Novel Coronavirus (2019-nCoV) Testing
This document provides testing guidelines for the novel coronavirus (2019-nCoV) associated with an outbreak of respiratory illness in Wuhan, China. This virus is considered a novel human coronavirus that is genetically distinct from the common human coronaviruses (229E, NL63, OC43, HKU1), which cause seasonal acute respiratory illness. It is also genetically distinct from the two newer human coronaviruses, MERS-CoV and SARS-CoV.
Laboratory testing of persons under investigation (PUIs) for infection with 2019-nCoV may be considered for patients with:
- Fever and acute respiratory illness, or with pneumonia; AND
- Presence in Wuhan within 14 days prior to symptom onset.
Note that definitive testing for 2019-nCoV is not currently available. Testing protocols will be revised as more information becomes available.
Testing for 2019-nCoV PUIs requires prior approval by the PHO Laboratory before submission and ideally after a physician has seen the patient. For approval, 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 2019-nCoV.
- PHO Laboratory verifies that the patient meets testing criteria, provides specimen collection and transportation advice, communicates an estimated turnaround time for results, and obtains contact information for reporting. Additional testing may be discussed.
- If the health unit becomes aware of a request prior to PHO Laboratory being contacted, they should direct the submitter to contact PHO Laboratory directly to discuss testing.
|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)
Viral throat swab (see Submission and Collection Notes below)
Swab in 1 ml universal transport media (UTM)
Lower respiratory tract (when possible): sputum, BAL, bronch wash, plueral fluid, lung tissue (see Submission and Collection Notes below)
Submission and Collection Notes
Respiratory Tract Specimens:
Collection of multiple specimens from both the upper and lower respiratory tract, where possible, is recommended.
I) Upper respiratory tract: submit both a nasopharyngeal swab (NPS) AND viral throat swab.
II) Lower respiratory tract specimens: submit when possible.
III) Sputum: collect if patient has a productive cough. Do not induce.
Complete all fields of the General Test Requisition form.
- Test requested – specify 2019-nCoV
- 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
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 specimens to the local PHO Laboratory in accordance with the Transportation of Dangerous Goods Regulations.
Test Frequency and Turnaround Time (TAT)
Testing for 2019-nCoV PUIs is performed at PHO Laboratory Toronto as required. NOTE: Turnaround time will vary according to geographical location and proximity to PHO Laboratory Toronto.
Testing for 2019-nCoV PUIs 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.
All specimens submitted to PHO Laboratory are sent to the National Microbiology Laboratory in Winnipeg, MB for parallel testing.
The turnaround time for viral respiratory testing is up to 4 days.
Results are reported to the ordering physician or health care provider as indicated on the requisition.
Currently, there is no specific test for the detection of 2019-nCoV. Until a definitive test is available, PHO Laboratory will conduct PCR and Sanger sequencing of a universal coronavirus target: RNA dependent RNA polymerase (RdRp) gene.
RdRp is a common coronavirus target designed to provide broad detection of Betacoronavirus clade C viruses. Although not evaluated in the laboratory setting, the sequences of 2019-nCoV released to date match the targets this assay was designed to detect.
The following publication contains additional technical information on the RdRp gene PCR protocol (which was developed as a component of MERS-CoV PCR): 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.
Serology for Wuhan Novel Coronavirus is not currently available.
PHO Testing Algorithm for 2019-nCoV PUIs (as of January 20, 2020)
A. Testing for other respiratory viruses:
- At least one respiratory specimen will be tested for influenza by molecular methods (PCR) and evaluated for possible avian influenza if influenza A is positive
- Specimens will also be tested for other respiratory viruses by a multiplex respiratory virus PCR (MRVP), which detects 11 respiratory virus targets. These include influenza A, influenza A H3 subtype, influenza A H1 (pdm09) subtype, influenza B, respiratory syncytial virus, parainfluenza, adenovirus, enterovirus, seasonal human coronaviruses*, rhinovirus and human metapneumovirus.
*Cross-reaction with 2019-nCoV is not expected based on available sequence data.
B. 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 pneumoniae/Chlamydophila pneumoniae duplex PCR:
i. Should be ordered on the same NP or throat swab submitted for novel coronavirus testing.
- Legionella testing:
i. Legionella PCR: can be ordered on the same lower respiratory tract specimens submitted for Wuhan NCoV testing (e.g. sputum, BAL, bronch wash, aspirates, lung tissue).
ii. Legionella urinary antigen testing (minimum urine volume 2 ml).
- Mycoplasma pneumoniae/Chlamydophila pneumoniae duplex PCR:
C. Testing for Wuhan NCoV
- A specific test for 2019-nCoV is not currently available as of January 10, 2020.
- In the interim, testing for 2019-nCoV offered by PHO will include a PCR targeting RNA dependent RNA polymerase (RdRp). RdRp is a common coronavirus target designed to provide broad detection of Betacoronavirus clade C viruses. Although not evaluated in the laboratory setting, the sequences released to date match well to the targets this assay was designed to detect. Other investigational testing approaches for the detection of 2019-nCoV will be applied as required.
NB. If a person under investigation is worsening or not improving, testing should be repeated, even if previous tests were positive for another pathogen.