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Volumn 8, Issue 6, 2013, Pages

HIV-1 Clade B pol Evolution following Primary Infection

Author keywords

[No Author keywords available]

Indexed keywords

ANTIRETROVIRUS AGENT; CD4 ANTIGEN; HLA ANTIGEN; NUCLEOTIDE; POL PROTEIN;

EID: 84879509059     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0068188     Document Type: Article
Times cited : (40)

References (34)
  • 1
    • 0034625771 scopus 로고    scopus 로고
    • Timing the ancestor of the HIV-1 pandemic strains
    • Korber B, Muldoon M, Theiler J, Gao F, Gupta R, et al. (2000) Timing the ancestor of the HIV-1 pandemic strains. Science 288: 1789-1796.
    • (2000) Science , vol.288 , pp. 1789-1796
    • Korber, B.1    Muldoon, M.2    Theiler, J.3    Gao, F.4    Gupta, R.5
  • 2
    • 0031010764 scopus 로고    scopus 로고
    • Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history
    • Leitner T, Kumar S, Albert J, (1997) Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history. J Virol 71: 4761-4770.
    • (1997) J Virol , vol.71 , pp. 4761-4770
    • Leitner, T.1    Kumar, S.2    Albert, J.3
  • 3
    • 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
  • 4
    • 0026476474 scopus 로고
    • Relationship of human immunodeficiency virus type 1 sequence heterogeneity to stage of disease
    • McNearney T, Hornickova Z, Markham R, Birdwell A, Arens M, et al. (1992) Relationship of human immunodeficiency virus type 1 sequence heterogeneity to stage of disease. Proc Natl Acad Sci U S A 89: 10247-10251.
    • (1992) Proc Natl Acad Sci U S A , vol.89 , pp. 10247-10251
    • McNearney, T.1    Hornickova, Z.2    Markham, R.3    Birdwell, A.4    Arens, M.5
  • 5
    • 0026695382 scopus 로고
    • HIV-1 genomic RNA diversification following sexual and parenteral virus transmission
    • Wolfs TF, Zwart G, Bakker M, Goudsmit J, (1992) HIV-1 genomic RNA diversification following sexual and parenteral virus transmission. Virology 189: 103-110.
    • (1992) Virology , vol.189 , pp. 103-110
    • Wolfs, T.F.1    Zwart, G.2    Bakker, M.3    Goudsmit, J.4
  • 6
    • 44649102135 scopus 로고    scopus 로고
    • Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
    • Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, et al. (2008) Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A 105: 7552-7557.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 7552-7557
    • Keele, B.F.1    Giorgi, E.E.2    Salazar-Gonzalez, J.F.3    Decker, J.M.4    Pham, K.T.5
  • 7
    • 33750297873 scopus 로고    scopus 로고
    • HIV evolutionary dynamics within and among hosts
    • Lemey P, Rambaut A, Pybus OG, (2006) HIV evolutionary dynamics within and among hosts. AIDS Rev 8: 125-140.
    • (2006) AIDS Rev , vol.8 , pp. 125-140
    • Lemey, P.1    Rambaut, A.2    Pybus, O.G.3
  • 9
    • 0037302428 scopus 로고    scopus 로고
    • Comprehensive epitope analysis of human immunodeficiency virus type 1 (HIV-1)-specific T-cell responses directed against the entire expressed HIV-1 genome demonstrate broadly directed responses, but no correlation to viral load
    • Addo MM, Yu XG, Rathod A, Cohen D, Eldridge RL, et al. (2003) Comprehensive epitope analysis of human immunodeficiency virus type 1 (HIV-1)-specific T-cell responses directed against the entire expressed HIV-1 genome demonstrate broadly directed responses, but no correlation to viral load. J Virol 77: 2081-2092.
    • (2003) J Virol , vol.77 , pp. 2081-2092
    • Addo, M.M.1    Yu, X.G.2    Rathod, A.3    Cohen, D.4    Eldridge, R.L.5
  • 10
  • 11
    • 72849114288 scopus 로고    scopus 로고
    • Quantifying differences in the tempo of human immunodeficiency virus type 1 subtype evolution
    • Abecasis AB, Vandamme AM, Lemey P, (2009) Quantifying differences in the tempo of human immunodeficiency virus type 1 subtype evolution. J Virol 83: 12917-12924.
    • (2009) J Virol , vol.83 , pp. 12917-12924
    • Abecasis, A.B.1    Vandamme, A.M.2    Lemey, P.3
  • 12
    • 36348971793 scopus 로고    scopus 로고
    • Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1
    • Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, et al. (2007) Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1. J Virol 81: 13050-13056.
    • (2007) J Virol , vol.81 , pp. 13050-13056
    • Gifford, R.J.1    de Oliveira, T.2    Rambaut, A.3    Pybus, O.G.4    Dunn, D.5
  • 13
    • 58849110598 scopus 로고    scopus 로고
    • A public health model for the molecular surveillance of HIV transmission in San Diego, California
    • Smith DM, May SJ, Tweeten S, Drumright L, Pacold ME, et al. (2009) A public health model for the molecular surveillance of HIV transmission in San Diego, California. AIDS 23: 225-232.
    • (2009) AIDS , vol.23 , pp. 225-232
    • Smith, D.M.1    May, S.J.2    Tweeten, S.3    Drumright, L.4    Pacold, M.E.5
  • 14
    • 0037043652 scopus 로고    scopus 로고
    • Antiretroviral-drug resistance among patients recently infected with HIV
    • Little SJ, Holte S, Routy JP, Daar ES, Markowitz M, et al. (2002) Antiretroviral-drug resistance among patients recently infected with HIV. N Engl J Med 347: 385-394.
    • (2002) N Engl J Med , vol.347 , pp. 385-394
    • Little, S.J.1    Holte, S.2    Routy, J.P.3    Daar, E.S.4    Markowitz, M.5
  • 15
    • 33748428894 scopus 로고    scopus 로고
    • A multicenter observational study of the potential benefits of initiating combination antiretroviral therapy during acute HIV infection
    • Hecht FM, Wang L, Collier A, Little S, Markowitz M, et al. (2006) A multicenter observational study of the potential benefits of initiating combination antiretroviral therapy during acute HIV infection. J Infect Dis 194: 725-733.
    • (2006) J Infect Dis , vol.194 , pp. 725-733
    • Hecht, F.M.1    Wang, L.2    Collier, A.3    Little, S.4    Markowitz, M.5
  • 16
    • 84155162517 scopus 로고    scopus 로고
    • Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men
    • Pacold ME, Pond SL, Wagner GA, Delport W, Bourque DL, et al. (2012) Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men. AIDS 26: 157-165.
    • (2012) AIDS , vol.26 , pp. 157-165
    • Pacold, M.E.1    Pond, S.L.2    Wagner, G.A.3    Delport, W.4    Bourque, D.L.5
  • 18
    • 73449085165 scopus 로고    scopus 로고
    • An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1
    • Kosakovsky Pond SL, Posada D, Stawiski E, Chappey C, Poon AF, et al. (2009) An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol 5: e1000581.
    • (2009) PLoS Comput Biol , vol.5
    • Kosakovsky Pond, S.L.1    Posada, D.2    Stawiski, E.3    Chappey, C.4    Poon, A.F.5
  • 19
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • Tamura K, Nei M, (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512-526.
    • (1993) Mol Biol Evol , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 20
    • 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
  • 21
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: a maximum likelihood approach
    • Felsenstein J, (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 22
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • Muse SV, Gaut BS, (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11: 715-724.
    • (1994) Mol Biol Evol , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 25
    • 33748919693 scopus 로고    scopus 로고
    • Selection on the human immunodeficiency virus type 1 proteome following primary infection
    • Liu Y, McNevin J, Cao J, Zhao H, Genowati I, et al. (2006) Selection on the human immunodeficiency virus type 1 proteome following primary infection. J Virol 80: 9519-9529.
    • (2006) J Virol , vol.80 , pp. 9519-9529
    • Liu, Y.1    McNevin, J.2    Cao, J.3    Zhao, H.4    Genowati, I.5
  • 26
    • 84855876436 scopus 로고    scopus 로고
    • Inconsistencies in estimating the age of HIV-1 subtypes due to heterotachy
    • Wertheim JO, Fourment M, Kosakovsky Pond SL, (2012) Inconsistencies in estimating the age of HIV-1 subtypes due to heterotachy. Mol Biol Evol 29: 451-456.
    • (2012) Mol Biol Evol , vol.29 , pp. 451-456
    • Wertheim, J.O.1    Fourment, M.2    Kosakovsky Pond, S.L.3
  • 27
    • 15444367844 scopus 로고    scopus 로고
    • Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups
    • Hue S, Pillay D, Clewley JP, Pybus OG, (2005) Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proc Natl Acad Sci U S A 102: 4425-4429.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 4425-4429
    • Hue, S.1    Pillay, D.2    Clewley, J.P.3    Pybus, O.G.4
  • 28
    • 50949117244 scopus 로고    scopus 로고
    • Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection
    • Brumme ZL, Brumme CJ, Carlson J, Streeck H, John M, et al. (2008) Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection. J Virol 82: 9216-9227.
    • (2008) J Virol , vol.82 , pp. 9216-9227
    • Brumme, Z.L.1    Brumme, C.J.2    Carlson, J.3    Streeck, H.4    John, M.5
  • 29
    • 84861214061 scopus 로고    scopus 로고
    • Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection
    • Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, et al. (2012) Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog 8: e1002529.
    • (2012) PLoS Pathog , vol.8
    • Henn, M.R.1    Boutwell, C.L.2    Charlebois, P.3    Lennon, N.J.4    Power, K.A.5
  • 30
    • 49849087657 scopus 로고    scopus 로고
    • Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection
    • Brumme ZL, Tao I, Szeto S, Brumme CJ, Carlson JM, et al. (2008) Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection. AIDS 22: 1277-1286.
    • (2008) AIDS , vol.22 , pp. 1277-1286
    • Brumme, Z.L.1    Tao, I.2    Szeto, S.3    Brumme, C.J.4    Carlson, J.M.5
  • 31
    • 34547643061 scopus 로고    scopus 로고
    • Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1
    • Brumme ZL, Brumme CJ, Heckerman D, Korber BT, Daniels M, et al. (2007) Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1. PLoS Pathog 3: e94.
    • (2007) PLoS Pathog , vol.3
    • Brumme, Z.L.1    Brumme, C.J.2    Heckerman, D.3    Korber, B.T.4    Daniels, M.5
  • 32
    • 55249118583 scopus 로고    scopus 로고
    • Transmission cluster of multiclass highly drug-resistant HIV-1 among 9 men who have sex with men in Seattle/King County, WA, 2005-2007
    • Buskin SE, Ellis GM, Pepper GG, Frenkel LM, Pergam SA, et al. (2008) Transmission cluster of multiclass highly drug-resistant HIV-1 among 9 men who have sex with men in Seattle/King County, WA, 2005-2007. J Acquir Immune Defic Syndr 49: 205-211.
    • (2008) J Acquir Immune Defic Syndr , vol.49 , pp. 205-211
    • Buskin, S.E.1    Ellis, G.M.2    Pepper, G.G.3    Frenkel, L.M.4    Pergam, S.A.5
  • 33
    • 12144254038 scopus 로고    scopus 로고
    • Transmission of HIV-1 during primary infection: relationship to sexual risk and sexually transmitted infections
    • Pao D, Fisher M, Hue S, Dean G, Murphy G, et al. (2005) Transmission of HIV-1 during primary infection: relationship to sexual risk and sexually transmitted infections. Aids 19: 85-90.
    • (2005) Aids , vol.19 , pp. 85-90
    • Pao, D.1    Fisher, M.2    Hue, S.3    Dean, G.4    Murphy, G.5
  • 34
    • 2142768288 scopus 로고    scopus 로고
    • HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy
    • Hue S, Clewley JP, Cane PA, Pillay D, (2004) HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy. AIDS 18: 719-728.
    • (2004) AIDS , vol.18 , pp. 719-728
    • Hue, S.1    Clewley, J.P.2    Cane, P.A.3    Pillay, D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.