HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma

PLoS ONE

Volumn 10, Issue 4, 2015, Pages

  Qiu, Ping ^a   Stevens, Richard ^a   Wei, Bo ^a   Lahser, Fred ^a   Howe, Anita Y M ^a   Klappenbach, Joel A ^a   Marton, Matthew J ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NONSTRUCTURAL PROTEIN 3; NONSTRUCTURAL PROTEIN 5A; NONSTRUCTURAL PROTEIN 5B;

ACCURACY; ARTICLE; BLOOD SAMPLING; BLOODSTREAM INFECTION; GENE SEQUENCE; GENE TARGETING; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOTYPING TECHNIQUE; HEPATITIS C VIRUS; HUMAN; LIMIT OF DETECTION; MIXED INFECTION; MOLECULAR PHYLOGENY; NEXT GENERATION SEQUENCING; NONHUMAN; PHYLOGENETIC TREE; VIRUS DETECTION; VIRUS LOAD; BLOOD; DNA SEQUENCE; GENETICS; GENOTYPE; HEPACIVIRUS; HEPATITIS C; HIGH THROUGHPUT SEQUENCING; MOLECULAR DIAGNOSIS; MOLECULAR TYPING; PHYLOGENY; VIROLOGY; VIRUS GENE;

HEPATITIS C VIRUS;

GENES, VIRAL; GENOTYPE; HEPACIVIRUS; HEPATITIS C; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; MOLECULAR TYPING; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84926667713     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0122082     Document Type: Article

References (35)

1. Lavanchy D. Evolving epidemiology of hepatitis C virus. Clin Microbiol Infect. 2011;17:107-115. doi: 10.1111/j.1469-0691.2010.03432.x PMID: 21091831
2. Lavanchy D. The global burden of hepatitis C. Liver Int. 2009;29 Suppl 1:74-81. doi: 10.1111/j.1478-3231.2008.01934.x PMID: 19207969
3. Choo QL, Kuo G, Weiner AJ, Overby LR, Bradley DW, Houghton M. Isolation of a cDNA clone derived from a bloodborne non-A, non-B hepatitis genome. Science 1989;244:359-362. PMID: 2523562
4. Kohli A, Shaffer A, Sherman A, Kottilil S. Treatment of hepatitis C: a systematic review. JAMA. 2014;2014(6):631-40. doi: 10.1001/jama.2014.7085 PMID: 25117132
5. Tokita H, Okamoto H, Luengrojanakul P, Vareesangthip K, Chainuvati T, Iizuka H et al. Hepatitis C virus variants from Thailand classifiable into five novel genotypes in the sixth (6b), seventh (7c, 7d) and ninth (9b, 9c) major genetic groups. J Gen Virol. 1995;76(Pt9):2329-2335. PMID: 7561773
6. Sandres-Saune K, Deny P, Pasquier C, Thibaut V, Duverlie G, Izopet J. Determining hepatitis C genotype by analyzing the sequence of the NS5b region. J Virol Methods 2003, 109:187-193. PMID: 12711062
7. Yang YC, Wang DY, Cheng HF, Chuang EY, Tsai MH. A reliable multiplex genotyping assay for HCV using a suspension bead array. Microb Biotechnol. 2014; doi: 10.1111/1751-7915.12140
8. Chevaliez S, Bouvier-Alias M, Brillet R, Pawlotsky JM. Hepatitis C virus (HCV) genotype 1 subtype identification in new HCV drug development and future clinical practice. PLoS One. 2009:4, p. e8209 doi: 10.1371/journal.pone.0008209 PMID: 19997618
9. Afdhal N, Zeuzem S, Kwo P, Chojkier M, Gitlin N, Puoti M et al. Ledipasvir and sofosbuvir for untreated HCVgenotype1 infection. N EnglJ Med. 2014;2014(20):1889-98. doi: 10.1056/NEJMoa1402454 PMID: 24725239
10. Bouchardeau F, Cantaloube JF, Chevaliez S, Portal C, Razer A, Lefrère JJ et al. Improvement of hepatitis C virus (HCV) genotype determination with the new version of the INNO-LiPA HCV assay. J Clin Microbiol, 2007;45:1140-1145 PMID: 17251399
11. Stelzl E, Van Der Meer C, Gouw R, Beld M, Grahovac M, Marth E, et al. Determination of the hepatitis C virus subtype: comparison of sequencing and reverse hybridization assays. Clin Chem Lab Med. 2007;45:167-170 PMID: 17311502
12. Martró E, González V, Buckton AJ, Saludes V, Fernández G, Matas L, et al. Evaluation of a new assay in comparison with reverse hybridization and sequencing methods for hepatitis C virus genotyping targeting both 5' noncoding and nonstructural 5b genomic regions. J Clin Microbiol. 2008;46:192-197 PMID: 17989191
13. Verbeeck J, Stanley MJ, Shieh J, Celis L, Huyck E, Wollants E, et al. Evaluation of Versant hepatitis C virus genotype assay (LiPA) 2.0. J Clin Microbiol 2008;46:1901-1906. doi: 10.1128/JCM.02390-07 PMID: 18400913
14. Ciotti M, Marcuccilli F, Guenci T, Babakir-Mina M, Chiodo F, Favarato M, et al. A multicenter evaluation of the Abbott RealTime HCV Genotype II assay. J Virol Methods. 2010;167:205-207 doi: 10.1016/j. jviromet.2010.03.017 PMID: 20362009
15. Sohn YH, Ko SY, Kim MH. Performance evaluation of the Abbott RealTime HCV Genotype II for hepatitis C virus genotyping. Clin Chem Lab Med. 2010:48:469-474 doi: 10.1515/CCLM.2010.093 PMID: 20128734
16. Al Balwi MA. Prevalence of mixed hepatitis C virus (HCV) genotypes among recently diagnosed dialysis patients with HCV infection. Saudi J Kidney Dis Transpl. 2011;2011(4):712-6. PMID: 21743215
17. Zanini B, Lanzini A. Antiviral treatment for chronic hepatitis C in illicit drug users: a systematic review. AntivirTher. 2009;2009(4):467-79. PMID: 19578232
18. Theodore Sy, Jamal M. Mazen Epidemiology of Hepatitis C Virus (HCV) Infection Int J Med Sci 2006;3(2):41-46. PMID: 16614741
19. Touzet S, Kraemer L, Colin C, Pradat P, Lanoir D, Bailly F et al. Epidemiology of hepatitis C virus infection in seven European Union countries: a critical analysis of the literature. HENCORE Group (Hepatitis C European Network for Cooperative Research). Eur J Gastroenterol Hepatol. 2000;12:667-678 PMID: 10912488
20. Beerenwinkel N, Zagordi O. Ultra-deep sequencing for the analysis of viral populations. Curr. Opin. Virol. 2011, 1:413-418. doi: 10.1016/j.coviro.2011.07.008 PMID: 22440844
21. Benjamini Y, Speed TP. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res. 2012;2012(10):e72. doi: 10.1093/nar/gks001 PMID: 22323520
22. Kanagawa T. Bias and artifacts in multitemplate polymerase chain reactions (PCR) J Biosci Bioeng. 2003;2003(4):317-323. PMID: 16233530
23. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 2008, 36(16):e105 doi: 10.1093/nar/gkn425 PMID: 18660515
24. Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 2011, 12(2):R18. doi: 10.1186/gb-2011-12-2-r18 PMID: 21338519
25. Dabney J, Meyer M. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques. 2012;2012(2):87-94. doi: 10.2144/000113809 PMID: 22313406
26. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:4673-4680. PMID: 7984417
27. Felsenstein J. 1989. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5:164-166.
28. Junier T and Zdobnov EM. The Newick Utilities: High-throughput Phylogenetic tree Processing in the UNIX Shell Bioinformatics 2010;26:1669-1670 doi: 10.1093/bioinformatics/btq243 PMID: 20472542
29. Magoc T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011;2011(21):2957-63. doi: 10.1093/bioinformatics/btr507 PMID: 21903629
30. Qiu P, Cai XY, Wang L, Greene JR, Malcolm B: Hepatitis C virus whole genome position weight matrix and robust primer design. BMC Microbiol 2002;2:29 PMID: 12323075
31. Qiu P, Cai XY, Ding W, Zhang Q, Norris ED, Greene JR. HCV genotyping using statistical classification approach. J Biomed Sci. 2009;16:62. doi: 10.1186/1423-0127-16-62 PMID: 19586537
32. Figlerowicz M, Jackowiak P, Formanowicz P, Kedziora P, Alejska M, Malinowska N et al. Hepatitis C virus quasispecies in chronically infected children subjected to interferon-ribavirin therapy. Arch Virol. 2010;14:1977-1987
33. Marascio N, Torti, Liberto MC and Focà A. Update on different aspects of HCV variability: focus on NS5B polymerase. BMC Infect Dis. 2014;14(Suppl 5):S1 doi: 10.1186/1471-2334-14-S5-S1 PMID: 25234810
34. Howe AY, Black S, Curry S, Ludmerer SW, Liu R, Barnard RJ, Newhard W, Hwang PM, Nickle D, Gilbert C, Caro L, Di Nubile MJ, Mobashery N. Virologic resistance analysis from a phase 2 study of MK-5172 combined with pegylated interferon/ribavirin in treatment-naive patients with hepatitis C virus genotype 1 infection. Clin Infect Dis. 2014, 59(12):1657-65. doi: 10.1093/cid/ciu696 PMID: 25266289
35. Fridell RA, Qiu D, Wang C, Valera L, Gao M. Resistance analysis of the hepatitis C virus NS5A inhibitor BMS-790052 in an in vitro replicon system. Antimicrob Agents Chemother 2010, 54(9):3641-50 doi: 10.1128/AAC.00556-10 PMID: 20585111