Coronavirus Disease 2019 (COVID-19) – PCR

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.

Background
This Test Information Sheet provides information on routine polymerase chain reaction (PCR) (molecular) testing for SARS-CoV-2, the causative agent of COVID-19. For other testing modalities, please refer to the following links:

Additional tests to be considered: Bacterial causes of community-acquired pneumonia:
Patients with pneumonia/parenchymal lung involvement may also be tested for bacterial causes of community acquired pneumonia (CAP). Recommended testing available at PHO’s laboratory includes:

Updates

Effective August 31, 2026, standalone COVID-19 PCR request will be replaced by the appropriate respiratory virus panels (FLUVID and MRVP), based on testing eligibility criteria. COVID-19 targets are included in both panels.
Both MRVP and FLUVID will be available at the following PHO locations: Toronto, London, Ottawa, Timmins, Hamilton, Kingston, and Thunder Bay.
For respiratory swab specimen (nasopharyngeal swab - NPS or throat), multiple swabs submitted in a single transport tube will not be accepted for testing. Please ensure that only one swab is submitted per UTM tube.
Pharmacy-based COVID-19 PCR testing has been discontinued. PHO no longer performs testing for specimens submitted through pharmacies.

*Uncontrolled print copy. Valid only on day of print: 01 Sep 2026.

Testing Indications

Who to test:
For test indications, please refer to Test-to-Treat COVID 19 guidance documents from the Ontario Ministry of Health.

people aged 65 years of age and older
people who are immunocompromised
people who are at increased risk due to a combination of age and other medical conditions or risk factors, based on an assessment by a health care provider
residents and patients in certain high-risk settings including hospitals and congregate living settings with medically and socially vulnerable individuals
people in the context of suspected or confirmed outbreaks, as directed by the local public health unit

PHO applies the above test-to-treat criteria to assign the appropriate testing platform for eligible COVID-19 testing requests, taking into account the patient care setting, vulnerable populations, and outbreak investigation needs (FLUVID vs. extended MRVP). Both testing platforms detect SARS-CoV-2

Acceptance/Rejection Criteria

As of October 1, 2024, asymptomatic patients are no longer eligible for COVID-19 testing and specimens from asymptomatic patients will be rejected for testing.

For respiratory swabs (NPS or throat), specimens received containing multiple swabs in a single transport tube will not be acceptable for testing. Please ensure one swab per UTM is submitted.

Specimen Collection Options for COVID-19 PCR Testing by Patient Characteristic

Specimen Collection Method	General Recommendations	Approximate Sensitivity Range^a
Nasopharyngeal (NP) swabbing	Preferred option for all patients (hospitalized or non-hospitalized)^b	95-100% ^{1, 2, 3, 4, 5, 6, 8, 9}
Combined oral/oropharyngeal (buccal/throat) and nasal (midturbinate) swabbing	Other preferred option for non-hospitalized patients^b	85-95% ^{1, 2, 10, 13, 14}
Saliva (neat or saline rinse)	Other preferred option for non-hospitalized patients^b,d	85-95% ^{1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12}
Lower respiratory tract (when possible): sputum^c, BAL, bronchial wash, pleural fluid, lung tissue, and tracheal aspirate	Other preferred option for hospitalized patients	95-100% ¹
Nasal (midturbinate) swabbing	Acceptable option for non-hospitalized patients	80-85% ^{1, 3, 7, 8, 9, 10, 11, 12, 13, 14}
Throat swabbing	Acceptable option for non-hospitalized patients	80-85% ^{1, 13, 14}
Non-respiratory: cerebrospinal fluid (CSF), other non-respiratory sterile fluid or tissues	Acceptable option for hospitalized patients	Not defined^d,1

^a Sensitivity may vary depending on training, collection quality, disease timeline, disease severity, virus lineage, and many other factors, therefore ranges are provided as approximate reference only. Values are approximated.

^b NP swabbing usually provides the highest sensitivity, however it may be less tolerated for some patients and is a regulated procedure, therefore not all settings can perform it. Alternatively, the combined oral and nasal swabbing option and the saliva option both provide relatively high sensitivity in the early infection phase and are suitable for most outpatient settings where NP swabbing is challenging to operationalize. Patients at risk of developing severe disease may still benefit from the higher sensitivity of NP swabbing.

^c Only if patient has self-productive cough (do not induce).

^d Saliva may be less feasible to collect in some patient populations with reduced salivary production or inability to reliably salivate into the collection tube. All PHO locations accept saliva specimens for COVID-19 PCR testing. However, some non-PHO laboratories may not be able to accept this specimen type. Contact your local laboratory provider if you have questions regarding the availability of COVID-19 saliva testing. Testing of respiratory viruses (including influenza) other than SARS-CoV-2 is not available on saliva specimens. Settings requiring testing of both SARS-CoV-2 and other respiratory viruses should select other collection options.

^e Considering the limited evidence for COVID-19 testing on non-respiratory specimens, these specimen types should not be routinely ordered. Testing should be reserved for atypical situations strongly suggestive of COVID-19 infection outside of the respiratory tract, and results should be interpreted with caution as test performance has not been verified for these specimen types. In such situations, common etiologies causing infections outside of the respiratory tract should be considered.

Specimen Collection and Handling

Specimen Requirements

Test Requested	Required Requisition(s)	Specimen Type	Minimum Volume	Collection Kit
COVID-19 PCR	General Test Requisition	Upper respiratory tract: Nasopharyngeal (swab) NPS	2.0 ml (including collection media)	Nasopharyngeal Collection Kit for Viral PCR order#: 390082
COVID-19 PCR	General Test Requisition	Upper respiratory tract: combined oral and nasal swabbing, nasal swabbing, or throat swabbing	Swab in universal transport media (UTM)	Large Swab Throat Collection Kit for Viral PCR order#: 390081
COVID-19 PCR	General Test Requisition	Saliva (neat or swish and gargle)	2.0 to 3.0 mL	Sterile container as provided in collection kit
COVID-19 PCR	General Test Requisition	Lower respiratory tract (when possible): sputum, BAL, bronchial wash, pleural fluid, lung tissue, tracheal aspirate	1.0 ml (if applicable)	Sterile container
COVID-19	General Test Requisition	Non-respiratory: Cerebrospinal fluid (CSF), other non-respiratory sterile fluid or tissue	1.0 ml (if applicable)	Sterile container

Submission and Collection Notes

Complete all fields of the General Test Requisition Form including:

Test(s) requested and indication for testing (e.g. immunocompromised)*
Clinical information including symptom onset date*
Medical condition that puts the patient at increased risk for severe illness*
Patient setting (e.g. inpatient, ICU/CCU, congregate living)*
Specimen type and collection date
Valid outbreak number (if applicable)*
Travel history (if applicable)
COVID-19 vaccination status
* Mandatory information. If the patient is eligible for public funded testing as per the Ministry of Health testing guidance,this must be indicated on the requisition.
FAILURE TO PROVIDE THE ABOVE INFORMATION MAY RESULT IN REJECTION OR TESTING DELAY.

For clinical specimens, label the specimen container(s) with the patient’s first and last name, date of collection, and one other unique identifier such as the patient’s date of birth or Health Card Number. For additional information see: Criteria for Acceptance of Patient Specimens. Failure to provide this information may result in rejection or testing delay.

Number of specimen submissions
For respiratory swabs (NPS or throat), multiple swabs submitted in a single transport tube will not be accepted for testing. Please ensure that only one swab is submitted per UTM.

Testing for other respiratory viruses
If patients meet testing criteria, Multiplex Respiratory Virus Panel (MRVP) or FLUVID testing can be ordered on the same specimen submitted for COVID-19 testing, except for saliva, which is not validated for seasonal respiratory virus testing. SARS-CoV-2 virus does not cross-react with other respiratory viruses in the MRVP assay. Refer to Respiratory Viruses (including influenza) Test Information for more details and acceptance criteria.

Eligible healthcare providers can also order Covid-19 supplies through the completing the PHO Requisition for Specimen Containers and Supplies on PHO website

Limitations

COVID-19 PCR testing is validated at PHO for testing of the respiratory specimen types described in the Specimen Collection Options table above. Non-respiratory specimens will be tested and reported with a disclaimer.

Storage and Transport

Place the specimen container in the biohazard bag and seal the bag; insert the completed requisition in the pocket on the outside of the sealed biohazard bag. To maintain optimal specimen integrity, specimens should be stored at 2-8°C following collection and should be transported to PHO on ice packs within 72 hours of collection. If longer storage/transit time is anticipated, specimens should be frozen at -70°C or lower and transported on dry ice.

Package and ship primary clinical specimens to a PHO location conducting respiratory PCR testing in accordance with the Transportation of Dangerous Goods Regulations.

Outbreak investigations
Respiratory outbreak specimens should be packaged and submitted following the Respiratory Outbreak Testing Prioritization Protocol.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

SARS-CoV-2 is included in PHO’s respiratory virus molecular testing and can be tested in the MRVP or FLUVID PCR.

The TAT for MRVP testing is up to 4 days after receipt by PHO
The TAT for FLUVID testing is up to 3 days after receipt by PHO

Note: Turnaround time may vary according to geographical location and proximity to PHO.

Table 1: Test Frequency of Respiratory Testing and PHO Testing Sites.

PHO Testing Site	FLUVID	MRVP	Business Days ^A
Toronto	Year Round	Year Round	Monday-Sunday
Kingston, London, Ottawa, Timmins	Year Round	Year Round	Monday-Saturday
Hamilton, Thunder Bay	Year Round	Year Round	Monday-Friday
Orillia, Peterborough, Sudbury Sault Ste. Marie	n/a	n/a	n/a

^ASaturday cut-off for same day testing is 11:00 am. Samples received after 11:00 am will be tested on the next available run.

Test Methods

Testing for COVID-19 is done by real-time reverse transcription PCR using the following validated assay which tests for the E gene*:
FLUVID – Respiratory virus quadplex PCR:

Laboratory developed test (LDT) validated at PHO
Detects SARS CoV-2 (COVID-19), influenza A, influenza B and RSV (A/B) and by nucleic acid amplification testing (NAAT)

MRVP – Multiplex Respiratory Virus PCR - In House assay:

Laboratory developed test (LDT) validated at PHO
Detects SARS CoV-2 (COVID-19), influenza A, influenza A H3 (seasonal H3N2) subtype, influenza A H1 (pdm09) subtype, influenza B, respiratory syncytial virus (RSV A/B), parainfluenza (1 – 4), adenovirus, enterovirus, seasonal human coronavirus (OC43, 229E, NL63, HKU1), rhinovirus and human metapneumovirus respiratory targets by multiplex NAAT

Note: The assay detects the different RSV, parainfluenza and seasonal human coronaviruses named above but does not differentiate between them.

*Based on Corman et. al (Euro Surveill 2020).

Interpretation

The following table provides possible test results with associated interpretations for FLUVID and MRVP:

Result	Interpretation	Comments
Not Detected	Virus not detected	Target virus not detected by real-time PCR
Detected	Virus detected	Target virus detected by real-time PCR
Indeterminate	Virus Indeterminate	An indeterminate PCR test result may be due to a low level of target genetic material in the specimen, inadequate specimen content, or a non-specific signal. Please resubmit another specimen for testing if clinically indicated.
Invalid	Invalid	Test results are invalid due to the failed amplification of the extraction control. Amplification failure may be due to inadequate specimen content, extraction failure, or PCR inhibition. Please resubmit another specimen for testing if clinically indicated.

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.

Specimens that are positive for COVID-19 are reported to the medical officer of health as per Health Protection and Promotion Act.

References

Tsang NNY, So HC, Ng KY, Cowling BJ, Leung GM, Ip DKM. Diagnostic performance of different sampling approaches for SARS-CoV-2 RT-PCR testing: a systematic review and meta-analysis. The Lancet Infectious Diseases [Internet]. 2021 Apr 12 [cited 2021 Apr 24];0(0). Available from: https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(21)00146-8/fulltext
Kandel CE, Young M, Serbanescu MA, Powis JE, Bulir D, Callahan J, et al. Detection of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in outpatients: A multicenter comparison of self-collected saline gargle, oral swab, and combined oral–anterior nasal swab to a provider collected nasopharyngeal swab. Infection Control & Hospital Epidemiology. 2021 Jan 13;1–5.
Jamal AJ, Mozafarihashjin M, Coomes E, Anceva-Sami S, Barati S, Crowl G, et al. Sensitivity of midturbinate versus nasopharyngeal swabs for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection Control & Hospital Epidemiology. 2020 Nov 18;42(8):1001–3.
Butler-Laporte G, Lawandi A, Schiller I, Yao M, Dendukuri N, McDonald EG, et al. Comparison of Saliva and Nasopharyngeal Swab Nucleic Acid Amplification Testing for Detection of SARS-CoV-2. JAMA Internal Medicine [Internet]. 2021 Mar 1 [cited 2021 Mar 16];181(3):353. Available from: https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/2775397
Kandel C, Zheng J, McCready J, Serbanescu M, Racher H, Desaulnier M, et al. Detection of SARS-CoV-2 from Saliva as Compared to Nasopharyngeal Swabs in Outpatients. Viruses. 2020 Nov 17;12(11):1314
Goldfarb DM, Tilley P, Al-Rawahi GN, Srigley JA, Ford G, Pedersen H, et al. Self-Collected Saline Gargle Samples as an Alternative to Health Care Worker-Collected Nasopharyngeal Swabs for COVID-19 Diagnosis in Outpatients. Tang Y-W, editor. Journal of Clinical Microbiology. 2021 Mar 19;59(4).
Kojima N, Turner F, Slepnev V, Bacelar A, Deming L, Kodeboyina S, et al. Self-Collected Oral Fluid and Nasal Swab Specimens Demonstrate Comparable Sensitivity to Clinician-Collected Nasopharyngeal Swab Specimens for the Detection of SARS-CoV-2. Clinical Infectious Diseases. 2020 Oct 19;
Teo AKJ, Choudhury Y, Tan IB, Cher CY, Chew SH, Wan ZY, et al. Saliva is more sensitive than nasopharyngeal or nasal swabs for diagnosis of asymptomatic and mild COVID-19 infection. Scientific Reports. 2021 Feb 4;11(1).
Lee RA, Herigon JC, Benedetti A, Pollock NR, Denkinger CM. Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: A Systematic Review and Meta-analysis. Journal of Clinical Microbiology. 2021 Jan 27;
Gertler M, Krause E, van Loon W, Krug N, Kausch F, Rohardt C, et al. Self-collected oral, nasal and saliva samples yield sensitivity comparable to professional-collected oro-nasopharyngeal swabs in SARS-CoV-2 diagnosis among symptomatic outpatients. International Journal of Infectious Diseases. 2021 Jul;
Grijalva CG, Rolfes M, Zhu Y, Chappell J, Halasa N, Kim A, et al. Performance of Self-Collected Anterior Nasal Swabs and Saliva Specimens for Detection of SARS-CoV-2 During Symptomatic and Asymptomatic Periods. Open Forum Infectious Diseases. 2021 Sep 25;8(11).
Marais G, Hsiao N, Iranzadeh A, Doolabh D, Enoch A, Chu C, et al. Saliva swabs are the preferred sample for Omicron detection. 2021 Dec 24;
Schrom J, Marquez C, Pilarowski G, Wang C-Y, Mitchell A, Puccinelli R, et al. Comparison of SARS-CoV-2 Reverse Transcriptase Polymerase Chain Reaction and BinaxNOW Rapid Antigen Tests at a Community Site During an Omicron Surge. Annals of Internal Medicine. 2022 Mar 15;
Goodall BL, LeBlanc JJ, Hatchette TF, Barrett L, Patriquin G. Investigating the Sensitivity of Nasal or Throat Swabs: Combination of Both Swabs Increases the Sensitivity of SARS-CoV-2 Rapid Antigen Tests. Martin RM, editor. Microbiology Spectrum. 2022 Aug 31;10(4).

Data and Analysis

Related Testing Resources