Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

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.

Laboratory testing for MERS-CoV is performed on patients who meet the criteria found on the MOHLTC’s MERS-CoV Guidance for Health Workers and Health Sector Employees website.
Testing for MERS-CoV requires prior approval by PHO Laboratory. Prior to submission - ideally after a physician has seen the patient but before respiratory specimens are collected - contact PHO Laboratory’s Customer Service Centre at 416-235-6556/1-877-604-4567 or the After-Hours Emergency Duty Officer at 416-605-3113.

PHO Laboratory reviews each request with the submitting physician or another healthcare provider (e.g. ER nurse, ICP) who has knowledge of how the patient’s clinical and epidemiological history meets criteria to justify performing laboratory testing for MERS-CoV. 

PHO Laboratory verifies that the patient meets testing criteria, provides advice concerning specimen collection and transportation, informs about turnaround time for results, and obtains contact information for results. Additional testing may be discussed. 

If the health unit becomes aware of a request prior to PHO Laboratory being contacted, they should request that the submitter make testing arrangements directly with PHO Laboratory.


IMPORTANT INSTRUCTIONS - Read before proceeding

Testing for MERS-CoV requires approval by Public Health Ontario (PHO) Laboratory prior to submission. See TESTING INDICATIONS for instructions.

Specimen Collection and Handling

Specimen Requirements

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


Upper respiratory tract: Nasopharyngeal swab (NPS) AND

Nasopharyngeal swab in 1 ml universal transport media (UTM)

Virus Respiratory Kit order#: 390082


Viral throat swab (see Submission and Collection Notes below)

Swab in 1 ml universal transport media (UTM)

Virus Culture Kit order#: 390081


Lower respiratory tract (where possible): sputum, BAL, bronch wash, pleural fluid, lung tissue (see Submission and Collection Notes below)

1.0 ml

Tuberculosis Kit order#: 390042


Stool (do not collect without PHO Laboratory approval-see Submission and Collection Notes below)

1 gram

Sterile container

Virus – Enteric Kit order#: 390087


Blood or serum (do not collect without PHO Laboratory approval-see Submission and Collection Notes below)

5.0 ml whole blood or 1.0 ml serum

Blood, clotted – vacutainer tubes (SST)

Submission and Collection Notes


Respiratory Tract Specimens:

Collection of multiple specimens from both the upper and lower respiratory tract, where possible, is recommended.
Upper respiratory tract: submit both a nasopharyngeal swab (NPS) AND viral throat swab. 
Lower respiratory tract specimens: submit where possible. 
Sputum: Collect if patient has a productive cough. Do not induce.


Additional specimens not routinely collected or tested – stool and blood for PCR: 

Stool: Only tested with consent of PHO Laboratory. Examples include: immunocompromised patients with possible atypical presentation with predominantly gastrointestinal symptoms; or if respiratory specimens are positive for MERS-CoV. Submit when available. Submission of respiratory specimens should not be delayed for stool collection. 
Blood for PCR: may be tested by PCR if respiratory tract or stool specimens are MERS-CoV positive by PCR, and will be considered in other situations after discussion with the PHO Laboratory microbiologist.


Serology for MERS-CoV is not currently available.


Testing for other respiratory viruses:

At least one respiratory specimen will be tested for influenza by molecular methods (PCR) on all patients.
Specimens will also be tested for other respiratory viruses.


Testing for bacterial causes of community-acquired pneumonia:

Patients with pneumonia/parenchymal lung involvement should also be tested for bacterial causes of community acquired pneumonia (CAP). Recommended testing available at PHO Laboratory includes:

Mycoplasma pneumonia/Chlamydophila pneumonia duplex PCR:
i. Can be ordered on the same NP or throat swab submitted for MERS-CoV testing.

Legionella testing:

i. Legionella PCR can be ordered on the same lower respiratory tract specimens submitted for MERS-CoV testing (e.g. sputum, BAL, bronch wash, aspirates, lung tissues).
ii. Legionella urinary antigen testing (minimum urine volume 2 ml).


If initial tests for MERS-CoV are negative, and a person under investigation is worsening or not improving, testing for MERS-CoV should be repeated, even if previous tests were positive for another pathogen.


Complete all fields of the General Test Requisition form.
Test requested – specify MERS-CoV
Specimen type
Reason for test – Diagnostic (serology is not available, including immune status)
Signs and symptoms – list all relevant
Onset date and date collected
Travel history within 14 days of symptom onset including all destinations and travel dates
Patient setting (e.g. ER, hospitalized, ICU)
Clinical information including whether the patient has pneumonia/lower respiratory tract infection and any associated risk factors as outlined in MOHLTC MERS-CoV Guidance for Health Care Workers and Health Sector Employees

Storage and Transport

Place specimen in biohazard bag and seal. Specimens should be stored at 2-8°C following collection and shipped to PHO Laboratory on ice packs. If transport of specimen to testing laboratory will be delayed more than 72 hours specimens should be frozen at -80°C and shipped on dry ice. 

Package and ship primary clinical specimens to the local PHO Laboratory in accordance with the Transportation of Dangerous Goods Regulations.

Public Health Agency of Canada issued Biosafety Advisory: Middle East Respiratory Coronavirus (MERS-CoV), (updated Oct 19, 2018 which provides guidelines for handling clinical material known or suspected to contain MERS-CoV.

Special Instructions

For respiratory specimens follow the instructions found in the Virus – Respiratory Kit Instruction Sheet.

For sputum, BAL, pleural fluid and lung tissue, see Tuberculosis Kit N-0042

For viral throat swab use Virus Culture Kit N0081.

For stools (if approved by PHO Laboratory) follow the instructions found in the Virus – Enteric Kit Instruction Sheet.

Instructions for using SST tubes are found in the Labstract, LAB-SD-008, Blood Collection using Serum Separator Tubes.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

MERS-CoV RT-PCR testing is performed at PHO Laboratory’s Toronto location as needed daily Monday to Friday. Testing is available on the weekend and holidays for hospitalized patients or in extraordinary circumstances. Note: turnaround time will vary according to the geographical location and proximity to PHO Laboratory’s Toronto location.

Testing for MERS-CoV requires prior approval by PHO Laboratory. Prior to submitting specimens, contact PHO Laboratory’s Customer Service Centre at 416-235-6556/1-877-604-4567 or After-Hours Emergency Duty Officer at 416-605-3113 to obtain approval and make arrangements if after-hours testing is desired.

Specimens that are positive by RT-PCR at PHO Laboratory are sent to NML, Winnipeg, MB for confirmation.

The turnaround time for further viral respiratory testing is up to 4 days.

Test Methods

Nucleic acid is extracted from the specimen and tested by real time PCR for the detection of MERS-CoV using protocols endorsed by the World Health Organization. Real time targets include upstream of the E region (UpE) and open reading frame (ORF) 1a of MERS-CoV. 

Specimens positive for one real time target will be tested by PCR and Sanger sequencing for two further targets: 

  1. RNA dependent  RNA polymerase (RdRp) gene and
  2. Nucleocapsid (N) gene

RdRp is a common coronavirus target designed to provide broad detection of Betacoronavirus clade C sequences including MERS-CoV as well as related viruses; the N gene target is specific for MERS-CoV.

A confirmed case should either have positive test results for at least two different sites in the virus genome tested by real time PCR, or a positive result for a single real time PCR target plus sequencing of a different site (RdRp or N gene) in the MERS-CoV genome.

Serology for MERS-CoV is not currently available.

The following contain additional technical information, including testing protocols: Assays for laboratory confirmation of novel human coronavirus (hCoV-EMC) infections and Detection of a novel human coronavirus by real-timereverse-transcription polymerase chain reaction.


Results are reported to the ordering physician or health care provider as indicated on the requisition, as well as to the Medical Officer of Health.

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Updated 20 July 2020