Coronavirus Disease 2019 (COVID-19) Testing

This document provides testing guidelines for the novel coronavirus disease 2019 (COVID-19, formerly known as 2019-nCoV) associated with an outbreak of respiratory illness that originated in Wuhan, Hubei Province, China in late 2019. The causative agent for COVID-19 disease is SARS-CoV-2 virus. For the purpose of clear communication, PHO uses the term COVID-19 to refer to both the virus and the disease.

Who to test:

Please refer to the testing guidelines from the Ministry of Health.

PHO is not currently recommending routine testing of asymptomatic persons for COVID-19. If the clinician would like to further discuss the role for testing, the PHO Microbiologists on-call are available and can be contacted through the 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.

Mandatory data accompanying testing requests:

In order to expedite testing, as of February 10, 2020 PHO Laboratory pre-approval for COVID-19 testing is no longer required, provided that the following mandatory information is included on the specific PHO COVID-19 Test Requisition. Refer to Submission and Collection Notes below.

Note: As of March 2, 2020, the respiratory virus multiplex PCR (MRVP) will no longer be performed on all specimens submitted for COVID-19 testing. MRVP will only be performed by request for patients that meet PHO Laboratory’s acceptance criteria for this testing (e.g. hospitalized, outbreaks, institutionalized). If patients meet testing criteria, MRVP can be ordered on the same swab submitted for COVID-19 testing. Refer to the Respiratory Viruses Test Information Sheet for more details and acceptance criteria.

Local public health unit notification:

The local public health unit should be contacted for all COVID-19 results. For contact and information on your local health unit, please see the Ministry of Health PHU Locator.

Specimen Collection and Handling

Due to global shortages, the following chart provides information on alternative collection kits for procurement that are acceptable for COVID-19 testing.

If you are ordering collection kits from PHOL.Warehouse@oahpp.ca using the Requisition for Specimen Containers and Supplies Form any of these kits may also be used to fulfill orders (see submission note #3 below).

Manufacturer

Vendor Catalogue

Description

Oxoid

OXRE12568

M6 Kit with Traditional-Tipped Flocked Swab

Oxoid

OXRE12569

M6 Kit with Micro-Tipped Flocked Swab

Copan

CA302MH

3mL UTM standard flock

Copan

CA305MH

3mL UTM Pernasal flock

Copan

CA56750CS01

Midturbinate - pediatrics swabs

BD

B220528

3mL Vial, one sterile Nylon flocked tip swab, scored plastic shaft

BD

B220531

3mL Vial, one sterile mini-tip swab, scored plastic shaft

Roche

07958021190

KIT COBAS PCR MEDIA DUAL SWB

Hologic

PRD-03546

Multitest Swabs

Specimen Requirements

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

COVID-19

Upper respiratory tract: Nasopharyngeal swab (NPS)

Nasopharyngeal swab in 1 ml universal transport media (UTM)

Virus Respiratory Kit order # 390082

COVID-19

Viral throat swab (see Submission and Collection Notes below)

Swab in 1 ml universal transport media (UTM)

Virus Culture Kit order #390081

COVID-19

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

1.0 ml

Tuberculosis Kit order#: 390042

Submission and Collection Notes

1

Respiratory tract specimens

Patients not admitted to hospital (including those in ER)

  • A single upper respiratory tract specimen will be accepted for COVID-19 testing. Upper respiratory tract specimens include a nasopharyngeal swab (NPS) OR viral throat swab collected in universal transport medium (UTM). NPS is the preferred specimen.

In-patients

Submission of both an upper and lower respiratory tract specimen is recommended when possible:

  • Upper respiratory tract: submit NPS. A viral throat swab collected in UTM may be submitted as an additional specimen, but is not required.
  • Lower respiratory tract specimens: submit when possible.
  • Sputum: collect if patient has a productive cough. Do not induce.
2

Use of laboratory testing for clearance of confirmed and probable COVID-19 cases from isolation

For each scenario below, cessation of isolation requires that the individual is afebrile and symptoms are improving.

  • For confirmed and probable cases at home: Laboratory testing is not required for discharge from isolation. These patients can be discharged from isolation and categorized as “resolved” 14 days following symptom onset.
  • For hospitalized patients: Isolate in hospital until two negative tests, obtained at least 24 hours apart. If discharged home within 14 days of symptom onset, follow advice for individuals at home.

For further information, please refer to the Ministry of Health COVID-19 Quick Reference Public Health Guidance on Testing and Clearance.

 
3

Alternative specimen collection kits

PHO Laboratory has done a limited evaluation on the alternative specimen collection kits listed above. These can be used for collection of nasopharyngeal specimens for COVID-19 testing.

PHO Laboratory will accept other swab types (except cotton-tipped swabs) and other liquid transport media (except gel or solid media) for COVID-19 testing; however, if the submitted swab and/or media type were not validated at PHO Laboratory for COVID-19 testing, the results will be reported with a disclaimer. Further information on alternative collection kits is available here: FAQs on Diagnostic Testing for SARS-CoV-2.

 
4

Complete all fields of the COVID-19 Test Requisition.

  • Test(s) requested and indication for testing (If confirmatory or clearance testing is requested, this must be indicated on the test requisition)
  • Travel history (if applicable)
  • Exposure history and details
  • Clinical information including symptom onset date
  • Specimen type and collection
  • Patient setting/population (If the patient belongs to a priority group, as per the Ministry of Health testing guidance, this must be indicated on the requisition)

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 or directly to a PHO Laboratory conducting COVID-19 testing in accordance with the Transportation of Dangerous Goods Regulations.

Current PHO Laboratory testing locations include Toronto, Hamilton, London, Kingston, and Ottawa. Refer to specimen acceptance hours and testing schedules at PHO Laboratory COVID-19 testing locations.

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.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Testing for COVID-19 is performed at PHO Laboratory as required. NOTE: Turnaround time will vary according to geographical location and proximity to a PHO Laboratory location that performs COVID-19 testing.

COVID-19 testing at PHO Laboratory is performed 7 days a week. The TAT for COVID-19 testing at PHO Laboratory is up to 4 days. If necessary, additional testing is conducted at the National Microbiology Laboratory (NML) in Winnipeg, which may increase TAT.

Testing for COVID-19 does not need to be sent as STAT specimens unless the result is needed to assist health-care providers in making swift patient care decisions in an urgent or emergency circumstance.

  • STAT samples must be shipped separately from routine specimens to a PHO Laboratory location that performs COVID-19 testing. Current PHO Laboratory testing locations include Toronto, Hamilton, Kingston, and Ottawa. Refer to specimen acceptance hours and testing schedules at PHO Laboratory COVID-19 testing locations.
  • For testing at PHO Laboratory Toronto, specimens must be sent to the shipping and receiving dock at 661 University Ave., Toronto, Ontario. For delivery instructions please see Directions to 661 University Shipping Dock for Clinical Samples
  • STAT samples must be placed in a clearly marked package indicating ‘STAT’ and handled in accordance with the Canadian Biosafety Standards and shipped in accordance with the Transportation of Dangerous Goods Regulations.
  • Failure to ship separately will delay testing, primarily due to delays in transportation, and will be processed as a routine sample.

Reporting

Final results of COVID-19 testing from PHO Laboratory are reported to the ordering health-care provider as indicated on the requisition.

As a disease of public health significance, all positive results will be reported to the local public health unit. As an interim measure we will also be reporting all negative results to the local public health unit.

Test Methods

Testing for COVID-19 is done by real-time PCR using protocols validated by PHO Laboratory and the NML. Targets include the envelope (E) gene and RNA-dependent RNA polymerase (RdRp) gene.

  • Specimens will be tested using the E gene real-time PCR assay, the more sensitive of the two PCR targets.
    • Specimens with an E gene target detected will be reported as COVID-19 virus detected, which is sufficient for laboratory confirmation of COVID-19 infection.
    • Specimens with an E gene target not detected will be reported as COVID-19 virus not detected.
  • Specimens with an E gene target result which is indeterminate* may be further investigated.
    • Additional testing will include the RdRp gene real-time PCR assay or Sanger sequencing for the COVID-19 virus RdRp gene.
    • Detection of COVID-19 virus by either RdRp gene assay, or detection of any other single gene target with a validated assay, is sufficient for laboratory confirmation.

Laboratory confirmation of COVID-19 at PHO Laboratory consists of:

  • Detection of one genome target by real-time PCR

OR

  • One or multiple targets is/are indeterminate* by real-time PCR AND detection of COVID-19 virus by sequencing.   

PHO Laboratory testing is considered INCONCLUSIVE if:

  • One or multiple targets is/are indeterminate* by real-time PCR (and no targets are detected)

AND

  • COVID-19 is not detected by sequencing.

*An indeterminate result on a real-time PCR assay is defined as a late amplification signal at a predetermined high cycle threshold (Ct) value range (Ct >38 in the PHOL COVID-19 laboratory developed assay). This may be due to low viral target quantity in the clinical specimen approaching the limit of detection of the assay, or alternatively may represent nonspecific reactivity (false signal) in the specimen. When clinically relevant, indeterminate samples should be investigated further by testing for an alternate gene target using a validated real-time PCR or nucleic acid sequencing assay at the community, hospital or reference laboratory that is equally or more sensitive than the initial assay or method used.

Specimens will be sent to NML for further testing if required.

Some hospital and community laboratories have implemented COVID-19 testing in-house and report final positive results, which is sufficient for case confirmation. Other hospital and community laboratories will report positives as preliminary positive during the early phases of implementation and will require confirmatory testing at PHO Laboratory. If confirmatory testing is requested, this should be indicated on the test requisition by the submitting hospital or community laboratory.

Details about the real-time PCR used at PHO Laboratory for COVID-19 testing are available at: Diagnostic detection of COVID-19 by real-time RT-PCR.

The following publication contains additional technical information on the RdRp gene PCR and sequencing assay which PHO Laboratory has adapted to be specific for COVID-19 virus detection: Assays for laboratory confirmation of novel human coronavirus (hCoV-EMC) infections.

To meet increasing submissions for COVID-19 testing, PHO Laboratory may also use a variety of commercial assays which are validated for clinical testing. The assay used will be identified on the report.

Serology for COVID-19 is not currently available at PHO Laboratory.

Algorithm

PHO Laboratory Testing Algorithm for COVID-19 (as of March 16, 2020)

A. Testing for COVID-19

  •  See Test Methods above.

B. Testing for other respiratory viruses:

  • Testing for other respiratory viruses by multiplex respiratory virus PCR (MRVP) can be ordered if patients meet PHO Laboratory’s acceptance criteria for this testing (e.g. hospitalized, outbreaks, institutionalized). Refer to the Respiratory Viruses Test Information Sheet for more details and acceptance criteria.
    *Cross-reaction with COVID-19 has not been detected based on in-house laboratory data and available sequence data. 

Note: Testing for other respiratory viruses and avian influenza must be ordered on the laboratory requisition if required and can be ordered on the same swab submitted for COVID-19 testing.

 

Additional tests to be considered:

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:

i. Mycoplasma pneumoniae/Chlamydophila pneumoniae duplex PCR:

  • Should be ordered on the same NP or throat swab submitted for COVID-19 testing.

ii. Legionella testing:

NB. If a person under investigation for COVID-19 is worsening or not improving, testing should be repeated, even if previous tests were positive for another pathogen.

contact lab

Contact Laboratory Customer Service

Laboratory Services

customerservicecentre@oahpp.ca

Updated 29 March 2020