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):3225–9.
PubMed
PubMed Central
CAS
Google Scholar
Domingo E, Sheldon J, Perales C. Viral quasispecies evolution. Microbiol Mol Biol Rev. 2012;76(2):159–216.
Article
PubMed
PubMed Central
CAS
Google Scholar
WHO: World Health Organization. Hepatitis C virus factsheet. http://www.who.int/mediacentre/factsheets/fs164/en/. Accessed February 15, 2018.
Smith DB, Bukh J, Kuiken C, Muerhoff AS, Rice CM, Stapleton JT, Simmonds P. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology. 2014;59(1):318–27.
Article
PubMed
Google Scholar
Messina JP, Humphreys I, Flaxman A, Brown A, Cooke GS, Pybus OG, Barnes E. Global distribution and prevalence of hepatitis C virus genotypes. Hepatology. 2015;61(1):77–87.
Article
PubMed
Google Scholar
Hezode C. Pan-genotypic treatment regimens for hepatitis C virus: advantages and disadvantages in high- and low-income regions. J Viral Hepat. 2017;24(2):92–101.
Article
PubMed
CAS
Google Scholar
Struble K, Chan-Tack K, Qi K, Naeger LK, Birnkrant D. Benefit-risk assessment for Sofosbuvir/Velpatasvir/Voxilaprevir based on patient population and HCV genotype: FDA's evaluation. Hepatology. 2017; https://doi.org/10.1002/hep.29601.
Welzel TM, Bhardwaj N, Hedskog C, Chodavarapu K, Camus G, McNally J, Brainard D, Miller MD, Mo H, Svarovskaia E, et al. Global epidemiology of HCV subtypes and resistance-associated substitutions evaluated by sequencing-based subtype analyses. J Hepatol. 2017;67(2):224–36.
Article
PubMed
Google Scholar
Sarrazin C. The importance of resistance to direct antiviral drugs in HCV infection in clinical practice. J Hepatol. 2016;64(2):486–504.
Article
PubMed
Google Scholar
EASL. EASL recommendations on treatment of hepatitis C 2016. J Hepatol. 2017;66(1):153–94.
Article
Google Scholar
Dietz J, Susser S, Vermehren J, Peiffer KH, Grammatikos G, Berger A, Ferenci P, Buti M, Mullhaupt B, Hunyady B, et al. Patterns of resistance-associated substitutions in patients with chronic HCV infection following treatment with direct-acting antivirals. Gastroenterology. 2017 https://doi.org/10.1053/j.gastro.2017.11.007.
Buti M, Riveiro-Barciela M, Esteban R. Management of direct-acting antiviral agent failures. J Hepatol. 2015;63(6):1511–22.
Article
PubMed
Google Scholar
Di Maio VC, Cento V, Lenci I, Aragri M, Rossi P, Barbaliscia S, Melis M, Verucchi G, Magni CF, Teti E, et al. Multiclass HCV resistance to direct-acting antiviral failure in real-life patients advocates for tailored second-line therapies. Liver Int. 2017;37(4):514–28.
Article
PubMed
CAS
Google Scholar
Lontok E, Harrington P, Howe A, Kieffer T, Lennerstrand J, Lenz O, McPhee F, Mo H, Parkin N, Pilot-Matias T, et al. Hepatitis C virus drug resistance-associated substitutions: state of the art summary. Hepatology. 2015;62(5):1623–32.
Article
PubMed
Google Scholar
Costantino A, Spada E, Equestre M, Bruni R, Tritarelli E, Coppola N, Sagnelli C, Sagnelli E, Ciccaglione AR. Naturally occurring mutations associated with resistance to HCV NS5B polymerase and NS3 protease inhibitors in treatment-naive patients with chronic hepatitis C. Virol J. 2015;12(1):186.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yang S, Xing H, Feng S, Ju W, Liu S, Wang X, Ou W, Cheng J, Pan CQ. Prevalence of NS5B resistance-associated variants in treatment-naive Asian patients with chronic hepatitis C. Arch Virol. 2017; https://doi.org/10.1007/s00705-017-3640-6.
Echeverria N, Betancour G, Gambaro F, Hernandez N, Lopez P, Chiodi D, Sanchez A, Boschi S, Fajardo A, Sonora M, et al. Naturally occurring NS3 resistance-associated variants in hepatitis C virus genotype 1: their relevance for developing countries. Virus Res. 2016;223:140–6.
Article
PubMed
CAS
Google Scholar
Perales C, Quer J, Gregori J, Esteban JI, Domingo E. Resistance of hepatitis C virus to inhibitors: complexity and clinical implications. Viruses. 2015;7(11):5746–66.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kai Y, Hikita H, Morishita N, Murai K, Nakabori T, Iio S, Hagiwara H, Imai Y, Tamura S, Tsutsui S, et al. Baseline quasispecies selection and novel mutations contribute to emerging resistance-associated substitutions in hepatitis C virus after direct-acting antiviral treatment. Sci Rep. 2017;7:41660.
Article
PubMed
PubMed Central
CAS
Google Scholar
Svarovskaia ES, Gane E, Dvory-Sobol H, Martin R, Doehle B, Hedskog C, Jacobson IM, Nelson DR, Lawitz E, Brainard DM, et al. L159F and V321A Sofosbuvir-associated hepatitis C virus NS5B substitutions. J Infect Dis. 2016;213(8):1240–7.
Article
PubMed
CAS
Google Scholar
Tong X, Le Pogam S, Li L, Haines K, Piso K, Baronas V, Yan JM, So SS, Klumpp K, Najera I. In vivo emergence of a novel mutant L159F/L320F in the NS5B polymerase confers low-level resistance to the HCV polymerase inhibitors mericitabine and sofosbuvir. J Infect Dis. 2014;209(5):668–75.
Article
PubMed
CAS
Google Scholar
Lam AM, Espiritu C, Bansal S, Micolochick Steuer HM, Niu C, Zennou V, Keilman M, Zhu Y, Lan S, Otto MJ, et al. Genotype and subtype profiling of PSI-7977 as a nucleotide inhibitor of hepatitis C virus. Antimicrob Agents Chemother. 2012;56(6):3359–68.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hedskog C, Dvory-Sobol H, Gontcharova V, Martin R, Ouyang W, Han B, Gane EJ, Brainard D, Hyland RH, Miller MD, et al. Evolution of the HCV viral population from a patient with S282T detected at relapse after sofosbuvir monotherapy. J Viral Hepat. 2015;22(11):871–81.
Article
PubMed
CAS
Google Scholar
Ji H, Kozak RA, Biondi MJ, Pilon R, Vallee D, Liang BB, La D, Kim J, Van Domselaar G, Leonard L, et al. Next generation sequencing of the hepatitis C virus NS5B gene reveals potential novel S282 drug resistance mutations. Virology. 2015;477:1–9.
Article
PubMed
CAS
Google Scholar
Komatsu TE, Boyd S, Sherwat A, Tracy L, Naeger LK, O'Rear JJ, Harrington PR. Regulatory analysis of effects of hepatitis C virus NS5A polymorphisms on efficacy of Elbasvir and Grazoprevir. Gastroenterology. 2017;152(3):586–97.
Article
PubMed
CAS
Google Scholar
Kanda T, Nirei K, Matsumoto N, Higuchi T, Nakamura H, Yamagami H, Matsuoka S, Moriyama M. Retreatment of patients with treatment failure of direct-acting antivirals: focus on hepatitis C virus genotype 1b. World J Gastroenterol. 2017;23(46):8120–7.
Article
PubMed
PubMed Central
Google Scholar
Fourati S, Pawlotsky JM. Virologic tools for HCV drug resistance testing. Viruses. 2015;7(12):6346–59.
Article
PubMed
PubMed Central
CAS
Google Scholar
Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, Stewart C, Volfovsky N, Levitsky A, Stephens RM, et al. Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of low-frequency drug resistance mutations in HIV-1 DNA. Retrovirology. 2013;10:18.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gorzer I, Guelly C, Trajanoski S, Puchhammer-Stockl E. The impact of PCR-generated recombination on diversity estimation of mixed viral populations by deep sequencing. J Virol Methods. 2010;169(1):248–52.
Article
PubMed
CAS
Google Scholar
Quer J, Rodriguez-Frias F, Gregori J, Tabernero D, Soria ME, Garcia-Cehic D, Homs M, Bosch A, Pinto RM, Esteban JI, et al. Deep sequencing in the management of hepatitis virus infections. Virus Res. 2017;239:115–25.
Article
PubMed
CAS
Google Scholar
Marukian S, Jones CT, Andrus L, Evans MJ, Ritola KD, Charles ED, Rice CM, Dustin LB. Cell culture-produced hepatitis C virus does not infect peripheral blood mononuclear cells. Hepatology. 2008;48(6):1843–50.
Article
PubMed
PubMed Central
Google Scholar
Perales C, Beach NM, Gallego I, Soria ME, Quer J, Esteban JI, Rice C, Domingo E, Sheldon J. Response of hepatitis C virus to long-term passage in the presence of alpha interferon: multiple mutations and a common phenotype. J Virol. 2013;87(13):7593–607.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lindenbach BD. Measuring HCV infectivity produced in cell culture and in vivo. Methods Mol Biol. 2009;510:329–36.
Article
PubMed
CAS
Google Scholar
Quer J, Gregori J, Rodriguez-Frias F, Buti M, Madejon A, Perez-del-Pulgar S, Garcia-Cehic D, Casillas R, Blasi M, Homs M, et al. High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods. J Clin Microbiol. 2015;53(1):219–26.
Article
PubMed
CAS
Google Scholar
Kwok S, Higuchi R. Avoiding false positives with PCR. Nature. 1989;339(6221):237–8.
Article
PubMed
CAS
Google Scholar
Gregori J, Esteban JI, Cubero M, Garcia-Cehic D, Perales C, Casillas R, Alvarez-Tejado M, Rodriguez-Frias F, Guardia J, Domingo E, et al. Ultra-deep pyrosequencing (UDPS) data treatment to study amplicon HCV minor variants. PLoS One. 2013;8(12):e83361.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ordeig L, Garcia-Cehic D, Gregori J, Soria ME, Nieto-Aponte L, Perales C, Llorens M, Chen Q, Riveiro-Barciela M, Buti M, et al. New hepatitis C virus genotype 1 subtype naturally harbouring resistance-associated mutations to NS5A inhibitors. J Gen Virol. 2018;99(1):97–102.
Article
PubMed
Google Scholar
Lu L, Xu Y, Yuan J, Li C, Murphy DG. The full-length genome sequences of nine HCV genotype 4 variants representing a new subtype 4s and eight unclassified lineages. Virology. 2015;482:111–6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Chueca N, Rivadulla I, Lovatti R, Reina G, Blanco A, Fernandez-Caballero JA, Cardenoso L, Rodriguez-Granjer J, Fernandez-Alonso M, Aguilera A, et al. Using NS5B sequencing for hepatitis C virus genotyping reveals discordances with commercial platforms. PLoS One. 2016;11(4):e0153754.
Article
PubMed
PubMed Central
CAS
Google Scholar
Liu CH, Liang CC, Liu CJ, Lin CL, Su TH, Yang HC, Chen PJ, Chen DS, Kao JH. Comparison of Abbott RealTime HCV genotype II with versant line probe assay 2.0 for hepatitis C virus genotyping. J Clin Microbiol. 2015;53(5):1754–7.
Article
PubMed
PubMed Central
CAS
Google Scholar
Poljak M. Next-generation sequencing: a diagnostic one-stop shop for hepatitis C? J Clin Microbiol. 2016;54(10):2427–30.
Article
PubMed
PubMed Central
CAS
Google Scholar
Rodriguez-Frias F, Nieto-Aponte L, Gregori J, Garcia-Cehic D, Casillas R, Tabernero D, Homs M, Blasi M, Vila M, Chen Q, et al. High HCV subtype heterogeneity in a chronically infected general population revealed by high-resolution hepatitis C virus subtyping. Clin Microbiol Infect. 2017;23(10):775.
Article
PubMed
Google Scholar
Hedskog C, Chodavarapu K, Ku KS, Xu S, Martin R, Miller MD, Mo H, Svarovskaia E. Genotype- and subtype-independent full-genome sequencing assay for hepatitis C virus. J Clin Microbiol. 2015;53(7):2049–59.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bull RA, Eltahla AA, Rodrigo C, Koekkoek SM, Walker M, Pirozyan MR, Betz-Stablein B, Toepfer A, Laird M, Oh S, et al. A method for near full-length amplification and sequencing for six hepatitis C virus genotypes. BMC Genomics. 2016;17:247.
Article
PubMed
PubMed Central
CAS
Google Scholar
Thomson E, Ip CL, Badhan A, Christiansen MT, Adamson W, Ansari MA, Bibby D, Breuer J, Brown A, Bowden R, et al. Comparison of next-generation sequencing Technologies for Comprehensive Assessment of full-length hepatitis C viral genomes. J Clin Microbiol. 2016;54(10):2470–84.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bartlett SR, Grebely J, Eltahla AA, Reeves JD, Howe AYM, Miller V, Ceccherini-Silberstein F, Bull RA, Douglas MW, Dore GJ, et al. Sequencing of hepatitis C virus for detection of resistance to direct-acting antiviral therapy: a systematic review. Hepatol Commun. 2017;1(5):379–90.
Article
PubMed
PubMed Central
Google Scholar
Lahr DJ, Katz LA. Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase. BioTechniques. 2009;47(4):857–66.
Article
PubMed
CAS
Google Scholar
Smith DB, Pathirana S, Davidson F, Lawlor E, Power J, Yap PL, Simmonds P. The origin of hepatitis C virus genotypes. J Gen Virol. 1997;78:321–8.
Article
PubMed
CAS
Google Scholar
Kuiken C, Combet C, Bukh J, Shin IT, Deleage G, Mizokami M, Richardson R, Sablon E, Yusim K, Pawlotsky JM, et al. A comprehensive system for consistent numbering of HCV sequences, proteins and epitopes. Hepatology. 2006;44(5):1355–61.
Article
PubMed
CAS
Google Scholar