Detection of noroviruses in fecal specimens by direct RT-PCR without RNA purification

Journal of Virological Methods

Volumn 163, Issue 2, 2010, Pages 282-286

  Nishimura, Naoyuki ^a   Nakayama, Hiroyuki ^a   Yoshizumi, Shima ^b   Miyoshi, Masahiro ^b   Tonoike, Hiroshi ^a   Shirasaki, Yoshinari ^a   Kojima, Kouichi ^a   Ishida, Setsuko ^b  

^a SHIMADZU CORPORATION   (Japan)

^b Department of Microbiology   (Japan)

Author keywords

Ampdirect ; Direct RT PCR; Norovirus; RNA; RT PCR; Virus

Indexed keywords

AGAR GEL ELECTROPHORESIS; ANALYTICAL EQUIPMENT; ARTICLE; CONTROLLED STUDY; FECES; HEAT TREATMENT; NONHUMAN; NOROVIRUS; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; RNA PURIFICATION; RNA VIRUS; SENSITIVITY AND SPECIFICITY; VIRUS DETECTION;

CALICIVIRIDAE INFECTIONS; ELECTROPHORESIS, AGAR GEL; FECES; GASTROENTERITIS; HUMANS; NOROVIRUS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SENSITIVITY AND SPECIFICITY;

NOROVIRUS; RNA VIRUSES;

EID: 73049087777     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2009.10.011     Document Type: Article

References (33)

1. Ando T., Monroe S.S., Gentsch J.R., Jin Q., Lewis D.C., and 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. 33 (1995) 64-71
2. Antonishyn N.A., Crozier N.A., McDonald R.R., Levett P.N., and Horsman G.B. Rapid detection of norovirus based on an automated extraction protocol and a real-time multiplexed single-step RT-PCR. J. Clin. Virol. 37 (2006) 156-161
3. Arnal C., Ferré-Aubineau V., Besse B., Mignotte B., Schwartzbrod L., and Billaudel S. Comparison of seven RNA extraction methods on stool and shellfish samples prior to hepatitis A virus amplification. J. Virol. Methods 77 (1999) 17-26
4. Atmar R.L., and Estes M.K. Diagnosis of noncultivatable gastroenteritis viruses, the human caliciviruses. Clin. Microbiol. Rev. 14 (2001) 15-37
5. Becker K.M., Moe C.L., Southwick K.L., and MacCormack J.N. Transmission of Norwalk virus during football game. N. Engl. J. Med. 343 (2000) 1223-1227
6. Bon F., Ambert-Balay K., Giraudon H., Kaplon J., Le Guyader S., Pommepuy M., Gallay A., Vaillant V., de Valk H., Chikhi-Brachet R., Flahaut A., Pothier P., and Kohli E. Molecular epidemiology of caliciviruses detected in sporadic and outbreak cases of gastroenteritis in France from December 1998 to February 2004. J. Clin. Microbiol. 43 (2005) 4659-4664
7. Clark B., and McKendrick M. A review of viral gastroenteritis. Curr. Opin. Infect. Dis. 17 (2004) 461-469
8. Fukuda S., Sasaki Y., Takao S., and Seno M. Recombinant norovirus implicated in gastroenteritis outbreaks in Hiroshima Prefecture. Jpn. J. Med. Virol. 80 (2008) 921-928
9. Gomes K.A., Stupka J.A., Gómez J., and Parra G.I. Molecular characterization of calicivirus strains detected in outbreaks of gastroenteritis in Argentina. J. Med. Virol. 79 (2007) 1703-1709
10. Green J., Norcott J.P., Lewis D., Arnold C., and Brown D.W.G. Norwalk-like viruses: demonstration of genomic diversity by polymerase chain reaction. J. Clin. Microbiol. 31 (1993) 3007-3012
11. Hale A.D., Green J., and Brown D.W. Comparison of four RNA extraction methods for the detection of small round structured viruses in faecal specimens. J. Virol. Methods 57 (1996) 195-201
12. Jiang X., Huang P.W., Zhong W.M., Farkas T., Cubitt D.W., and Matson D.O. Design and evaluation of a primer pair that detects both Norwalk- and Sapporo-like caliciviruses by RT-PCR. J. Virol. Methods 83 (1999) 145-154
13. Jiang X., Wang M., Wang K., and Estes M.K. Sequence and genomic organization of Norwalk virus. Virology 195 (1993) 51-61
14. Kageyama T., Kojima S., Shinohara M., Uchida K., Fukushi S., Hoshino F.B., Takeda N., and Katayama K. Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR. J. Clin. Microbiol. 41 (2003) 1548-1557
15. Kageyama T., Shinohara M., Uchida K., Fukushi S., Hoshino F.B., Kojima S., Takai R., Oka T., Takeda N., and Katayama K. Coexistence of multiple genotypes, including newly identified genotypes, in outbreaks of gastroenteritis due to norovirus in Japan. J. Clin. Microbiol. 42 (2004) 2988-2995
16. Kok T., Wati S., Bayly B., Devonshire-Gill D., and Higgins G. Comparison of six nucleic acid extraction methods for detection of viral DNA or RNA sequences in four different non-serum specimen types. J. Clin. Virol. 16 (2000) 59-63
17. Lambden P.R., Caul E.O., Ashley C.R., and Clarke I.N. Sequence and genome organization of a human small round-structured (Norwalk-like) virus. Science 259 (1993) 516-519
18. Lantz P.G., Matsson M., Wadström T., and Rådström P. Removal of PCR inhibitors from human faecal samples through the use of an aqueous two-phase system for sample preparation prior to PCR. J. Microbiol. Methods 28 (1997) 159-167
19. Marks P.J., Vipond I.B., Regan F.M., Wedgwood K., Fey R.E., and Caul E.O. A school outbreak of Norwalk-like virus: evidence for airborne transmission. Epidemiol. Infect. 131 (2003) 727-736
20. Marshall J.A., Dimitriadis A., and Wright P.J. Molecular and epidemiological features of norovirus-associated gastroenteritis outbreaks in Victoria, Australia in 2001. J. Med. Virol. 75 (2005) 321-331
21. Nishimura N., Nakayama T., Tonoike H., Kojima K., and Kato S. Direct polymerase chain reaction from whole blood without DNA isolation. Ann. Clin. Biochem. 37 (2000) 674-680
22. Nishimura N., Nakayama T., Tonoike H., Kojima K., Shirasaki Y., Kondoh K., and Yamada T. Various applications of direct PCR using blood samples. Clin. Lab. 48 (2002) 377-384
23. Okamoto H., Takano E., Sugao T., Kage K., Okamoto E., Nishimura N., and Ueda K. Direct amplification of Escherichia coli O157 vero toxin genes from human faeces by the polymerase chain reaction. Ann. Clin. Biochem. 36 (1999) 642-648
24. Pang X., Lee B., Chui L., Preiksaitis J.K., and Monroe S.S. Evaluation and validation of real-time reverse transcription-PCR assay using the LightCycler system for detection and quantitation of norovirus. J. Clin. Microbiol. 42 (2004) 4679-4685
25. Pang X.L., Preiksaitis J.K., and Lee B. Multiplex real time RT-PCR for the detection and quantitation of norovirus genogroups I and II in patients with acute gastroenteritis. J. Clin. Virol. 33 (2005) 168-171
26. Rasool N.B., Monroe S.S., and Glass R.I. Determination of a universal nucleic acid extraction procedure for PCR detection of gastroenteritis viruses in faecal specimens. J. Virol. Methods 100 (2002) 1-16
27. Reuter G., Krisztalovics K., Vennema H., Koopmans M., and Szucs G. Evidence of the etiological predominance of norovirus in gastroenteritis outbreaks-emerging new-variant and recombinant noroviruses in Hungary. J. Med. Virol. 76 (2005) 598-607
28. Richards G.P., Watson M.A., Fankhauser R.L., and Monroe S.S. Genogroup I and II noroviruses detected in stool samples by real-time reverse transcription-PCR using highly degenerate universal primers. Appl. Environ. Microbiol. 70 (2004) 7179-7184
29. Scipioni A., Mauroy A., Ziant D., Saegerman C., and Thiry E. A SYBR Green RT-PCR assay in single tube to detect human and bovine noroviruses and control for inhibition. Virol. J. 5 (2008) 94-101
30. Vainio K., and Myrmel M. Molecular epidemiology of norovirus outbreaks in Norway during 2000 to 2005 and comparison of four norovirus real-time reverse transcriptase PCR assays. J. Clin. Microbiol. 44 (2006) 3695-3702
31. Wilde J., Eiden J., and Yolken R. Removal of inhibitory substances from human fecal specimens for detection of group A rotaviruses by reverse transcriptase and polymerase chain reactions. J. Clin. Microbiol. 28 (1990) 1300-1307
32. Wilson I.G. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63 (1997) 3741-3751
33. Witlox K.J., Nguyen T.N., Bruggink L.D., Catton M.G., and Marshall J.A. A comparative evaluation of the sensitivity of two automated and two manual nucleic acid extraction methods for the detection of norovirus by RT-PCR. J. Virol. Methods 150 (2008) 70-72