ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens

F1000Research

Volumn 4, Issue , 2015, Pages

  Bowden, Rory ^c   Bonsall, David ^a   Ansari, M Azim ^a,b   Ip, Camilla ^c   Trebes, Amy ^c   Brown, Anthony ^a   Klenerman, Paul ^a,d   Buck, David ^c   Piazza, Paolo ^c   Barnes, Eleanor ^a,d  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d JOHN RADCLIFFE HOSPITAL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GENE AMPLIFICATION; GENETIC VARIABILITY; HEPATITIS C VIRUS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; METAGENOMICS; OLIGONUCLEOTIDE PROBE; TARGET ORGANISM; VIRUS GENOME;

EID: 84965053929     PISSN: 20461402     EISSN: 1759796X     Source Type: Journal    
DOI: 10.12688/f1000research.7111.1     Document Type: Article

References (33)

1. Mohd Hanafiah K Groeger J Flaxman AD: Global epidemiology of hepatitis C virus infection: new estimates of age-specific antibody to HCV seroprevalence. Hepatology. 2013;57(4):1333-1342. 23172780 10.1002/hep.26141
2. Messina JP Humphreys I Flaxman A: Global distribution and prevalence of hepatitis C virus genotypes. Hepatology. 2015;61(1):77-87. 25069599 10.1002/hep.27259 4303918
3. Jacobson IM Gordon SC Kowdley KV: Sofosbuvir for hepatitis C genotype 2 or 3 in patients without treatment options. N Engl J Med. 2013;368(20):1867-1877. 23607593 10.1056/NEJMoa1214854
4. Lawitz E Mangia A Wyles D: Sofosbuvir for previously untreated chronic hepatitis C infection. N Engl J Med. 2013;368(20):1878-1887. 23607594 10.1056/NEJMoa1214853
5. Shah N Pierce T Kowdley KV: Review of direct-acting antiviral agents for the treatment of chronic hepatitis C. Expert Opin Investig Drugs. 2013;22(9):1107-1121. 23735127 10.1517/13543784.2013.806482
6. Asboe D Aitken C Boffito M: British HIV Association guidelines for the routine investigation and monitoring of adult HIV-1-infected individuals 2011. HIV Med. 2012;13(1):1-44. 22171742 10.1111/j.1468-1293.2011.00971.x
7. Gordon SC Muir AJ Lim JK: Safety profile of boceprevir and telaprevir in chronic hepatitis C: real world experience from HCV-TARGET. J Hepatol. 2015;62(2):286-293. 25218788 10.1016/j.jhep.2014.08.052
8. Hutchison C Kwong A Ray S: Accelerating drug development through collaboration: the Hepatitis C Drug Development Advisory Group. Clin Pharmacol Ther. 2014;96(2):162-165. 24853733 10.1038/clpt.2014.113
9. Hedskog C Chodavarapu K Ku KS: Genotype- and Subtype-Independent Full-Genome Sequencing Assay for Hepatitis C Virus. J Clin Microbiol. 2015;53(7):2049-59. 25878342 10.1128/JCM.02624-14 4473213
10. Smith DB Bukh J Kuiken C: Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource. Hepatology. 2014;59(1):318-327. 24115039 10.1002/hep.26744 4063340
11. Humphreys I Fleming V Fabris P: Full-length characterization of hepatitis C virus subtype 3a reveals novel hypervariable regions under positive selection during acute infection. J Virol. 2009;83(22):11456-11466. 19740991 10.1128/JVI.00884-09 2772701
12. Lauck M Alvarado-Mora MV Becker EA: Analysis of hepatitis C virus intrahost diversity across the coding region by ultradeep pyrosequencing. J Virol. 2012;86(7):3952-3960. 22278255 10.1128/JVI.06627-11 3302523
13. Batty EM Wong TH Trebes A: A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. PLoS One. 2013;8(6):e66129. 23762474 10.1371/journal.pone.0066129 3677912
14. Ninomiya M Ueno Y Funayama R: Use of Illumina deep sequencing technology to differentiate hepatitis C virus variants. J Clin Microbiol. 2012;50(3):857-866. 22205816 10.1128/JCM.05715-11 3295113
15. Iles JC Njouom R Foupouapouognigni Y: Characterization of Hepatitis C Virus Recombination in Cameroon by Use of Nonspecific Next-Generation Sequencing. J Clin Microbiol. 2015;53(10):3155-64. 26202126 10.1128/JCM.00483-15
16. Matranga CB Andersen KG Winnicki S: Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples. Genome Biol. 2014;15(11):519. 25403361 10.1186/PREACCEPT-1698056557139770 4262991
17. Depledge DP Palser AL Watson SJ: Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS One. 2011;6(11):e27805. 22125625 10.1371/journal.pone.0027805 3220689
18. Brown AC Bryant JM Einer-Jensen K: Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples. J Clin Microbiol. 2015;53(7):2230-7. 25972414 10.1128/JCM.00486-15 4473240
19. Lamble S Batty E Attar M: Improved workflows for high throughput library preparation using the transposome-based Nextera system. BMC Biotechnol. 2013;13:104. 24256843 10.1186/1472-6750-13-104 4222894
20. Gaidatzis D Lerch A Hahne F: QuasR: quantification and annotation of short reads in R. Bioinformatics. 2015;31(7):1130-2. 25417205 10.1093/bioinformatics/btu781 4382904
21. Martin M: Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal. 2011;17(1): Next Generation Sequencing Data Analysis. 10.14806/ej.17.1.200
22. Langmead B Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-359. 22388286 10.1038/nmeth.1923 3322381
23. Yang X Charlebois P Gnerre S: De novo assembly of highly diverse viral populations. BMC Genomics. 2012;13:475. 22974120 10.1186/1471-2164-13-475 3469330
24. Lee WP Stromberg MP Ward A: MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One. 2014;9(3):e90581. 24599324 10.1371/journal.pone.0090581 3944147
25. Yang X Charlebois P Macalalad A: V-Phaser 2: variant inference for viral populations. BMC Genomics. 2013;14:674. 24088188 10.1186/1471-2164-14-674 3907024
26. Henn MR Boutwell CL Charlebois P: Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog. 2012;8(3):e1002529. 22412369 10.1371/journal.ppat.1002529 3297584
27. Dohm JC Lottaz C Borodina T: Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 2008;36(16):e105. 18660515 10.1093/nar/gkn425 2532726
28. Melnikov A Galinsky K Rogov P: Hybrid selection for sequencing pathogen genomes from clinical samples. Genome Biol. 2011;12(8):R73. 21835008 10.1186/gb-2011-12-8-r73 3245613
29. Paolucci S Fiorina L Piralla A: Naturally occurring mutations to HCV protease inhibitors in treatment-naïve patients. Virol J. 2012;9:245. 23095680 10.1186/1743-422X-9-245 3493344
30. Afdhal N Reddy KR Nelson DR: Ledipasvir and sofosbuvir for previously treated HCV genotype 1 infection. N Engl J Med. 2014;370(16):1483-1493. 24725238 10.1056/NEJMoa1316366
31. Susser S Welsch C Wang Y: Characterization of resistance to the protease inhibitor boceprevir in hepatitis C virus-infected patients. Hepatology. 2009;50(6):1709-1718. 19787809 10.1002/hep.23192
32. Zhou Y Bartels DJ Hanzelka BL: Phenotypic characterization of resistant Val 36 variants of hepatitis C virus NS3-4A serine protease. Antimicrob Agents Chemother. 2008;52(1):110-120. 17938182 10.1128/AAC.00863-07 2223918
33. Cheval J Sauvage V Frangeul L: Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples. J Clin Microbiol. 2011;49(9):3268-3275. 21715589 10.1128/JCM.00850-11 3165575