Norovirus whole-genome sequencing by SureSelect target enrichment: A robust and sensitive method

Journal of Clinical Microbiology

Volumn 54, Issue 10, 2016, Pages 2530-2537

  Brown, Julianne R ^a,b   Roy, Sunando ^b   Ruis, Christopher ^b   Yara Romero, Erika ^b   Shah, Divya ^a,b   Williams, Rachel ^b   Breuer, Judy ^a,b  

^a GREAT ORMOND STREET HOSPITAL   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS OF VARIANCE; ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA SYNTHESIS; ENRICHMENT CULTURE; GENE AMPLIFICATION; GENETIC ANALYSIS; GENETIC HETEROGENEITY; GENETIC PROCEDURES; GENETIC VARIABILITY; GENOTYPE; NONHUMAN; NOROVIRUS; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; SURESELECT TARGET ENRICHMENT; VIRUS CAPSID; VIRUS GENOME; VIRUS TITRATION; WHOLE GENOME SEQUENCING; CALICIVIRUS INFECTION; DNA SEQUENCE; FECES; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MALE; NUCLEIC ACID HYBRIDIZATION; PROCEDURES; SPECIMEN HANDLING; VIROLOGY;

VIRUS RNA;

CALICIVIRIDAE INFECTIONS; FECES; GENOME, VIRAL; HUMANS; MALE; NOROVIRUS; NUCLEIC ACID HYBRIDIZATION; RNA, VIRAL; SEQUENCE ANALYSIS, DNA; SPECIMEN HANDLING;

EID: 84991219412     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.01052-16     Document Type: Article

References (24)

1. de Wit MA, Koopmans MP, Kortbeek LM, Wannet WJ, Vinje J, van Leusden F, Bartelds AI, van Duynhoven YT. 2001. Sensor, a population-based cohort study on gastroenteritis in the Netherlands: incidence and etiology. Am J Epidemiol 154:666-674. http://dx.doi.org/10.1093/aje/154.7.666.
2. Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson MA, Roy SL, Jones JL, Griffin PM. 2011. Foodborne illness acquired in the United States: major pathogens. Emerg Infect Dis 17:7-15. http://dx.doi.org/10.3201/eid1701.P11101.
3. Ahmed SM, Hall AJ, Robinson AE, Verhoef L, Premkumar P, Parashar UD, Koopmans M, Lopman BA. 2014. Global prevalence of norovirus in cases of gastroenteritis: a systematic review and meta-analysis. Lancet Infect Dis 14:725-730. http://dx.doi.org/10.1016/S1473-3099(14)70767-4.
4. Lopman BA, Reacher MH, Vipond IB, Hill D, Perry C, Halladay T, Brown DW, Edmunds WJ, Sarangi J. 2004. Epidemiology and cost of nosocomial gastroenteritis, Avon, England, 2002-2003. Emerg Infect Dis 10:1827-1834. http://dx.doi.org/10.3201/eid1010.030941.
5. Koo HL, Neill FH, Estes MK, Munoz FM, Cameron A, Dupont HL, Atmar RL. 2013. Noroviruses: the most common pediatric viral enteric pathogen at a large university hospital after introduction of rotavirus vaccination. J Pediatr Infect Dis Soc 2:57-60. http://dx.doi.org/10.1093/jpids/pis070.
6. Payne DC, Vinje J, Szilagyi PG, Edwards KM, Staat MA, Weinberg GA, Hall CB, Chappell J, Bernstein DI, Curns AT, Wikswo M, Shirley SH, Hall AJ, Lopman B, Parashar UD. 2013. Norovirus and medically attended gastroenteritis in U.S. children. N Engl J Med 368:1121-1130. http://dx.doi.org/10.1056/NEJMsa1206589.
7. Verhoef L, Williams KP, Kroneman A, Sobral B, van Pelt W, Koopmans M. 2012. Selection of a phylogenetically informative region of the norovirus genome for outbreak linkage. Virus Genes 44:8-18. http://dx.doi.org/10.1007/s11262-011-0673-x.
8. Jones MK, Watanabe M, Zhu S, Graves CL, Keyes LR, Grau KR, Gonzalez-Hernandez MB, Iovine NM, Wobus CE, Vinje J, Tibbetts SA, Wallet SM, Karst SM. 2014. Enteric bacteria promote human and mouse norovirus infection of B cells. Science 346:755-759. http://dx.doi.org/10.1126/science.1257147.
9. Kundu S, Lockwood J, Depledge DP, Chaudhry Y, Aston A, Rao K, Hartley JC, Goodfellow I, Breuer J. 2013. Next-generation whole genome sequencing identifies the direction of norovirus transmission in linked patients. Clin Infect Dis 57:407-414. http://dx.doi.org/10.1093/cid/cit287.
10. Cotten M, Petrova V, Phan MV, Rabaa MA, Watson SJ, Ong SH, Kellam P, Baker S. 2014. Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting. J Virol 88:11056-11069. http://dx.doi.org/10.1128/JVI.01333-14.
11. Won YJ, Park JW, Han SH, Cho HG, Kang LH, Lee SG, Ryu SR, Paik SY. 2013. Full-genomic analysis of a human norovirus recombinant GII.12/13 novel strain isolated from South Korea. PLoS One 8:e85063. http://dx.doi.org/10.1371/journal.pone.0085063.
12. Chhabra P, Walimbe AM, Chitambar SD. 2010. Complete genome characterization of genogroup II norovirus strains from India: evidence of recombination in ORF2/3 overlap. Infect Genet Evol 10:1101-1109. http://dx.doi.org/10.1016/j.meegid.2010.07.007.
13. Nakamura S, Yang CS, Sakon N, Ueda M, Tougan T, Yamashita A, Goto N, Takahashi K, Yasunaga T, Ikuta K, Mizutani T, Okamoto Y, Tagami M, Morita R, Maeda N, Kawai J, Hayashizaki Y, Nagai Y, Horii T, Iida T, Nakaya T. 2009. Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One 4:e4219. http://dx.doi.org/10.1371/journal.pone.0004219.
14. Wong TH, Dearlove BL, Hedge J, Giess AP, Piazza P, Trebes A, Paul J, Smit E, Smith EG, Sutton JK, Wilcox MH, Dingle KE, Peto TE, Crook DW, Wilson DJ, Wyllie DH. 2013. Whole genome sequencing and de novo assembly identifies Sydney-like variant noroviruses and recombinants during the winter 2012/2013 outbreak in England. Virol J 10:335. http://dx.doi.org/10.1186/1743-422X-10-335.
15. Batty EM, Wong TH, Trebes A, Argoud K, Attar M, Buck D, Ip CL, Golubchik T, Cule M, Bowden R, Manganis C, Klenerman P, Barnes E, Walker AS, Wyllie DH, Wilson DJ, Dingle KE, Peto TE, Crook DW, Piazza P. 2013. A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. PLoS One 8:e66129. http://dx.doi.org/10.1371/journal.pone.0066129.
16. Bavelaar HH, Rahamat-Langendoen J, Niesters HG, Zoll J, Melchers WJ. 2015. Whole genome sequencing of fecal samples as a tool for the diagnosis and genetic characterization of norovirus. J Clin Virol 72:122-125. http://dx.doi.org/10.1016/j.jcv.2015.10.003.
17. Brown AC, Bryant JM, Einer-Jensen K, Holdstock J, Houniet DT, Chan JZ, Depledge DP, Nikolayevskyy V, Broda A, Stone MJ, Christiansen MT, Williams R, McAndrew MB, Tutill H, Brown J, Melzer M, Rosmarin C, McHugh TD, Shorten RJ, Drobniewski F, Speight G, Breuer J. 2015. Rapid whole-genome sequencing of Mycobacterium tuberculosis isolates directly from clinical samples. J Clin Microbiol 53:2230-2237. http://dx.doi.org/10.1128/JCM.00486-15.
18. Christiansen MT, Brown AC, Kundu S, Tutill HJ, Williams R, Brown JR, Holdstock J, Holland MJ, Stevenson S, Dave J, Tong CY, Einer-Jensen K, Depledge DP, Breuer J. 2014. Whole-genome enrichment and sequencing of Chlamydia trachomatis directly from clinical samples. BMC Infect Dis 14:591. http://dx.doi.org/10.1186/s12879-014-0591-3.
19. Depledge DP, Palser AL, Watson SJ, Lai IY, Gray ER, Grant P, Kanda RK, Leproust E, Kellam P, Breuer J. 2011. Specific capture and whole-genome sequencing of viruses from clinical samples. PLoS One 6:e27805. http://dx.doi.org/10.1371/journal.pone.0027805.
20. Kroneman A, Vennema H, Deforche K, Avoort HVD, Penaranda S, Oberste MS, Vinje J, Koopmans M. 2011. An automated genotyping tool for enteroviruses and noroviruses. J Clin Virol 51:121-125. http://dx.doi.org/10.1016/j.jcv.2011.03.006.
21. Kent WJ. 2002. BLAT: the BLAST-like alignment tool. Genome Res 12:656-664. http://dx.doi.org/10.1101/gr.229202.
22. Brown JR, Gilmour K, Breuer J. 2016. Norovirus infections occur in B-cell-deficient patients. Clin Infect Dis 62:1136-1138. http://dx.doi.org/10.1093/cid/ciw060.
23. Eden JS, Tanaka MM, Boni MF, Rawlinson WD, White PA. 2013. Recombination within the pandemic norovirus GII.4 lineage. J Virol 87:6270-6282. http://dx.doi.org/10.1128/JVI.03464-12.
24. Brown JR, Shah D, Breuer J. Viral gastrointestinal infections and norovirus genotypes in a paediatric UK hospital, 2014-2015. J Clin Virol, in press.