Molecular Detection and Genotyping
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Reference Details
Molecular detection and genotyping of Norovirus by PCR.
- Gastroenteritis
- Stool - ≥ 1.0 g (solid) or ≥ 0.5 mL (liquid). Preferred specimen type as the virus is present for longer than other specimen types.
- Rectal Swab - Not recommended as the small quantity of faecal material obtained is inadequate for use.
- Vomitus - may be collected to supplement stool specimens.
- Stool - Collect within 48-72 hours after illness onset, while stools are still liquid or semisolid because the level of virus is greatest at this time. Place stool in sterile leak proof container, no special medium required. For outbreak investigations, collect stool specimens from at least 2, but not more than 6 outbreak-associated ill persons.
- Vomitus - Collect as stool specimens.
Store samples frozen at ≤-20°C until shipped for testing. Ship frozen on dry ice.
Shipping of specimens shall be done by a TDG certified individual in accordance with TDG regulations. For additional information regarding classification of specimens for the purposes of shipping, consult either Part 2 Appendix 3 of the TDG Regulations or section 3.6.2 of the IATA Dangerous Goods Regulations as applicable.
Suspected Norovirus infection.
Completed Enteroviruses and Enteric viruses requisition form. If possible include clinical, outbreak information such as lab outbreak number, setting (e.g., long term care facility), transmission (e.g., person to person), suspected source and any lab test results completed at local or provincial laboratories.
Labs that perform their own norovirus PCR testing should submit positive samples for genotyping surveillance.
Laboratory Surveillance noroviruses involves several methods:
- Real-time RT-PCR for detection and initial genogrouping of noroviruses: A broadly reactive genogroup specific (GI and GII) real-time PCR assays that target the conserved ORF1-ORF2 junction region of the genome are used to detect and genogroup noroviruses. Results are reported positive or negative for NoV GI and GII.
- RT-PCR and sequencing of partial regions of the NoV VP1 gene: Sequences generated from partial regions of the VP1 gene (region C, D and P2) to group strains into genotypes and subtypes. The NoV genotype is reported.
21 calendar days. Stat testing available upon request.
- A., Trujillo, K. McCaustland, D. Zheng,L. Hadley, G. Vaughn,S. Adams,T. Ando, R. Glass, and S. Monroe. Use of TaqMan real-time reverse transcriptase-PCR for rapid detection, quantification, and typing of noroviruses. 2006 J. Clin. Microbiol. 44:1405-12
- S. Kojima, T. Kageyama, S. Fukushi, F.B. Hoshino, M. Shinohara, K. Uchida, K. Natori, N. Takeda, and K. Katayama, K. Genogroup-specific PCR primers for detection of Norwalk-like firuses. 2002 J. Virol. Methods 100:107-14
- J. Vinje, R.A. Hamidjaja, and M.D. Sobsey, Development and application of a capsid VP1 (region D) based reverse transcription PCR assay for genotyping of genogroup I and II noroviruses. 2004 J. Virol. Methods 116:109-17.
- D.P. Zheng, T. Ando, R.L. Fankhauser, R.S. Beard, R.I. Glass, and S.S. Monroe. Norovirus classification and proposed strain nomenclature. 2006 Virology 346:312-23.
- A. Kroneman A, H. Vennema, K. Deforche, H.v.d. Avoort, S. Peñaranda, M.S, Oberste, J. Vinjé, M. Koopmans. An automated genotyping tool for enteroviruses and noroviruses. 2011 J Clin Virol. Jun; 51(2):121-5).