Hepatitis C virus whole genome sequencing: Current methods/issues and future challenges

References

• European Association for the Study of the Liver. EASL recommendations on treatment of hepatitis C 2015. J Hepatol 2015;63:199–236
   PubMed Web of Science ®Google Scholar
• WHO|Hepatitis C. WHO. Available from: http://www.who.int/mediacentre/factsheets/fs164/en/ [last accessed 13 Apr 2015]
   Google Scholar
• Wedemeyer H, Dore GJ, Ward JW. Estimates on HCV disease burden worldwide – filling the gaps. J Viral Hepat 2015;22:1–5
   PubMed Web of Science ®Google Scholar
• Pawlotsky J-M. New hepatitis C virus (HCV) drugs and the hope for a cure: concepts in anti-HCV drug development. Semin Liver Dis 2014;34:22–9
   PubMed Web of Science ®Google Scholar
• O’Brien TR, Pfeiffer RM, Paquin A, et al. Comparison of functional variants in IFNL4 and IFNL3 for association with HCV clearance. J Hepatol 2015;63:1103–10
   PubMed Web of Science ®Google Scholar
• Rupp D, Bartenschlager R. Targets for antiviral therapy of hepatitis C. Semin Liver Dis 2014;34:9–21
   PubMed Web of Science ®Google Scholar
• Florian J, Mishra P, Arya V, et al. Direct-acting antiviral drugs for the treatment of chronic hepatitis c virus infection: interferon free is now. Clin Pharmacol Ther 2015;98:394–402
   PubMed Web of Science ®Google Scholar
• AASLD/IDSA HCV Guidance Panel. Hepatitis C guidance: AASLD-IDSA recommendations for testing, managing, and treating adults infected with hepatitis C virus. Hepatology 2015;62:932–54
   PubMed Web of Science ®Google Scholar
• Choo QL, Kuo G, Weiner AJ, et al. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 1989;244:359–62
   PubMed Web of Science ®Google Scholar
• Friebe P, Bartenschlager R. Genetic analysis of sequences in the 3' nontranslated region of hepatitis C virus that are important for RNA replication. J Virol 2002;76:5326–38
   PubMed Web of Science ®Google Scholar
• Moriishi K, Matsuura Y. Exploitation of lipid components by viral and host proteins for hepatitis c virus infection. Front Microbiol 2012;3:54
   PubMed Web of Science ®Google Scholar
• Neumann AU, Lam NP, Dahari H, et al. Hepatitis C viral dynamics in vivo and the antiviral efficacy of interferon-alpha therapy. Science 1998;282:103–7
   PubMed Web of Science ®Google Scholar
• Ogata N, Alter HJ, Miller RH, Purcell RH. Nucleotide sequence and mutation rate of the H strain of hepatitis C virus. Proc Natl Acad Sci USA 1991;88:3392–6
   PubMed Web of Science ®Google Scholar
• Gonzalez-Candelas F, Lopez-Labrador FX, Bracho MA. Recombination in Hepatitis C Virus. Viruses 2011;3:2006–24
   PubMed Web of Science ®Google Scholar
• Galli A, Bukh J. Comparative analysis of the molecular mechanisms of recombination in hepatitis C virus. Trends Microbiol 2014;22:354–64
   PubMed Web of Science ®Google Scholar
• Smith DB, Bukh J, Kuiken C, et al. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology 2014;59:318–27
   PubMed Web of Science ®Google Scholar
• Echeverría N, Moratorio G, Cristina J, Moreno P. Hepatitis C virus genetic variability and evolution. World J Hepatol 2015;7:831–45
   PubMed Web of Science ®Google Scholar
• Jacka B, Lamoury F, Simmonds P, et al. Sequencing of the hepatitis C virus: a systematic review. PLoS One 2013;8:e67073
   PubMed Web of Science ®Google Scholar
• Schnell G, Tripathi R, Beyer J, et al. Hepatitis C virus genotype 4 resistance and subtype demographic characterization of patients treated with Ombitasvir Plus Paritaprevir/Ritonavir. Antimicrob Agents Chemother 2015;59:6807–15
   PubMed Web of Science ®Google Scholar
• Cento V, Chevaliez S, Perno CF. Resistance to direct-acting antiviral agents: clinical utility and significance. Curr Opin HIV AIDS 2015;10:381–9
   PubMed Web of Science ®Google Scholar
• Lontok E, Harrington P, Howe A, et al. Hepatitis C virus drug resistance-associated substitutions: state of the art summary. Hepatology 2015;62:1623–32
   PubMed Web of Science ®Google Scholar
• Xia X, Zhao W, Tee KK, et al. Complete genome sequencing and phylogenetic analysis of HCV isolates from China reveals a new subtype, designated 6u. J Med Virol 2008;80:1740–6
   PubMed Web of Science ®Google Scholar
• Hussain A, Idrees M. The first complete genome sequence of HCV-1a from Pakistan and a phylogenetic analysis with complete genomes from the rest of the world. Virol J 2013;10:211
   PubMed Web of Science ®Google Scholar
• Stoddard MB, Li H, Wang S, et al. Identification, molecular cloning, and analysis of full-length hepatitis C virus transmitted/founder genotypes 1, 3, and 4. MBio 2015;6:e02518
   Web of Science ®Google Scholar
• Campo DS, Dimitrova Z, Yamasaki L, et al. Next-generation sequencing reveals large connected networks of intra-host HCV variants. BMC Genomics 2014;15:S4
   PubMed Web of Science ®Google Scholar
• Bull RA, Luciani F, McElroy K, et al. Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection. PLoS Pathog 2011;7:e1002243
   PubMed Web of Science ®Google Scholar
• Samimi-Rad K, Asgari F, Nasiritoosi M, et al. Patient-to-patient transmission of hepatitis C at Iranian Thalassemia centers shown by genetic characterization of viral strains. Hepat Mon 2013;13: e7699
   PubMed Web of Science ®Google Scholar
• Lecuit M, Eloit M. The diagnosis of infectious diseases by whole genome next generation sequencing: a new era is opening. Front Cell Infect Microbiol 2014;4:25
   PubMed Web of Science ®Google Scholar
• Lamoury FMJ, Jacka B, Bartlett S, et al. The influence of hepatitis C virus genetic region on phylogenetic clustering analysis. PLoS One 2015;10:e0131437
   Web of Science ®Google Scholar
• Cunningham EB, Applegate TL, Lloyd AR, et al. Mixed HCV infection and reinfection in people who inject drugs-impact on therapy. Nat Rev Gastroenterol Hepatol 2015;12:218–30
   PubMed Web of Science ®Google Scholar
• Sarrazin C, Dvory-Sobol H, Svarovskaia E, et al. Baseline and Post-baseline Resistance Analyses of Phase 2/3 Studies of Ledipasvir/Sofosbuvir ± RBV. AASLD Liver Meeting. Boston, 2014 Nov 7–12, Abstract 1926
   Google Scholar
• Jia H, Guo Y, Zhao W, Wang K. Long-range PCR in next-generation sequencing: comparison of six enzymes and evaluation on the MiSeq sequencer. Sci Rep 2014;4:5737
   Web of Science ®Google Scholar
• Qiu P, Cai X-Y, Wang L, et al. Hepatitis C virus whole genome position weight matrix and robust primer design. BMC Microbiol 2002;2:29
   PubMed Web of Science ®Google Scholar
• Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977;74:5463–7
   PubMed Web of Science ®Google Scholar
• Volpicella M, Leoni C, Costanza A, et al. Genome walking by next generation sequencing approaches. Biology 2012;1:495–507
   PubMedGoogle Scholar
• Zhang EZ, Bartels DJ, Frantz JD, et al. Development of a sensitive RT-PCR method for amplifying and sequencing near full-length HCV genotype 1 RNA from patient samples. Virol J 2013;10:53
   PubMed Web of Science ®Google Scholar
• Li C, Barnes E, Newton PN, et al. An expanded taxonomy of hepatitis C virus genotype 6: characterization of 22 new full-length viral genomes. Virology 2015;476:355–63
   PubMed Web of Science ®Google Scholar
• Lu L, Nakano T, Li C, et al. Hepatitis C virus complete genome sequences identified from China representing subtypes 6k and 6n and a novel, as yet unassigned subtype within genotype 6. J Gen Virol 2006;87:629–34
   PubMed Web of Science ®Google Scholar
• Li C, Lu L, Wu X, et al. Complete genomic sequences for hepatitis C virus subtypes 4b, 4c, 4d, 4g, 4k, 4l, 4m, 4n, 4o, 4p, 4q, 4r and 4t. J Gen Virol 2009;90:1820–6
   PubMed Web of Science ®Google Scholar
• Choudhary MC, Gupta E, Pandey P, et al. Identification and full-length molecular characterization of rare hepatitis C virus genotype 5a from India. Arch Virol 2015;160:329–33
   PubMed Web of Science ®Google Scholar
• Lu L, Li C, Xu Y, Murphy DG. Full-length genomes of 16 hepatitis C virus genotype 1 isolates representing subtypes 1c, 1d, 1e, 1g, 1h, 1i, 1j and 1k, and two new subtypes 1m and 1n, and four unclassified variants reveal ancestral relationships among subtypes. J Gen Virol 2014;95:1479–87
   PubMed Web of Science ®Google Scholar
• Gededzha MP, Selabe SG, Blackard JT, et al. Near full-length genome analysis of HCV genotype 5 strains from South Africa. Infect Genet Evol 2014;21:118–23
   PubMed Web of Science ®Google Scholar
• Xu R, Tong W, Gu L, et al. A panel of 16 full-length HCV genomes was characterized in China belonging to genotypes 1-6 including subtype 2f and two novel genotype 6 variants. Infect Genet Evol 2013;20:225–9
   PubMed Web of Science ®Google Scholar
• Yao E, Tavis JE. A general method for nested RT-PCR amplification and sequencing the complete HCV genotype 1 open reading frame. Virol J 2005;2:88
   PubMed Web of Science ®Google Scholar
• Kalinina O, Norder H, Mukomolov S, Magnius LO. A natural intergenotypic recombinant of hepatitis C virus identified in St. Petersburg. J Virol 2002;76:4034–43
   PubMed Web of Science ®Google Scholar
• Kalinina O, Norder H, Magnius LO. Full-length open reading frame of a recombinant hepatitis C virus strain from St. Petersburg: proposed mechanism for its formation. J Gen Virol 2004;85:1853–7
   PubMed Web of Science ®Google Scholar
• Bhattacharya D, Accola MA, Ansari IH, et al. Naturally occurring genotype 2b/1a hepatitis C virus in the United States. Virol J 2011;8:458
   PubMed Web of Science ®Google Scholar
• Noppornpanth S, Lien TX, Poovorawan Y, et al. Identification of a naturally occurring recombinant genotype 2/6 hepatitis C virus. J Virol 2006;80:7569–77
   PubMed Web of Science ®Google Scholar
• Shi W, Freitas IT, Zhu C, et al. Recombination in hepatitis C virus: identification of four novel naturally occurring inter-subtype recombinants. PloS One 2012;7:e41997
   PubMed Web of Science ®Google Scholar
• Kuntzen T, Berical A, Ndjomou J, et al. A set of reference sequences for the hepatitis C genotypes 4d, 4f and 4k covering the full open reading frame. J Med Virol 2008;80:1370
   PubMed Web of Science ®Google Scholar
• Glenn TC. Field guide to next-generation DNA sequencers. Mol Ecol Resour 2011;11:759–69
   PubMed Web of Science ®Google Scholar
• Fox EJ, Reid-Bayliss KS, Emond MJ, Loeb LA. Accuracy of next generation sequencing platforms. Next Gener Seq Appl 2014;1:pii. 1000106
   PubMedGoogle Scholar
• Lauck M, Alvarado-Mora MV, Becker EA, et al. analysis of hepatitis C virus intrahost diversity across the coding region by ultradeep pyrosequencing. J Virol 2012;86:3952–60
   PubMed Web of Science ®Google Scholar
• Nasu A, Marusawa H, Ueda Y, et al. Genetic heterogeneity of hepatitis C virus in association with antiviral therapy determined by ultra-deep sequencing. PLoS ONE 2011;6:e24907
   PubMed Web of Science ®Google Scholar
• Wang GP, Sherrill-Mix SA, Chang K-M, et al. Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. J Virol 2010;84:6218–28
   PubMed Web of Science ®Google Scholar
• Ohtsuru S, Ueda Y, Marusawa H, et al. Dynamics of defective hepatitis c virus clones in reinfected liver grafts in liver transplant recipients: ultradeep sequencing analysis. J Clin Microbiol 2013;51:3645–52
   PubMed Web of Science ®Google Scholar
• Cuypers L, Snoeck J, Vrancken B, et al. A near-full length genotypic assay for HCV1b. J Virol Methods 2014;209:126–35
   PubMed Web of Science ®Google Scholar
• Newman RM, Kuntzen T, Weiner B, et al. Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants. J Infect Dis 2013;208:17–31
   PubMed Web of Science ®Google Scholar
• Ramiere C, Trémeaux P, Caporossi A, et al. Recent evidence of underestimated circulation of hepatitis C virus intergenotypic recombinant strain RF2k/1b in the Rhone-Alpes region, France, January to August 2014: implications for antiviral treatment. Euro Surveill 2014;19:pii: 20944
   PubMedGoogle Scholar
• Hedskog C, Chodavarapu K, Ku KS, et al. Genotype- and subtype-independent full-genome sequencing assay for hepatitis C virus. J Clin Microbiol 2015;53:2049–59
   PubMed Web of Science ®Google Scholar
• Hedskog C, Doehle B, Chodavarapu K, et al. Characterization of hepatitis C virus intergenotypic recombinant strains and associated virological response to sofosbuvir/ribavirin. Hepatology 2015;61:471–80
   PubMed Web of Science ®Google Scholar
• Bartolini B, Giombini E, Abbate I, et al. Near full length hepatitis C virus genome reconstruction by next generation sequencing based on genotype-independent amplification. Dig Liver Dis 2015;47:608–12
   PubMedGoogle Scholar
• Ninomiya M, Ueno Y, Funayama R, et al. Use of illumina deep sequencing technology to differentiate hepatitis c virus variants. J Clin Microbiol 2012;50:857–66
   PubMed Web of Science ®Google Scholar
• Iles JC, Njouom R, Foupouapouognigni Y, et al. Characterisation of hepatitis C virus recombination in Cameroon using non-specific next generation sequencing. J Clin Microbiol 2015;53:3155–64
   PubMed Web of Science ®Google Scholar
• Prosperi MCF, Yin L, Nolan DJ, et al. Empirical validation of viral quasispecies assembly algorithms: state-of-the-art and challenges. Sci Rep 2013;3:2837
   PubMed Web of Science ®Google Scholar
• Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005;437:376–80
   PubMed Web of Science ®Google Scholar
• Li R, Zhu H, Ruan J, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010;20:265–72
   PubMed Web of Science ®Google Scholar
• Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008;18:821–9
   PubMed Web of Science ®Google Scholar
• Henn MR, Boutwell CL, Charlebois P, et al. Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog 2012;8:e1002529
   PubMed Web of Science ®Google Scholar
• Yang X, Charlebois P, Gnerre S, et al. De novo assembly of highly diverse viral populations. BMC Genomics 2012;13:475
   PubMed Web of Science ®Google Scholar
• Chin C-S, Alexander DH, Marks P, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013;10:563–9
   PubMed Web of Science ®Google Scholar
• McElroy K, Thomas T, Luciani F. Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions. Microb Inform Exp 2014;4:1
   PubMedGoogle Scholar
• Audebert C, Hot D, Lemoine Y, Caboche S. High-throughput sequencing: towards a genome-based diagnosis in infectious diseases. Med Sci (Paris) 2014;30:1144–51
   PubMed Web of Science ®Google Scholar
• Munroe DJ, Harris TJR. Third-generation sequencing fireworks at Marco Island. Nat Biotechnol 2010;28:426–8
   PubMed Web of Science ®Google Scholar