Coronavirus Disease 2019 (COVID-19) – PCR

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:

Updates (February 3, 2023):
Overall simplification of testing information, and updated the summary table of specimen collection methods with linked instructions. Some key changes include:

  • combined oral/oropharyngeal (buccal/throat) and nasal swabbing” now represents:
    • combined oral (buccal)
    • deep nasal swab
    • combined swab of throat and both nares
  • saliva” now represents:
    • saliva – neat – funnel
    • saliva – neat – straw
    • saliva: mouth rinse – swish and gargle – funnel
    • saliva: mouth rinse – swish and gargle – straw.
  • Provision of expected performance ranges by specimen type.

Testing Indications

For test indications, please refer to the testing guidance documents from the Ontario Ministry of Health.

Specimen Collection and Handling

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

Specimen Collection Method General Recommendations Approximate Sensitivity Rangea
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 patientsb 85-95% 1, 2, 10, 13, 14
Saliva (neat or saline rinse) Other preferred option for non-hospitalized patientsb, d 85-95% 1, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12
Lower respiratory tract (when possible): sputumc, BAL, bronch 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 definede,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. Risk factors for severe disease are listed in the Ontario Ministry of Health testing guidance.
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 laboratory 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 Requirements

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

COVID-19 PCR

Upper respiratory tract: NP swabbing, combined oral and nasal swabbing, saliva, nasal swabbing, or throat swabbing

2.0 ml (including collection media if used)

See COVID-19 PCR Collection Kits

COVID-19 PCR

Lower respiratory tract (when possible): sputum, BAL, bronch wash, pleural fluid, lung tissue, tracheal aspirate (see Submission and Collection Notes #1)

1 ml

Sterile container

COVID-19

Non-respiratory: Cerebrospinal fluid (CSF), other non-respiratory sterile fluid or tissue

1.0 ml

Sterile container

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), combined oropharyngeal/throat plus both anterior nares/nostrils, combined oral (buccal) and deep nasal swab, deep nasal swab, oropharyngeal/throat swab, or swab of both anterior nares, collected in universal transport medium (UTM) or other viral media as described above. 
  • Upper respiratory tract specimens can also include saliva collected neat or as a saline mouth rinse “swish and gargle”. Please see all notes associated with this specimen type in the table “Preferred and Acceptable Specimen Types for COVID-19 testing by Patient Characteristic” above. Saliva sample should not be collected from symptomatic patients residing in institutional settings (e.g. retirement homes or long-term care facility) or hospitalized patients. Saliva samples are not suitable and cannot be accepted for testing for respiratory viruses (e.g. influenza virus, RSV) other than SARS-CoV-2 NOTE: only limited non-PHO laboratories are accepting saliva testing for COVID-19 PCR.

In-patients

For in-patients, PHO Laboratory will accept multiple specimen submissions. If done, this should be done from different collection sites:

  • Upper respiratory tract: submit NPS, combined swab of oropharyngeal/throat plus both anterior nares/nostris, or deep nasal swab. A viral throat swab collected in UTM may be submitted as an additional specimen, but is not required. PHO Laboratory will accept multiple swabs (e.g NP swab, throat swab) placed into one transport medium. This combined submission will be run and reported as a single test.
  • 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

Respiratory Virus Multiplex PCR (MRVP)

As of March 2, 2020, MRVP is no longer performed on all specimens submitted for COVID-19 testing. MRVP is 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 Respiratory Viruses Test Information for more details and acceptance criteria.

 

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 or if asymptomatic
  • COVID-19 vaccination status
  • 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)
5

Respiratory outbreak specimens should be submitted following the Respiratory Outbreak Testing Prioritization Protocol

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.

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 -70°C or below 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 PCR testing in accordance with the Transportation of Dangerous Goods Regulations. Current PHO Laboratory testing locations include Toronto, Hamilton, Kingston, London, Ottawa, Timmins and Thunder Bay. Refer to COVID-19 PCR  specimen acceptance hours and testing schedules for further details.

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)

COVID-19 testing is performed 7 days a week at PHO’s laboratory. Most results are expected to be completed within 24 hours, however turnaround time may vary according to geographical location and proximity to a PHO Laboratory location that performs COVID-19 PCR testing. 

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.

URGENT samples must be shipped separately from routine specimens to a PHO’s laboratory location that performs COVID-19 PCR testing. Failure to ship COVID specimens separately may delay testing, primarily due to delays in transportation. Specimen may inadvertently be processed as a routine sample.

URGENT samples must be placed in a package that has been clearly marked ‘URGENT’ and handled in accordance with the Canadian Biosafety Standards and shipped in accordance with the Transportation of Dangerous Goods Regulations.

Reporting

COVID-19 PCR results are reported to the ordering healthcare provider as indicated on the test requisition.

As a disease of public health significance, all positive results will be reported to the local public health unit.

If specimens submitted to PHO’s laboratory are forwarded to another laboratory for testing as part of Ontario’s response to the COVID-19 pandemic, the reporting of results to the ordering healthcare provider, as well as any required health unit notifications, will be performed by the testing laboratory.

Test Methods

Testing for COVID-19 is done by real-time reverse transcription PCR using either one of the following validated assays:

Current Assays in Use at PHO Laboratory and Associated Gene Targets

Assay Gene Targets

PHO’s laboratory-developed test (LDT)

E gene*

Roche Cobas

Orf1a/b gene, E gene

Thermofisher Amplitude

Orf1a/b gene, S gene, N gene

E – Envelope; Orf1a/b – open reading frame 1a/b; N – Nucleocapsid; S- Spike
*Based on Corman et. al (Euro Surveill 2020).

Specimens with a single gene target detected will be reported as COVID-19 virus detected. The detection of any gene target is sufficient to confirm a COVID-19 diagnosis in most situations.

Specimens with a single gene target detected at a late amplification signal within a predetermined high cycle threshold (Ct) value range (Ct ≥ 35 and ≤ 38 for PHO’s LDT) will be reported as COVID-19 virus (low level) detected. The low level detection of any gene target is sufficient to confirm a COVID-19 diagnosis in most situations. The low level positivity may further correlate with either a very early or very late stage of the COVID-19 infection, and this additional information may assist public health units in defining transmission risk.

Specimens with a gene target detected at a very late amplification signal within a predetermined high cycle threshold (Ct) value range (Ct > 38 and <40 for PHO’s LDT) will be reported as COVID-19 virus indeterminate. An indeterminate result may be due to very low viral target quantity in the clinical specimen approaching the limit of detection of the assay, or may represent nonspecific reactivity (false signal) in the specimen. The presence of indeterminate gene target result(s) in the absence of other detected gene target(s), and where gene target result(s) remain undetected or indeterminate on an alternative molecular test assay, is inconclusive for COVID-19, and repeat testing is usually warranted.

Specimens with no gene target(s) detected will be reported as COVID-19 virus not detected. The absence of detected gene target(s) is sufficient to exclude a COVID-19 diagnosis in many situations. Additional considerations may be needed to rule out disease in a symptomatic person with very high pre-test likelihood of disease. Due to the viral dynamics of COVID-19 infection over time, a negative result in an asymptomatic person tested early after exposure cannot be used to rule out the development of subsequent disease.

Tests may be reported as invalid if gene target results are uninterpretable. This could be for various reasons, most commonly due to failed detection of the assay’s internal control. Each invalid result is accompanied with a specific comment to explain the cause. When possible, specimens that are invalid are repeated on the same test system and/or retested on an alternate testing assay at PHO’s laboratory.

Algorithm

Additional tests to be considered:

Testing for 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:

This testing can be performed on the same upper or lower respiratory specimen submitted for COVID-19 PCR testing except saliva specimens.

  • Legionella testing:

-Legionella PCRcan be ordered on the same lower respiratory tract specimen (e.g. sputum, BAL, bronchial wash, aspirates, lung tissue) submitted for COVID-19 PCR testing.
- Legionella urinary antigen testing (minimum urine volume 2 ml).

Note: If the clinical status of a person under investigation for COVID-19 is deteriorating or not improving, repeat COVID-19 PCR testing should be considered even if previous tests were positive for another pathogen as co-infection or superimposed infection may occur. 

References:

  1. 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
  2. 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.
  3. 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.
  4. 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
  5. 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
  6. 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).
  7. 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;
  8. 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).
  9. 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;
  10. 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;
  11. 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).
  12. 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;
  13. 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;
  14. 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

PHO has developed the following testing resources:

contact lab

Contact Laboratory Customer Service

Laboratory Services

customerservicecentre@oahpp.ca

Updated 16 Nov 2021