Measles – Diagnostic – PCR

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Background:

This page provides diagnostic polymerase chain reaction (PCR) testing information for Measles at Public Health Ontario (PHO). For information regarding other testing options, including Cerebral Spinal Fluid (CSF) for Subacute sclerosing panencephalitis (SSPE) refer to:

Measles Serology TIS

Updates:

Effective August 5, 2025, a new measles multiplex PCR assay will be implemented at PHO’s Toronto laboratory, combining measles diagnostic PCR and vaccine strain typing in a single assay. PHO’s regional laboratory sites will continue to use Measles PCR standalone testing and send positives to Toronto for vaccine strain testing. Refer to Method and Algorithm section for details.

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Testing Indications

Measles PCR is a diagnostic test for the detection of viral RNA in clinical specimens collected from patients suspected of having Measles and is useful during the early phase of the disease following symptom onset.

Measles molecular testing (PCR) is the preferred testing method during periods of significant community transmission such as the current multi-jurisdictional outbreak in Ontario. Measles serology testing may provide additional diagnostic value however, blood collection may cause additional health care visits and community exposure and therefore is not mandated. The decision to collect blood for serology remains at the discretion of the health care provider or public health unit.

Testing for immune status (IgG) is not routinely recommended for unvaccinated, under-vaccinated individuals, and unknown vaccination status. Measles-containing vaccine should be offered as the ideal protective measure in accordance with Canadian Immunization Guide.

For suspected cases of Measles, contact your local public health unit (PHU) prior to collecting specimens.

Acceptance/Rejection Criteria

Specimens received in incorrect containers or expired kits will be rejected.

Specimen Collection and Handling

Specimen Requirements

Test Requested	Required Requisition(s)	Specimen Type	Minimum Volume	Collection Kit
Measles Virus Diagnostic PCR	General Test Requisition	Nasopharyngeal swab^3,4	1 swab in transport media contained in kit	Nasopharyngeal Collection Kit for Viral PCR order#: 390082
Measles Virus Diagnostic PCR	General Test Requisition	Throat swab^3,5	1 swab in transport media contained in kit	Large Swab Throat Collection Kit for Viral PCR order#: 390081
Measles Virus Diagnostic PCR	General Test Requisition	Urine^3,6	Minimum volume 10mL	Sterile container

Submission and Collection Notes

Complete all fields of the requisition form, including:

Test(s) requests and indications for testing
Patient setting
Clinical information (symptom and symptom onset), MMR/MMRV vaccination status and travel history (including date of travel/return).

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.

For diagnosis of symptomatic patients, collect either a nasopharyngeal (NP) swab or throat swab for PCR testing. Collecting a urine specimen along with an NP/throat swab may improve sensitivity of testing. Collection of blood specimen for measles serology testing may add a diagnostic value in certain clinical scenarios. See next section for the recommended timing of specimen collection.

Refer to the Nasopharyngeal Specimen Collection Instructions for collecting nasopharyngeal swab specimens.

Refer to the Throat Specimen Collection Instructions for collecting throat swab specimens.

Urine specimen collected in other media (i.e. CTNG specimen container) will be rejected for testing.

For submission of other specimen types please contact PHO’s Laboratory Customer Service Centre at 416-235-6556 or 1-877-604-4567.

Timing of Specimen Collection

Nasopharyngeal swab or aspirate and/or a throat swab should be collected within 7 days of rash onset.

Urine should be collected within 14 days of rash onset and submitted in a sterile container.

In certain situations, such as when there is a high index of suspicion for measles (e.g. compatible illness in a returned traveler or contact of a laboratory confirmed case), it may be warranted to test beyond the above time periods when specimens could not be collected earlier in the illness. This can be discussed with PHO’s laboratory on a case-by-case basis.

Testing of individuals exhibiting prodromal symptoms without a rash, who have a strong epidemiologic link to a confirmed case, is acceptable. Result should be interpreted with caution.

Storage and Transport

Place specimen in biohazard bag and seal. Specimens should be stored at stored at 2-8°C within 72 hours of collection and shipped to PHO’s laboratory on ice packs. If longer storage/transit time is anticipated, specimens should be frozen at -70°C or lower and transported on dry ice.

All clinical specimens must be shipped in accordance to the Transportation of Dangerous Good Act.

To assist with laboratory workflow and identifying specimens for priority testing, Measles specimens should be sent separate from routine specimens and mark STAT on the outside of the package.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Test	Turnaround Time	Test Location	Frequency	Sample receipt cut-offs*
Measles Multiplex PCR	Up to 3 business days from receipt at PHO Laboratory	Toronto	Monday to Sunday	11AM
Measles standalone PCR	Up to 3 business days from receipt at PHO Laboratory	Ottawa Kingston Timmins	Monday to Saturday	11AM
Measles standalone PCR	Up to 3 business days from receipt at PHO Laboratory	Thunder Bay Hamilton London	Monday to Friday	11AM^a
Measles Vaccine Genotype PCR	Up to 3 business days after the confirmation of Measles PCR positive (by Measles PCR standalone assay)	Toronto	Monday to Sunday	N/A
Measles full Genotype (NML)	Up to 21 days from the receipt at NML	National Microbiology Laboratory	N/A	N/A

*Samples must arrive at PHO’s laboratory at the time listed in this column to be included in the same day testing, samples that arrive later than time listed here will be tested on the next available run.

^aSamples received after 11am on Friday in London, Hamilton and Thunder Bay will be directed to Toronto for testing on Saturday.

STAT and Critical Specimens Testing

Refer to the above cut-off hours in the ‘Frequency and turnaround time’ section for priority specimen testing.

Critical measles testing for vulnerable populations/patient settings may be available outside of regular hours upon special request and approval from a PHO microbiologist. For consultation, please contact PHO’s Laboratory Customer Service at 416-235-6556 / 1-877-604-4567, or after-hours, contact the Duty Officer at 416-605-3113.

Test Methods

Measles multiplex is performed using polymerase chain reaction (PCR) – Laboratory developed test validated at PHO’s laboratory; not Health Canada approved. This assay detects measles targets (H1, F1 and N3) and measles vaccine strain.

Measles standalone is performed using polymerase chain reaction (PCR) – Laboratory developed test validated at PHO’s laboratory; not Health Canada approved. This assay detects measles targets (H1, F1 and N3).

Measles Vaccine Genotype is performed using polymerase chain reaction (PCR) – Laboratory developed test validated at PHO’s laboratory; not Health Canada approved. This assay detects the measles vaccine strain only.

Algorithm

The new measles multiplex PCR test detects 3 viral targets (H1, F1 and N3) of the measles virus and confirms if it is measles vaccine strain (Genotype A). All specimens in which one or more of the Measles viral targets are detected, and the in-house measles vaccine PCR is not detected (implying a wild-type virus), will be referred to the NML for full genotyping. The multiplex test is performed in Toronto only.

Regional sites (Hamilton, London, Ottawa, Kingston, Thunder Bay and Timmins) will continue to use the measles standalone PCR. All specimens that are detected by the measles PCR will be sent to Toronto for testing by the in-house measles vaccine genotype PCR. Specimens that are not detected by the in-house measles vaccine genotype PCR will be referred to the NML for full genotyping.

Due to the recent increase in measles cases, the NML has implemented a triage and selection process for prioritizing measles genotyping based on:

Cases with no know epidemiological link (unknown source/acquisition)
Travel related cases
Hospitalized cases
First 5-10 cases in a new jurisdiction
Random sampling on a proportion of the submitted specimens linked to the current outbreak

(Note, for specimens not selected as part of the sampling, NML will issue a cancellation report for genotyping result.)

Refer to the NML for more information on measles genotyping.

Interpretation

Results for both the multiplex and standalone assays will be reported as DETECTED, NOT DETECTED, INDETERMINATE, or INVALID for each of the three measles virus targets and measles vaccine target.

DETECTED indicates that this target was detected in the specimen.
NOT DETECTED indicates that this target was not detected in the specimen. Note: a negative result does NOT exclude the possible presence of measles virus in the patient.
INDETERMINATE results may be due to a low level of target genetic material in the specimen, inadequate specimen content, or a non-specific signal. Please submit another specimen for testing if clinically indicated.
INVALID results indicates failed amplification of the extraction control which may be due to inadequate specimen content, extraction failure, or PCR inhibition. It is recommended to resubmit another specimen for testing if clinically indicated.
This result must be interpreted within the context of the clinical history and epidemiological information.

Results will be reported as DETECTED/NOT DETECTED for measles vaccine genotype PCR.

Reporting

Results are reported to the physician, or authorized health care provider (General O. Reg 45/22, s.18) or submitter as indicated on the requisition.

Specimens that are positive for Measles are reported to the Medical Officer of Health as per Health Protection and Promotion Act.

Information for Health Care Providers

NOTE: Measles: Information for Health Care Providers

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Microbiologie et des services de laboratoire

customerservicecentre@oahpp.ca

Mis à jour le 5 août 2025