Genotype- and subtype-independent full-genome sequencing assay for hepatitis C virus

Journal of Clinical Microbiology

Volumn 53, Issue 7, 2015, Pages 2049-2059

  Hedskog, Charlotte ^a   Chodavarapu, Krishna ^a   Ku, Karin S ^a   Xu, Simin ^a   Martin, Ross ^a   Miller, Michael D ^a   Mo, Hongmei ^a   Svarovskaia, Evguenia ^a  

^a GILEAD SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ANTIVIRAL RESISTANCE; ARTICLE; CLINICAL ARTICLE; CONSENSUS SEQUENCE; CONTROLLED STUDY; FULL LENGTH GENOME SEQUENCING ASSAY; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPING TECHNIQUE; HEPATITIS C VIRUS; HEPATITIS C VIRUS GENOTYPE 2; HEPATITIS C VIRUS GENOTYPE 3; HEPATITIS C VIRUS GENOTYPE 4; HEPATITIS C VIRUS GENOTYPE 5; HEPATITIS C VIRUS GENOTYPE 6; HEPATITIS C VIRUS SUBTYPE 1A; HEPATITIS C VIRUS SUBTYPE 1B; HEPATITIS C VIRUS SUBTYPE 2A; HEPATITIS C VIRUS SUBTYPE 2B; HEPATITIS C VIRUS SUBTYPE 2C; HEPATITIS C VIRUS SUBTYPE 2J; HEPATITIS C VIRUS SUBTYPE 3A; HEPATITIS C VIRUS SUBTYPE 3I; HEPATITIS C VIRUS SUBTYPE 4A; HEPATITIS C VIRUS SUBTYPE 4D; HEPATITIS C VIRUS SUBTYPE 5A; HEPATITIS C VIRUS SUBTYPE 6A; HEPATITIS C VIRUS SUBTYPE 6E; HEPATITIS C VIRUS SUBTYPE 6J; HUMAN; IN VITRO STUDY; MOLECULAR EVOLUTION; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; VIRUS GENOME; VIRUS LOAD; CLINICAL TRIAL; DNA SEQUENCE; GENETICS; HEPACIVIRUS; HEPATITIS C; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; PHASE 2 CLINICAL TRIAL; PHASE 3 CLINICAL TRIAL; PROCEDURES; VIROLOGY;

HEPATITIS C VIRUS;

VIRUS RNA;

GENOME, VIRAL; HEPACIVIRUS; HEPATITIS C; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; RNA, VIRAL; SEQUENCE ANALYSIS, DNA;

EID: 84932649981     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.02624-14     Document Type: Article

References (25)

1. Smith DB, Bukh J, Kuiken C, Muerhoff AS, Rice CM, Stapleton JT, Simmonds P. 2014. Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology 59:318-327. http://dx.doi.org/10.1002/hep.26744.
2. Simmonds P. 2004. Genetic diversity and evolution of hepatitis C virus-15 years on. J Gen Virol 85:3173-3188. http://dx.doi.org/10.1099/vir.0.80401-0.
3. Smith DB, Pathirana S, Davidson F, Lawlor E, Power J, Yap PL, Simmonds P. 1997. The origin of hepatitis C virus genotypes. J Gen Virol 78(Pt 2):321-328.
4. Morel V, Fournier C, François C, Brochot E, Helle F, Duverlie G, Castelain S. 2011. Genetic recombination of the hepatitis C virus: clinical implications. J Viral Hepat 18:77-83. http://dx.doi.org/10.1111/j.1365-2893.2010.01367.x.
5. Kalinina O, Norder H, Mukomolov S, Magnius LO. 2002. A natural intergenotypic recombinant of hepatitis C virus identified in St. Petersburg. J Virol 76:4034-4043. http://dx.doi.org/10.1128/JVI.76.8.4034-4043.2002.
6. Hedskog C, Doehle B, Chodavarapu K, Gontcharova V, Crespo Garcia J, De Knegt R, Drenth JP, McHutchison JG, Brainard D, Stamm LM, Miller MD, Svarovskaia E, Mo H. 2014. Characterization of hepatitis C virus intergenotypic recombinant strains and associated virologic response to sofosbuvir/ribavirin. Hepatology 61:471-480. http://dx.doi.org/10.1002/hep.27361.
7. Gane EJ, Stedman CA, Hyland RH, Ding X, Svarovskaia E, Symonds WT, Hindes RG, Berrey MM. 2013. Nucleotide polymerase inhibitor sofosbuvir plus ribavirin for hepatitis C. N Engl J Med 368:34-44. http://dx.doi.org/10.1056/NEJMoa1208953.
8. Murphy DG, Willems B, Deschenes M, Hilzenrat N, Mousseau R, Sabbah S. 2007. Use of sequence analysis of the NS5B region for routine genotyping of hepatitis C virus with reference to C/E1 and 5' untranslated region sequences. J Clin Microbiol 45:1102-1112. http://dx.doi.org/10.1128/JCM.02366-06.
9. Newman RM, Kuntzen T, Weiner B, Berical A, Charlebois P, Kuiken C, Murphy DG, Simmonds P, Bennett P, Lennon NJ, Birren BW, Zody MC, Allen TM, Henn MR. 2013. Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants. J Infect Dis 208:17-31. http://dx.doi.org/10.1093/infdis/jis679.
10. Okamoto H, Kurai K, Okada S, Yamamoto K, Lizuka H, Tanaka T, Fukuda S, Tsuda F, Mishiro S. 1992. Full-length sequence of a hepatitis C virus genome having poor homology to reported isolates: comparative study of four distinct genotypes. Virology 188:331-341. http://dx.doi.org/10.1016/0042-6822(92)90762-E.
11. Hmaied F, Legrand-Abravanel F, Nicot F, Garrigues N, Chapuy-Regaud S, Dubois M, Njouom R, Izopet J, Pasquier C. 2007. Full-length genome sequences of hepatitis C virus subtype 4f. J Gen Virol 88:2985-2990. http://dx.doi.org/10.1099/vir.0.83151-0.
12. Aizaki H, Aoki Y, Harada T, Ishii K, Suzuki T, Nagamori S, Toda G, Matsuura Y, Miyamura T. 1998. Full-length complementary DNA of hepatitis C virus genome from an infectious blood sample. Hepatology 27:621-627. http://dx.doi.org/10.1002/hep.510270242.
13. Lauck M, Alvarado-Mora MV, Becker EA, Bhattacharya D, Striker R, Hughes AL, Carrilho FJ, O'Connor DH, Rebello Pinho JR. 2012. Analysis of hepatitis C virus intrahost diversity across the coding region by ultradeep pyrosequencing. J Virol 86:3952-3960. http://dx.doi.org/10.1128/JVI.06627-11.
14. Ninomiya M, Ueno Y, Funayama R, Nagashima T, Nishida Y, Kondo Y, Inoue J, Kakazu E, Kimura O, Nakayama K, Shimosegawa T. 2012. Use of illumina deep sequencing technology to differentiate hepatitis C virus variants. J Clin Microbiol 50:857-866. http://dx.doi.org/10.1128/JCM.05715-11.
15. Malboeuf CM, Yang X, Charlebois P, Qu J, Berlin AM, Casali M, Pesko KN, Boutwell CL, DeVincenzo JP, Ebel GD, Allen TM, Zody MC, Henn MR, Levin JZ. 2013. Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification. Nucleic Acids Res 41:e13. http://dx.doi.org/10.1093/nar/gks794.
16. Kurn N, Chen P, Heath JD, Kopf-Sill A, Stephens KM, Wang S. 2005. Novel isothermal, linear nucleic acid amplification systems for highly multiplexed applications. Clin Chem 51:1973-1981. http://dx.doi.org/10.1373/clinchem.2005.053694.
17. Yang X, Charlebois P, Gnerre S, Coole MG, Lennon NJ, Levin JZ, Qu J, Ryan EM, Zody MC, Henn MR. 2012. De novo assembly of highly diverse viral populations. BMC Genomics 13:475. http://dx.doi.org/10.1186/1471-2164-13-475.
18. Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT. 2014. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One 9:e90581. http://dx.doi.org/10.1371/journal.pone.0090581.
19. Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. J Comput Biol 7:203-214. http://dx.doi.org/10.1089/10665270050081478.
20. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948. http://dx.doi.org/10.1093/bioinformatics/btm404.
21. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731-2739. http://dx.doi.org/10.1093/molbev/msr121.
22. Odeberg J, Ahmadian A, Williams C, Uhlen M, Ponten F, Lundeberg J. 1999. Context-dependent Taq-polymerase-mediated nucleotide alterations, as revealed by direct sequencing of the ZNF189 gene: implications for mutation detection. Gene 235:103-109. http://dx.doi.org/10.1016/S0378-1119(99)00205-X.
23. Gray RR, Parker J, Lemey P, Salemi M, Katzourakis A, Pybus OG. 2011. The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evol Biol 11:131. http://dx.doi.org/10.1186/1471-2148-11-131.
24. Dou XG, Talekar G, Chang J, Dai X, Li L, Bonafonte MT, Holloway B, Fields HA, Khudyakov YE. 2002. Antigenic heterogeneity of the hepatitis C virus NS5A protein. J Clin Microbiol 40:61-67. http://dx.doi.org/10.1128/JCM.40.1.61-67.2002.
25. Vallet S, Viron F, Henquell C, Le Guillou-Guillemette H, Lagathu G, Abravanel F, Trimoulet P, Soussan P, Schvoerer E, Rosenberg A, Gouriou S, Colson P, Izopet J, Payan C, ANRS AC11 HCV Group. 2011. NS3 protease polymorphism and natural resistance to protease inhibitors in French patients infected with HCV genotypes 1-5. Antiviral therapy 16:1093-1102. http://dx.doi.org/10.3851/IMP1900.