Application of next-generation sequencing to investigation of norovirus diversity in shellfish collected from two coastal sites in Japan from 2013 to 2014

Japanese Journal of Veterinary Research

Volumn 64, Issue 2, 2016, Pages 113-122

  Imamura, Saiki ^a   Haruna, Mika ^a   Goshima, Tomoko ^a   Kanezashi, Hiromi ^a   Okada, Tsukasa ^b   Akimoto, Keiko ^a  

^a NATIONAL VETERINARY ASSAY LABORATORY   (Japan)

^b Custom Biotechnology Service Group   (Japan)

Author keywords

Crassostrea gigas; Mitilus galloprovincialis; Next generation sequencing; Noroviruses

Indexed keywords

VIRUS RNA;

ANIMAL; CRASSOSTREA; GENETIC VARIATION; GENETICS; GENOTYPE; ISOLATION AND PURIFICATION; JAPAN; MYTILUS; NOROVIRUS; VIROLOGY;

ANIMALS; CRASSOSTREA; GENETIC VARIATION; GENOTYPE; JAPAN; MYTILUS; NOROVIRUS; RNA, VIRAL;

EID: 84975029744     PISSN: 00471917     EISSN: None     Source Type: Journal    
DOI: 10.14943/jjvr.64.2.113     Document Type: Article

References (36)

1. Boxman, I. L., Tilburg, J. J., Te Loeke, N. A., Vennema, H., Jonker, K., de Boer, E. and Koopmans, M. 2006. Detection of noroviruses in shellfish in the Netherlands. Int. J. Food Microbiol., 108: 391-396.
2. Bruggink, L. D., Dunbar, N. L. and Marshall, J. A. 2015. Norovirus genotype diversity in community-based sporadic gastroenteritis incidents: A five-year study. J. Med. Virol., 87: 961-969.
3. Bull, R. A., Hansman, G. S., Clancy, L. E., Tanaka, M. M., Rawlinson, W. D. and White, P. A. 2005. Norovirus recombination in ORF1/ ORF2 overlap. Emerg. Infect. Dis., 11: 1079-1085.
4. Burkhardt, W 3rd. and Calci, K. R. 2000. Selective accumulation may account for shellfish-associated viral illness. Appl. Environ. Microbiol., 66: 1375-1378.
5. Croci, L., Losio, M. N., Suffredini, E., Pavoni, E., Di Pasquale, S., Fallacara, F. and Arcangeli, G. 2007. Assessment of human enteric viruses in shellfish from the northern Adriatic sea. Int. J. Food Microbiol., 114: 252-257.
6. Fankhauser, R. L., Monroe, S. S., Noel, J. S., Humphrey, C. D., Bresee, J. S., Parashar, U. D., Ando, T. and Glass, R. I. 2002. Epidemiologic and molecular trends of “Norwalk-like viruses” associated with outbreaks of gastroenteritis in the United States. J. Infect. Dis., 186: 1-7.
7. [EFSA] European Food Safety Authority 2011. Panel on Biological Hazard (BIOHAZ). Scientific opinion on an update on the present knowledge on the occurrence and control of foodborne viruses. EFSA journal, 9: 2190 [96 pp.]
8. Gallimore, C. I., Cheesbrough, J. S., Lamden, K., Bingham, C. and Gray, J. J. 2005. Multiple norovirus genotypes characterised from an oyster-associated outbreak of gastroenteritis. Int. J. Food Microbiol., 103: 323-330.
9. Gentry, J., Vinjé, J., Guadagnoli, D. and Lipp, E. K. 2009. Norovirus distribution within an estuarine environment. Appl. Environ. Microbiol., 75: 5474-5480.
10. Green, J., Norcott, J. P., Lewis, D., Arnold, C. and Brown, D. W. Norwalk-like viruses: demonstration of genomic diversity by polymerase chain reaction. J. Clin. Microbiol., 31: 3007-3012.
11. Huhti, L., Szakal, E. D., Puustinen, L., Salminen, M., Huhtala, H., Valve, O., Blazevic, V. and Vesikari, T. 2011. Norovirus GII-4 causes a more severe gastroenteritis than other noroviruses in young children. J. Infect. Dis., 203: 1442-1444.
12. [ISO/TS 15216-1] 2013. Microbiology of food and animal feed -Horizontal method for determination of hepatitis A virus and norovirus in food using real-time RT-PCR-. pp. 10.
13. [Japanese Committee for Standardization Virus of Detection in Food] available at: http://www.nihs.go.jp/fhm/csvdf/kentest/csvdf001_wg_100820.pdf
14. Kageyama, T., Kojima, S., Shinohara, M., Uchida, K., Fukushi, S., Hoshino, F. B., Takeda, N. and Katayama, K. 2003. Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR. J Clin. Microbiol., 41: 1548-1557.
15. Kou, X., Wu, Q., Zhang, J. and Fan, H. 2007. Rapid detection of noroviruses in fecal samples and shellfish by nucleic acid sequence-based amplification. J. Microbiol., 44: 403-408.
16. Kroneman, A., Vega, E., Vennema, H., Vinjé, J., White, P. A., Hansman, G., Green, K., Martella, V., Katayama, K. and Koopmans, M. 2013. Proposal for a unified norovirus nomenclature and genotyping. Arch. Virol., 158: 2059-2068.
17. Kroneman, A., Verhoef, L., Harris, J., Vennema, H., Duizer, E., van Duynhoven, Y., Gray, J., Iturriza, M., Böttiger, B., Falkenhorst, G., Johnsen, C., von Bonsdorff, C. H., Maunula, L., Kuusi, M., Pothier, P., Gallay, A., Schreier, E., Höhne, M., Koch, J., Szücs, G., Reuter, G., Krisztalovics, K., Lynch, M., McKeown, P., Foley, B., Coughlan, S., Ruggeri, F. M., Di Bartolo, I., Vainio, K., Isakbaeva, E., Poljsak-Prijatelj, M., Grom, A. H., Mijovski, J. Z., Bosch, A., Buesa, J., Fauquier, A. S., Hernandéz-Pezzi, G., Hedlund, K. O. and Koopmans, M. 2008. Analysis of integrated virological and epidemiological reports of norovirus outbreaks collected within the Foodborne Viruses in Europe network from 1 July 2001 to 30 June 2006. J. Clin. Microbiol., 46: 2959-2965.
18. Le Guyader, F., Neill, F. H., Estes, M. K., Monroe, S. S., Ando, T. and Atmer, R. L. 1996. Detection and analysis of a small round-structured virus strain in oysters implicated in an outbreak of acute gastroenteritis. Appl. Environ. Microbiol., 62: 4268-4272.
19. Lewis, T., Loman, N. J., Bingle, L., Jumaa, P., Weinstock, G. M., Mortiboy, D. and Pallen, M. J. 2010. High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak. J. Hosp. Infect., 75: 37-41
20. Lindesmith, L., Moe, C., Marionneau, S., Ruvoen, N., Jiang, X., Lindblad, L., Stewart, P., LePendu, J. and Baric, R. 2003. Human susceptibility and resistance to Norwalk virus infection. Nat. Med., 9: 548-553.
21. Ma, L. P., Zhao, F., Yao, L., Li, X. G., Zhou, D. Q. and Zhang, R. L. 2013. The presence of genogroup II norovirus in retail shellfish from seven coastal cities in China. Food Environ. Virol., 5: 81-86.
22. Maalouf, H., Zakhour, M., Le Pendu, J., Le Saux, J. C., Atmar, R. L. and Le Guyader, F. S. 2010. Distribution in tissue and seasonal variation of Norovirus genogroup I and II ligands in oysters. Appl. Environ. Microbiol., 76: 5621-5630.
23. [MHLW] Ministry of Health, Labour and Welfare 2014. Infectious Agents Surveillance Report. Available at: http://www.nih.go.jp/niid/ja/iasr-vol35/4830-iasr-413.html
24. Myrmel, M., Berg, E. M., Rimstad, E. and Grinde, B. 2004. Detection of enteric viruses in shellfish from the Norwegian coast. Appl. Environ. Microbiol., 70: 2678-2684.
25. Nishida, T., Kimura, H., Saitoh, M., Shinohara, M., Kato, M., Fukuda, S., Munemura, T., Mikami, T., Kawamoto, A., Akiyama, M., Kato, Y., Nishi, K., Kozawa, K. and Nishio, O. 2003. Detection, quantitation, and phylogenetic analysis of noroviruses in Japanese oysters. Appl. Environ. Microbiol., 69: 5782-5786.
26. O’Sullivan, D. J., 2000. Methods for analysis of the intestinal microflora. Curr. Issues Intest. Microbiol., 1: 39-50.
27. Singh, P., Foley, S. L., Nayak, R. and Kwon, Y. M. 2013. Massively parallel sequencing of enriched target amplicons for high-resolution genotyping of Salmonella serovars. Mol. Cell Probes., 27: 80-85.
28. Sugieda, M., Nakajima, K. and Nakajima, S. 1996. Outbreaks of Norwalk-like virus-associated gastroenteritis traced to shellfish: coexistence of two genotypes in one specimen. Epidemiol. Infect., 116: 339-346.
29. Taboada, E. N., Clark, C. G., Sproston, E. L. and Carrillo, C. D. 2013. Current methods for molecular typing of Campylobacter species. J. Microbiol. Methods, 95: 24-31.
30. Terio, V., Martella, V., Moschidou, P., Di Pinto, P., Tantillo, G. and Buonavoglia, C. 2010. Norovirus in retail shellfish. Food Microbiol., 27: 29-32.
31. Tuladhar, E., Hazeleger, W. C., Koopmans, M., Zwietering, M. H., Beumer, R. R. and Duizer, E. 2012. Residual viral and bacterial contamination of surfaces after cleaning and disinfection. Appl. Environ. Microbiol., 78: 7769-7775.
32. Vega, E., Barclay, L., Gregoricus, N., Shirley, S. H., Lee, D. and Vinjé, J. 2014. Genotypic and epidemiologic trends of norovirus outbreaks in the United States, 2009 to 2013. J. Clin. Microbiol., 52: 147-155.
33. Verhoef, L. P., Kroneman, A., van Duynhoven, Y., Boshuizen, H., van Pelt, W. and Koopmans, M. 2009. Selection tool for foodborne norovirus outbreaks. Emerg. Infect. Dis., 15: 31-38.
34. Wang, J. and Deng, Z. 2015. Modeling and Prediction of Oyster Norovirus Outbreaks along Gulf of Mexico Coast. Environ. Health Perspect., In press.
35. Yan, H., Yagyu, F., Okitsu, S., Nishio, O. and Ushijima, H. 2003. Detection of norovirus (GI, GII), Sapovirus and astrovirus in fecal samples using reverse transcription single-round multiplex PCR. J. Virol. Methods, 114: 37-44.
36. Zheng, D. P., Ando, T., Fankhauser, R. L., Beard, R. S., Glass, R. I. and Monroe, S. S. 2006. Norovirus classification and proposed strain nomenclature. Virology, 346: 312-323.