Molecular Identification and Genetic Analysis of Norovirus Genogroups I and II in Water Environments: Comparative Analysis of Different Reverse Transcription-PCR Assays

Overview

Journal Appl Environ Microbiol

Specialties Environmental Health
Microbiology

Date 2007 May 8

PMID 17483265

Citations 26

Authors

G La Rosa

S Fontana

A Di Grazia

M Iaconelli

M Pourshaban

M Muscillo

Affiliations

Soon will be listed here.

Abstract

Noroviruses have received increased attention in recent years because their role as etiologic agents in acute gastroenteritis outbreaks is now clearly established. Our inability to grow them in cell culture and the lack of an animal model hinder the characterization of these viruses. More recently, molecular approaches have been used to study the genetic relationships that exist among them. In the present study, environmental samples from seawater, estuarine water, and effluents of sewage treatment plants were analyzed in order to evaluate the role of environmental surface contamination as a possible vehicle for transmission of norovirus genogroups I and II. Novel broad-range reverse transcription-PCR/nested assays targeting the region coding for the RNA-dependent RNA polymerase were developed, amplifying fragments of 516 bp and 687 bp in the nested reactions for genogroups II and I, respectively. The assays were evaluated and compared against widely used published assays. The newly designed assays provide long regions for high-confidence BLAST searches in public databases and therefore are useful diagnostic tools for molecular diagnosis and typing of human noroviruses in clinical and environmental samples, as well as for the study of molecular epidemiology and the evolution of these viruses.

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References

Trujillo A, McCaustland K, Zheng D, Hadley L, Vaughn G, Adams S . Use of TaqMan real-time reverse transcription-PCR for rapid detection, quantification, and typing of norovirus. J Clin Microbiol. 2006; 44(4):1405-12. PMC: 1448641. DOI: 10.1128/JCM.44.4.1405-1412.2006. View

Zheng D, Ando T, Fankhauser R, Beard R, Glass R, Monroe S . Norovirus classification and proposed strain nomenclature. Virology. 2005; 346(2):312-23. DOI: 10.1016/j.virol.2005.11.015. View

Rutjes S, Van Den Berg H, Lodder W, de Roda Husman A . Real-time detection of noroviruses in surface water by use of a broadly reactive nucleic acid sequence-based amplification assay. Appl Environ Microbiol. 2006; 72(8):5349-58. PMC: 1538714. DOI: 10.1128/AEM.00751-06. View

Ramirez S, De Grazia S, Giammanco G, Milici M, Colomba C, Ruggeri F . Detection of the norovirus variants GGII.4 hunter and GGIIb/hilversum in Italian children with gastroenteritis. J Med Virol. 2006; 78(12):1656-62. DOI: 10.1002/jmv.20751. View

Atmar R, Estes M . The epidemiologic and clinical importance of norovirus infection. Gastroenterol Clin North Am. 2006; 35(2):275-90, viii. DOI: 10.1016/j.gtc.2006.03.001. View

Queiroz A, Santos F, Sassaroli A, Harsi C, Monezi T, Mehnert D . Electropositive filter membrane as an alternative for the elimination of PCR inhibitors from sewage and water samples. Appl Environ Microbiol. 2001; 67(10):4614-8. PMC: 93211. DOI: 10.1128/AEM.67.10.4614-4618.2001. View

Beuret C, Kohler D, Baumgartner A, Luthi T . Norwalk-like virus sequences in mineral waters: one-year monitoring of three brands. Appl Environ Microbiol. 2002; 68(4):1925-31. PMC: 123876. DOI: 10.1128/AEM.68.4.1925-1931.2002. View

Subekti D, Tjaniadi P, Lesmana M, Simanjuntak C, Komalarini S, Digdowirogo H . Characterization of Norwalk-like virus associated with gastroenteritis in Indonesia. J Med Virol. 2002; 67(2):253-8. DOI: 10.1002/jmv.2215. View

Martinez N, Espul C, Cuello H, Zhong W, Jiang X, Matson D . Sequence diversity of human caliciviruses recovered from children with diarrhea in Mendoza, Argentina, 1995-1998. J Med Virol. 2002; 67(2):289-98. DOI: 10.1002/jmv.2220. View

10.

Fankhauser R, Monroe S, Noel J, Humphrey C, Bresee J, Parashar U . Epidemiologic and molecular trends of "Norwalk-like viruses" associated with outbreaks of gastroenteritis in the United States. J Infect Dis. 2002; 186(1):1-7. DOI: 10.1086/341085. View

11.

Buesa J, Collado B, Rodriguez Diaz J, GARCIA DIAZ A, Prat J, Guix S . Molecular epidemiology of caliciviruses causing outbreaks and sporadic cases of acute gastroenteritis in Spain. J Clin Microbiol. 2002; 40(8):2854-9. PMC: 120653. DOI: 10.1128/JCM.40.8.2854-2859.2002. View

12.

Schvoerer E, Bonnet F, Dubois V, Rogues A, Gachie J, Lafon M . A hospital outbreak of gastroenteritis possibly related to the contamination of tap water by a small round structured virus. J Hosp Infect. 1999; 43(2):149-54. DOI: 10.1053/jhin.1999.0632. View

13.

Kukkula M, Maunula L, SILVENNOINEN E, von Bonsdorff C . Outbreak of viral gastroenteritis due to drinking water contaminated by Norwalk-like viruses. J Infect Dis. 1999; 180(6):1771-6. DOI: 10.1086/315145. View

14.

Lodder W, Vinje J, van De Heide R, de Roda Husman A, Leenen E, Koopmans M . Molecular detection of Norwalk-like caliciviruses in sewage. Appl Environ Microbiol. 1999; 65(12):5624-7. PMC: 91771. DOI: 10.1128/AEM.65.12.5624-5627.1999. View

15.

Hafliger D, Hubner P, Luthy J . Outbreak of viral gastroenteritis due to sewage-contaminated drinking water. Int J Food Microbiol. 2000; 54(1-2):123-6. DOI: 10.1016/s0168-1605(99)00176-2. View

16.

Koopmans M, Vinje J, de Wit M, Leenen I, van der Poel W, van Duynhoven Y . Molecular epidemiology of human enteric caliciviruses in The Netherlands. J Infect Dis. 2000; 181 Suppl 2:S262-9. DOI: 10.1086/315573. View

17.

Ando T, Noel J, Fankhauser R . Genetic classification of "Norwalk-like viruses. J Infect Dis. 2000; 181 Suppl 2:S336-48. DOI: 10.1086/315589. View

18.

Schaub S, Oshiro R . Public health concerns about caliciviruses as waterborne contaminants. J Infect Dis. 2000; 181 Suppl 2:S374-80. DOI: 10.1086/315580. View

19.

Nakata S, Honma S, Numata K, Kogawa K, Ukae S, Morita Y . Members of the family caliciviridae (Norwalk virus and Sapporo virus) are the most prevalent cause of gastroenteritis outbreaks among infants in Japan. J Infect Dis. 2000; 181(6):2029-32. DOI: 10.1086/315500. View

20.

Foley B, OMahony J, Morgan S, Hill C, Morgan J . Detection of sporadic cases of Norwalk-like virus (NLV) and astrovirus infection in a single Irish hospital from 1996 to 1998. J Clin Virol. 2000; 17(2):109-17. DOI: 10.1016/s1386-6532(00)00083-4. View