Gastroenteritis – Stool Viruses

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Background
This page provides information on polymerase chain reaction (PCR) testing for enteric viruses for the diagnosis of Gastroenteritis at Public Health Ontario (PHO). The causative agent(s) of gastroenteritis tested include Adenovirus, Norovirus and Rotavirus.

For information regarding other testing options, refer to the following PHO webpages:

Updates

June 2025: Updated acceptable patient setting to include suspected enteric outbreaks in community settings, under investigation by the public health unit(s).

* Copie d'impression non contrôlée. Valide uniquement le jour de l'impression : 30 juin 2025.

Testing Indications

Public Health Ontario utilizes a testing algorithm for gastroenteritis viruses which is based on patient setting.

Gastroenteritis Virus Testing Available at PHO

Patient Setting¹	Testing
In-patient (ICU/CCU² or ward) Congregate Living settings (non-outbreak) e.g. long-term care homes, correctional facilities	Multiplex Gastrointestinal Viral PCR (MGVP)³
Gastrointestinal infection outbreaks, or suspected outbreaks in community settings, under investigation by the public health unit(s)⁴	MGVP³ for up to 5 outbreak specimens
Emergency Room patients¹	MGVP³ testing is only available if symptoms have persisted for ≥ 72 hours. MGVP³ testing will not be performed if date of onset and date of collection are not provided on the PHO Laboratory requisition.
Ambulatory¹	MGVP³ testing is only available if symptoms have persisted for ≥ 72 hours. MGVP3 testing will not be performed if date of onset and date of collection are not provided on the PHO Laboratory requisition.

Table footnotes:

Patient setting and duration of symptoms prior to submission must be provided on the requisition to help triaging of specimens. If patient setting and duration of symptoms are not provided the specimen will NOT be tested.
ICU - Intensive Care Unit; CCU - Critical Care Units.
Multiplex gastrointestinal viral real-time PCR (MGVP) detects adenovirus, rotavirus, norovirus GI, norovirus GII. Note: testing for sapovirus, astrovirus and torovirus are not currently available at PHO Laboratory or the National Microbiology Laboratory.
A limit of 5 outbreak specimens are routinely accepted for testing. Testing will cease once the same gastrointestinal virus is found in two or more samples from the outbreak. Outbreak settings may include congregated living settings, gatherings, events, and etc. For outbreaks with special concerns, including requests for additional testing, contact PHO Laboratory’s Customer Service Centre.

Acceptance/Rejection Criteria

Samples received in Virus or Multi-Organism transport media are not suitable for testing.

Specimen Collection and Handling

Specimen Requirements

Test Requested

Required Requisition(s)

Specimen Type

Minimum Volume

Collection Kit

Gastroenteritis Virus Detection (Molecular)

General Test Requisition

Stool⁵

1.0-2.0 grams

Virus - Enteric Kit order#: 390087

Submission and Collection Notes

Complete the following fields of the General Test Requisition Form if diagnostic testing is requested:

symptoms
onset date
outbreak number if applicable

Refer to the Virus-Enteric Kit Instruction Sheet for detailed specimen collection instructions.

If you suspect an outbreak, contact your local public health unit.

Label the specimen container with the patient’s full name, date of collection and one other unique identifier such as the patient’s date of birth or Health Card Number. For additional information see: Criteria for Acceptance of Patient Specimens. Failure to provide this information may result in rejection or testing delay

Other specimen types (ex. Rectal swab, tissue) may be acceptable subject to microbiologist approval. These specimens will be reported with a disclaimer

Timing of Specimen Collection

For inpatient, institutional or outbreak specimens, collect within 48 hours of onset when possible.

Collect specimen for all other settings (ER or ambulatory) only if symptoms persist for more than 72 hours.

Storage and Transport

Place the specimen container in the biohazard bag and seal the bag; insert the completed requisition in the pocket on the outside of the sealed biohazard bag. To maintain optimal viability of the virus, specimens should be stored at 2-8°C following collection and transported to PHO on ice packs within 72 hours of collection. If longer storage/transit time is anticipated, specimens should be frozen at -70°C or lower and transported on dry ice.

All clinical specimens must be shipped in accordance to the Transportation of Dangerous Good Act.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Gastroenteritis virus testing is performed Monday to Friday.

Turnaround time is up to 4 days.

Test Methods

PHO Laboratory uses a laboratory developed multiplex gastrointestinal viral real-time PCR (MGVP) assay which detects and differentiates adenovirus, rotavirus, norovirus GI and norovirus GII.

Note: testing for sapovirus, torovirus and astrovirus are not currently available at PHO Laboratory or the National Microbiology Laboratory.

Interpretation

The following table provides possible test results with associated interpretations for each of the viral target of the multiplex assay:

Result	Interpretation	Comments
Not Detected	Virus Not detected by PCR	Target virus not detected by real-time PCR
Detected	Virus Detected by PCR	Target virus detected by real-time PCR
Indeterminate	Virus Indeterminate by PCR	An indeterminate PCR test result may be due to a low level of target genetic material in the specimen, inadequate specimen content, or a non-specific signal. Please resubmit another specimen for testing if clinically indicated.
Invalid	Invalid	Test results are Invalid due to the failed amplification of the extraction control. Amplification failure may be due to inadequate specimen content, extraction failure, or PCR inhibition. Please resubmit another specimen for testing if clinically indicated.

Reporting

Results are reported to the ordering physician or health care provider as indicated on the requisition.

Outbreak specimens that are positive for enteric viruses are reported to the Medical Officer of health as per Health Protection and Promotion Act.

References

Real-time PCR with an internal control for detection of all known human adenovirus serotypes. Damen M1, Minnaar R, Glasius P, van der Ham A, Koen G, Wertheim P, Beld M. J Clin Microbiol. 2008 Dec ;46(12) :3997-4003. Doi : 10.1128/JCM.00563-08. Epub 2008 Oct 15.
Rapid and sensitive detection of noroviruses by using TaqMan-based one-step reverse transcription-PCR assays and application to naturally contaminated shellfish samples. Jothikumar N1, Lowther JA, Henshilwood K, Lees DN, Hill VR, Vinjé J. Appl Environ Microbiol. 2005 Apr;71(4):1870-5.
One-step quantitative RT-PCR for the detection of rotavirus in acute gastroenteritis. Zeng SQ1, Halkosalo A, Salminen M, Szakal ED, Puustinen L, Vesikari T. J Virol Methods. 2008 Nov;153(2):238-40. Doi: 10.1016/j.jviromet.2008.08.004. Epub 2008 Sep 17.
Use of bacteriophage MS2 as an internal control in viral reverse transcription-PCR assays. Dreier J1, Störmer M, Kleesiek K. J Clin Microbiol. 2005 Sep;43(9):4551-7.