메뉴 건너뛰기




Volumn 88, Issue 13, 2014, Pages 7628-7644

Statistical linkage analysis of substitutions in patient-derived sequences of genotype 1a Hepatitis C virus nonstructural protein 3 exposes targets for immunogen design

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; HELICASE; NONSTRUCTURAL PROTEIN 3; PROTEINASE; NS3 PROTEIN, HEPATITIS C VIRUS; VIRUS PROTEIN;

EID: 84901999754     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.03812-13     Document Type: Article
Times cited : (35)

References (74)
  • 1
    • 84901975872 scopus 로고    scopus 로고
    • World Health Organization. World Health Organization, Geneva, Switzerland.
    • World Health Organization. 2013. Factsheet, hepatitis C. World Health Organization, Geneva, Switzerland.
    • (2013) Factsheet, hepatitis C
  • 2
    • 0035811625 scopus 로고    scopus 로고
    • Hepatitis C virus infection
    • Lauer G, Walker B. 2001. Hepatitis C virus infection. N. Engl. J. Med. 345:41-52. http://dx.doi.org/10.1056/NEJM200107053450107.
    • (2001) N. Engl. J. Med. , vol.345 , pp. 41-52
    • Lauer, G.1    Walker, B.2
  • 3
    • 4444365401 scopus 로고    scopus 로고
    • The natural history of hepatitis C
    • Afdhal NH. 2004. The natural history of hepatitis C. Semin. Liver Dis. 24:3-8. http://dx.doi.org/10.1055/s-2004-832922.
    • (2004) Semin. Liver Dis. , vol.24 , pp. 3-8
    • Afdhal, N.H.1
  • 4
    • 0036829649 scopus 로고    scopus 로고
    • National Institutes of Health Consensus Development Conference statement: management of hepatitis C: 2002-June 10-12, 2002
    • National Institutes of Health.
    • National Institutes of Health. 2002. National Institutes of Health Consensus Development Conference statement: management of hepatitis C: 2002-June 10-12, 2002. Hepatology 36(Suppl 1):S3-S20. http://dx.doi .org/10.1053/jhep.2002.37117.
    • (2002) Hepatology , vol.36 , Issue.SUPPL. 1
  • 5
    • 33645965496 scopus 로고    scopus 로고
    • Cost effectiveness of interferon alpha or peginterferon alpha with ribavirin for histologically mild chronic hepatitis C
    • Grieve R, Roberts J, Wright M, Sweeting M, DeAngelis D, Rosenberg W, Bassendine M, Main J, Thomas H. 2006. Cost effectiveness of interferon alpha or peginterferon alpha with ribavirin for histologically mild chronic hepatitis C. Gut 55:1332-1338. http://dx.doi.org/10.1136/gut .2005.064774.
    • (2006) Gut , vol.55 , pp. 1332-1338
    • Grieve, R.1    Roberts, J.2    Wright, M.3    Sweeting, M.4    DeAngelis, D.5    Rosenberg, W.6    Bassendine, M.7    Main, J.8    Thomas, H.9
  • 6
    • 1442282958 scopus 로고    scopus 로고
    • New therapies for chronic hepatitis C virus infection
    • Dev A, Patel K, McHutchison J. 2004. New therapies for chronic hepatitis C virus infection. Curr. Gastroenterol. Rep. 6:77-86. http://dx.doi .org/10.1007/s11894-004-0030-5.
    • (2004) Curr. Gastroenterol. Rep. , vol.6 , pp. 77-86
    • Dev, A.1    Patel, K.2    McHutchison, J.3
  • 7
    • 0034950181 scopus 로고    scopus 로고
    • Clinical guidelines on the management of hepatitis C
    • The Royal College of Physicians of London and the British Society of Gastroenterology.
    • Booth JC, O'Grady J, Neuberger J; The Royal College of Physicians of London and the British Society of Gastroenterology. 2001. Clinical guidelines on the management of hepatitis C. Gut 49:I1-I21. http://dx.doi .org/10.1136/gut.49.suppl_1.I1.
    • (2001) Gut , vol.49
    • Booth, J.C.1    O'Grady, J.2    Neuberger, J.3
  • 9
    • 79957622306 scopus 로고    scopus 로고
    • Vaccination for hepatitis C virus: closing in on an evasive target
    • Halliday J, Klenerman P, Barnes E. 2011. Vaccination for hepatitis C virus: closing in on an evasive target. Expert Rev. Vaccines 10:659-672. http://dx.doi.org/10.1586/erv.11.55.
    • (2011) Expert Rev. Vaccines , vol.10 , pp. 659-672
    • Halliday, J.1    Klenerman, P.2    Barnes, E.3
  • 10
    • 34249024924 scopus 로고    scopus 로고
    • Replication of hepatitis C virus
    • Moradpour D, Penin F, Rice CM. 2007. Replication of hepatitis C virus. Nat. Rev. Microbiol. 5:453-463. http://dx.doi.org/10.1038/nrmicro1645.
    • (2007) Nat. Rev. Microbiol. , vol.5 , pp. 453-463
    • Moradpour, D.1    Penin, F.2    Rice, C.M.3
  • 11
    • 37849016609 scopus 로고    scopus 로고
    • Identification of a broadly cross-reacting and neutralizing human monoclonal antibody directed against the hepatitis C virus E2 protein
    • Perotti M, Mancini N, Diotti RA, Tarr AW, Ball JK, Owsianka A, Adair R, Patel AH, Clementi M, Burioni R. 2008. Identification of a broadly cross-reacting and neutralizing human monoclonal antibody directed against the hepatitis C virus E2 protein. J. Virol. 82:1047-1052. http://dx .doi.org/10.1128/JVI.01986-07.
    • (2008) J. Virol. , vol.82 , pp. 1047-1052
    • Perotti, M.1    Mancini, N.2    Diotti, R.A.3    Tarr, A.W.4    Ball, J.K.5    Owsianka, A.6    Adair, R.7    Patel, A.H.8    Clementi, M.9    Burioni, R.10
  • 13
    • 84863724325 scopus 로고    scopus 로고
    • T cell responses in hepatitis C: the good, the bad and the unconventional
    • Klenerman P, Thimme R. 2012. T cell responses in hepatitis C: the good, the bad and the unconventional. Gut 61:1226-1234. http://dx.doi.org/10 .1136/gutjnl-2011-300620.
    • (2012) Gut , vol.61 , pp. 1226-1234
    • Klenerman, P.1    Thimme, R.2
  • 16
    • 84855240713 scopus 로고    scopus 로고
    • Hepatitis C virus-T-cell responses and viral escape mutations
    • Petrovic D, Dempsey E, Doherty DG, Kelleher D, Long A. 2012. Hepatitis C virus-T-cell responses and viral escape mutations. Eur. J. Immunol. 42:17-26. http://dx.doi.org/10.1002/eji.201141593.
    • (2012) Eur. J. Immunol. , vol.42 , pp. 17-26
    • Petrovic, D.1    Dempsey, E.2    Doherty, D.G.3    Kelleher, D.4    Long, A.5
  • 25
    • 0030806820 scopus 로고    scopus 로고
    • Lymphocyte reactivity to hepatitis C virus (HCV) antigens shows evidence for exposure toHCVin HCV-seronegative spouses of HCV-infected patients
    • Bronowicki JP, Vetter D, Uhl G, Hudziak H, Uhrlacher A, Vetter JM, Doffoel M. 1997. Lymphocyte reactivity to hepatitis C virus (HCV) antigens shows evidence for exposure toHCVin HCV-seronegative spouses of HCV-infected patients. J. Infect. Dis. 176:518-522. http://dx.doi.org/10 .1086/517279.
    • (1997) J. Infect. Dis. , vol.176 , pp. 518-522
    • Bronowicki, J.P.1    Vetter, D.2    Uhl, G.3    Hudziak, H.4    Uhrlacher, A.5    Vetter, J.M.6    Doffoel, M.7
  • 26
    • 0036500976 scopus 로고    scopus 로고
    • The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding
    • Pang PS, Jankowsky E, Planet PJ, Pyle AM. 2002. The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding. EMBO J. 21:1168-1176. http://dx.doi.org/10.1093/emboj/21 .5.1168.
    • (2002) EMBO J. , vol.21 , pp. 1168-1176
    • Pang, P.S.1    Jankowsky, E.2    Planet, P.J.3    Pyle, A.M.4
  • 28
    • 77954931489 scopus 로고    scopus 로고
    • Hepatitis C virus non-structural protein 3 (HCV NS3): a multifunctional antiviral target
    • Raney KD, Sharma SD, Moustafa IM, Cameron CE. 2010. Hepatitis C virus non-structural protein 3 (HCV NS3): a multifunctional antiviral target. J. Biol. Chem. 285:22725-22731. http://dx.doi.org/10.1074/jbc .R110.125294.
    • (2010) J. Biol. Chem. , vol.285 , pp. 22725-22731
    • Raney, K.D.1    Sharma, S.D.2    Moustafa, I.M.3    Cameron, C.E.4
  • 29
    • 84875546274 scopus 로고    scopus 로고
    • Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design
    • Ferguson A, Mann J, Omarjee S, Ndung'u T, Walker BD, Chakraborty AK. 2013. Translating HIV sequences into quantitative fitness landscapes predicts viral vulnerabilities for rational immunogen design. Immunity 38:606-617. http://dx.doi.org/10.1016/j.immuni.2012.11.022.
    • (2013) Immunity , vol.38 , pp. 606-617
    • Ferguson, A.1    Mann, J.2    Omarjee, S.3    Ndung'u, T.4    Walker, B.D.5    Chakraborty, A.K.6
  • 32
    • 68749107059 scopus 로고    scopus 로고
    • Protein sectors: evolutionary units of three-dimensional structure
    • Halabi N, Rivoire O, Leibler S, Ranganathan R. 2009. Protein sectors: evolutionary units of three-dimensional structure. Cell 138:774-786. http://dx.doi.org/10.1016/j.cell.2009.07.038.
    • (2009) Cell , vol.138 , pp. 774-786
    • Halabi, N.1    Rivoire, O.2    Leibler, S.3    Ranganathan, R.4
  • 33
    • 84879373530 scopus 로고    scopus 로고
    • T-cell responses in hepatitis B and C virus infection: similarities and differences
    • e15
    • Schmidt J, Blum HE, Thimme R. 2013. T-cell responses in hepatitis B and C virus infection: similarities and differences. Emerg. Microbes Infect. 2:e15. http://dx.doi.org/10.1038/emi.2013.14.
    • (2013) Emerg. Microbes Infect. , vol.2
    • Schmidt, J.1    Blum, H.E.2    Thimme, R.3
  • 34
    • 61749095537 scopus 로고    scopus 로고
    • Genome-wide hepatitis C virus amino acid covariance networks can predict response to antiviral therapy in humans
    • Aurora R, Donlin M. 2009. Genome-wide hepatitis C virus amino acid covariance networks can predict response to antiviral therapy in humans. J. Clin. Invest. 119:225-236. http://dx.doi.org/10.1172/JCI37085.
    • (2009) J. Clin. Invest. , vol.119 , pp. 225-236
    • Aurora, R.1    Donlin, M.2
  • 35
    • 79952610453 scopus 로고    scopus 로고
    • Coevolution of the hepatitis Cvirus polyprotein sites in patients on combined pegylated interferon and ribavirin therapy
    • Lara J, Xia G, Purdy M, Khudyakov Y. 2011. Coevolution of the hepatitis Cvirus polyprotein sites in patients on combined pegylated interferon and ribavirin therapy. J. Virol. 85:3649-3663. http://dx.doi.org/10.1128/JVI .02197-10.
    • (2011) J. Virol. , vol.85 , pp. 3649-3663
    • Lara, J.1    Xia, G.2    Purdy, M.3    Khudyakov, Y.4
  • 40
    • 13844253602 scopus 로고    scopus 로고
    • The Los Alamos hepatitis C sequence database
    • Kuiken C, Yusim K, Boykin L, Richardson R. 2005. The Los Alamos hepatitis C sequence database. Bioinformatics 21:379-384. http://dx.doi .org/10.1093/bioinformatics/bth485.
    • (2005) Bioinformatics , vol.21 , pp. 379-384
    • Kuiken, C.1    Yusim, K.2    Boykin, L.3    Richardson, R.4
  • 43
    • 78149452459 scopus 로고    scopus 로고
    • Financial applications of random matrix theory: a short review
    • Akemann G, Baik J, and Di Francesco P (ed), Oxford University Press, Oxford, United Kingdom.
    • Bouchaud J-P, Potters M. 2011. Financial applications of random matrix theory: a short review, p 824-850. In Akemann G, Baik J, and Di Francesco P (ed), The Oxford handbook of random matrix theory. Oxford University Press, Oxford, United Kingdom.
    • (2011) The Oxford handbook of random matrix theory , pp. 824-850
    • Bouchaud, J.-P.1    Potters, M.2
  • 44
    • 46749116893 scopus 로고    scopus 로고
    • Sample eigenvalue based detection of high-dimensional signals in white noise using relatively few samples
    • Nadakuditi RR, Edelman A. 2008. Sample eigenvalue based detection of high-dimensional signals in white noise using relatively few samples. IEEE Trans. Signal Process. 56:2625-2638. http://dx.doi.org/10.1109/TSP.2008 .917356.
    • (2008) IEEE Trans. Signal Process. , vol.56 , pp. 2625-2638
    • Nadakuditi, R.R.1    Edelman, A.2
  • 46
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey JD, Tibshirani R. 2003. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U. S. A. 100:9440-9445. http://dx.doi.org /10.1073/pnas.1530509100.
    • (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 47
    • 84867683811 scopus 로고    scopus 로고
    • Discovery of an allosteric mechanism for the regulation of HCV NS3 protein function
    • Saalau-Bethell S, Woodhead A. 2012. Discovery of an allosteric mechanism for the regulation of HCV NS3 protein function. Nat. Chem. Biol. 8:920-925. http://dx.doi.org/10.1038/nchembio.1081.
    • (2012) Nat. Chem. Biol. , vol.8 , pp. 920-925
    • Saalau-Bethell, S.1    Woodhead, A.2
  • 48
    • 33645645084 scopus 로고    scopus 로고
    • Structural and biological identification of residues on the surface of NS3 helicase required for optimal replication of the hepatitis C virus
    • Mackintosh SG, Lu JZ, Jordan JB, Harrison MK, Sikora B, Sharma SD, Cameron CE, Raney KD, Sakon J. 2006. Structural and biological identification of residues on the surface of NS3 helicase required for optimal replication of the hepatitis C virus. J. Biol. Chem. 281:3528-3535. http: //dx.doi.org/10.1074/jbc.M512100200.
    • (2006) J. Biol. Chem. , vol.281 , pp. 3528-3535
    • Mackintosh, S.G.1    Lu, J.Z.2    Jordan, J.B.3    Harrison, M.K.4    Sikora, B.5    Sharma, S.D.6    Cameron, C.E.7    Raney, K.D.8    Sakon, J.9
  • 49
    • 0141940269 scopus 로고    scopus 로고
    • Mining residue contacts in proteins using local structure predictions
    • Zaki M, Jin S, Bystroff C. 2003. Mining residue contacts in proteins using local structure predictions. IEEE Trans. Syst. Man. Cybern. B Cybern. 33:789-801. http://dx.doi.org/10.1109/TSMCB.2003.816916.
    • (2003) IEEE Trans. Syst. Man. Cybern. B Cybern. , vol.33 , pp. 789-801
    • Zaki, M.1    Jin, S.2    Bystroff, C.3
  • 50
    • 23144463510 scopus 로고    scopus 로고
    • PRISM: protein interactions by structural matching
    • Ogmen U, Keskin O, Aytuna AS, Nussinov R, Gursoy A. 2005. PRISM: protein interactions by structural matching. Nucleic Acids Res. 33(Web Server issue):W331-W336. http://dx.doi.org/10.1093/nar/gki585.
    • (2005) Nucleic Acids Res. , vol.33 , Issue.WEB SERVER ISSUE
    • Ogmen, U.1    Keskin, O.2    Aytuna, A.S.3    Nussinov, R.4    Gursoy, A.5
  • 51
    • 0036010981 scopus 로고    scopus 로고
    • HLA-Cw* 04 and hepatitis C virus persistence
    • Thio C, Gao X, Goedert J. 2002. HLA-Cw* 04 and hepatitis C virus persistence. J. Virol. 76:4792-4797. http://dx.doi.org/10.1128/JVI.76.10 .4792-4797.2002.
    • (2002) J. Virol. , vol.76 , pp. 4792-4797
    • Thio, C.1    Gao, X.2    Goedert, J.3
  • 55
    • 37749020935 scopus 로고    scopus 로고
    • Evidence for human leukocyte antigen heterozygote advantage against hepatitis C virus infection
    • Hraber P, Kuiken C, Yusim K. 2007. Evidence for human leukocyte antigen heterozygote advantage against hepatitis C virus infection. Hepatology 46:1713-1721. http://dx.doi.org/10.1002/hep.21889.
    • (2007) Hepatology , vol.46 , pp. 1713-1721
    • Hraber, P.1    Kuiken, C.2    Yusim, K.3
  • 56
    • 77954348400 scopus 로고    scopus 로고
    • Hepatitis C infection in HIV-1 natural viral suppressors
    • Sajadi M, Shakeri N, Talwani R, Redfield R. 2010. Hepatitis C infection in HIV-1 natural viral suppressors. AIDS 24:1689-1695. http://dx.doi.org /10.1097/QAD.0b013e32833a2a32.
    • (2010) AIDS , vol.24 , pp. 1689-1695
    • Sajadi, M.1    Shakeri, N.2    Talwani, R.3    Redfield, R.4
  • 59
    • 34548472899 scopus 로고    scopus 로고
    • High-resolution HLA alleles and haplotypes in the United States population
    • Maiers M, Gragert L, Klitz W. 2007. High-resolution HLA alleles and haplotypes in the United States population. Hum. Immunol. 68:779-788. http://dx.doi.org/10.1016/j.humimm.2007.04.005.
    • (2007) Hum. Immunol. , vol.68 , pp. 779-788
    • Maiers, M.1    Gragert, L.2    Klitz, W.3
  • 61
    • 84879198048 scopus 로고    scopus 로고
    • Correction for founder effects in host-viral association studies via principal components
    • pii: /j/sagmb.2012.11.issue-4/1544-6115.1827/1544-6115.1827.xml
    • Reeves KL, McKinnon EJ, James IR. 2012. Correction for founder effects in host-viral association studies via principal components. Stat. Appl. Genet. Mol. Biol. 11:pii: /j/sagmb.2012.11.issue-4/1544-6115.1827/1544-6115.1827.xml. http://dx.doi.org/10.1515/1544-6115.1827.
    • (2012) Stat. Appl. Genet. Mol. Biol. , vol.11
    • Reeves, K.L.1    McKinnon, E.J.2    James, I.R.3
  • 64
    • 22344447485 scopus 로고    scopus 로고
    • Divergent and convergent evolution after a common-source outbreak of hepatitis C virus
    • Ray SC, Fanning L, Wang X-H, Netski DM, Kenny-Walsh E, Thomas DL. 2005. Divergent and convergent evolution after a common-source outbreak of hepatitis C virus. J. Exp. Med. 201:1753-1759. http://dx.doi .org/10.1084/jem.20050122.
    • (2005) J. Exp. Med. , vol.201 , pp. 1753-1759
    • Ray, S.C.1    Fanning, L.2    Wang, X.-H.3    Netski, D.M.4    Kenny-Walsh, E.5    Thomas, D.L.6
  • 67
    • 79955647061 scopus 로고    scopus 로고
    • New opportunities in anti-hepatitis C virus drug discovery: targeting NS4B
    • Rai R, Deval J. 2011. New opportunities in anti-hepatitis C virus drug discovery: targeting NS4B. Antiviral Res. 90:93-101. http://dx.doi.org/10 .1016/j.antiviral.2011.01.009.
    • (2011) Antiviral Res. , vol.90 , pp. 93-101
    • Rai, R.1    Deval, J.2
  • 68
    • 33646876613 scopus 로고    scopus 로고
    • Entropy and diversity
    • Jost L. 2006. Entropy and diversity. Oikos 113:363-375. http://dx.doi.org /10.1111/j.2006.0030-1299.14714.x.
    • (2006) Oikos , vol.113 , pp. 363-375
    • Jost, L.1
  • 69
    • 70349730223 scopus 로고    scopus 로고
    • The long and winding road leading to the identification of the hepatitis C virus
    • Houghton M. 2009. The long and winding road leading to the identification of the hepatitis C virus. J. Hepatol. 51:939-948. http://dx.doi.org/10 .1016/j.jhep.2009.08.004.
    • (2009) J. Hepatol. , vol.51 , pp. 939-948
    • Houghton, M.1
  • 70
    • 0000263234 scopus 로고
    • Distribution of eigenvalues for some sets of random matrices
    • Marčenko V, Pastur L. 1967. Distribution of eigenvalues for some sets of random matrices. Math. USSR-Sbornik 1:457-483. http://dx.doi.org/10 .1070/SM1967v001n04ABEH001994.
    • (1967) Math. USSR-Sbornik , vol.1 , pp. 457-483
    • Marčenko, V.1    Pastur, L.2
  • 71
    • 0001436319 scopus 로고
    • A limit theorem for the norm of random matrices
    • Geman S. 1980. A limit theorem for the norm of random matrices. Ann. Probab. 8:252-261. http://dx.doi.org/10.1214/aop/1176994775.
    • (1980) Ann. Probab. , vol.8 , pp. 252-261
    • Geman, S.1
  • 72
    • 0001629248 scopus 로고
    • The smallest eigenvalue of a large dimensional Wishart matrix
    • Silverstein J. 1985. The smallest eigenvalue of a large dimensional Wishart matrix. Ann. Probab. 13:1364-1368. http://dx.doi.org/10.1214/aop /1176992819.
    • (1985) Ann. Probab. , vol.13 , pp. 1364-1368
    • Silverstein, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.