메뉴 건너뛰기




Volumn 60, Issue 6, 2006, Pages 1165-1176

Evolution of intrahost HIV-1 genetic diversity during chronic infection

Author keywords

Approximate Bayesian computation; Demography; Effective population size; HIV 1; Metapopulation

Indexed keywords

BAYESIAN ANALYSIS; EVOLUTION; GENETIC VARIATION; INFECTIOUS DISEASE; METAPOPULATION; MUTATION; POPULATION GENETICS; POPULATION SIZE;

EID: 33748541658     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1554/05-473.1     Document Type: Article
Times cited : (39)

References (53)
  • 2
    • 2442502566 scopus 로고    scopus 로고
    • Mitochondrial cytochrome b DNA variation in the high fecundity Atlantic cod: Trans-Atlantic clines and shallow gene genealogy
    • Árnason, E. 2004. Mitochondrial cytochrome b DNA variation in the high fecundity Atlantic cod: trans-Atlantic clines and shallow gene genealogy. Genetics 166:1871-1875.
    • (2004) Genetics , vol.166 , pp. 1871-1875
    • Árnason, E.1
  • 3
    • 0036964474 scopus 로고    scopus 로고
    • Approximate Bayesian computation in population genetics
    • Beaumont, M. A., W. Zhang, and D. J. Balding. 2002. Approximate Bayesian computation in population genetics. Genetics 162:2025-2035.
    • (2002) Genetics , vol.162 , pp. 2025-2035
    • Beaumont, M.A.1    Zhang, W.2    Balding, D.J.3
  • 5
    • 0038463589 scopus 로고    scopus 로고
    • Selection in a subdivided population with local extinction and recolonization
    • Cherry, J. L. 2003. Selection in a subdivided population with local extinction and recolonization. Genetics 164:789-795.
    • (2003) Genetics , vol.164 , pp. 789-795
    • Cherry, J.L.1
  • 8
    • 0028874989 scopus 로고
    • Effective population size/adult population size ratios in wildlife: A review
    • Frankham, R. 1995. Effective population size/adult population size ratios in wildlife: a review. Genet. Res. 66:95-107.
    • (1995) Genet. Res. , vol.66 , pp. 95-107
    • Frankham, R.1
  • 11
    • 0034082076 scopus 로고    scopus 로고
    • Genetic drift in an infinite population: The pseudohitchhiking model
    • Gillespie, J. H. 2000. Genetic drift in an infinite population: the pseudohitchhiking model. Genetics 155:909-919.
    • (2000) Genetics , vol.155 , pp. 909-919
    • Gillespie, J.H.1
  • 12
    • 0032912338 scopus 로고    scopus 로고
    • Population dynamics of HIV-1 inferred from gene sequences
    • Grassly, N. C., P. H. Harvey, and E. C. Holmes. 1999. Population dynamics of HIV-1 inferred from gene sequences. Genetics 151:427-438.
    • (1999) Genetics , vol.151 , pp. 427-438
    • Grassly, N.C.1    Harvey, P.H.2    Holmes, E.C.3
  • 14
    • 0032568603 scopus 로고    scopus 로고
    • Multiple modes of cellular activation and virus transmission in HIV infection: A role for chronically and latently infected cells in sustaining viral replication
    • Grossman, Z., M. B. Feinberg, and W. E. Paul. 1998. Multiple modes of cellular activation and virus transmission in HIV infection: a role for chronically and latently infected cells in sustaining viral replication. Proc. Natl. Acad. Sci. USA 95:6314-6319.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 6314-6319
    • Grossman, Z.1    Feinberg, M.B.2    Paul, W.E.3
  • 15
    • 0037015074 scopus 로고    scopus 로고
    • Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus)
    • Hauser, L., G. J. Adcock, P. J. Smith, J. H. Bernal Ramírez, and G. R. Carvalho. 2002. Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proc. Natl. Acad. Sci. USA 99:11742-11747.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 11742-11747
    • Hauser, L.1    Adcock, G.J.2    Smith, P.J.3    Bernal Ramírez, J.H.4    Carvalho, G.R.5
  • 16
    • 0015389841 scopus 로고
    • Effective size of populations with overlapping generations
    • Hill, W. G. 1972. Effective size of populations with overlapping generations. Theor. Popul. Biol. 3:278-289.
    • (1972) Theor. Popul. Biol. , vol.3 , pp. 278-289
    • Hill, W.G.1
  • 19
    • 0038192127 scopus 로고    scopus 로고
    • Selective sweeps in the presence of interference among partially linked loci
    • Kim, Y., and W. Stephan. 2003. Selective sweeps in the presence of interference among partially linked loci. Genetics 164:389-398.
    • (2003) Genetics , vol.164 , pp. 389-398
    • Kim, Y.1    Stephan, W.2
  • 20
    • 0002743467 scopus 로고
    • Exchangeability and the evolution of large populations
    • G. Koch and F. Spizzichino, eds. North-Holland, Amsterdam
    • Kingman, J. F. C. 1982a. Exchangeability and the evolution of large populations. Pp. 97-112 in: G. Koch and F. Spizzichino, eds. Exchangeability in Probability and Statistics. North-Holland, Amsterdam.
    • (1982) Exchangeability in Probability and Statistics , pp. 97-112
    • Kingman, J.F.C.1
  • 21
    • 0002556819 scopus 로고
    • On the genealogy of large populations
    • _. 1982b. On the genealogy of large populations. J. Appl. Prob. 19A:27-43.
    • (1982) J. Appl. Prob. , vol.19 A , pp. 27-43
  • 23
    • 0004732896 scopus 로고    scopus 로고
    • Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population
    • Leigh Brown, A. J. 1997. Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population. Proc. Natl. Acad. Sci. USA 94:1862-1865.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 1862-1865
    • Leigh Brown, A.J.1
  • 25
    • 0036838723 scopus 로고    scopus 로고
    • Intrapatient diversity and its correlation with viral set point in human immunodeficiency virus type 1 CRF02-A/GIbNG infection
    • Mani, I., P. Gilbert, J. L. Sankale, G. Eisen, S. Mboup, and P. J. Kanki. 2002. Intrapatient diversity and its correlation with viral set point in human immunodeficiency virus type 1 CRF02-A/GIbNG infection. J. Virol. 76:10745-10755.
    • (2002) J. Virol. , vol.76 , pp. 10745-10755
    • Mani, I.1    Gilbert, P.2    Sankale, J.L.3    Eisen, G.4    Mboup, S.5    Kanki, P.J.6
  • 26
    • 0030060447 scopus 로고    scopus 로고
    • Forward mutation rate of human immunodeficiency virus type 1 in a T lymphoid cell line
    • Mansky, L. M. 1996. Forward mutation rate of human immunodeficiency virus type 1 in a T lymphoid cell line. AIDS Res. Hum. Retroviruses 12:307-314.
    • (1996) AIDS Res. Hum. Retroviruses , vol.12 , pp. 307-314
    • Mansky, L.M.1
  • 28
    • 0037385686 scopus 로고    scopus 로고
    • A novel antiviral intervention results in more accurate assessment of human immunodeficiency virus type 1 replication dynamics and T-cell decay in vivo
    • Markowitz, M., M. Louie, A. Hurley, E. Sun, M. Di Mascio, A. S. Perelson, and D. D. Ho. 2003. A novel antiviral intervention results in more accurate assessment of human immunodeficiency virus type 1 replication dynamics and T-cell decay in vivo. J. Virol. 77:5037-5038.
    • (2003) J. Virol. , vol.77 , pp. 5037-5038
    • Markowitz, M.1    Louie, M.2    Hurley, A.3    Sun, E.4    Di Mascio, M.5    Perelson, A.S.6    Ho, D.D.7
  • 29
    • 0019297501 scopus 로고
    • Genetic variability and effective population size when local extinction and recolonization of subpopulations are frequent
    • Maruyama, T., and M. Kimura. 1980. Genetic variability and effective population size when local extinction and recolonization of subpopulations are frequent. Proc. Natl. Acad. Sci. USA 77:6710-6714.
    • (1980) Proc. Natl. Acad. Sci. USA , vol.77 , pp. 6710-6714
    • Maruyama, T.1    Kimura, M.2
  • 30
    • 0000913208 scopus 로고    scopus 로고
    • Coalescent theory
    • D. J. Balding, M. Bishop, and C. Cannings, eds. John Wiley & Sons, New York
    • Nordborg, M. 2001. Coalescent theory. Pp. 179-212 in D. J. Balding, M. Bishop, and C. Cannings, eds. Handbook of statistical genetics. John Wiley & Sons, New York.
    • (2001) Handbook of Statistical Genetics , pp. 179-212
    • Nordborg, M.1
  • 31
    • 0038650624 scopus 로고    scopus 로고
    • Coalescence in a metapopulation with recurrent local extinction and recolonization
    • Pannell, J. R. 2003. Coalescence in a metapopulation with recurrent local extinction and recolonization. Evolution 57:949-961.
    • (2003) Evolution , vol.57 , pp. 949-961
    • Pannell, J.R.1
  • 32
    • 0032809938 scopus 로고    scopus 로고
    • Neutral genetic diversity in a metapopulation with recurrent local extinction and recolonization
    • Pannell, J. R., and B. Charlesworth. 1999. Neutral genetic diversity in a metapopulation with recurrent local extinction and recolonization. Evolution 53:664-676.
    • (1999) Evolution , vol.53 , pp. 664-676
    • Pannell, J.R.1    Charlesworth, B.2
  • 34
    • 0031694637 scopus 로고    scopus 로고
    • Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade a human immunodeficiency virus type 1
    • Poss, M., A. G. Rodrigo, J. J. Gosink, G. H. Learn, D. de Vange Panteleeff, H. L. Martin Jr., J. Bwayo, J. K. Kreiss, and J. Overbaugh. 1998. Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1. J. Virol. 72:8240-8251.
    • (1998) J. Virol. , vol.72 , pp. 8240-8251
    • Poss, M.1    Rodrigo, A.G.2    Gosink, J.J.3    Learn, G.H.4    De Vange Panteleeff, D.5    Martin Jr., H.L.6    Bwayo, J.7    Kreiss, J.K.8    Overbaugh, J.9
  • 38
    • 17544386547 scopus 로고    scopus 로고
    • Natural selection and the organ-specific differentiation of HIV-1 V3 hypervariable region
    • Sanjuán, R., F. M. Codoñer, A. Moya, and S. F. Elena. 2004. Natural selection and the organ-specific differentiation of HIV-1 V3 hypervariable region. Evolution 58:1185-1194.
    • (2004) Evolution , vol.58 , pp. 1185-1194
    • Sanjuán, R.1    Codoñer, F.M.2    Moya, A.3    Elena, S.F.4
  • 39
    • 0036234481 scopus 로고    scopus 로고
    • Estimation of effective population size of HIV-1 within a host: A pseudomaximum-likelihood approach
    • Seo, T.-K., J. L. Thorne, M. Hasegawa, and H. Kishino. 2002. Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach. Genetics 160:1283-1293.
    • (2002) Genetics , vol.160 , pp. 1283-1293
    • Seo, T.-K.1    Thorne, J.L.2    Hasegawa, M.3    Kishino, H.4
  • 42
    • 4644245699 scopus 로고    scopus 로고
    • Pervasive genomic recombination of HIV-1 in vivo
    • Shriner, D., A. G. Rodrigo, D. C. Nickle, and J. I. Mullins. 2004b. Pervasive genomic recombination of HIV-1 in vivo. Genetics 167:1573-1583.
    • (2004) Genetics , vol.167 , pp. 1573-1583
    • Shriner, D.1    Rodrigo, A.G.2    Nickle, D.C.3    Mullins, J.I.4
  • 43
    • 0017731844 scopus 로고
    • Gene flow and genetic drift in a species subject to frequent local extinctions
    • Slatkin, M. 1977. Gene flow and genetic drift in a species subject to frequent local extinctions. Theor. Popul. Biol. 12:253-262.
    • (1977) Theor. Popul. Biol. , vol.12 , pp. 253-262
    • Slatkin, M.1
  • 45
    • 0024313579 scopus 로고
    • Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
    • Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
    • (1989) Genetics , vol.123 , pp. 585-595
    • Tajima, F.1
  • 46
    • 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., R. A. Reichert, A. E. Weisstein, X.-F. Yu, and R. B. Markham. 2004. Selection in context: patterns of natural selection in the glycoprotein 120 region of human immunodeficiency virus 1 within infected individuals. Genetics 167:1547-1561.
    • (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
  • 47
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 48
    • 0034758281 scopus 로고    scopus 로고
    • Gene genealogies in a metapopulation
    • Wakeley, J., and N. Aliacar. 2001. Gene genealogies in a metapopulation. Genetics 159:893-905.
    • (2001) Genetics , vol.159 , pp. 893-905
    • Wakeley, J.1    Aliacar, N.2
  • 49
    • 0016491430 scopus 로고
    • On the number of segregating sites in genetical models without recombination
    • Watterson, G. A. 1975. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7:256-276.
    • (1975) Theor. Popul. Biol. , vol.7 , pp. 256-276
    • Watterson, G.A.1
  • 50
    • 0038124402 scopus 로고    scopus 로고
    • Fixation probability and time in subdivided populations
    • Whitlock, M. C. 2003. Fixation probability and time in subdivided populations. Genetics 164:767-779.
    • (2003) Genetics , vol.164 , pp. 767-779
    • Whitlock, M.C.1
  • 51
    • 0025599681 scopus 로고
    • Some population genetic consequences of colony formation and extinction: Genetic correlations within founding groups
    • Whitlock, M. C., and D. E. McCauley. 1990. Some population genetic consequences of colony formation and extinction: genetic correlations within founding groups. Evolution 44:1717-1724.
    • (1990) Evolution , vol.44 , pp. 1717-1724
    • Whitlock, M.C.1    McCauley, D.E.2
  • 52
    • 14544287462 scopus 로고    scopus 로고
    • A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients
    • Williamson, S., S. M. Perry, C. D. Bustamante, M. E. Orive, M. N. Stearns, and J. K. Kelly. 2005. A statistical characterization of consistent patterns of human immunodeficiency virus evolution within infected patients. Mol. Biol. Evol. 22:456-468.
    • (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
  • 53
    • 0001771498 scopus 로고
    • Evolution in Mendelian populations
    • Wright, S. 1931. Evolution in Mendelian populations. Genetics 16:97-159.
    • (1931) Genetics , vol.16 , pp. 97-159
    • Wright, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.