메뉴 건너뛰기




Volumn 18, Issue 9, 2011, Pages 608-618

Evidence for separation of HCV subtype 1a into two distinct clades

Author keywords

bioinformatics; drug resistance; hepatitis C virus; phylogeny; selection pressure

Indexed keywords

AMINO ACID; POLYPROTEIN; PROTEINASE INHIBITOR; RNA POLYMERASE;

EID: 79960937707     PISSN: 13520504     EISSN: 13652893     Source Type: Journal    
DOI: 10.1111/j.1365-2893.2010.01342.x     Document Type: Article
Times cited : (58)

References (55)
  • 1
    • 34250679750 scopus 로고    scopus 로고
    • Epidemiology of hepatitis C virus infection
    • Alter MJ,. Epidemiology of hepatitis C virus infection. World J Gastroenterol 2007; 13 (17): 2436-2441. (Pubitemid 46929498)
    • (2007) World Journal of Gastroenterology , vol.13 , Issue.17 , pp. 2436-2441
    • Alter, M.J.1
  • 3
    • 0035050164 scopus 로고    scopus 로고
    • Evidence for a new hepatitis C virus antigen encoded in an overlapping reading frame
    • DOI 10.1017/S1355838201010111
    • Walewski JL, Keller TR, Stump DD, Branch AD,. Evidence for a new hepatitis C virus antigen encoded in an overlapping reading frame. RNA, 2001; 7 (5): 710-721. (Pubitemid 32405868)
    • (2001) RNA , vol.7 , Issue.5 , pp. 710-721
    • Walewski, J.L.1    Keller, T.R.2    Stump, D.D.3    Branch, A.D.4
  • 4
    • 0142040119 scopus 로고    scopus 로고
    • Two Alternative Translation Mechanisms Are Responsible for the Expression of the HCV ARFP/F/Core+1 Coding Open Reading Frame
    • DOI 10.1074/jbc.M305504200
    • Vassilaki N, Mavromara P,. Two alternative translation mechanisms are responsible for the expression of the HCV ARFP/F/core+1 coding open reading frame. J Biol Chem 2003; 278 (42): 40503-40513. (Pubitemid 37280860)
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.42 , pp. 40503-40513
    • Vassilaki, N.1    Mavromara, P.2
  • 5
    • 33645849521 scopus 로고    scopus 로고
    • Human ribosomal protein L18a interacts with hepatitis C virus internal ribosome entry site
    • Dhar D, Mapa K, Pudi R, Srinivasan P, Bodhinathan K, Das S,. Human ribosomal protein L18a interacts with hepatitis C virus internal ribosome entry site. Arch Virol 2006; 151 (3): 509-524.
    • (2006) Arch Virol , vol.151 , Issue.3 , pp. 509-524
    • Dhar, D.1    Mapa, K.2    Pudi, R.3    Srinivasan, P.4    Bodhinathan, K.5    Das, S.6
  • 6
    • 0034623002 scopus 로고    scopus 로고
    • Human la antigen is required for the hepatitis C virus internal ribosome entry site-mediated translation
    • Ali N, Pruijn GJ, Kenan DJ, Keene JD, Siddiqui A,. Human La antigen is required for the hepatitis C virus internal ribosome entry site-mediated translation. J Biol Chem 2000; 275 (36): 27531-27540.
    • (2000) J Biol Chem , vol.275 , Issue.36 , pp. 27531-27540
    • Ali, N.1    Pruijn, G.J.2    Kenan, D.J.3    Keene, J.D.4    Siddiqui, A.5
  • 7
    • 7444256169 scopus 로고    scopus 로고
    • Genetic diversity and evolution of hepatitis C virus - 15 years on
    • DOI 10.1099/vir.0.80401-0
    • Simmonds P,. Genetic diversity and evolution of hepatitis C virus-15 years on. J Gen Virol 2004; 85 (Pt 11): 3173-3188. (Pubitemid 39445434)
    • (2004) Journal of General Virology , vol.85 , Issue.11 , pp. 3173-3188
    • Simmonds, P.1
  • 8
    • 0027974113 scopus 로고
    • Evolution and selection of hepatitis C virus variants in patients with chronic hepatitis C
    • DOI 10.1006/viro.1994.1631
    • Kurosaki M, Enomoto N, Marumo F, Sato C,. Evolution and selection of hepatitis C virus variants in patients with chronic hepatitis C. Virology 1994; 205 (1): 161-169. (Pubitemid 24360602)
    • (1994) Virology , vol.205 , Issue.1 , pp. 161-169
    • Kurosaki, M.1    Enomoto, N.2    Marumo, F.3    Sato, C.4
  • 9
    • 0034060990 scopus 로고    scopus 로고
    • Hepatitis C virus: Kinetics and quasispecies evolution during anti-viral therapy
    • Zeuzem S,. Hepatitis C virus: kinetics and quasispecies evolution during anti-viral therapy. Forum (Genova) 2000; 10 (1): 32-42. (Pubitemid 30160684)
    • (2000) FORUM - Trends in Experimental and Clinical Medicine , vol.10 , Issue.1 , pp. 32-42
    • Zeuzem, S.1
  • 11
    • 0028945033 scopus 로고
    • Genetic heterogeneity of hepatitis C virus: Quasispecies and genotypes
    • Bukh J, Miller RH, Purcell RH,. Genetic heterogeneity of hepatitis C virus: quasispecies and genotypes. Semin Liver Dis 1995; 15 (1): 41-63.
    • (1995) Semin Liver Dis , vol.15 , Issue.1 , pp. 41-63
    • Bukh, J.1    Miller, R.H.2    Purcell, R.H.3
  • 13
    • 0037179698 scopus 로고    scopus 로고
    • Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection
    • Fried MW, Shiffman ML, Reddy KR, et al. Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection. N Eng J Med 2002; 347 (13): 975-982.
    • (2002) N Eng J Med , vol.347 , Issue.13 , pp. 975-982
    • Fried, M.W.1    Shiffman, M.L.2    Reddy, K.R.3
  • 14
    • 33645992473 scopus 로고    scopus 로고
    • Extended treatment duration for hepatitis C virus type 1: Comparing 48 versus 72 weeks of peginterferon-alfa-2a plus ribavirin
    • Berg T, von Wagner M, Nasser S, et al. Extended treatment duration for hepatitis C virus type 1: comparing 48 versus 72 weeks of peginterferon-alfa-2a plus ribavirin. Gastroenterology 2006; 130 (4): 1086-1097.
    • (2006) Gastroenterology , vol.130 , Issue.4 , pp. 1086-1097
    • Berg, T.1    Von Wagner, M.2    Nasser, S.3
  • 16
    • 48349131253 scopus 로고    scopus 로고
    • Hepatitis C virus diversity and evolution in the full open-reading frame during antiviral therapy
    • Cannon NA, Donlin MJ, Fan X, Aurora R, Tavis JE,. Hepatitis C virus diversity and evolution in the full open-reading frame during antiviral therapy. PLoS ONE 2008; 3 (5): e2123.
    • (2008) PLoS ONE , vol.3 , Issue.5
    • Cannon, N.A.1    Donlin, M.J.2    Fan, X.3    Aurora, R.4    Tavis, J.E.5
  • 17
    • 34548758435 scopus 로고    scopus 로고
    • Telaprevir and pegylated interferon-alpha-2a inhibit wild-type and resistant genotype 1 hepatitis C virus replication in patients
    • DOI 10.1002/hep.21781
    • Kieffer TL, Sarrazin C, Miller JS, et al. Telaprevir and pegylated interferon-alpha-2a inhibit wild-type and resistant genotype 1 hepatitis C virus replication in patients. Hepatology (Baltimore, MD) 2007; 46 (3): 631-639. (Pubitemid 47436107)
    • (2007) Hepatology , vol.46 , Issue.3 , pp. 631-639
    • Kieffer, T.L.1    Sarrazin, C.2    Miller, J.S.3    Welker, M.W.4    Forestier, N.5    Reesink, H.W.6    Kwong, A.D.7    Zeuzem, S.8
  • 20
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • DOI 10.1093/nar/gkh340
    • Edgar RC,. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32 (5): 1792-1797. (Pubitemid 38832724)
    • (2004) Nucleic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 21
    • 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 JD, Higgins DG, Gibson TJ,. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22 (22): 4673-4680. (Pubitemid 24354800)
    • (1994) Nucleic Acids Research , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 22
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • DOI 10.1093/molbev/msm092
    • Tamura K, Dudley J, Nei M, Kumar S,. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 2007; 24 (8): 1596-1599. (Pubitemid 47236692)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 23
    • 0002222776 scopus 로고    scopus 로고
    • HIV signature and sequence variation analysis
    • Rodrigo A.G. Learn G.H. eds. Dordrecht, Netherlands: Kluwer Academic Publishers
    • Korber B,. HIV signature and sequence variation analysis. In:, Rodrigo AG, Learn GH, eds. Computational Analysis of HIV Molecular Sequences. Dordrecht, Netherlands: Kluwer Academic Publishers, 2000: 55-72.
    • (2000) Computational Analysis of HIV Molecular Sequences , pp. 55-72
    • Korber, B.1
  • 24
    • 68649123160 scopus 로고    scopus 로고
    • Evolution and dispersal of St Louis encephalitis virus in the Americas
    • Auguste AJ, Pybus OG, Carrington CV,. Evolution and dispersal of St Louis encephalitis virus in the Americas. Infect Genet Evol 2009; 9 (4): 709-715.
    • (2009) Infect Genet Evol , vol.9 , Issue.4 , pp. 709-715
    • Auguste, A.J.1    Pybus, O.G.2    Carrington, C.V.3
  • 25
    • 42249097434 scopus 로고    scopus 로고
    • The evolution of human influenza A viruses from 1999 to 2006: A complete genome study
    • Bragstad K, Nielsen LP, Fomsgaard A,. The evolution of human influenza A viruses from 1999 to 2006: a complete genome study. Virol J 2008; 5: 40.
    • (2008) Virol J , vol.5 , pp. 40
    • Bragstad, K.1    Nielsen, L.P.2    Fomsgaard, A.3
  • 26
    • 53049089301 scopus 로고    scopus 로고
    • Analysis of HCV resistance mutations during combination therapy with protease inhibitor boceprevir and PEG-IFN alpha-2b using TaqMan mismatch amplification mutation assay
    • Curry S, Qiu P, Tong X,. Analysis of HCV resistance mutations during combination therapy with protease inhibitor boceprevir and PEG-IFN alpha-2b using TaqMan mismatch amplification mutation assay. J Virol Methods 2008; 153 (2): 156-162.
    • (2008) J Virol Methods , vol.153 , Issue.2 , pp. 156-162
    • Curry, S.1    Qiu, P.2    Tong, X.3
  • 27
    • 58149388300 scopus 로고    scopus 로고
    • Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naive patients
    • (Baltimore, MD)
    • Kuntzen T, Timm J, Berical A, et al. Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naive patients. Hepatology (Baltimore, MD) 2008; 48 (6): 1769-1778.
    • (2008) Hepatology , vol.48 , Issue.6 , pp. 1769-1778
    • Kuntzen, T.1    Timm, J.2    Berical, A.3
  • 28
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • Nei M, Gojobori T,. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986; 3 (5): 418-426. (Pubitemid 16010523)
    • (1986) Molecular Biology and Evolution , vol.3 , Issue.5 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 29
    • 33845642217 scopus 로고    scopus 로고
    • Establishment of a pipeline to analyse non-synonymous SNPs in Bos taurus
    • Lee MA, Keane OM, Glass BC, et al. Establishment of a pipeline to analyse non-synonymous SNPs in Bos taurus. BMC Genomics 2006; 7: 298.
    • (2006) BMC Genomics , vol.7 , pp. 298
    • Lee, M.A.1    Keane, O.M.2    Glass, B.C.3
  • 30
    • 0013936167 scopus 로고
    • Codon - Anticodon pairing: The wobble hypothesis
    • Crick FH,. Codon-anticodon pairing: the wobble hypothesis. J Mol Biol 1966; 19 (2): 548-555.
    • (1966) J Mol Biol , vol.19 , Issue.2 , pp. 548-555
    • Crick, F.H.1
  • 31
    • 0031897964 scopus 로고    scopus 로고
    • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    • Yang Z,. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 1998; 15 (5): 568-573. (Pubitemid 28194621)
    • (1998) Molecular Biology and Evolution , vol.15 , Issue.5 , pp. 568-573
    • Yang, Z.1
  • 32
    • 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,. Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J Virol 1997; 71 (1): 663-677. (Pubitemid 26412340)
    • (1997) Journal of Virology , vol.71 , Issue.1 , pp. 663-677
    • Ganeshan, S.1    Dickover, R.E.2    Korber, B.T.M.3    Bryson, Y.J.4    Wolinsky, S.M.5
  • 33
    • 0041418109 scopus 로고    scopus 로고
    • Comparison of serologic and genetic porB-based typing of Neisseria gonorrhoeae: Consequences for future characterization
    • DOI 10.1128/JCM.41.9.4141-4147.2003
    • Unemo M, Olcen P, Albert J, Fredlund H,. Comparison of serologic and genetic porB-based typing of Neisseria gonorrhoeae: consequences for future characterization. J Clin Microbiol 2003; 41 (9): 4141-4147. (Pubitemid 37099677)
    • (2003) Journal of Clinical Microbiology , vol.41 , Issue.9 , pp. 4141-4147
    • Unemo, M.1    Olcen, P.2    Albert, J.3    Fredlund, H.4
  • 35
    • 33847015308 scopus 로고    scopus 로고
    • Hepatitis C Virus Continuously Escapes From Neutralizing Antibody and T-Cell Responses During Chronic Infection In Vivo
    • DOI 10.1053/j.gastro.2006.12.008, PII S0016508506025662
    • von Hahn T, Yoon JC, Alter H, et al. Hepatitis C virus continuously escapes from neutralizing antibody and T-cell responses during chronic infection in vivo. Gastroenterology 2007; 132 (2): 667-678. (Pubitemid 46274668)
    • (2007) Gastroenterology , vol.132 , Issue.2 , pp. 667-678
    • Von Hahn, T.1    Yoon, J.C.2    Alter, H.3    Rice, C.M.4    Rehermann, B.5    Balfe, P.6    McKeating, J.A.7
  • 37
    • 0031982502 scopus 로고    scopus 로고
    • Comparison of the rate of sequence variation in the hypervariable region of E2/NS1 region of hepatitis C virus in normal and hypogammaglobulinemic patients
    • DOI 10.1002/hep.510270134
    • Booth JC, Kumar U, Webster D, Monjardino J, Thomas HC,. Comparison of the rate of sequence variation in the hypervariable region of E2/NS1 region of hepatitis C virus in normal and hypogammaglobulinemic patients. Hepatology (Baltimore, MD) 1998; 27 (1): 223-227. (Pubitemid 28041558)
    • (1998) Hepatology , vol.27 , Issue.1 , pp. 223-227
    • Booth, J.C.L.1    Kumar, U.2    Webster, D.3    Monjardino, J.4    Thomas, H.C.5
  • 38
    • 43249089764 scopus 로고    scopus 로고
    • Hepatitis C virus envelope glycoprotein co-evolutionary dynamics during chronic hepatitis C
    • Li H, McMahon BJ, McArdle S, et al. Hepatitis C virus envelope glycoprotein co-evolutionary dynamics during chronic hepatitis C. Virology 2008; 375 (2): 580-591.
    • (2008) Virology , vol.375 , Issue.2 , pp. 580-591
    • Li, H.1    McMahon, B.J.2    McArdle, S.3
  • 39
    • 1842510015 scopus 로고    scopus 로고
    • High-Resolution Phylogenetic Analysis of Hepatitis C Virus Adaptation and Its Relationship to Disease Progression
    • DOI 10.1128/JVI.78.7.3447-3454.2004
    • Sheridan I, Pybus OG, Holmes EC, Klenerman P,. High-resolution phylogenetic analysis of hepatitis C virus adaptation and its relationship to disease progression. J Virol 2004; 78 (7): 3447-3454. (Pubitemid 38568286)
    • (2004) Journal of Virology , vol.78 , Issue.7 , pp. 3447-3454
    • Sheridan, I.1    Pybus, O.G.2    Holmes, E.C.3    Klenerman, P.4
  • 40
    • 0030587469 scopus 로고    scopus 로고
    • A hyperimmune serum against a synthetic peptide corresponding to the hypervariable region 1 of hepatitis C virus can prevent viral infection in cell cultures
    • DOI 10.1006/viro.1996.0497
    • Shimizu YK, Igarashi H, Kiyohara T, et al. A hyperimmune serum against a synthetic peptide corresponding to the hypervariable region 1 of hepatitis C virus can prevent viral infection in cell cultures. Virology 1996; 223 (2): 409-412. (Pubitemid 26319606)
    • (1996) Virology , vol.223 , Issue.2 , pp. 409-412
    • Shimizu, Y.K.1    Igarashi, H.2    Kiyohara, T.3    Cabezon, T.4    Farci, P.5    Purcell, R.H.6    Yoshikura, H.7
  • 43
    • 0028274958 scopus 로고
    • Characterization and mapping of a B-cell immunogenic domain in hepatitis C virus E2 glycoprotein using a yeast peptide library
    • DOI 10.1006/viro.1994.1182
    • Mink MA, Benichou S, Madaule P, Tiollais P, Prince AM, Inchauspe G,. Characterization and mapping of a B-cell immunogenic domain in hepatitis C virus E2 glycoprotein using a yeast peptide library. Virology 1994; 200 (1): 246-255. (Pubitemid 24170474)
    • (1994) Virology , vol.200 , Issue.1 , pp. 246-255
    • Mink, M.A.1    Benichou, S.2    Madaule, P.3    Tiollais, P.4    Prince, A.M.5    Inchauspe, G.6
  • 44
    • 0032964973 scopus 로고    scopus 로고
    • Immunodominant B-cell domains of hepatitis C virus envelope proteins E1 and E2 identified during early and late time points of infection
    • DOI 10.1016/S0168-8278(99)80059-2
    • Zibert A, Kraas W, Ross RS, et al. Immunodominant B-cell domains of hepatitis C virus envelope proteins E1 and E2 identified during early and late time points of infection. J Hepatol 1999; 30 (2): 177-184. (Pubitemid 29071177)
    • (1999) Journal of Hepatology , vol.30 , Issue.2 , pp. 177-184
    • Zibert, A.1    Kraas, W.2    Ross, R.S.3    Meisel, H.4    Lechner, S.5    Jung, G.6    Roggendorf, M.7
  • 45
    • 0026581290 scopus 로고
    • Interaction of immune sera with synthetic peptides corresponding to the structural protein region of hepatitis C virus
    • Ching WM, Wychowski C, Beach MJ, et al. Interaction of immune sera with synthetic peptides corresponding to the structural protein region of hepatitis C virus. Proc Natl Acad Sci USA 1992; 89 (8): 3190-3194.
    • (1992) Proc Natl Acad Sci USA , vol.89 , Issue.8 , pp. 3190-3194
    • Ching, W.M.1    Wychowski, C.2    Beach, M.J.3
  • 48
    • 0033600812 scopus 로고    scopus 로고
    • Identification of the major phosphorylation site of the hepatitis C virus H strain NS5A protein as serine 2321
    • Reed KE, Rice CM,. Identification of the major phosphorylation site of the hepatitis C virus H strain NS5A protein as serine 2321. J Biol Chem 1999; 274 (39): 28011-28018.
    • (1999) J Biol Chem , vol.274 , Issue.39 , pp. 28011-28018
    • Reed, K.E.1    Rice, C.M.2
  • 49
    • 34249817897 scopus 로고    scopus 로고
    • Characterization of hepatitis C virus subgenomic replicon resistance to cyclosporine in vitro
    • DOI 10.1128/JVI.02524-06
    • Robida JM, Nelson HB, Liu Z, Tang H,. Characterization of hepatitis C virus subgenomic replicon resistance to cyclosporine in vitro. J Virol 2007; 81 (11): 5829-5840. (Pubitemid 46847020)
    • (2007) Journal of Virology , vol.81 , Issue.11 , pp. 5829-5840
    • Robida, J.M.1    Nelson, H.B.2    Liu, Z.3    Tang, H.4
  • 52
    • 36349034692 scopus 로고    scopus 로고
    • Sensitivity of hepatitis C virus to cyclosporine A depends on nonstructural proteins NS5A and NS5B
    • DOI 10.1002/hep.21809
    • Fernandes F, Poole DS, Hoover S, et al. Sensitivity of hepatitis C virus to cyclosporine A depends on nonstructural proteins NS5A and NS5B. Hepatology (Baltimore, MD) 2007; 46 (4): 1026-1033. (Pubitemid 350144767)
    • (2007) Hepatology , vol.46 , Issue.4 , pp. 1026-1033
    • Fernandes, F.1    Poole, D.S.2    Hoover, S.3    Middleton, R.4    Andrei, A.-C.5    Gerstner, J.6    Striker, R.7
  • 54
    • 37549041381 scopus 로고    scopus 로고
    • Hepatitis C virus and the controversial role of the interferon sensitivity determining region in the response to interferon treatment
    • Torres-Puente M, Cuevas JM, Jimenez-Hernandez N, et al. Hepatitis C virus and the controversial role of the interferon sensitivity determining region in the response to interferon treatment. J Med Virol 2008; 80 (2): 247-253.
    • (2008) J Med Virol , vol.80 , Issue.2 , pp. 247-253
    • Torres-Puente, M.1    Cuevas, J.M.2    Jimenez-Hernandez, N.3
  • 55


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.