Development and validation of a microarray for the confirmation and typing of norovirus RT-PCR products

Journal of Virological Methods

Volumn 173, Issue 2, 2011, Pages 233-250

  Mattison, Kirsten ^a,b   Corneau, Nathalie ^a   Berg, Ingvild ^c   Bosch, Albert ^d   Duizer, Erwin ^e   Gutiérrez Aguirre, Ion ^f   L'Homme, Yvan ^g   Lucero, Yalda ^h   Luo, Zhiyao ^g   Martyres, Alexander ^b   Myrmel, Mette ^c   O'Ryan, Miguel ^h   Pagotto, Franco ^a,b   Sano, Daisuke ^d,i   Svraka, Sanela ^e,j   Urzua, Ulises ^h   Bidawid, Sabah ^a  

^a HEALTH CANADA   (Canada)

^b UNIVERSITY OF OTTAWA   (Canada)

^c NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^d UNIVERSITY OF BARCELONA   (Spain)

^e NATIONAL INSTITUTE FOR PUBLIC HEALTH AND THE ENVIRONMENT   (Netherlands)

^f NATIONAL INSTITUTE OF BIOLOGY   (Slovenia)

^g CANADIAN FOOD INSPECTION AGENCY   (Canada)

^h UNIVERSITY OF CHILE   (Chile)

ⁱ HOKKAIDO UNIVERSITY   (Japan)

^j Central Laboratory for Bacteriology and Serology   (Netherlands)

more..

Author keywords

Genotyping; Microarray; Norovirus

Indexed keywords

DNA POLYMERASE; VIRUS DNA;

AMPLICON; ARTICLE; CANADA; CONTROLLED STUDY; DNA MICROARRAY; GENE INTERACTION; GENE SEQUENCE; GENETIC ANALYSIS; GENOTYPE; LABORATORY TEST; NONHUMAN; NOROVIRUS; NUCLEIC ACID HYBRIDIZATION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STRAIN DIFFERENCE; VIRUS CAPSID; VIRUS STRAIN; VIRUS TYPING;

GENOTYPE; HUMANS; MICROARRAY ANALYSIS; MOLECULAR TYPING; NOROVIRUS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

MIRIDAE; NOROVIRUS;

EID: 79954610452     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2011.02.011     Document Type: Article

References (32)

1. Anderson A.D., Heryford A.G., Sarisky J.P., Higgins C., Monroe S.S., Beard R.S., Newport C.M., Cashdollar J.L., Fout G.S., Robbins D.E., Seys S.A., Musgrave K.J., Medus C., Vinje J., Bresee J.S., Mainzer H.M., Glass R.I. A waterborne outbreak of Norwalk-like virus among snowmobilers-Wyoming, 2001. J. Infect. Dis. 2003, 187:303-306.
2. Ando T., Monroe S.S., Gentsch J.R., Jin Q., Lewis D.C., Glass R.I. Detection and differentiation of antigenically distinct small round-structured viruses (Norwalk-like viruses) by reverse transcription-PCR and southern hybridization. J. Clin. Microbiol. 1995, 33:64-71.
3. Ayodeji M., Kulka M., Jackson S.A., Patel I., Mammel M., Cebula T.A., Goswami B.B. A microarray based approach for the identification of common foodborne viruses. Open Virol. J. 2009, 3:7-20.
4. Brinkman N.E., Fout G.S. Development and evaluation of a generic tag array to detect and genotype noroviruses in water. J. Virol. Methods 2009, 156:8-18.
5. Butot S., Le Guyader F.S., Krol J., Putallaz T., Amoroso R., Sanchez G. Evaluation of various real-time RT-PCR assays for the detection and quantitation of human norovirus. J. Virol. Methods 2010, 167:90-94.
6. Chan M.C., Sung J.J., Lam R.K., Chan P.K., Lee N.L., Lai R.W., Leung W.K. Fecal viral load and norovirus-associated gastroenteritis. Emerg. Infect. Dis. 2006, 12:1278-1280.
7. Chizhikov V., Wagner M., Ivshina A., Hoshino Y., Kapikian A.Z., Chumakov K. Detection and genotyping of human group A rotaviruses by oligonucleotide microarray hybridization. J. Clin. Microbiol. 2002, 40:2398-2407.
8. Clark B., McKendrick M. A review of viral gastroenteritis. Curr. Opin. Infect. Dis. 2004, 17:461-469.
9. Eklund A.C., Friis P., Wernersson R., Szallasi Z. Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization. Nucleic Acids Res. 2010, 38:e27.
10. Gall A., Hoffmann B., Harder T., Grund C., Hoper D., Beer M. Design and validation of a microarray for detection, hemagglutinin subtyping, and pathotyping of avian influenza viruses. J. Clin. Microbiol. 2009, 47:327-334.
11. Jaaskelainen A.J., Maunula L. Applicability of microarray technique for the detection of noro- and astroviruses. J. Virol. Methods 2006, 136:210-216.
12. Kageyama T., Kojima S., Shinohara M., Uchida K., Fukushi S., Hoshino F.B., Takeda N., Katayama K. Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR. J. Clin. Microbiol. 2003, 41:1548-1557.
13. Kageyama T., Shinohara M., Uchida K., Fukushi S., Hoshino F.B., Kojima S., Takai R., Oka T., Takeda N., Katayama K. Coexistence of multiple genotypes, including newly identified genotypes, in outbreaks of gastroenteritis due to Norovirus in Japan. J. Clin. Microbiol. 2004, 42:2988-2995.
14. Kojima S., Kageyama T., Fukushi S., Hoshino F.B., Shinohara M., Uchida K., Natori K., Takeda N., Katayama K. Genogroup-specific PCR primers for detection of Norwalk-like viruses. J. Virol. Methods 2002, 100:107-114.
15. Leparc G.G., Tuchler T., Striedner G., Bayer K., Sykacek P., Hofacker I.L., Kreil D.P. Model-based probe set optimization for high-performance microarrays. Nucleic Acids Res. 2009, 37:e18.
16. Lopman B. Noroviruses: simple detection for complex epidemiology. Clin. Infect. Dis. 2006, 42:970-971.
17. Magulski T., Paulmann D., Bischoff B., Becker B., Steinmann E., Steinmann J., Goroncy-Bermes P., Steinmann J. Inactivation of murine norovirus by chemical biocides on stainless steel. BMC Infect. Dis. 2009, 9:107.
18. Mattison K., Grudeski E., Auk B., Charest H., Drews S.J., Fritzinger A., Gregoricus N., Hayward S., Houde A., Lee B.E., Pang X.L., Wong J., Booth T.F., Vinje J. Multicenter comparison of two norovirus ORF2-based genotyping protocols. J. Clin. Microbiol. 2009, 47:3927-3932.
19. Menton J.F., Kearney K., Morgan J.G. Development of a real-time RT-PCR and reverse line probe hybridisation assay for the routine detection and genotyping of Noroviruses in Ireland. Virol. J. 2007, 4:86.
20. Noel J.S., Ando T., Leite J.P., Green K.Y., Dingle K.E., Estes M.K., Seto Y., Monroe S.S., Glass R.I. Correlation of patient immune responses with genetically characterized small round-structured viruses involved in outbreaks of nonbacterial acute gastroenteritis in the United States, 1990 to 1995. J. Med. Virol. 1997, 53:372-383.
21. Pagotto F., Mattison K., Corneau N., Bidawid S. Development of a DNA microarray for the simultaneous detection and genotyping of noroviruses. J. Food Prot. 2008, 71:1434-1441.
22. Svraka S., van der Veer B., Duizer E., Dekkers J., Koopmans M., Vennema H. Novel approach for detection of enteric viruses to enable syndrome surveillance of acute viral gastroenteritis. J. Clin. Microbiol. 2009, 47:1674-1679.
23. Terpstra F.G., van den Blink A.E., Bos L.M., Boots A.G., Brinkhuis F.H., Gijsen E., van Remmerden Y., Schuitemaker H., van't Wout A.B. Resistance of surface-dried virus to common disinfection procedures. J. Hosp. Infect. 2007, 66:332-338.
24. Teunis P.F., Moe C.L., Liu P., Miller S.E., Lindesmith L., Baric R.S., Le Pendu J., Calderon R.L. Norwalk virus: how infectious is it?. J. Med. Virol. 2008, 80:1468-1476.
25. Ueki Y., Sano D., Watanabe T., Akiyama K., Omura T. Norovirus pathway in water environment estimated by genetic analysis of strains from patients of gastroenteritis, sewage, treated wastewater, river water and oysters. Water Res. 2005, 39:4271-4280.
26. Vennema H., de Bruin E., Koopmans M. Rational optimization of generic primers used for Norwalk-like virus detection by reverse transcriptase polymerase chain reaction. J. Clin. Virol. 2002, 25:233-235.
27. Verhoef L., Vennema H., van Pelt W., Lees D., Boshuizen H., Henshilwood K., Koopmans M. Use of norovirus genotype profiles to differentiate origins of foodborne outbreaks. Emerg. Infect. Dis. 2010, 16:617-624.
28. Vinje J., Koopmans M.P. Molecular detection and epidemiology of small round-structured viruses in outbreaks of gastroenteritis in the Netherlands. J. Infect. Dis. 1996, 174:610-615.
29. Vinje J., Koopmans M.P. Simultaneous detection and genotyping of "Norwalk-like viruses" by oligonucleotide array in a reverse line blot hybridization format. J. Clin. Microbiol. 2000, 38:2595-2601.
30. Vinje J., Hamidjaja R.A., Sobsey M.D. Development and application of a capsid VP1 (region D) based reverse transcription PCR assay for genotyping of genogroup I and II noroviruses. J. Virol. Methods 2004, 116:109-117.
31. Wang D., Coscoy L., Zylberberg M., Avila P.C., Boushey H.A., Ganem D., DeRisi J.L. Microarray-based detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:15687-15692.
32. Zheng D.P., Ando T., Fankhauser R.L., Beard R.S., Glass R.I., Monroe S.S. Norovirus classification and proposed strain nomenclature. Virology 2006, 346:312-323.