Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

Specimen Collection and Handling

Specimen Requirements

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

Upper respiratory tract: Nasopharyngeal swab (NPS)

Swab in 1 ml universal transport media (UTM)

Virus Respiratory Kit order#: 390082

Viral throat swab

Swab in 1 ml universal transport media (UTM)

Virus Culture Kit order#: 390081

Lower respiratory tract: sputum, (BAL) (where possible), pleural fluid, lung tissue

1.0 ml

Tuberculosis Kit order#: 390042


1 gram

Sterile container

Virus – Enteric Kit order#: 390087

Blood or serum

5.0 ml whole blood or 1.0 ml serum

Blood, clotted – vacutainer tubes (SST)

Submission and Collection Notes


Contact Public Health Ontario customer service at 1-877-604-4567 prior to submitting samples and to obtain PHO Medical/Clinical Microbiologist approval for after-hours testing. 

Preparation Prior to 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 samples 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 Corona Virus (MERS-CoV), (updated July 7, 2015) 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 stools 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.

For sputum, BAL, pleural fluid and lung tissue, see Tuberculosis Kit N-0042. For viral throat swab use Virus Culture Kit N0081.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

The MERS-CoV test is performed as needed daily Monday to Friday. Testing on the weekend will be done for hospitalized patients. Contact Public Health Ontario customer service at 1-877-604-4567 prior to submitting samples and to obtain PHO Medical/Clinical Microbiologist approval for after-hours testing.

The Turnaround time for RT-PCR is up to 3 days after receipt at testing site. Note: Turnaround time will vary according to geographical location and proximity to Toronto PHO laboratory.

Samples that are positive by PCR at PHOL are sent to NML, Winnipeg, MB for confirmation.

The turnaround time for rapid respiratory virus culture (R-Mix TOO) is up to 4 days.


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.

Test Methods

The specimen nucleic acid is 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), open reading frame (ORF) 1a, and/or ORF1b 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 

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.

Serologic assays are in development at NML, Winnipeg, Manitoba. Serology testing is being used in Canada for surveillance purposes, and not for diagnosis. Serology will not be reported on PCR-negative patients.

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.

Prior to Submission

Contact PHO laboratory's Customer Service Centre at 416-235-6556/1-877-604-4567 prior to submission

PHO laboratory reviews each request with the submitting physician or another healthcare provider who has knowledge of the patient and how they meet the case definition (e.g. ER nurse, ICP). If health unit becomes aware of a request prior to PHO laboratory being contacted, ask the submitter to call PHO laboratory before submission, ideally prior to specimen collection and after a physician has seen the patient. PHO laboratory will then verify that the patient meets criteria, determine testing priority, obtain contact information for results and provide advice concerning specimen collection, transportation and turnaournd time. Additional testing may be discussed. 

Laboratory testing for MERS-CoV should be done on any person with acute respiratory infection (ARI) with or without lower respiratory tract involvement (e.g., pneumonia or ARDS) and appropriate epidemiology such as contact with a confirmed case or onset of symptoms during travel to or within 14 days of return from a MERS-CoV endemic area. All cases to date have been linked to countries in the Middle East, or have been direct contacts of confirmed cases who acquired infection in the region, with some secondary chains of transmission (see MOHLTC: MERS-CoV Guidance for Health Workers and Health Sector Employees)

The following specimens are recommended for MERS-CoV testing on persons under investigation.

  • Respiratory Tract Specimens
    • Collection of multiple specimens from both the upper and lower respiratory tract, where possible, is recommended.
    • Upper respiratory tract specimens: both a nasopharyngeal (NP) swab AND a viral throat swab.
    • Lower respiratory tract specimens: sputum (if patient has a productive cough), bronchoalveolar lavage (BAL) (where possible), pleural fluid, lung tissue.
  • Additional specimens which may be considered for submission.
    • If the patient has gastrointestinal symptoms (diarrhea), submit a stool specimen in a dry sterile container – do NOT use other transportation media containers such as Cary-Blair.
      • Stool samples will be tested if respiratory specimens are positive for MERS-CoV, or if the patient is immunocompromised and is considered to have an atypical presentation with predominant gastrointestinal symptoms.
    • Acute (when patient first seen with acute respiratory illness) and convalescent (21 to 28 days after illness onset) serology. Serum may also be tested by PCR if respiratory tract or stool specimens are positive for MERS-CoV, and will be considered in other situations after discussion with the PHO laboratory microbiologist.
      • Serology testing is being used in Canada for surveillance purposes, and not for diagnostic purposes. A laboratory report may not be provided on samples tested.

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 using Rapid Respiratory Virus Culture.

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 CAP pathogen testing available at PHO laboratory include:

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.

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Updated 4 Jan 2019