National case definition: Coronavirus disease (COVID-19)

Last updated: December 17, 2021

On this page

• Preamble
• National notification
• Type of surveillance
• National surveillance case definitions for COVID-19
  • Confirmed case
  • Probable case
  • Deceased case
  • Resolved case
  • Reinfection case
    • Laboratory-based reinfection
    • Time-based reinfection
• Laboratory comments
  • Laboratory-based tests
  • Point-of-care tests
  • Serology tests
• Clinical features
• ICD code(s)
• Comments
• Previous case definitions

Preamble

The primary surveillance objective for COVID-19 is the detection of cases and identification of outbreaks in Canada. The secondary objective is to characterize the clinical and epidemiologic features of COVID-19 in order to better inform prevention and control efforts.

This document outlines surveillance case definitions for the identification of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Surveillance case definitions are provided for the purpose of standardized case classification and reporting to the Public Health Agency of Canada. They are based on the current level of epidemiological evidence and uncertainty, and public health response goals, and are subject to change as new information becomes available.

National notification

The Public Health Agency of Canada should be notified of any confirmed and probable cases of COVID-19.

Type of surveillance

Routine case-by-case notification to the Public Health Agency of Canada.

Detailed information on the reporting of COVID-19 cases in Canada can be found in the National surveillance for Coronavirus Disease (COVID-19).

National surveillance case definitions for COVID-19

Confirmed case

A person with confirmation of infection with SARS-CoV-2 documented by:

• The detection of at least 1 specific gene target by a validated laboratory-based nucleic acid amplification test (NAAT) assay (e.g. real-time PCR or nucleic acid sequencing) performed at a community, hospital, or reference laboratory (the National Microbiology Laboratory or a provincial public health laboratory)
  or
• The detection of at least 1 specific gene target by a validated point-of-care (POC) NAAT that has been deemed acceptable to provide a final result (i.e. does not require confirmatory testing)
  or
• Seroconversion or diagnostic rise (at least 4-fold or greater from baseline) in viral specific antibody titre in serum or plasma using a validated laboratory-based serological assay for SARS-CoV-2

See Laboratory comments for further details.

Probable case

A person who:

• 1. Has symptoms compatible with COVID-19
  • and
  • Had a high-risk exposure with a confirmed COVID-19 case (i.e. close contact) or was exposed to a known cluster^{Footnote 1} or outbreak^{Footnote 2} of COVID-19^{Footnote 3}
    and
    • Has not had a laboratory-based NAAT assay for SARS-CoV-2 completed or the result is inconclusive
      or
    • Had SARS-CoV-2 antibodies detected in a single serum, plasma, or whole blood sample using a validated laboratory-based serological assay for SARS-CoV-2 collected within 4 weeks of symptom onset
• or
• 2. Had a POC NAAT or POC antigen test for SARS-CoV-2 completed and the result is preliminary (presumptive) positive
• or
• 3. Had a validated POC antigen test for SARS-CoV-2 completed and the result is positive

See Clinical features for further details.

See Laboratory comments for further details.

Deceased case

A probable or confirmed COVID-19 case whose death resulted from a clinically compatible illness, unless there is a clear alternative cause of death identified (e.g., trauma, poisoning, drug overdose).

A Medical Officer of Health, relevant public health authority, or coroner may use their discretion when determining if a death was due to COVID-19, and their judgement will supersede the above-mentioned criteria.

A death due to COVID-19 may be attributed when COVID-19 is the cause of death or is a contributing factor.

Resolved case

A case is considered resolved when:

• 1. Fever has resolved without the use of fever reducing medication, and other symptoms have improved^{Footnote 4}
  
  • and
    • If the case is not immunocompromised and does not have severe illness, at least 10 days have passed since symptom onset or, if asymptomatic, the episode date
      or
    • If the case is immunocompromised or has severe illness (e.g. admitted to hospital due to COVID-19), a minimum of 20 days have passed since symptom onset
• or
• 2. Two consecutive validated laboratory-based NAAT tests for SARS-CoV-2 have been collected at least 24 hours apart and both have returned negative

See Comments for further details.

Notes

A Medical Officer of Health or relevant public health authority (which may include other infection prevention and control experts) may use their discretion when determining if a COVID-19 case requires continued public health management, and their judgement will supersede the above-mentioned criteria.

A COVID-19 case which is classified as resolved may still have ongoing clinical indications and symptoms, but should no longer require isolation measures or public health follow up.

If symptom onset date is unavailable or the case is asymptomatic, the earliest of the following dates (i.e. the episode date) could be used as proxy for classification: laboratory specimen collection date, laboratory testing date or reported date. If a case is lost to follow-up or information required for classification is unavailable, the case can be classified as resolved a minimum of 20 days after the initial report.

Reinfection case

Laboratory-based reinfection

A confirmed case that was previously classified as resolved, that has a subsequent infection of SARS-CoV-2 where there is laboratory evidence supporting two different infections.

Laboratory evidence includes:

• Genome sequencing^{Footnote 5} or variant of concern (VOC) screening PCR testing indicates two distinct SARS-CoV-2 infections
• or
• One of the infections was confirmed to be a variant of interest (VOI)/VOC or mutations associated with VOI/VOC based on genome sequencing^{Footnote 5} or VOC screening PCR testing
• and
• The other infection occurred when the VOI/VOC was not circulating in Canada

Note: A viral lineage is a group of viruses defined by a founding variant and its descendants

To determine when VOC/VOI's were circulating in Canada, download the national genomic surveillance dataset as of November 5, 2021 in Excel format (19 KB).

Text description: National genomic surveillance dataset as of November 5, 2021

Variable names and definitions

Lineage:

The name of the identified variant of concern (VOC) or variant of interest (VOI).

WHO label:

The variant naming system as defined by the WHO (currently Greek letter system). Includes parent lineage and all sub-lineages.

Parent lineage:

The parental lineage of the identified VOC or VOI (lineage).

Original designation:

The Canadian defined variant classification - variant of concern (VOC) or variant of interest (VOI). Included as historical reference in the event that a variant from this list has been de-escalated as a VOC/VOI.

First observed collection date (focd):

The earliest collection date in the Canadian genomic surveillance dataset.

Previous focd:

If first observed collection date changes in a subsequent report the first seen collection date from the previous month's report (previous focd) will also be reported. If first observed collection date does not change between reports, the value previous focd will be blank.

Last observed collection date (locd):

The most recent collection date in the Canadian genomic surveillance dataset.

Previous locd:

It is assumed last observed collection date will change frequently with monthly updates and last seen collection date from the previous month (previous locd) will be reported each month. If last observed collection date does not change between reports, the value previous locd will be blank.

National genomic surveillance dataset as of November 5, 2021

Lineage	Who label	Parent lineage	Original designation	First observed collection date	Previous focd	Last observed collection date	Previous locd
B.1.1.7	Alpha	N/A	VOC	2020-11-08	n/a	2021-10-15	n/a
Q.1	Alpha	B.1.1.7	VOC	2021-02-10	n/a	2021-08-10	n/a
Q.3	Alpha	B.1.1.7	VOC	2021-05-08	n/a	2021-05-27	n/a
Q.4	Alpha	B.1.1.7	VOC	2021-01-13	n/a	2021-08-02	n/a
Q.8	Alpha	B.1.1.7	VOC	2021-01-06	n/a	2021-09-01	n/a
B.1.351	Beta	N/A	VOC	2020-12-19	n/a	2021-07-31	n/a
B.1.351.2	Beta	B.1.351	VOC	2021-02-07	n/a	2021-04-22	n/a
B.1.351.3	Beta	B.1.351	VOC	2021-03-02	n/a	2021-07-19	n/a
AY.1	Delta	B.1.617.2	VOC	2021-05-05	n/a	2021-09-24	n/a
AY.2	Delta	B.1.617.2	VOC	2021-06-18	n/a	2021-07-13	n/a
AY.3	Delta	B.1.617.2	VOC	2021-06-26	n/a	2021-10-14	n/a
AY.3.1	Delta	B.1.617.2	VOC	2021-07-31	n/a	2021-10-03	n/a
AY.4	Delta	B.1.617.2	VOC	2021-06-15	n/a	2021-10-08	n/a
AY.4.2	Delta	B.1.617.2	VOC	2021-07-19	n/a	2021-09-30	n/a
AY.4.3	Delta	B.1.617.2	VOC	2021-09-13	n/a	2021-09-13	n/a
AY.4.4	Delta	B.1.617.2	VOC	2021-07-23	n/a	2021-08-11	n/a
AY.4.5	Delta	B.1.617.2	VOC	2021-08-04	n/a	2021-08-04	n/a
AY.5	Delta	B.1.617.2	VOC	2021-07-09	n/a	2021-10-05	n/a
AY.5.2	Delta	B.1.617.2	VOC	2021-05-10	n/a	2021-09-17	n/a
AY.6	Delta	B.1.617.2	VOC	2021-06-30	n/a	2021-09-27	n/a
AY.7.1	Delta	B.1.617.2	VOC	2021-08-26	n/a	2021-09-07	n/a
AY.7.2	Delta	B.1.617.2	VOC	2021-08-07	n/a	2021-08-27	n/a
AY.8	Delta	B.1.617.2	VOC	2021-08-30	n/a	2021-08-30	n/a
AY.9	Delta	B.1.617.2	VOC	2021-07-10	n/a	2021-10-08	n/a
AY.10	Delta	B.1.617.2	VOC	2021-04-13	n/a	2021-10-04	n/a
AY.12	Delta	B.1.617.2	VOC	2021-04-25	n/a	2021-09-22	n/a
AY.13	Delta	B.1.617.2	VOC	2021-08-03	n/a	2021-09-08	n/a
AY.14	Delta	B.1.617.2	VOC	2021-04-20	n/a	2021-09-29	n/a
AY.15	Delta	B.1.617.2	VOC	2021-04-24	n/a	2021-10-09	n/a
AY.16	Delta	B.1.617.2	VOC	2021-04-08	n/a	2021-09-07	n/a
AY.17	Delta	B.1.617.2	VOC	2021-04-14	n/a	2021-08-11	n/a
AY.18	Delta	B.1.617.2	VOC	2021-05-11	n/a	2021-07-30	n/a
AY.19	Delta	B.1.617.2	VOC	2021-06-02	n/a	2021-07-22	n/a
AY.20	Delta	B.1.617.2	VOC	2021-04-28	n/a	2021-10-07	n/a
AY.21	Delta	B.1.617.2	VOC	2021-08-05	n/a	2021-08-08	n/a
AY.23	Delta	B.1.617.2	VOC	2021-04-06	n/a	2021-10-13	n/a
AY.24	Delta	B.1.617.2	VOC	2021-05-08	n/a	2021-09-23	n/a
AY.25	Delta	B.1.617.2	VOC	2021-04-01	n/a	2021-10-16	n/a
AY.26	Delta	B.1.617.2	VOC	2021-05-17	n/a	2021-10-11	n/a
AY.27	Delta	B.1.617.2	VOC	2021-04-16	n/a	2021-10-16	n/a
AY.28	Delta	B.1.617.2	VOC	2021-08-08	n/a	2021-08-30	n/a
AY.29	Delta	B.1.617.2	VOC	2021-08-05	n/a	2021-09-03	n/a
AY.29.1	Delta	B.1.617.2	VOC	2021-08-03	n/a	2021-08-03	n/a
AY.32	Delta	B.1.617.2	VOC	2021-08-03	n/a	2021-08-30	n/a
AY.33	Delta	B.1.617.2	VOC	2021-06-07	n/a	2021-10-05	n/a
AY.34	Delta	B.1.617.2	VOC	2021-06-16	n/a	2021-10-06	n/a
AY.35	Delta	B.1.617.2	VOC	2021-04-16	n/a	2021-08-20	n/a
AY.36	Delta	B.1.617.2	VOC	2021-05-23	n/a	2021-10-08	n/a
AY.37	Delta	B.1.617.2	VOC	2021-04-19	n/a	2021-10-06	n/a
AY.38	Delta	B.1.617.2	VOC	2021-06-04	n/a	2021-07-10	n/a
AY.39	Delta	B.1.617.2	VOC	2021-04-11	n/a	2021-10-12	n/a
AY.39.1	Delta	B.1.617.2	VOC	2021-07-21	n/a	2021-10-12	n/a
AY.40	Delta	B.1.617.2	VOC	2021-05-30	n/a	2021-10-10	n/a
AY.41	Delta	B.1.617.2	VOC	2021-07-19	n/a	2021-09-09	n/a
AY.46	Delta	B.1.617.2	VOC	2021-05-04	n/a	2021-10-08	n/a
AY.46.1	Delta	B.1.617.2	VOC	2021-06-22	n/a	2021-09-26	n/a
AY.46.2	Delta	B.1.617.2	VOC	2021-06-16	n/a	2021-09-11	n/a
AY.46.3	Delta	B.1.617.2	VOC	2021-07-22	n/a	2021-07-22	n/a
AY.46.4	Delta	B.1.617.2	VOC	2021-06-08	n/a	2021-10-07	n/a
AY.46.6	Delta	B.1.617.2	VOC	2021-05-09	n/a	2021-09-16	n/a
AY.47	Delta	B.1.617.2	VOC	2021-04-17	n/a	2021-10-13	n/a
B.1.617.2	Delta	n/a	VOC	2021-03-21	n/a	2021-10-16	n/a
B.1.427	Epsilon	n/a	VOI	2020-12-30	n/a	2021-05-05	n/a
B.1.429	Epsilon	n/a	VOI	2020-12-05	n/a	2021-07-16	n/a
B.1.525	Eta	n/a	VOI	2020-12-14	n/a	2021-07-12	n/a
P.1	Gamma	n/a	VOC	2021-02-19	n/a	2021-09-07	n/a
P.1.2	Gamma	P.1	VOC	2021-08-10	n/a	2021-08-10	n/a
P.1.7	Gamma	P.1	VOC	2021-07-27	n/a	2021-08-01	n/a
P.1.10	Gamma	P.1	VOC	2021-02-16	n/a	2021-06-04	n/a
P.1.12	Gamma	P.1	VOC	2021-02-23	n/a	2021-10-07	n/a
P.1.14	Gamma	P.1	VOC	2021-01-12	n/a	2021-09-18	n/a
P.1.15	Gamma	P.1	VOC	2021-04-10	n/a	2021-06-27	n/a
P.1.16	Gamma	P.1	VOC	2021-03-21	n/a	2021-03-23	n/a
P.1.17	Gamma	P.1	VOC	2021-03-22	n/a	2021-07-30	n/a
B.1.526	Iota	n/a	VOI	2021-01-23	n/a	2021-08-09	n/a
B.1.617.1	Kappa	n/a	VOI	2021-03-02	n/a	2021-05-31	n/a
C.37	Lambda	n/a	VOI	2021-02-15	n/a	2021-08-10	n/a
B.1.621	Mu	n/a	VOI	2021-03-11	n/a	2021-09-09	n/a
B.1.621.1	Mu	n/a	VOI	2021-05-10	n/a	2021-09-10	n/a
P.3	Theta	n/a	VOI	2021-02-09	n/a	2021-07-29	n/a
P.2	Zeta	n/a	VOI	2020-11-24	n/a	2021-05-07	n/a
AZ.1	n/a	B.1.1.318	VOI	2021-02-19	n/a	2021-07-29	n/a
AZ.2	n/a	B.1.1.318	VOI	2021-06-03	n/a	2021-06-03	n/a
AZ.5	n/a	B.1.1.318	VOI	2021-03-01	n/a	2021-03-09	n/a
AZ.6	n/a	B.1.1.318	VOI	2021-02-20	n/a	2021-06-14	n/a
B.1.1.318	n/a	n/a	VOI	2021-02-06	n/a	2021-08-18	n/a
B.1.617.3	n/a	n/a	VOI	2021-03-31	n/a	2021-04-21	n/a

Notes

• Data are extracted monthly. These data were extracted from national genomic surveillance dataset on November 5, 2021; PANGO lineage definitions from version posted October 18, 2021.
• Data comes from the national genomic surveillance dataset (doesn't include data from the national case database). These results can't be linked to case data including severity indicators or case demographics.
• Dates may be updated retrospectively due to re-classification of samples with updated PANGO lineage information or retrospective testing of samples.
• WHO name classification and parent lineage will be reported as applicable. If a sub-lineage is subsequently determined to be a separate VOI or VOC (apart from the initial parent lineage) these 2 categories will be updated.

Time-based reinfection

A confirmed case that was previously classified as resolved* that has a subsequent confirmed infection of SARS-CoV-2 at least 90 days after the previous infection using episode date**

and

Does not meet the laboratory-based reinfection case definition

Notes

*Public health or clinical judgement should be used to rule out situations where a possible reinfection has been attributed to prolonged viral shedding (i.e., consider if prolonged viral shedding is more likely than reinfection).

** If case is symptomatic, then episode date uses symptom onset date and if symptom onset date is unavailable or the case is asymptomatic, then the earliest of the following dates could be used as proxy for classification: laboratory specimen collection date, laboratory testing date or reported date.

The judgement of a Medical Officer of Health or relevant public health authority may be used to identify reinfection cases based on new exposures or symptoms if the above criteria are not met.

Laboratory comments

Laboratory tests are evolving for this emerging pathogen, and laboratory testing recommendations will change as new assays are developed and validated. Assays that have been licensed by Health Canada are preferred.

Any case classified as probable based on an epidemiological link, which subsequently tests negative for the SARS-CoV-2 virus should no longer be classified as a case. Exceptions may be made for negative results from a compromised sample or if NAAT testing is delayed (e.g. >10 to 14 days following symptom onset), whereby such persons remain as probable cases.

Laboratory-based tests

NAATs must be validated for SARS-CoV-2 detection.

An inconclusive result on a real-time PCR assay is defined as an indeterminate result on a single or multiple real-time PCR target(s) without sequencing confirmation, or a positive result from an assay for which limited performance data are available.

An indeterminate result on a real-time PCR assay is defined as a late amplification signal in a real-time PCR reaction at a predetermined high cycle threshold value. This may be due to low viral target quantity in the clinical specimen approaching the limit of detection (LOD) of the assay, or may represent nonspecific reactivity (false signal) in the specimen. When clinically relevant, indeterminate samples should be investigated further in the laboratory (e.g. by testing for an alternate gene target using a validated real-time PCR or nucleic acid sequencing that is equally or more sensitive than the initial assay or method used) or by collection and testing of another sample from the patient.

Point-of-care tests

Local validation and provincial (and/or federal) evaluation is required for all POC tests (molecular and/or antigen-based), with the reference testing done in a licensed/accredited laboratory. If validation is not completed prior to clinical use at an individual location, a simultaneous sample should be obtained from the individual and tested using a validated laboratory-based NAAT at a licensed/accredited laboratory until at least 10 to 20 positives and 30 to 50 negatives are assessed with the POC test and acceptable performance data are obtained. If discrepant results from simultaneous testing are obtained, a case should be re-classified based on the results from the laboratory-based NAAT testing.

If reporting occurs prior to completion of validation and jurisdictional evaluation, or testing occurs in a non-licensed setting, a positive POC result should be considered a preliminary positive (also referred to as presumptive positive in some jurisdictions) and the case should be classified as a probable case while awaiting results of the validated laboratory-based NAAT.

If no laboratory-based NAAT test result is obtained (or repeat specimen collected >24 hours after the preliminary POC collection and laboratory-based result is negative), the case status should remain as probable.

Each jurisdiction may decide if/when a positive or negative POC NAAT test can be considered a confirmed final positive or negative result, respectively, without the need for confirmation in a licensed/accredited laboratory. Acceptable performance is based on a jurisdiction's own evaluation and/or evaluations conducted by interprovincial/national partners, and would likely include analysis of initial data accumulated for the specific assay. Due to differing performance among different assays using the same technology, this analysis is recommended for each individual POC NAAT assay in use.

Specimens with preliminary (or presumptive) positive or final positive POC antigen test results require confirmation with a laboratory-based NAAT. At this time, such patients are considered probable cases while awaiting NAAT test results. This recommendation may change as more data are accumulated on POC antigen test performance in Canada.

Serology tests

SARS-CoV-2 antibody testing must be conducted using a validated assay by a licensed/accredited laboratory. Currently, SARS-CoV-2 IgM and serology POC tests are not widely available and are not recommended for use at this time due to a lack of adequate performance data. A diagnostic rise in antibody titre can be established using paired acute and convalescent sera taken 2 to 4 weeks apart and tested by an end-point enzyme immunoassay (EIA), quantitative EIA, or neutralizing antibody titres (e.g. plaque reduction neutralization (PRN)); however, these assays are not yet widely available and are not currently recommended for routine diagnostic testing. Since an individual can have detectable antibody levels for many months, a single positive serology result (i.e. no documented seroconversion or diagnostic rise) may not reflect recent infection.

In populations with low disease prevalence (<5%) or in individuals with a low pre-test probability, there is a risk of false positive results, even with an assay with high performance characteristics. In such cases, an orthogonal testing algorithm may be considered to increase the positive predictive value (PPV). In an effective orthogonal algorithm, a specimen that tests positive initially is tested with a second unique assay (i.e. uses a different antigen).

At this time, serology testing should not be used for classification of cases who have been previously diagnosed with COVID-19 or who have received a SARS-CoV-2 vaccination. SARS-CoV-2 serology tests should not be used for screening or the routine diagnosis of acute infection. It may be considered as an adjunct to SARS-CoV-2 NAAT in individuals with compatible symptoms who present late and therefore may test negative, and in the diagnosis of multisystem inflammatory syndrome in children (MIS-C) and multisystem inflammatory syndrome in adults (MIS-A).

Clinical features

COVID-19 presents with varied clinical features, and symptoms can vary from person to person, and among different age groups. Each province and territory has its own list of clinical presentation and these can be found on provincial and territorial health ministry websites.

Please refer to the Public Health Agency of Canada's COVID-19 signs, symptoms and severity of disease: A clinician guide for a comprehensive list of common and infrequently reported COVID-19 symptoms.

ICD code(s)

• U07.1 COVID-19, virus identified
• U07.2 COVID-19, virus not identified
• U07.3 Multisystem inflammatory syndrome associated with COVID-19
• U07.4 Post COVID-19 condition as diagnosis type (3)/other problem
• U07.5 Personal history of COVID-19 as diagnosis type (3)/other problem

Comments

The resolved case definition was developed for surveillance purposes and is not related to clinical management of cases. It is based on existing evidence to determine when a case of COVID-19 is no longer infectious or capable of transmitting the SARS-CoV-2 virus. Some cases may remain infectious beyond the time period specified, and the judgement of a Medical Officer of Health or relevant public health authority supersedes the specified criteria. Classification of cases as resolved by laboratory testing is not routinely recommended and should be used with discretion.

Previous case definitions

Previous versions of the COVID-19 case definition are available upon request. Please email COVID19Surveillance@canada.ca to request a copy or for more information.