Martell M, Esteban JI, Quer J, Genesca J, Weiner A, Esteban R, Guardia J, Gomez J: Hepatitis C virus (HCV) circulates as a population of different but closely related genomes: quasispecies nature of HCV genome distribution. J Virol. 1992, 66 (5): 3225-3229.
CAS
PubMed
PubMed Central
Google Scholar
Duarte EA, Novella IS, Weaver SC, Domingo E, Wain-Hobson S, Clarke DK, Moya A, Elena SF, de la Torre JC, Holland JJ: RNA virus quasispecies: significance for viral disease and epidemiology. Infect Agents Dis. 1994, 3 (4): 201-214.
CAS
PubMed
Google Scholar
Kato N, Ootsuyama Y, Ohkoshi S, Nakazawa T, Sekiya H, Hijikata M, Shimotohno K: Characterization of hypervariable regions in the putative envelope protein of hepatitis C virus. Biochem Biophys Res Commun. 1992, 189 (1): 119-127. 10.1016/0006-291X(92)91533-V.
Article
CAS
PubMed
Google Scholar
Di Lorenzo C, Angus AG, Patel AH: Hepatitis C virus evasion mechanisms from neutralizing antibodies. Viruses. 2011, 3 (11): 2280-2300.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kato N, Sekiya H, Ootsuyama Y, Nakazawa T, Hijikata M, Ohkoshi S, Shimotohno K: Humoral immune response to hypervariable region 1 of the putative envelope glycoprotein (gp70) of hepatitis C virus. J Virol. 1993, 67 (7): 3923-3930.
CAS
PubMed
PubMed Central
Google Scholar
Guglietta S, Garbuglia AR, Pacciani V, Scotta C, Perrone MP, Laurenti L, Spada E, Mele A, Capobianchi MR, Taliani G, Folgori A, Vitelli A, Ruggeri L, Nicosia A, Piccolella E, Del Porto P: Positive selection of cytotoxic T lymphocyte escape variants during acute hepatitis C virus infection. Eur J Immunol. 2005, 35 (9): 2627-2637. 10.1002/eji.200526067.
Article
CAS
PubMed
Google Scholar
Zoulim F, Chevallier M, Maynard M, Trepo C: Clinical consequences of hepatitis C virus infection. Rev Med Virol. 2003, 13 (1): 57-68. 10.1002/rmv.371.
Article
CAS
PubMed
Google Scholar
Hoofnagle JH: Hepatitis C: the clinical spectrum of disease. Hepatology. 1997, 26 (3 Suppl 1): 15S-20S.
Article
CAS
PubMed
Google Scholar
Farci P, Shimoda A, Coiana A, Diaz G, Peddis G, Melpolder JC, Strazzera A, Chien DY, Munoz SJ, Balestrieri A, Purcell RH, Alter HJ: The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies. Science. 2000, 288 (5464): 339-344. 10.1126/science.288.5464.339.
Article
CAS
PubMed
Google Scholar
Laskus T, Wilkinson J, Gallegos-Orozco JF, Radkowski M, Adair DM, Nowicki M, Operskalski E, Buskell Z, Seeff LB, Vargas H, Rakela J: Analysis of hepatitis C virus quasispecies transmission and evolution in patients infected through blood transfusion. Gastroenterology. 2004, 127 (3): 764-776. 10.1053/j.gastro.2004.06.005.
Article
CAS
PubMed
Google Scholar
McHutchison JG, Poynard T, Pianko S, Gordon SC, Reid AE, Dienstag J, Morgan T, Yao R, Albrecht J: The impact of interferon plus ribavirin on response to therapy in black patients with chronic hepatitis C. The International Hepatitis Interventional Therapy Group. Gastroenterology. 2000, 119 (5): 1317-1323. 10.1053/gast.2000.19289.
Article
CAS
PubMed
Google Scholar
Lam NP, Pitrak D, Speralakis R, Lau AH, Wiley TE, Layden TJ: Effect of obesity on pharmacokinetics and biologic effect of interferon-alpha in hepatitis C. Dig Dis Sci. 1997, 42 (1): 178-185. 10.1023/A:1018865928308.
Article
CAS
PubMed
Google Scholar
Asselah T, Estrabaud E, Bieche I, Lapalus M, De Muynck S, Vidaud M, Saadoun D, Soumelis V, Marcellin P: Hepatitis C: viral and host factors associated with non-response to pegylated interferon plus ribavirin. Liver Int. 2010, 30 (9): 1259-1269. 10.1111/j.1478-3231.2010.02283.x.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ijichi S, Izumo S, Nagai M, Shinmyozu K, Hall WW, Osame M: Anti-viral and immunomodulatory effects of interferon-alpha on cultured lymphocytes from patients with human T lymphotropic virus type I-associated myelopathy (HAM/TSP). J Neuroimmunol. 1995, 61 (2): 213-221. 10.1016/0165-5728(95)00101-7.
Article
CAS
PubMed
Google Scholar
Shindo M, Hamada K, Koya S, Arai K, Sokawa Y, Okuno T: The clinical significance of changes in genetic heterogeneity of the hypervariable region 1 in chronic hepatitis C with interferon therapy. Hepatology. 1996, 24 (5): 1018-1023. 10.1002/hep.510240507.
Article
CAS
PubMed
Google Scholar
Polyak SJ, McArdle S, Liu SL, Sullivan DG, Chung M, Hofgartner WT, Carithers RL, McMahon BJ, Mullins JI, Corey L, Gretch DR, Diaz G, Balestrieri A, Purcell RH: Evolution of hepatitis C virus quasispecies in hypervariable region 1 and the putative interferon sensitivity-determining region during interferon therapy and natural infection. J Virol. 1998, 72 (5): 4288-4296.
CAS
PubMed
PubMed Central
Google Scholar
Sandres K, Dubois M, Pasquier C, Payen JL, Alric L, Duffaut M, Vinel JP, Pascal JP, Puel J, Izopet J: Genetic heterogeneity of hypervariable region 1 of the hepatitis C virus (HCV) genome and sensitivity of HCV to alpha interferon therapy. J Virol. 2000, 74 (2): 661-668. 10.1128/JVI.74.2.661-668.2000.
Article
CAS
PubMed
PubMed Central
Google Scholar
Farci P, Strazzera R, Alter HJ, Farci S, Degioannis D, Coiana A, Peddis G, Usai F, Serra G, Chessa L, et al: Early changes in hepatitis C viral quasispecies during interferon therapy predict the therapeutic outcome. Proc Natl Acad Sci U S A. 2002, 99 (5): 3081-3086. 10.1073/pnas.052712599.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pawlotsky JM, Germanidis G, Frainais PO, Bouvier M, Soulier A, Pellerin M, Dhumeaux D: Evolution of the hepatitis C virus second envelope protein hypervariable region in chronically infected patients receiving alpha interferon therapy. J Virol. 1999, 73 (8): 6490-6499.
CAS
PubMed
PubMed Central
Google Scholar
Cuevas JM, Torres-Puente M, Jimenez-Hernandez N, Bracho MA, Garcia-Robles I, Carnicer F, Olmo JD, Ortega E, Moya A, Gonzalez-Candelas F: Refined analysis of genetic variability parameters in hepatitis C virus and the ability to predict antiviral treatment response. J Viral Hepat. 2008, 15 (8): 578-590. 10.1111/j.1365-2893.2008.00991.x.
Article
CAS
PubMed
Google Scholar
Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW: Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res. 2007, 17 (8): 1195-1201. 10.1101/gr.6468307.
Article
CAS
PubMed
PubMed Central
Google Scholar
Simen BB, Simons JF, Hullsiek KH, Novak RM, Macarthur RD, Baxter JD, Huang C, Lubeski C, Turenchalk GS, Braverman MS, Desany B, Rothberg JM, Egholm M, Kozal MJ, Terry Beirn Community Programs for Clinical Research on AIDS: Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis. 2009, 199 (5): 693-701. 10.1086/596736.
Article
PubMed
Google Scholar
Spear GT, Sikaroodi M, Zariffard MR, Landay AL, French AL, Gillevet PM: Comparison of the diversity of the vaginal microbiota in HIV-infected and HIV-uninfected women with or without bacterial vaginosis. J Infect Dis. 2008, 198 (8): 1131-1140. 10.1086/591942.
Article
PubMed
PubMed Central
Google Scholar
Bull RA, Luciani F, McElroy K, Gaudieri S, Pham ST, Chopra A, Cameron B, Maher L, Dore GJ, White PA, Lloyd AR: Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection. PLoS Pathog. 2011, 7 (9): e1002243-10.1371/journal.ppat.1002243.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nasu A, Marusawa H, Ueda Y, Nishijima N, Takahashi K, Osaki Y, Yamashita Y, Inokuma T, Tamada T, Fujiwara T, Sato F, Shimizu K, Chiba T: Genetic heterogeneity of hepatitis C virus in association with antiviral therapy determined by ultra-deep sequencing. PLoS ONE. 2011, 6 (9): e24907-10.1371/journal.pone.0024907.
Article
CAS
PubMed
PubMed Central
Google Scholar
Caraballo Cortes K, Zagordi O, Laskus T, Ploski R, Bukowska-Osko I, Pawelczyk A, Berak H, Radkowski M: Ultradeep pyrosequencing of hepatitis C virus hypervariable region 1 in quasispecies analysis. Biomed Res Int. 2013, 2013: 626083-
Article
PubMed
PubMed Central
Google Scholar
Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N: ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinformatics. 2011, 12: 119-10.1186/1471-2105-12-119.
Article
PubMed
PubMed Central
Google Scholar
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011, 28 (10): 2731-2739. 10.1093/molbev/msr121.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tamura K, Nei M: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol. 1993, 10 (3): 512-526.
CAS
PubMed
Google Scholar
Librado P, Rozas J: DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009, 25 (11): 1451-1452. 10.1093/bioinformatics/btp187.
Article
CAS
PubMed
Google Scholar
Abbate I, Cappiello G, Lo Iacono O, Longo R, Ferraro D, Antonucci G, Di Marco V, Di Stefano R, Craxi A, Solmone MC, Spanò A, Ippolito G, Capobianchi MR: Heterogeneity of HVR-1 quasispecies is predictive of early but not sustained virological response in genotype 1b-infected patients undergoing combined treatment with PEG- or STD-IFN plus RBV. J Biol Regul Homeost Agents. 2003, 17 (2): 162-165.
CAS
PubMed
Google Scholar
Abbate I, Lo Iacono O, Di Stefano R, Cappiello G, Girardi E, Longo R, Ferraro D, Antonucci G, Di Marco V, Solmone M, Craxì A, Ippolito G, Capobianchi MR: HVR-1 quasispecies modifications occur early and are correlated to initial but not sustained response in HCV-infected patients treated with pegylated- or standard-interferon and ribavirin. J Hepatol. 2004, 40 (5): 831-836. 10.1016/j.jhep.2004.01.019.
Article
CAS
PubMed
Google Scholar
Morishima C, Polyak SJ, Ray R, Doherty MC, Di Bisceglie AM, Malet PF, Bonkovsky HL, Sullivan DG, Gretch DR, Rothman AL, Koziel MJ, Lindsay KL, Hepatitis C Antiviral Long-Term Treatment Against Cirrhosis Trial Group: Hepatitis C virus-specific immune responses and quasi-species variability at baseline are associated with nonresponse to antiviral therapy during advanced hepatitis C. J Infect Dis. 2006, 193 (7): 931-940. 10.1086/500952.
Article
CAS
PubMed
Google Scholar
Saludes V, Bracho MA, Valero O, Ardevol M, Planas R, Gonzalez-Candelas F, Ausina V, Martro E: Baseline prediction of combination therapy outcome in hepatitis C virus 1b infected patients by discriminant analysis using viral and host factors. PLoS ONE. 2010, 5 (11): e14132-10.1371/journal.pone.0014132.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pawlotsky JM, Pellerin M, Bouvier M, Roudot-Thoraval F, Germanidis G, Bastie A, Darthuy F, Remire J, Soussy CJ, Dhumeaux D: Genetic complexity of the hypervariable region 1 (HVR1) of hepatitis C virus (HCV): influence on the characteristics of the infection and responses to interferon alfa therapy in patients with chronic hepatitis C. J Med Virol. 1998, 54 (4): 256-264. 10.1002/(SICI)1096-9071(199804)54:4<256::AID-JMV4>3.0.CO;2-3.
Article
CAS
PubMed
Google Scholar
Lopez-Labrador FX, Ampurdanes S, Gimenez-Barcons M, Guilera M, Costa J, Jimenez de Anta MT, Sanchez-Tapias JM, Rodes J, Saiz JC: Relationship of the genomic complexity of hepatitis C virus with liver disease severity and response to interferon in patients with chronic HCV genotype 1b infection [correction of interferon]. Hepatology. 1999, 29 (3): 897-903. 10.1002/hep.510290306.
Article
CAS
PubMed
Google Scholar
Cuevas JM, Torres-Puente M, Jimenez-Hernandez N, Bracho MA, Garcia-Robles I, Wrobel B, Carnicer F, del Olmo J, Ortega E, Moya A, González-Candelas F: Genetic variability of hepatitis C virus before and after combined therapy of interferon plus ribavirin. PLoS ONE. 2008, 3 (8): e3058-10.1371/journal.pone.0003058.
Article
PubMed
PubMed Central
Google Scholar
Torres-Puente M, Cuevas JM, Jimenez-Hernandez N, Bracho MA, Garcia-Robles I, Wrobel B, Carnicer F, Del Olmo J, Ortega E, Moya A, González-Candelas F: Genetic variability in hepatitis C virus and its role in antiviral treatment response. J Viral Hepat. 2008, 15 (3): 188-199.
Article
CAS
PubMed
Google Scholar
Gilles A, Meglecz E, Pech N, Ferreira S, Malausa T, Martin JF: Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics. 2011, 12: 245-10.1186/1471-2164-12-245.
Article
PubMed
PubMed Central
Google Scholar
Beerenwinkel N, Zagordi O: Ultra-deep sequencing for the analysis of viral populations. Curr Opin Virol. 2011, 1 (5): 413-418. 10.1016/j.coviro.2011.07.008.
Article
CAS
PubMed
Google Scholar