메뉴 건너뛰기




Volumn 6, Issue 8, 2011, Pages

Daily sampling of an HIV-1 patient with slowly progressing disease displays persistence of multiple env subpopulations consistent with neutrality

Author keywords

[No Author keywords available]

Indexed keywords

CD4 ANTIGEN; NUCLEIC ACID BASE; NUCLEOTIDE; VIRUS RNA;

EID: 79960976088     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0021747     Document Type: Article
Times cited : (7)

References (78)
  • 1
    • 58149175798 scopus 로고    scopus 로고
    • Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression
    • Lee HY, Perelson AS, Park SC, Leitner T, (2008) Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression. PLoS Comput Biol 4: e1000240.
    • (2008) PLoS Comput Biol , vol.4
    • Lee, H.Y.1    Perelson, A.S.2    Park, S.C.3    Leitner, T.4
  • 2
    • 0032710838 scopus 로고    scopus 로고
    • Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection
    • Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, et al. (1999) Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol 73: 10489-10502.
    • (1999) J Virol , vol.73 , pp. 10489-10502
    • Shankarappa, R.1    Margolick, J.B.2    Gange, S.J.3    Rodrigo, A.G.4    Upchurch, D.5
  • 3
    • 33847246314 scopus 로고    scopus 로고
    • Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics
    • Lemey P, Kosakovsky Pond SL, Drummond AJ, Pybus OG, Shapiro B, et al. (2007) Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Comput Biol 3: e29.
    • (2007) PLoS Comput Biol , vol.3
    • Lemey, P.1    Kosakovsky Pond, S.L.2    Drummond, A.J.3    Pybus, O.G.4    Shapiro, B.5
  • 4
    • 0037389643 scopus 로고    scopus 로고
    • Rapid evolution of the neutralizing antibody response to HIV type 1 infection
    • Richman DD, Wrin T, Little SJ, Petropoulos CJ, (2003) Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc Natl Acad Sci U S A 100: 4144-4149.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 4144-4149
    • Richman, D.D.1    Wrin, T.2    Little, S.J.3    Petropoulos, C.J.4
  • 5
    • 0036841716 scopus 로고    scopus 로고
    • The functional CD8 T cell response to HIV becomes type-specific in progressive disease
    • Lee SK, Xu Z, Lieberman J, Shankar P, (2002) The functional CD8 T cell response to HIV becomes type-specific in progressive disease. J Clin Invest 110: 1339-1347.
    • (2002) J Clin Invest , vol.110 , pp. 1339-1347
    • Lee, S.K.1    Xu, Z.2    Lieberman, J.3    Shankar, P.4
  • 6
    • 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, (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929-936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 7
    • 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 MA, Nickle DC, Mittler JE, et al. (2004) Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection. Genetics 166: 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
  • 8
    • 0004732896 scopus 로고    scopus 로고
    • Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population
    • Brown AJ, (1997) Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population. Proc Natl Acad Sci U S A 94: 1862-1865.
    • (1997) Proc Natl Acad Sci U S A , vol.94 , pp. 1862-1865
    • Brown, A.J.1
  • 9
    • 0029967721 scopus 로고    scopus 로고
    • HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time
    • Perelson AS, Neumann AU, Markowitz M, Leonard JM, Ho DD, (1996) HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271: 1582-1586.
    • (1996) Science , vol.271 , pp. 1582-1586
    • Perelson, A.S.1    Neumann, A.U.2    Markowitz, M.3    Leonard, J.M.4    Ho, D.D.5
  • 10
    • 33751021082 scopus 로고    scopus 로고
    • Stochastic or deterministic: what is the effective population size of HIV-1?
    • Kouyos RD, Althaus CL, Bonhoeffer S, (2006) Stochastic or deterministic: what is the effective population size of HIV-1? Trends Microbiol 14: 507-511.
    • (2006) Trends Microbiol , vol.14 , pp. 507-511
    • Kouyos, R.D.1    Althaus, C.L.2    Bonhoeffer, S.3
  • 11
    • 0032564366 scopus 로고    scopus 로고
    • Stochastic processes strongly influence HIV-1 evolution during suboptimal protease-inhibitor therapy
    • Nijhuis M, Boucher CA, Schipper P, Leitner T, Schuurman R, et al. (1998) Stochastic processes strongly influence HIV-1 evolution during suboptimal protease-inhibitor therapy. Proc Natl Acad Sci U S A 95: 14441-14446.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 14441-14446
    • Nijhuis, M.1    Boucher, C.A.2    Schipper, P.3    Leitner, T.4    Schuurman, R.5
  • 12
    • 33748541658 scopus 로고    scopus 로고
    • Evolution of intrahost HIV-1 genetic diversity during chronic infection
    • Shriner D, Liu Y, Nickle DC, Mullins JI, (2006) Evolution of intrahost HIV-1 genetic diversity during chronic infection. Evolution 60: 1165-1176.
    • (2006) Evolution , vol.60 , pp. 1165-1176
    • Shriner, D.1    Liu, Y.2    Nickle, D.C.3    Mullins, J.I.4
  • 13
    • 4944263648 scopus 로고    scopus 로고
    • A robust measure of HIV-1 population turnover within chronically infected individuals
    • Achaz G, Palmer S, Kearney M, Maldarelli F, Mellors JW, et al. (2004) A robust measure of HIV-1 population turnover within chronically infected individuals. Mol Biol Evol 21: 1902-1912.
    • (2004) Mol Biol Evol , vol.21 , pp. 1902-1912
    • Achaz, G.1    Palmer, S.2    Kearney, M.3    Maldarelli, F.4    Mellors, J.W.5
  • 14
    • 0025124532 scopus 로고
    • Human immunodeficiency virus-infected individuals contain provirus in small numbers of peripheral mononuclear cells and at low copy numbers
    • Simmonds P, Balfe P, Peutherer JF, Ludlam CA, Bishop JO, et al. (1990) Human immunodeficiency virus-infected individuals contain provirus in small numbers of peripheral mononuclear cells and at low copy numbers. J Virol 64: 864-872.
    • (1990) J Virol , vol.64 , pp. 864-872
    • Simmonds, P.1    Balfe, P.2    Peutherer, J.F.3    Ludlam, C.A.4    Bishop, J.O.5
  • 15
    • 41949124934 scopus 로고    scopus 로고
    • Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing
    • Salazar-Gonzalez JF, Bailes E, Pham KT, Salazar MG, Guffey MB, et al. (2008) Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing. J Virol 82: 3952-3970.
    • (2008) J Virol , vol.82 , pp. 3952-3970
    • Salazar-Gonzalez, J.F.1    Bailes, E.2    Pham, K.T.3    Salazar, M.G.4    Guffey, M.B.5
  • 16
    • 1242274541 scopus 로고    scopus 로고
    • Unselected mutations in the human immunodeficiency virus type 1 genome are mostly nonsynonymous and often deleterious
    • Gao F, Chen Y, Levy DN, Conway JA, Kepler TB, et al. (2004) Unselected mutations in the human immunodeficiency virus type 1 genome are mostly nonsynonymous and often deleterious. J Virol 78: 2426-2433.
    • (2004) J Virol , vol.78 , pp. 2426-2433
    • Gao, F.1    Chen, Y.2    Levy, D.N.3    Conway, J.A.4    Kepler, T.B.5
  • 17
    • 0029075130 scopus 로고
    • Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase
    • Mansky LM, Temin HM, (1995) Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J Virol 69: 5087-5094.
    • (1995) J Virol , vol.69 , pp. 5087-5094
    • Mansky, L.M.1    Temin, H.M.2
  • 18
    • 76749139978 scopus 로고    scopus 로고
    • Recombination rate and selection strength in HIV intra-patient evolution
    • Neher RA, Leitner T, (2010) Recombination rate and selection strength in HIV intra-patient evolution. PLoS Comput Biol 6: e1000660.
    • (2010) PLoS Comput Biol , vol.6
    • Neher, R.A.1    Leitner, T.2
  • 19
    • 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
  • 20
    • 0027453041 scopus 로고
    • Statistical tests of neutrality of mutations
    • Fu YX, Li WH, (1993) Statistical tests of neutrality of mutations. Genetics 133: 693-709.
    • (1993) Genetics , vol.133 , pp. 693-709
    • Fu, Y.X.1    Li, W.H.2
  • 21
    • 0033911640 scopus 로고    scopus 로고
    • Hitchhiking under positive Darwinian selection
    • Fay JC, Wu CI, (2000) Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
    • (2000) Genetics , vol.155 , pp. 1405-1413
    • Fay, J.C.1    Wu, C.I.2
  • 22
    • 33751338031 scopus 로고    scopus 로고
    • Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection
    • Edwards CT, Holmes EC, Pybus OG, Wilson DJ, Viscidi RP, et al. (2006) Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection. Genetics 174: 1441-1453.
    • (2006) Genetics , vol.174 , pp. 1441-1453
    • Edwards, C.T.1    Holmes, E.C.2    Pybus, O.G.3    Wilson, D.J.4    Viscidi, R.P.5
  • 23
    • 84857959077 scopus 로고    scopus 로고
    • Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response
    • Troyer RM, McNevin J, Liu Y, Zhang SC, Krizan RW, et al. (2009) Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response. PLoS Pathog 5: e1000365.
    • (2009) PLoS Pathog , vol.5
    • Troyer, R.M.1    McNevin, J.2    Liu, Y.3    Zhang, S.C.4    Krizan, R.W.5
  • 25
    • 27144513224 scopus 로고    scopus 로고
    • Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution
    • Allen TM, Altfeld M, Geer SC, Kalife ET, Moore C, et al. (2005) Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution. J Virol 79: 13239-13249.
    • (2005) J Virol , vol.79 , pp. 13239-13249
    • Allen, T.M.1    Altfeld, M.2    Geer, S.C.3    Kalife, E.T.4    Moore, C.5
  • 26
    • 77649195668 scopus 로고    scopus 로고
    • Compartmentalization and clonal amplification of HIV-1 variants in the cerebrospinal fluid during primary infection
    • Schnell G, Price RW, Swanstrom R, Spudich S, (2010) Compartmentalization and clonal amplification of HIV-1 variants in the cerebrospinal fluid during primary infection. J Virol 84: 2395-2407.
    • (2010) J Virol , vol.84 , pp. 2395-2407
    • Schnell, G.1    Price, R.W.2    Swanstrom, R.3    Spudich, S.4
  • 28
    • 0036720436 scopus 로고    scopus 로고
    • Compartmentalization of surface envelope glycoprotein of human immunodeficiency virus type 1 during acute and chronic infection
    • Zhang L, Rowe L, He T, Chung C, Yu J, et al. (2002) Compartmentalization of surface envelope glycoprotein of human immunodeficiency virus type 1 during acute and chronic infection. J Virol 76: 9465-9473.
    • (2002) J Virol , vol.76 , pp. 9465-9473
    • Zhang, L.1    Rowe, L.2    He, T.3    Chung, C.4    Yu, J.5
  • 29
    • 70349377626 scopus 로고    scopus 로고
    • Lack of in vivo compartmentalization among HIV-1 infected naive and memory CD4+ T cell subsets
    • Heeregrave EJ, Geels MJ, Brenchley JM, Baan E, Ambrozak DR, et al. (2009) Lack of in vivo compartmentalization among HIV-1 infected naive and memory CD4+ T cell subsets. Virology 393: 24-32.
    • (2009) Virology , vol.393 , pp. 24-32
    • Heeregrave, E.J.1    Geels, M.J.2    Brenchley, J.M.3    Baan, E.4    Ambrozak, D.R.5
  • 30
    • 0033786824 scopus 로고    scopus 로고
    • Differential coreceptor expression allows for independent evolution of non-syncytium-inducing and syncytium-inducing HIV-1
    • van Rij RP, Blaak H, Visser JA, Brouwer M, Rientsma R, et al. (2000) Differential coreceptor expression allows for independent evolution of non-syncytium-inducing and syncytium-inducing HIV-1. J Clin Invest 106: 1039-1052.
    • (2000) J Clin Invest , vol.106 , pp. 1039-1052
    • van Rij, R.P.1    Blaak, H.2    Visser, J.A.3    Brouwer, M.4    Rientsma, R.5
  • 31
    • 0037456827 scopus 로고    scopus 로고
    • Antibody neutralization and escape by HIV-1
    • Wei X, Decker JM, Wang S, Hui H, Kappes JC, et al. (2003) Antibody neutralization and escape by HIV-1. Nature 422: 307-312.
    • (2003) Nature , vol.422 , pp. 307-312
    • Wei, X.1    Decker, J.M.2    Wang, S.3    Hui, H.4    Kappes, J.C.5
  • 32
    • 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 EM, Pisas L, van Nuenen AC, Schuitemaker H, (2008) Autologous neutralizing humoral immunity and evolution of the viral envelope in the course of subtype B human immunodeficiency virus type 1 infection. J Virol 82: 7932-7941.
    • (2008) J Virol , vol.82 , pp. 7932-7941
    • Bunnik, E.M.1    Pisas, L.2    van Nuenen, A.C.3    Schuitemaker, H.4
  • 33
    • 0025267919 scopus 로고
    • Rapid development of isolate-specific neutralizing antibodies after primary HIV-1 infection and consequent emergence of virus variants which resist neutralization by autologous sera
    • Albert J, Abrahamsson B, Nagy K, Aurelius E, Gaines H, et al. (1990) Rapid development of isolate-specific neutralizing antibodies after primary HIV-1 infection and consequent emergence of virus variants which resist neutralization by autologous sera. AIDS 4: 107-112.
    • (1990) AIDS , vol.4 , pp. 107-112
    • Albert, J.1    Abrahamsson, B.2    Nagy, K.3    Aurelius, E.4    Gaines, H.5
  • 34
    • 29444442970 scopus 로고    scopus 로고
    • Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection
    • Frost SD, Wrin T, Smith DM, Kosakovsky Pond SL, Liu Y, et al. (2005) Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc Natl Acad Sci U S A 102: 18514-18519.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 18514-18519
    • Frost, S.D.1    Wrin, T.2    Smith, D.M.3    Kosakovsky Pond, S.L.4    Liu, Y.5
  • 35
    • 59449083486 scopus 로고    scopus 로고
    • The generation and maintenance of genetic variation by frequency-dependent selection: constructing polymorphisms under the pairwise interaction model
    • Trotter MV, Spencer HG, (2008) The generation and maintenance of genetic variation by frequency-dependent selection: constructing polymorphisms under the pairwise interaction model. Genetics 180: 1547-1557.
    • (2008) Genetics , vol.180 , pp. 1547-1557
    • Trotter, M.V.1    Spencer, H.G.2
  • 36
    • 0036135771 scopus 로고    scopus 로고
    • Frequency-dependent selection in human immunodeficiency virus type 1
    • Yuste E, Moya A, Lopez-Galindez C, (2002) Frequency-dependent selection in human immunodeficiency virus type 1. J Gen Virol 83: 103-106.
    • (2002) J Gen Virol , vol.83 , pp. 103-106
    • Yuste, E.1    Moya, A.2    Lopez-Galindez, C.3
  • 37
    • 34249744471 scopus 로고    scopus 로고
    • Frequency-Dependent Selection in a Periodic Environment
    • Forster R, Wilke CO, (2007) Frequency-Dependent Selection in a Periodic Environment. Physica A 381: 255-264.
    • (2007) Physica A , vol.381 , pp. 255-264
    • Forster, R.1    Wilke, C.O.2
  • 39
    • 44149089266 scopus 로고    scopus 로고
    • Genetic drift of norovirus genotype GII-4 in seven consecutive epidemic seasons in Hungary
    • Reuter G, Pankovics P, Szucs G, (2008) Genetic drift of norovirus genotype GII-4 in seven consecutive epidemic seasons in Hungary. J Clin Virol 42: 135-140.
    • (2008) J Clin Virol , vol.42 , pp. 135-140
    • Reuter, G.1    Pankovics, P.2    Szucs, G.3
  • 40
    • 0036928543 scopus 로고    scopus 로고
    • Sequence diversity of the capsid gene and the nonstructural gene NS2B of dengue-3 virus in vivo
    • Wang WK, Sung TL, Lee CN, Lin TY, King CC, (2002) Sequence diversity of the capsid gene and the nonstructural gene NS2B of dengue-3 virus in vivo. Virology 303: 181-191.
    • (2002) Virology , vol.303 , pp. 181-191
    • Wang, W.K.1    Sung, T.L.2    Lee, C.N.3    Lin, T.Y.4    King, C.C.5
  • 41
    • 33846007284 scopus 로고    scopus 로고
    • Stochastic processes are key determinants of short-term evolution in influenza a virus
    • Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, et al. (2006) Stochastic processes are key determinants of short-term evolution in influenza a virus. PLoS Pathog 2: e125.
    • (2006) PLoS Pathog , vol.2
    • Nelson, M.I.1    Simonsen, L.2    Viboud, C.3    Miller, M.A.4    Taylor, J.5
  • 42
    • 0034049454 scopus 로고    scopus 로고
    • Evolutionary rate and genetic drift of hepatitis C virus are not correlated with the host immune response: studies of infected donor-recipient clusters
    • Allain JP, Dong Y, Vandamme AM, Moulton V, Salemi M, (2000) Evolutionary rate and genetic drift of hepatitis C virus are not correlated with the host immune response: studies of infected donor-recipient clusters. J Virol 74: 2541-2549.
    • (2000) J Virol , vol.74 , pp. 2541-2549
    • Allain, J.P.1    Dong, Y.2    Vandamme, A.M.3    Moulton, V.4    Salemi, M.5
  • 43
    • 0036234481 scopus 로고    scopus 로고
    • Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach
    • Seo TK, Thorne JL, Hasegawa M, Kishino H, (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
  • 44
    • 77955653140 scopus 로고    scopus 로고
    • Genetic composition of replication competent clonal HIV-1 variants isolated from peripheral blood mononuclear cells (PBMC), HIV-1 proviral DNA from PBMC and HIV-1 RNA in serum in the course of HIV-1 infection
    • Edo-Matas D, van Gils MJ, Bowles EJ, Navis M, Rachinger A, et al. (2010) Genetic composition of replication competent clonal HIV-1 variants isolated from peripheral blood mononuclear cells (PBMC), HIV-1 proviral DNA from PBMC and HIV-1 RNA in serum in the course of HIV-1 infection. Virology 405: 492-504.
    • (2010) Virology , vol.405 , pp. 492-504
    • Edo-Matas, D.1    van Gils, M.J.2    Bowles, E.J.3    Navis, M.4    Rachinger, A.5
  • 45
    • 77957199746 scopus 로고    scopus 로고
    • Genetic analyses of HIV-1 env sequences demonstrate limited compartmentalization in breast milk and suggest viral replication within the breast that increases with mastitis
    • Gantt S, Carlsson J, Heath L, Bull ME, Shetty AK, et al. (2010) Genetic analyses of HIV-1 env sequences demonstrate limited compartmentalization in breast milk and suggest viral replication within the breast that increases with mastitis. J Virol 84: 10812-10819.
    • (2010) J Virol , vol.84 , pp. 10812-10819
    • Gantt, S.1    Carlsson, J.2    Heath, L.3    Bull, M.E.4    Shetty, A.K.5
  • 46
    • 67049134469 scopus 로고    scopus 로고
    • Cross-sectional characterization of HIV-1 env compartmentalization in cerebrospinal fluid over the full disease course
    • Harrington PR, Schnell G, Letendre SL, Ritola K, Robertson K, et al. (2009) Cross-sectional characterization of HIV-1 env compartmentalization in cerebrospinal fluid over the full disease course. AIDS 23: 907-915.
    • (2009) AIDS , vol.23 , pp. 907-915
    • Harrington, P.R.1    Schnell, G.2    Letendre, S.L.3    Ritola, K.4    Robertson, K.5
  • 47
    • 66149133580 scopus 로고    scopus 로고
    • Major coexisting human immunodeficiency virus type 1 env gene subpopulations in the peripheral blood are produced by cells with similar turnover rates and show little evidence of genetic compartmentalization
    • Ince WL, Harrington PR, Schnell GL, Patel-Chhabra M, Burch CL, et al. (2009) Major coexisting human immunodeficiency virus type 1 env gene subpopulations in the peripheral blood are produced by cells with similar turnover rates and show little evidence of genetic compartmentalization. J Virol 83: 4068-4080.
    • (2009) J Virol , vol.83 , pp. 4068-4080
    • Ince, W.L.1    Harrington, P.R.2    Schnell, G.L.3    Patel-Chhabra, M.4    Burch, C.L.5
  • 48
    • 0242331608 scopus 로고    scopus 로고
    • HIV-1 in genital tract and plasma of women: compartmentalization of viral sequences, coreceptor usage, and glycosylation
    • Kemal KS, Foley B, Burger H, Anastos K, Minkoff H, et al. (2003) HIV-1 in genital tract and plasma of women: compartmentalization of viral sequences, coreceptor usage, and glycosylation. Proc Natl Acad Sci U S A 100: 12972-12977.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 12972-12977
    • Kemal, K.S.1    Foley, B.2    Burger, H.3    Anastos, K.4    Minkoff, H.5
  • 49
    • 0035162203 scopus 로고    scopus 로고
    • Despite high concordance, distinct mutational and phenotypic drug resistance profiles in human immunodeficiency virus type 1 RNA are observed in gastrointestinal mucosal biopsy specimens and peripheral blood mononuclear cells compared with plasma
    • Poles MA, Elliott J, Vingerhoets J, Michiels L, Scholliers A, et al. (2001) Despite high concordance, distinct mutational and phenotypic drug resistance profiles in human immunodeficiency virus type 1 RNA are observed in gastrointestinal mucosal biopsy specimens and peripheral blood mononuclear cells compared with plasma. J Infect Dis 183: 143-148.
    • (2001) J Infect Dis , vol.183 , pp. 143-148
    • Poles, M.A.1    Elliott, J.2    Vingerhoets, J.3    Michiels, L.4    Scholliers, A.5
  • 50
    • 0028874048 scopus 로고
    • Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection
    • Ho DD, Neumann AU, Perelson AS, Chen W, Leonard JM, et al. (1995) Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 373: 123-126.
    • (1995) Nature , vol.373 , pp. 123-126
    • Ho, D.D.1    Neumann, A.U.2    Perelson, A.S.3    Chen, W.4    Leonard, J.M.5
  • 51
    • 0028811974 scopus 로고
    • Viral dynamics in human immunodeficiency virus type 1 infection
    • Wei X, Ghosh SK, Taylor ME, Johnson VA, Emini EA, et al. (1995) Viral dynamics in human immunodeficiency virus type 1 infection. Nature 373: 117-122.
    • (1995) Nature , vol.373 , pp. 117-122
    • Wei, X.1    Ghosh, S.K.2    Taylor, M.E.3    Johnson, V.A.4    Emini, E.A.5
  • 52
    • 70349204366 scopus 로고    scopus 로고
    • Evidence for limited genetic compartmentalization of HIV-1 between lung and blood
    • Heath L, Fox A, McClure J, Diem K, van't Wout AB, et al. (2009) Evidence for limited genetic compartmentalization of HIV-1 between lung and blood. PLoS One 4: e6949.
    • (2009) PLoS One , vol.4
    • Heath, L.1    Fox, A.2    McClure, J.3    Diem, K.4    van't Wout, A.B.5
  • 53
    • 0026064626 scopus 로고
    • Discontinuous sequence change of human immunodeficiency virus (HIV) type 1 env sequences in plasma viral and lymphocyte-associated proviral populations in vivo: implications for models of HIV pathogenesis
    • Simmonds P, Zhang LQ, McOmish F, Balfe P, Ludlam CA, et al. (1991) Discontinuous sequence change of human immunodeficiency virus (HIV) type 1 env sequences in plasma viral and lymphocyte-associated proviral populations in vivo: implications for models of HIV pathogenesis. J Virol 65: 6266-6276.
    • (1991) J Virol , vol.65 , pp. 6266-6276
    • Simmonds, P.1    Zhang, L.Q.2    McOmish, F.3    Balfe, P.4    Ludlam, C.A.5
  • 54
    • 33748925430 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection, and these modifications affect antibody neutralization sensitivity
    • Sagar M, Wu X, Lee S, Overbaugh J, (2006) Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection, and these modifications affect antibody neutralization sensitivity. J Virol 80: 9586-9598.
    • (2006) J Virol , vol.80 , pp. 9586-9598
    • Sagar, M.1    Wu, X.2    Lee, S.3    Overbaugh, J.4
  • 55
    • 0031060165 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease
    • Ganeshan S, Dickover RE, Korber BT, Bryson YJ, Wolinsky SM, (1997) Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J Virol 71: 663-677.
    • (1997) J Virol , vol.71 , pp. 663-677
    • Ganeshan, S.1    Dickover, R.E.2    Korber, B.T.3    Bryson, Y.J.4    Wolinsky, S.M.5
  • 56
    • 0027957791 scopus 로고
    • Nevirapine resistance mutations of human immunodeficiency virus type 1 selected during therapy
    • Richman DD, Havlir D, Corbeil J, Looney D, Ignacio C, et al. (1994) Nevirapine resistance mutations of human immunodeficiency virus type 1 selected during therapy. J Virol 68: 1660-1666.
    • (1994) J Virol , vol.68 , pp. 1660-1666
    • Richman, D.D.1    Havlir, D.2    Corbeil, J.3    Looney, D.4    Ignacio, C.5
  • 57
    • 24644460976 scopus 로고    scopus 로고
    • Human immunodeficiency virus mutagenesis during antiviral therapy: impact of drug-resistant reverse transcriptase and nucleoside and nonnucleoside reverse transcriptase inhibitors on human immunodeficiency virus type 1 mutation frequencies
    • Chen R, Yokoyama M, Sato H, Reilly C, Mansky LM, (2005) Human immunodeficiency virus mutagenesis during antiviral therapy: impact of drug-resistant reverse transcriptase and nucleoside and nonnucleoside reverse transcriptase inhibitors on human immunodeficiency virus type 1 mutation frequencies. J Virol 79: 12045-12057.
    • (2005) J Virol , vol.79 , pp. 12045-12057
    • Chen, R.1    Yokoyama, M.2    Sato, H.3    Reilly, C.4    Mansky, L.M.5
  • 58
    • 0028821731 scopus 로고
    • Long-term survivors of HIV-1 infection
    • Klein MR, Miedema F, (1995) Long-term survivors of HIV-1 infection. Trends Microbiol 3: 386-391.
    • (1995) Trends Microbiol , vol.3 , pp. 386-391
    • Klein, M.R.1    Miedema, F.2
  • 59
    • 0034691639 scopus 로고    scopus 로고
    • An AB recombinant and its parental HIV type 1 strains in the area of the former Soviet Union: low requirements for sequence identity in recombination. UNAIDS Virus Isolation Network
    • Liitsola K, Holm K, Bobkov A, Pokrovsky V, Smolskaya T, et al. (2000) An AB recombinant and its parental HIV type 1 strains in the area of the former Soviet Union: low requirements for sequence identity in recombination. UNAIDS Virus Isolation Network. AIDS Res Hum Retroviruses 16: 1047-1053.
    • (2000) AIDS Res Hum Retroviruses , vol.16 , pp. 1047-1053
    • Liitsola, K.1    Holm, K.2    Bobkov, A.3    Pokrovsky, V.4    Smolskaya, T.5
  • 60
    • 84856117275 scopus 로고    scopus 로고
    • (1996) Se-Al: Sequence Alignment Editor, Available from
    • Rambaut A, (1996) (1996) Se-Al: Sequence Alignment Editor, Available fromhttp://tree.bio.ed.ac.uk/software/seal/.
    • (1996)
    • Rambaut, A.1
  • 61
    • 0031773680 scopus 로고    scopus 로고
    • MODELTEST: testing the model of DNA substitution
    • Posada D, Crandall KA, (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 62
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S, Gascuel O, (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
    • (2003) Syst Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 63
    • 33645108873 scopus 로고    scopus 로고
    • LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
    • Kuhner MK, (2006) LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 22: 768-770.
    • (2006) Bioinformatics , vol.22 , pp. 768-770
    • Kuhner, M.K.1
  • 66
    • 55049120771 scopus 로고    scopus 로고
    • An exploratory algorithm to identify intra-host recombinant viral sequences
    • Salemi M, Gray RR, Goodenow MM, (2008) An exploratory algorithm to identify intra-host recombinant viral sequences. Mol Phylogenet Evol 49: 618-628.
    • (2008) Mol Phylogenet Evol , vol.49 , pp. 618-628
    • Salemi, M.1    Gray, R.R.2    Goodenow, M.M.3
  • 67
    • 1542347067 scopus 로고    scopus 로고
    • Neighbor-net: an agglomerative method for the construction of phylogenetic networks
    • Bryant D, Moulton V, (2004) Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21: 255-265.
    • (2004) Mol Biol Evol , vol.21 , pp. 255-265
    • Bryant, D.1    Moulton, V.2
  • 68
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson DH, Bryant D, (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254-267.
    • (2006) Mol Biol Evol , vol.23 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2
  • 69
    • 33646167864 scopus 로고    scopus 로고
    • A simple and robust statistical test for detecting the presence of recombination
    • Bruen TC, Philippe H, Bryant D, (2006) A simple and robust statistical test for detecting the presence of recombination. Genetics 172: 2665-2681.
    • (2006) Genetics , vol.172 , pp. 2665-2681
    • Bruen, T.C.1    Philippe, H.2    Bryant, D.3
  • 70
    • 0022211482 scopus 로고
    • Statistical properties of the number of recombination events in the history of a sample of DNA sequences
    • Hudson RR, Kaplan NL, (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164.
    • (1985) Genetics , vol.111 , pp. 147-164
    • Hudson, R.R.1    Kaplan, N.L.2
  • 72
    • 14544275616 scopus 로고    scopus 로고
    • A genetic algorithm approach to detecting lineage-specific variation in selection pressure
    • Pond SL, Frost SD, (2005) A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol Biol Evol 22: 478-485.
    • (2005) Mol Biol Evol , vol.22 , pp. 478-485
    • Pond, S.L.1    Frost, S.D.2
  • 73
    • 17744395033 scopus 로고    scopus 로고
    • Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
    • Pond SL, Frost SD, (2005) Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21: 2531-2533.
    • (2005) Bioinformatics , vol.21 , pp. 2531-2533
    • Pond, S.L.1    Frost, S.D.2
  • 74
    • 15844406550 scopus 로고    scopus 로고
    • HyPhy: hypothesis testing using phylogenies
    • Pond SL, Frost SD, Muse SV, (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679.
    • (2005) Bioinformatics , vol.21 , pp. 676-679
    • Pond, S.L.1    Frost, S.D.2    Muse, S.V.3
  • 76
    • 77649338614 scopus 로고    scopus 로고
    • The evolutionary rate dynamically tracks changes in HIV-1 epidemics: Application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data
    • In Press, Corrected Proof
    • Maljkovic Berry I, Athreya G, Kothari M, Daniels M, Bruno WJ, et al. (2009) The evolutionary rate dynamically tracks changes in HIV-1 epidemics: Application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data. Epidemics In Press, Corrected Proof.
    • (2009) Epidemics
    • Maljkovic Berry, I.1    Athreya, G.2    Kothari, M.3    Daniels, M.4    Bruno, W.J.5
  • 77
    • 34648830194 scopus 로고    scopus 로고
    • Unequal Evolutionary Rates in the Human Immunodeficiency Virus Type 1 (HIV-1) Pandemic: the Evolutionary Rate of HIV-1 Slows Down When the Epidemic Rate Increases
    • Maljkovic Berry I, Ribeiro R, Kothari M, Athreya G, Daniels M, et al. (2007) Unequal Evolutionary Rates in the Human Immunodeficiency Virus Type 1 (HIV-1) Pandemic: the Evolutionary Rate of HIV-1 Slows Down When the Epidemic Rate Increases. J Virol 81: 10625-10635.
    • (2007) J Virol , vol.81 , pp. 10625-10635
    • Maljkovic Berry, I.1    Ribeiro, R.2    Kothari, M.3    Athreya, G.4    Daniels, M.5
  • 78
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
    • (2007) BMC Evol Biol , vol.7 , pp. 214
    • Drummond, A.J.1    Rambaut, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.