Parechovirus – PCR and Genotyping

Consistent with O. Reg. 671/92 of the French Language Services Act, laboratory testing information on this page is only available in English because it is scientific or technical in nature and is for use only by qualified health care providers and not by members of the public.

This page provides routine PCR detection and genotyping information for parechovirus at Public Health Ontario (PHO). The genus Parechovirus is comprised of six species (A to F), of which Parechovirus A (PeV-A)is primarily known to cause human infection. PeV-Ais further differentiated into 19 genotypes (PeV-A1 to PeV-A19), of which PeV-A1 and PeV-A3are most commonly associated with disease.

The test information below is limited to testing of Parechovirus. For testing of Enterovirus, another member of the Picornaviridae potentially causing similar clinical presentations, please refer to the following link:

Who to test:
Human parechovirus infections have a wide spectrum of manifestations including febrile illness, exanthema, neonatal sepsis, meningitis, encephalitis, myocarditis, hepatitis, gastroenteritis, and respiratory tract infections. Most parechovirus infections are self-limited and do not require testing. However, testing should be considered in patients with severe presentation, including those with neurologic or cardiac involvement, especially in patients under 1 year of age.

Testing will be routinely performed if requested on patients under 1 year of age with severe, neurologic, and/or cardiac manifestations. Testing for patients above 1 year of age requires contacting PHO’s customer service for approval by a PHO laboratory microbiologist.

Specimen Collection and Handling

Specimen Requirements

Test Requested Required Requisition(s) Specimen Type Minimum Volume Collection Kit


Stool sample1

2 x 0.5 grams

Virus - Enteric Kit order#: 390087


Nasal, nasopharyngeal, or throat swabs.

1 swab in transport media provided in the kit

Virus Respiratory Kit order#: 390082


Bronchoalveolar lavage (BAL)/bronchial wash (BW), pleural fluid, sputum

2.0 ml

Sterile container


Cerebrospinal fluid (CSF), blood, tissue, or other sterile fluid

1.0 ml

Sterile container

Submission and Collection Notes


Stool is the preferred specimen for Parechovirus testing. It is recommended to submit 2 stool specimens, preferably taken 2 days apart, to detect intermittent viral shedding.


Complete all fields of the General Test Requisition Form, including:

    • Test(s) requested and indication for testing
    • Relevant travel history (if applicable)
    • Relevant close contact exposure history (if applicable)
    • Relevant vaccination history
    • Clinical information including symptom onset date
      • Include any signs or symptoms of paralysis, vomiting, myocarditis, aseptic meningitis, hand-foot-mouth disease, diarrhea, pericarditis, herpangina, epidemic pleurodynia, acute hemorrhagic conjunctivitis, or other clinical presentation
    • Patient setting/population
      • Include if hospitalized as inpatient
    • Outbreak number (if applicable)

Label the specimen container with the patient’s first and last name, date of collection and one other unique identifier such as the patient’s date of birth or Health Card Number. Failure to provide this information may result in rejection or testing delay.


Submission of multiple specimen types may enhance the likelihood of detection, however sensitivity can vary by specimen type. Stool specimens remain positive for longer than other specimen types, and a positive result could represent either active infection or prolonged asymptomatic carriage from a prior infection. Detection in sterile specimens is usually definitive of active infection. A negative result does not rule out the presence of parechovirus.

Intermittent shedding may occur, therefore 2 stool specimens, taken 2 days apart, are recommended. A negative result may also be due to PCR inhibitors present in the patient sample or the viral load of the sample is below the level of detection of the assay.

Special Instructions

Place specimen in biohazard bag and seal. Specimens should be stored at 2-8°C following collection and shipped to the PHO’s laboratory on ice packs as soon as possible. Freeze the specimen at -70°C if more than 72 hours are expected between the time of specimen collection and testing.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Parechovirus testing is referred out to the National Microbiology Laboratory (NML) in Winnipeg. Turnaround time is up to 21 days from receipt at NML. Testing may be expedited upon request by contacting PHO’s microbiologist. See NML’s Non-polio Enterovirus (NPEV) and Human Parechovirus (HPeV) Molecular Detection and Typing guide to services.

Test Methods

Parechovirus testing is referred out to the NML in Winnipeg. NML performs reverse transcriptase semi-nested PCR (RT-snPCR) using generic primers targeting the viral envelope protein 1 (VP1) gene of all human parechovirus genotypes to date. Specimens with positive PCR results will be further sequenced for genotyping of the viral agent. See NML’s Non-polio Enterovirus (NPEV) and Human Parechovirus (HPeV) Molecular Detection and Typing guide to services.


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

Updated 25 June 2024