Middle East Respiratory Syndrome Coronavirus (MERS-CoV) – Real-time PCR

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Background
This page provides testing information for Middle East Respiratory Syndrome (MERS) at Public Health Ontario (PHO). MERS is a viral respiratory illness caused by the Middle East Respiratory Syndrome coronavirus (MERS-CoV).

* Copie d'impression non contrôlée. Valide uniquement le jour de l'impression : 23 mai 2025.

Testing Indications

Laboratory testing for MERS-CoV is performed on patients with acute respiratory illness with onset within 14 days of travel to the Kingdom of Saudi Arabia. Travellers returning from other MERS affected areas should have one or more of the following risk factors:

visited a health care facility as a patient, worker or visitor in the affected area
had contact with camels or camel products, such as raw milk or meat, secretions or excretions (including urine)

In addition, patients are also eligible for testing if they’ve had:

close contact with a confirmed or probable case of MERS or
close contact with a traveller arriving from or resident of an affected area with acute respiratory illness

Testing for MERS-CoV requires prior approval by a PHO microbiologist or designate. Prior to submission — ideally after a physician has seen the patient but prior to specimen collection — contact PHO’s Laboratory Customer Service Centre at 416-235-6556/1-877-604-4567 or the After-Hours Emergency Duty Officer at 416-605-3113.
PHO reviews each request with the ordering physician or another healthcare provider (e.g. ER nurse, Infection Control & Prevention) who has knowledge of how the patient’s clinical and epidemiological history meets MERS-CoV testing criteria.
PHO verifies 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.

Health units should advise submitters to make testing arrangements directly with PHO.

IMPORTANT INSTRUCTIONS - Read before proceeding

Testing for MERS-CoV requires approval by the Public Health Ontario 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
MERS-CoV PCR	General Test Requisition	Upper respiratory tract: Nasopharyngeal swab (NPS) AND Throat swab¹	Nasopharyngeal/Throat swab in 1 ml universal transport media (UTM)	Nasopharyngeal swab Virus Respiratory Kit order#: 390082 Throat swab Virus Culture Kit order#: 390081
MERS-CoV PCR	General Test Requisition	Lower respiratory tract (where possible): sputum, BAL, bronch wash, pleural fluid, lung tissue¹	1.0 ml, if applicable	Tuberculosis Kit order#: 390042
MERS-CoV PCR	General Test Requisition	Stool² (do not collect without PHO’s approval)	1 gram	Sterile container Virus – Enteric Kit order#: 390087
MERS-CoV PCR	General Test Requisition	Blood or serum (do not collect without PHO’s approval²)	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 Microbiologist. 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 Microbiologist.

Serology for MERS-CoV is not currently available.

Additional Tests can be performed upon request and should be included under Test Requested on the requisition.

Testing for other respiratory viruses:

Multiplex Respiratory Virus PCR (MRVP) can be performed at PHO on one of the respiratory specimens upon request.

Testing for bacterial causes of community-acquired pneumonia:

Patients with pneumonia/parenchymal lung involvement should consider testing bacterial causes of community acquired pneumonia (CAP). Recommended testing available at PHO includes:
1. Mycoplasma pneumonia/Chlamydophila pneumonia duplex PCR: can be ordered on the same NP or throat swab submitted for MERS-CoV testing.
2. Legionella testing:

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).
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 and additional tests
Specimen type and date collected
Reason for test – diagnostic
Signs and symptoms – list all relevant
Onset date
Travel history within 14 days of symptom onset including all destinations and travel dates
Patient setting (e.g. ER, hospitalized, ICU)

Storage and Transport

Place specimen in biohazard bag and seal. Specimens should be stored at 2-8°C following collection and shipped to PHO 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 in accordance with the Transportation of Dangerous Goods Regulations.

Refer to Biosafety Advisory: Middle East Respiratory Corona Virus (MERS-CoV) from Public Health Agency of Canada 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) follow the instructions found in the Virus – Enteric Kit Instruction Sheet.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

MERS-CoV RT-PCR testing is routinely performed at PHO’s laboratory, Toronto location, as needed on Monday to Friday.

Turnaround time is up to 3 days from receipt at PHO.

The turnaround time for further viral respiratory testing is up to 4 days after MERS-CoV RT-PCR is performed.

Stat and Critical Specimens Testing

Testing on weekends and/or holidays may be performed under special circumstances. 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 for consultation.

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 PCR targets include upstream of the E region (UpE) and open reading frame (ORF) 1a of MERS-CoV.

Specimens positive for a single target will be tested by PCR and Sanger sequencing for two additional targets:

RNA dependent RNA polymerase (RdRp) gene and
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 contains 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-time reverse-transcription polymerase chain reaction.

Algorithm

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

Interpretation

Result	Interpretation	Comments
Not Detected	Middle East respiratory syndrome coronavirus NOT detected by PCR
Detected	Middle East respiratory syndrome coronavirus Detected by PCR
Indeterminate	Indeterminate for Middle East respiratory syndrome coronavirus.	An indeterminate result may represent a low level of genetic material in this specimen.
Invalid	Middle East Respiratory Syndrome coronavirus invalid by PCR	Test results are uninterpretable due to the failed amplification of the extraction control. Unable to report MERS Coronavirus PCR result. Amplification failure may be due to inadequate specimen content, extraction failure, or PCR inhibition.

Reporting

Results are reported to the physician, authorized health care provider (General O. Reg 45/22, s.18) or submitter as indicated on the requisition.

Positive specimens are reported to the Medical Officer of Health as per the Ontario Health Protection and Promotion Act.

* Copie d'impression non contrôlée. Valide uniquement le jour de l'impression : 23 mai 2025.

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Mis à jour le 1 mai 2025