mutants by growth in the presence of a mixture of monoclonal antihemagglutinin antibodies. J Virol 1986, 57: 623–628.
PubMed Central
CAS
PubMed
Google Scholar
Gerhard W, Yewdell J, Frankel M: Antigenic structure of influenza virus haemagglutinin defined by hybridoma antibodies. Nature 1981, 290: 713–717.
Article
CAS
PubMed
Google Scholar
Lambkin R, McLain L, Jones SE, Aldridge SL, Dimmock NJ: Neutralization escape mutants of type A influenza virus are readily selected by antisera from mice immunized with whole virus: a possible mechanism for antigenic drift. J Gen Virol 1994, 75: 3493–3502.
Article
CAS
PubMed
Google Scholar
Cleveland SM, Taylor HP, Dimmock NJ: Selection of neutralizing antibody escape mutants with type A influenza virus HA-specific polyclonal antisera: possible significance for antigenic drift. Epidemiol Infect 1997, 118: 149–154. 10.1017/S0950268896007303
Article
PubMed Central
CAS
PubMed
Google Scholar
Putney SD, Matthews TJ, Robey WG, Lynn DL, Robert-Guroff M, Mueller WT, Langlois AJ, Ghrayeb J, Petteway SR Jr, Weinhold KJ, Fischinger PJ, Wong-Staal F, Gallo RC, Bolognesi DP: HTLV-III/LAV-neutralizing antibodies to an E. coli-produced fragment of the virus envelope. Science 1986, 234: 1392–1395.
Article
CAS
PubMed
Google Scholar
Goudsmit J, Debouck C, Meloen RH, Smit L, Bakker M, Asher DM, Wolff AV, Gibbs CJ Jr, Gajdusek DC: Human immunodeficiency virus type 1 neutralization epitope with conserved architecture elicits early type-specific antibodies in experimentally infected chimpanzees. Proc Natl Acad Sci U S A 1988, 85: 4478–4482.
Article
PubMed Central
CAS
PubMed
Google Scholar
Javaherian K, Langlois AJ, McDanal C, Ross KL, Eckler LI, Jellis CL, Profy AT, Rusche JR, Bolognesi DP, Putney SD, Matthews TJ: Principal neutralizing domain of the human immunodeficiency virus type 1 envelope protein. Proc Natl Acad Sci U S A 1989, 86: 6768–6772.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nowak MA, Anderson RM, McLean AR, Wolfs TF, Goudsmit J, May RM: Antigenic diversity thresholds and the development of AIDS. Science 1991, 254: 963–969.
Article
CAS
PubMed
Google Scholar
Wolinsky SM, Korber BT, Neumann AU, Daniels M, Kunstman KJ, Whetsell AJ, Furtado MR, Cao Y, Ho DD, Safrit JT: Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 1996, 272: 537–542.
Article
CAS
PubMed
Google Scholar
Delwart EL, Pan H, Sheppard HW, Wolpert D, Neumann AU, Korber B, Mullins JI: Slower evolution of human immunodefiency virus type 1 quasispecies during progression to AIDS. J Virol 1997, 71: 7498–7508.
PubMed Central
CAS
PubMed
Google Scholar
Lukashov VV, Kuiken CL, Goudsmit J: Intrahost human immunodeficiency virus type 1 evolution is related to length of the immunocompetent period. J Virol 1995, 69: 6911–6916.
PubMed Central
CAS
PubMed
Google Scholar
Liu S, Schacker T, Musey L, Shriner D, McElrath MJ, Corey L, Mullins JI: Divergent patterns of progression to AIDS after infection from the same source: human immunodeficiency virus type 1 evolution and antiviral responses. J Virol 1997, 71: 4284–4295.
PubMed Central
CAS
PubMed
Google Scholar
Ganeshan S, Dickover RE, Korber BT, Bryson YJ, Wolinsky SM: Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J Virol 1997, 71: 663–677.
PubMed Central
CAS
PubMed
Google Scholar
Fitch WM, Leiter JM, Li XQ, Palese P: Positive Darwinian evolution in human influenza A viruses. Proc Natl Acad Sci U S A 1991, 88: 4270–4274.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mindell DP: Positive selection and rates of evolution in immunodeficiency viruses from humans and chimpanzees. Proc Natl Acad Sci U S A 1996, 93: 3284–3288.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yamaguchi Y, Gojobori T: Evolutionary mechanisms and population dynamics of the third variable enveloperegion of HIV within single hosts. Proc Natl Acad Sci U S A 1997, 94: 1264–1269.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhang L, Diaz RS, Ho DD, Mosley JW, Busch MP, Mayer A: Host-specific driving force in human immunodeficiency virus type 1 evolution in vivo. J Virol 1997, 71: 2555–2561.
PubMed Central
CAS
PubMed
Google Scholar
Poss M, Rodrigo AG, Gosink JJ, Learn GH, de Vange Panteleeff D, Martin HLJ, Bwayo J, Kreiss JK, Overbaugh J: Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1. J Virol 1998, 72: 8240–8251.
PubMed Central
CAS
PubMed
Google Scholar
Shankarappa R, Gupta P, Learn GHJ, Rodrigo AG, Rinaldo CRJ, Gorry MC, Mullins JI, Nara PL, Ehrlich GD: Evolution of human immunodeficiency virus type 1 envelope sequences in infected individuals with differing disease progression profiles. Virology 1998, 241: 251–259. 10.1006/viro.1997.8996
Article
CAS
PubMed
Google Scholar
Ida S, Gatanaga H, Shioda T, Nagai Y, Kobayashi N, Shimada K, Kimura S, Iwamoto A, Oka S: HIV type 1 V3 variation dynamics in vivo: long-term persistence of non-syncytium-inducing genotypes and transient presence of syncytium-inducing genotypes during the course of progressive AIDS. AIDS Res Hum Retroviruses 1997, 13: 1597–1609.
Article
CAS
PubMed
Google Scholar
Cichutek K, Merget H, Norley S, Linde R, Kreuz W, Gahr M, Kurth R: Development of a quasispecies of human immunodeficiency virus type 1 in vivo. Proc Natl Acad Sci U S A 1992, 89: 7365–7369.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nei M, Gojobori T: Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986, 3: 418–426.
CAS
PubMed
Google Scholar
Li W-H, Tanimura M, Sharp PM: Rates and dates of divergence between AIDS virus nucleotide sequences. Mol Biol Evol 1988, 5: 313–330.
CAS
PubMed
Google Scholar
Simmonds P, Balfe P, Ludlam CA, Bishop JO, Brown AJ: Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1. J Virol 1990, 64: 5840–5850.
PubMed Central
CAS
PubMed
Google Scholar
Goodenow M, Huet T, Saurin W, Kwok S, Sninsky J, Wain-Hobson S: HIV-I isolates are rapidly evolving quasispecies: evidence for viral mixtures and preferred nucleotide substitutions. J. AIDS 1989, 2: 344–352.
CAS
Google Scholar
Bonhoeffer S, Holmes EC, Nowak MA: Causes of HIV diversity. Nature 1995, 376: 125.
Article
CAS
PubMed
Google Scholar
Suzuki Y, Gojobori T: A method for detecting positive selection at single amino acid sites. Mol Biol Evol 1999, 16: 1315–1328.
Article
CAS
PubMed
Google Scholar
Nielsen R: The ratio of replacement to silent divergence and tests of neutrality. J. Evol. Biol. 1997, 10: 217–231. 10.1007/s000360050019
Article
Google Scholar
Bush RM, Fitch WM, Bender CA, Cox NJ: Positive selection on the H3 hemagglutinin gene of human influenza virus A. Mol Biol Evol 1999, 16: 1457–1465.
Article
CAS
PubMed
Google Scholar
Graham CM, Warren AP, Thomas DB: Do antigenic drift residues in influenza hemagglutinins of the H3 subtype qualify as contact sites for MHC class II interaction? Int Immunol 1992, 4: 917–922.
Article
CAS
PubMed
Google Scholar
Bush RM, Bender CA, Subbarao K, Cox NJ, Fitch WM: Predicting the Evolution of Human Influenza A. Science 1999, 286: 1921–1925. 10.1126/science.286.5446.1921
Article
CAS
PubMed
Google Scholar
Wiley DC, Wilson IA, Skehel JJ: Structural identification of the antibody-binding sites of Hong Kong influenza haemagglutinin and their involvement in antigenic variation. Nature 1981, 289: 373–378.
Article
CAS
PubMed
Google Scholar
Wilson IA, Skehel JJ, Wiley DC: Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3Å resolution. Nature 1981, 289: 366–373.
Article
CAS
PubMed
Google Scholar
Wiley DC, Skehel JJ: The structure and function of the hemagglutinin membrane glycoprotein of influenza virus. Annu Rev Biochem 1987, 56: 365–394.
Article
CAS
PubMed
Google Scholar
Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J: Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 1998, 393: 648–659.
Article
CAS
PubMed
Google Scholar
Wyatt R, Kwong PD, Desjardins E, Sweet RW, Robinson J, Hendrickson WA, Sodroski JG: The antigenic structure of the HIV gp120 envelope glycoprotein. Nature 1998, 393: 705–711.
Article
CAS
PubMed
Google Scholar
Ho DD, McKeating JA, Li XL, Moudgil T, Daar ES, Sun NC, Robinson JE: Conformational epitope on gp120 important in CD4 binding and human immunodeficiency virus type 1 neutralization identified by a human monoclonal antibody. J Virol 1991, 65: 489–493.
PubMed Central
CAS
PubMed
Google Scholar
Moore JP, Sodroski J: Antibody cross-competition analysis of the human immunodeficiency virus type 1 gp120 exterior envelope glycoprotein. J Virol 1996, 70: 1863–1872.
PubMed Central
CAS
PubMed
Google Scholar
Korber B, Moore J, Brander C, Koup R, Haynes B, Walker B: HIV Molecular Immunology Database 1997.
Google Scholar
Wildemann B, Haas J, Ehrhart K, Wagner H, Lynen N, Storch-Hagenlocher B: In vivo comparison of zidovudine resistance mutations in blood and CSF of HIV-1-infected patients. Neurology 1993, 43: 2659–2663.
Article
CAS
PubMed
Google Scholar
Wong JK, Ignacio CC, Torriani F, Havlir D, Fitch NJS, Richman DD: In vitro compartmentalization of human immunodeficiency virus: evidence from the examination of pol sequences from autopsy tissues. J Virol 1997, 71: 2059–2071.
PubMed Central
CAS
PubMed
Google Scholar
Zheng NN, Hurren L, Neilan BA, Cooper DA, Delaney SF, McQueen PW: Sequence analyses of the reverse transcriptase region of HIV type 1 isolates from Sydney, Australia. AIDS Res Hum Retroviruses 1996, 12: 1731–1732.
Article
CAS
PubMed
Google Scholar
Mellors JW, Schinazi RF, Larder BA: Mutations in retroviral genes associated with drug resistance. In: Human Retroviruses and AIDS. Edited by Meyers G, Korber B, Foley B, Jeang K, Mellors JW, Wain-Hobson S. Los Alamos: Los Alamos National Laboratory; 1996.
Google Scholar
Boucher CA, O'Sullivan E, Mulder JW, Ramautarsing C, Kellam P, Darby G, Lange JM, Goudsmit J, Larder BA: Ordered appearance of zidovudine resistance mutations during treatment of 18 human immunodeficiency virus-positive subjects. J Infect Dis 1992, 165: 105–110.
Article
CAS
PubMed
Google Scholar
Yang Z: Phylogenetic Analysis by Maximum Likelihood (PAML). In: Phylogenetic Analysis by Maximum Likelihood (PAML), 1.3 ed. City; 1997.
Google Scholar
Shannon CE: The mathematical theory of communication. Urbana: University of Illinois Press; 1949.
Google Scholar
GCG: Wisconsin Package. In: Wisconsin Package, 9.1 ed. City: Genetics Computer Group; 1997.
Google Scholar
Morgenstern B, Frech K, Dress A, Werner T: DIALIGN: Finding local similarities by multiple sequence alignment. Bioinformatics 1998, 14: 290–294. 10.1093/bioinformatics/14.3.290
Article
CAS
PubMed
Google Scholar
Rocha EP, Xu X, Hall HE, Allen JR, Regnery HL, Cox NJ: Comparison of 10 influenza A (H1N1 and H3N2) haemagglutinin sequences obtained directly from clinical specimens to those of MDCK cell- and egg-grown viruses. J Gen Virol 1993, 74: 2513–2518.
Article
CAS
PubMed
Google Scholar
Kodihalli S, Justewicz DM, Gubareva LV, Webster RG: Selection of a single amino acid substitution in the hemagglutinin molecule by chicken eggs can render influenza A virus (H3) candidate vaccine ineffective. J Virol 1995, 69: 4888–4897.
PubMed Central
CAS
PubMed
Google Scholar
Nicholls A: Graphical Representation and Analysis of Surface Properties (GRASP). In: Graphical Representation and Analysis of Surface Properties (GRASP). City: Columbia University; 1992.
Google Scholar
Starcich BR, Hahn BH, Shaw GM, McNeely PD, Modrow S, Wolf H, Parks ES, Parks WP, Josephs SF, Gallo RC, et al.: Identification and characterization of conserved and variable regions in the envelope gene of HTLV-III/LAV, the retrovirus of AIDS. Cell 1986, 45: 637–648.
Article
CAS
PubMed
Google Scholar