메뉴 건너뛰기




Volumn 8, Issue 2, 2008, Pages 110-120

Disease progression and evolution of the HIV-1 env gene in 24 infected infants

Author keywords

Disease progression; env; HIV 1; Recombination; Selection

Indexed keywords

DIDANOSINE; VIRUS ENVELOPE PROTEIN; ZIDOVUDINE;

EID: 39649118635     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2007.10.009     Document Type: Article
Times cited : (21)

References (65)
  • 1
    • 0029088866 scopus 로고
    • Neonatal predictors of infection status and early death among 332 infants at risk of HIV-1 infection monitored prospectively from birth. New York City Perinatal HIV Transmission Collaborative Study Group
    • Abrams E.J., Matheson P.B., Thomas P.A., Thea D.M., Krasinski K., Lambert G., Shaffer N., Bamji M., Hutson D., Grimm K., et al. Neonatal predictors of infection status and early death among 332 infants at risk of HIV-1 infection monitored prospectively from birth. New York City Perinatal HIV Transmission Collaborative Study Group. Pediatrics 96 (1995) 451-458
    • (1995) Pediatrics , vol.96 , pp. 451-458
    • Abrams, E.J.1    Matheson, P.B.2    Thomas, P.A.3    Thea, D.M.4    Krasinski, K.5    Lambert, G.6    Shaffer, N.7    Bamji, M.8    Hutson, D.9    Grimm, K.10
  • 2
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike H. A new look at the statistical model identification. IEEE Trans. Autom. Control 19 (1974) 716-723
    • (1974) IEEE Trans. Autom. Control , vol.19 , pp. 716-723
    • Akaike, H.1
  • 3
    • 27144440023 scopus 로고    scopus 로고
    • Stochastic interplay between mutation and recombination during the acquisition of drug resistance mutations in human immunodeficiency virus type 1
    • Althaus C.L., and Bonhoeffer S. Stochastic interplay between mutation and recombination during the acquisition of drug resistance mutations in human immunodeficiency virus type 1. J. Virol. 79 (2005) 13572-13578
    • (2005) J. Virol. , vol.79 , pp. 13572-13578
    • Althaus, C.L.1    Bonhoeffer, S.2
  • 4
    • 0042208362 scopus 로고    scopus 로고
    • Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
    • Anisimova M., Nielsen R., and Yang Z. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164 (2003) 1229-1236
    • (2003) Genetics , vol.164 , pp. 1229-1236
    • Anisimova, M.1    Nielsen, R.2    Yang, Z.3
  • 5
    • 33644911496 scopus 로고    scopus 로고
    • Recombination estimation under complex evolutionary models with the coalescent composite likelihood method
    • Carvajal-Rodriguez A., Crandall K.A., and Posada D. Recombination estimation under complex evolutionary models with the coalescent composite likelihood method. Mol. Biol. Evol. 23 (2006) 817-827
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 817-827
    • Carvajal-Rodriguez, A.1    Crandall, K.A.2    Posada, D.3
  • 6
    • 34249693632 scopus 로고    scopus 로고
    • Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy
    • Carvajal-Rodriguez A., Crandall K.A., and Posada D. Recombination favors the evolution of drug resistance in HIV-1 during antiretroviral therapy. Infect. Genet. Evol. 7 (2007) 476-483
    • (2007) Infect. Genet. Evol. , vol.7 , pp. 476-483
    • Carvajal-Rodriguez, A.1    Crandall, K.A.2    Posada, D.3
  • 8
    • 0033028201 scopus 로고    scopus 로고
    • Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection
    • Crandall K.A., Kelsey C.R., Imamichi H., Lane C.H., and Salzman N.P. Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol. Biol. Evol. 16 (1999) 372-382
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 372-382
    • Crandall, K.A.1    Kelsey, C.R.2    Imamichi, H.3    Lane, C.H.4    Salzman, N.P.5
  • 10
    • 39649099394 scopus 로고    scopus 로고
    • Drummond, A.J., Rambaut, A., 2006. BEAST v1.4.
    • Drummond, A.J., Rambaut, A., 2006. BEAST v1.4.
  • 12
    • 0031060165 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease
    • Ganeshan S., Dickover R.E., Korber B.M., Bryson Y.J., and Wolinsky S.M. Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J. Virol. 71 (1997) 663-677
    • (1997) J. Virol. , vol.71 , pp. 663-677
    • Ganeshan, S.1    Dickover, R.E.2    Korber, B.M.3    Bryson, Y.J.4    Wolinsky, S.M.5
  • 14
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 15
    • 33646586721 scopus 로고    scopus 로고
    • A Dirichlet process model for detecting positive selection in protein-coding DNA sequences
    • Huelsenbeck J.P., Jain S., Frost S.W., and Pond S.L. A Dirichlet process model for detecting positive selection in protein-coding DNA sequences. Proc. Natl. Acad. Sci. U.S.A. 103 (2006) 6263-6268
    • (2006) Proc. Natl. Acad. Sci. U.S.A. , vol.103 , pp. 6263-6268
    • Huelsenbeck, J.P.1    Jain, S.2    Frost, S.W.3    Pond, S.L.4
  • 16
    • 0028874043 scopus 로고
    • Retroviral recombination can lead to linkage of reverse transcriptase mutations that confer increased zidovudine resistance
    • Kellam P., and Larder B.A. Retroviral recombination can lead to linkage of reverse transcriptase mutations that confer increased zidovudine resistance. J. Virol. 69 (1995) 669-674
    • (1995) J. Virol. , vol.69 , pp. 669-674
    • Kellam, P.1    Larder, B.A.2
  • 18
    • 0030947397 scopus 로고    scopus 로고
    • Divergent patterns of progression to AIDS after infection from the same source: human immunodeficiency virus type 1 evolution and antiviral responses
    • Liu S.L., Schacker T., Musey L., Shriner D., McElrath M.J., Corey L., and Mullins J.I. Divergent patterns of progression to AIDS after infection from the same source: human immunodeficiency virus type 1 evolution and antiviral responses. J. Virol. 71 (1997) 4284-4295
    • (1997) J. Virol. , vol.71 , pp. 4284-4295
    • Liu, S.L.1    Schacker, T.2    Musey, L.3    Shriner, D.4    McElrath, M.J.5    Corey, L.6    Mullins, J.I.7
  • 20
    • 0036199914 scopus 로고    scopus 로고
    • A coalescent based-method for detecting and estimating recombination from gene sequences
    • McVean G.A.T., Awadalla P., and Fearnhead P. A coalescent based-method for detecting and estimating recombination from gene sequences. Genetics 160 (2002) 1231-1241
    • (2002) Genetics , vol.160 , pp. 1231-1241
    • McVean, G.A.T.1    Awadalla, P.2    Fearnhead, P.3
  • 21
    • 0032844935 scopus 로고    scopus 로고
    • Mosaic structure of the human immunodeficiency virus type 1 genome infecting lymphoid cells and the brain: evidence for frequent in vivo recombination events in the evolution of regional populations
    • Morris A., Marsden M., Halcrow K., Hughes E.S., Brettle R.P., Bell J.E., and Simmonds P. Mosaic structure of the human immunodeficiency virus type 1 genome infecting lymphoid cells and the brain: evidence for frequent in vivo recombination events in the evolution of regional populations. J. Virol. 73 (1999) 8720-8731
    • (1999) J. Virol. , vol.73 , pp. 8720-8731
    • Morris, A.1    Marsden, M.2    Halcrow, K.3    Hughes, E.S.4    Brettle, R.P.5    Bell, J.E.6    Simmonds, P.7
  • 22
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • Muse S.V., and Gaut B.S. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11 (1994) 715-724
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 23
    • 0036999990 scopus 로고    scopus 로고
    • Genetic recombination and its role in the development of the HIV-1 pandemic
    • Nájera R., Delgado E., Pérez-Alvarez L., and Thomson M.M. Genetic recombination and its role in the development of the HIV-1 pandemic. AIDS 16 Suppl. 4 (2002) S3-S16
    • (2002) AIDS , vol.16 , Issue.SUPPL. 4
    • Nájera, R.1    Delgado, E.2    Pérez-Alvarez, L.3    Thomson, M.M.4
  • 24
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood methods for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R., and Yang Z. Likelihood methods for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148 (1998) 929-936
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 28
    • 27844569825 scopus 로고    scopus 로고
    • Site-to-site variation of synonymous substitution rates
    • Pond S.K., and Muse S.V. Site-to-site variation of synonymous substitution rates. Mol. Biol. Evol. 22 (2005) 2375-2385
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 2375-2385
    • Pond, S.K.1    Muse, S.V.2
  • 29
    • 17744396121 scopus 로고    scopus 로고
    • Not so different after all: a comparison of methods for detecting amino acid sites under selection
    • Pond S.L.K., and Frost S.D. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol. 22 (2005) 1208-1222
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1208-1222
    • Pond, S.L.K.1    Frost, S.D.2
  • 30
    • 17744395033 scopus 로고    scopus 로고
    • Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
    • Pond S.L.K., and Frost S.D.W. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21 (2005) 2531-2533
    • (2005) Bioinformatics , vol.21 , pp. 2531-2533
    • Pond, S.L.K.1    Frost, S.D.W.2
  • 31
    • 15844406550 scopus 로고    scopus 로고
    • HyPhy: hypothesis testing using phylogenies
    • Pond S.L.K., Frost S.D.W., and Muse S.V. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21 (2005) 676-679
    • (2005) Bioinformatics , vol.21 , pp. 676-679
    • Pond, S.L.K.1    Frost, S.D.W.2    Muse, S.V.3
  • 32
    • 0031773680 scopus 로고    scopus 로고
    • Modeltest: testing the model of DNA substitution
    • Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 33
    • 0034988391 scopus 로고    scopus 로고
    • Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1)
    • Posada D., and Crandall K.A. Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1). Mol. Biol. Evol. 18 (2001) 897-906
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 897-906
    • Posada, D.1    Crandall, K.A.2
  • 34
    • 33646468974 scopus 로고    scopus 로고
    • Genetic analyses reveal structured HIV-1 populations in serially sampled T lymphocytes of patients receiving HAART
    • Potter S.J., Lemey P., Dyer W.B., Sullivan J.S., Chew C.B., Vandamme A.M., Dwyer D.E., and Saksena N.K. Genetic analyses reveal structured HIV-1 populations in serially sampled T lymphocytes of patients receiving HAART. Virology 348 (2006) 35-46
    • (2006) Virology , vol.348 , pp. 35-46
    • Potter, S.J.1    Lemey, P.2    Dyer, W.B.3    Sullivan, J.S.4    Chew, C.B.5    Vandamme, A.M.6    Dwyer, D.E.7    Saksena, N.K.8
  • 35
    • 0034044313 scopus 로고    scopus 로고
    • Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies
    • Rambaut A. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 16 (2000) 395-399
    • (2000) Bioinformatics , vol.16 , pp. 395-399
    • Rambaut, A.1
  • 38
    • 0036828069 scopus 로고    scopus 로고
    • Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration
    • Ross H.A., and Rodrigo A.G. Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J. Virol. 76 (2002) 11715-11720
    • (2002) J. Virol. , vol.76 , pp. 11715-11720
    • Ross, H.A.1    Rodrigo, A.G.2
  • 39
    • 20444366581 scopus 로고    scopus 로고
    • Evolution of human immunodeficiency virus under selection and weak recombination
    • Rouzine I.M., and Coffin J.M. Evolution of human immunodeficiency virus under selection and weak recombination. Genetics 170 (2005) 7-18
    • (2005) Genetics , vol.170 , pp. 7-18
    • Rouzine, I.M.1    Coffin, J.M.2
  • 40
    • 0347513220 scopus 로고    scopus 로고
    • DnaSP, DNA polymorphism analyses by the coalescent and other methods
    • Rozas J., Sanchez-DelBarrio J.C., Messeguer X., and Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
    • (2003) Bioinformatics , vol.19 , pp. 2496-2497
    • Rozas, J.1    Sanchez-DelBarrio, J.C.2    Messeguer, X.3    Rozas, R.4
  • 41
    • 33749827106 scopus 로고    scopus 로고
    • Robust inference of positive selection from recombining coding sequences
    • Scheffler K., Martin D.P., and Seoighe C. Robust inference of positive selection from recombining coding sequences. Bioinformatics 22 (2006) 2493-2499
    • (2006) Bioinformatics , vol.22 , pp. 2493-2499
    • Scheffler, K.1    Martin, D.P.2    Seoighe, C.3
  • 42
    • 0029095624 scopus 로고
    • Natural selection on the gag, pol, and env, genes of human immunodeficiency virus 1 (HIV-1)
    • Seibert S.A., Howell C.Y., Hughes M.K., and Hughes A.L. Natural selection on the gag, pol, and env, genes of human immunodeficiency virus 1 (HIV-1). Mol. Biol. Evol. 12 (1995) 803-813
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 803-813
    • Seibert, S.A.1    Howell, C.Y.2    Hughes, M.K.3    Hughes, A.L.4
  • 44
    • 0037986694 scopus 로고    scopus 로고
    • Potential impact of recombination on sitewise approaches for detecting positive natural selection
    • Shriner D., Nickle D.C., Jensen M.A., and Mullins J.I. Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet. Res. 81 (2003) 115-121
    • (2003) Genet. Res. , vol.81 , pp. 115-121
    • Shriner, D.1    Nickle, D.C.2    Jensen, M.A.3    Mullins, J.I.4
  • 45
    • 1942421715 scopus 로고    scopus 로고
    • Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection
    • Shriner D., Shankarappa R., Jensen M.A., Nickle D.C., Mittler J.E., Margolick J.B., and Mullins J.I. Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection. Genetics 166 (2004) 1155-1164
    • (2004) Genetics , vol.166 , pp. 1155-1164
    • Shriner, D.1    Shankarappa, R.2    Jensen, M.A.3    Nickle, D.C.4    Mittler, J.E.5    Margolick, J.B.6    Mullins, J.I.7
  • 47
    • 0028818258 scopus 로고
    • Convergent evolution within the V3 loop domain of human immunodeficiency virus type 1 in association with disease progression
    • Strunnikova N., Ray S.C., Livingston R.A., Rubalcaba E., and Viscidi R.P. Convergent evolution within the V3 loop domain of human immunodeficiency virus type 1 in association with disease progression. J. Virol. 69 (1995) 7548-7558
    • (1995) J. Virol. , vol.69 , pp. 7548-7558
    • Strunnikova, N.1    Ray, S.C.2    Livingston, R.A.3    Rubalcaba, E.4    Viscidi, R.P.5
  • 48
    • 0032009638 scopus 로고    scopus 로고
    • Evolution of human immunodeficiency virus type 1 in relation to disease progression in children
    • Strunnikova N., Ray S.C., Lancioni C., Nguyen M., and Viscidi R.P. Evolution of human immunodeficiency virus type 1 in relation to disease progression in children. J. Hum. Virol. 1 (1998) 224-239
    • (1998) J. Hum. Virol. , vol.1 , pp. 224-239
    • Strunnikova, N.1    Ray, S.C.2    Lancioni, C.3    Nguyen, M.4    Viscidi, R.P.5
  • 49
    • 0032849322 scopus 로고    scopus 로고
    • A method for detecting positive selection at single amino acid sites
    • Suzuki Y., and Gojobori T. A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16 (1999) 1315-1328
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1315-1328
    • Suzuki, Y.1    Gojobori, T.2
  • 51
    • 39649107373 scopus 로고    scopus 로고
    • Team, R.D.C., 2006. R: a language and environment for statistical computing. http://www.R-project.org (online).
    • Team, R.D.C., 2006. R: a language and environment for statistical computing. http://www.R-project.org (online).
  • 52
    • 4644278569 scopus 로고    scopus 로고
    • Selection in context: patterns of natural selection in the glycoprotein 120 region of human immunodeficiency virus 1 within infected individuals
    • Templeton A.R., Reichert R.A., Weisstein A.E., Yu X.-F., and Markham R.B. Selection in context: patterns of natural selection in the glycoprotein 120 region of human immunodeficiency virus 1 within infected individuals. Genetics 167 (2004) 1547-1561
    • (2004) Genetics , vol.167 , pp. 1547-1561
    • Templeton, A.R.1    Reichert, R.A.2    Weisstein, A.E.3    Yu, X.-F.4    Markham, R.B.5
  • 54
    • 0031574072 scopus 로고    scopus 로고
    • The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24 (1997) 4876-4882
    • (1997) Nucleic Acids Res. , vol.24 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 55
    • 0008890772 scopus 로고    scopus 로고
    • The evolution of HIV. HIV evolution and disease progression via longitudinal studies
    • Crandall K.A. (Ed), The Johns Hopkins University Press
    • Viscidi R. The evolution of HIV. HIV evolution and disease progression via longitudinal studies. In: Crandall K.A. (Ed). The Evolution of HIV (1999), The Johns Hopkins University Press 346-389
    • (1999) The Evolution of HIV , pp. 346-389
    • Viscidi, R.1
  • 57
    • 0016491430 scopus 로고
    • On the number of segregating sites in genetical models without recombination
    • Watterson G.A. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7 (1975) 256-276
    • (1975) Theor. Popul. Biol. , vol.7 , pp. 256-276
    • Watterson, G.A.1
  • 58
    • 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. 20 (2003) 1318-1325
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 1318-1325
    • Williamson, S.1
  • 59
    • 14544287462 scopus 로고    scopus 로고
    • A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients
    • Williamson S., Perry S.M., Bustamante C.D., Orive M.E., Stearns M.N., and Kelly J.K. A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients. Mol. Biol. Evol. 22 (2005) 456-468
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 456-468
    • Williamson, S.1    Perry, S.M.2    Bustamante, C.D.3    Orive, M.E.4    Stearns, M.N.5    Kelly, J.K.6
  • 60
    • 33645229840 scopus 로고    scopus 로고
    • Estimating diversifying selection and functional constraint in the presence of recombination
    • Wilson D.J., and McVean G. Estimating diversifying selection and functional constraint in the presence of recombination. Genetics 172 (2006) 1411-1425
    • (2006) Genetics , vol.172 , pp. 1411-1425
    • Wilson, D.J.1    McVean, G.2
  • 62
    • 0033995286 scopus 로고    scopus 로고
    • Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes
    • Yamaguchi-Kabata Y., and Gojobori T. Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes. J. Virol. 74 (2000) 4335-4350
    • (2000) J. Virol. , vol.74 , pp. 4335-4350
    • Yamaguchi-Kabata, Y.1    Gojobori, T.2
  • 63
    • 0030683599 scopus 로고    scopus 로고
    • PAML: a program package for phylogenetic analysis by maximum likelihood
    • Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13 (1997) 555-556
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 64
    • 0032737463 scopus 로고    scopus 로고
    • Genealogical evidence for positive selection in the nef gene of HIV-1
    • Zanotto P.M.D.A., Kallas E.G., de Souza R.F., and Holmes E.C. Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 153 (1999) 1077-1089
    • (1999) Genetics , vol.153 , pp. 1077-1089
    • Zanotto, P.M.D.A.1    Kallas, E.G.2    de Souza, R.F.3    Holmes, E.C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.