Monkeypox Virus

Testing Indications

This document provides testing information for Monkeypox virus (Poxviridae family, Orthopoxvirus genus). For testing information of poxviruses other than Monkeypox virus and Variola virus, please refer to the following link:

General Background:
Monkeypox is a viral illness endemic to parts of Central and West Africa. It is spread to people through direct contact with the bodily fluids or lesions of infected animals or people, via respiratory droplets from an infected person, or from mother to fetus. Symptoms include fever, headache, swollen lymph nodes, and lethargy, followed by the development of a rash (usually 1 to 3 days after fever onset). 

Since May 20, 2022, several countries in which monkeypox is not endemic, including Canada, have documented clusters of cases of Monkeypox virus infection. All infections characterized so far among the recent clusters have been due to the West African clade.

Who to test:
Individuals with a compatible clinical illness where monkeypox is suspected should be tested. Consult with Public Health Ontario if you have any questions regarding testing indications, specimen collection or transportation.

Specimen Collection and Handling

Specimen Requirements

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

Monkeypox Virus

Lesion fluid, crust material or scab2

Not Applicable

Sterile tube/ container or Virus Culture Collection kit order#: 390081

Monkeypox Virus

Swab of lesion2,4

Not Applicable

Place swab in a sterile tube/ container6 or Virus Culture Collection kit order#: 390081

Monkeypox Virus

Nasopharyngeal and/or throat swab3,4

Particularly useful specimens if testing during the prodrome (e.g. pre-rash in febrile patients who are contacts of cases, patients with macular or papular rash) – and may be collected on all patients

Sterile tube/ container or Virus Culture Collection kit order#: 390081

Monkeypox Virus


≥0.5 ml

Red top or serum separator tubes

Monkeypox Virus

Cerebrospinal fluid (CSF)

≥0.5 ml may be submitted on patients with meningitis/encephalitis

Sterile tube /container

Monkeypox Virus


50 ml 

Sterile container

Monkeypox Virus

Frozen tissues/ Formalin-fixed, or paraffin embedded tissues Entire blocks, or four to six 10-micron block sections Sterile container (clearly label if formalin fixed)

Submission and Collection Notes


Approval for testing and notification of specimen submission is not required. Contact PHO Customer Service (416-235-6556/1-877-604-4567) or the on-call Duty Officer (416-605-3113) after hours if you wish to consult prior to sample collection and shipment.


Submit a maximum of three skin lesion specimens per patient – based on PHO’s laboratory data, detection sensitivity from individual skin specimens is high (approximately 90%) in patients with laboratory-confirmed monkeypox infection.


Nasopharyngeal/throat swabs and blood specimens are generally not recommended in patients who have skin lesions that can be swabbed, or have skin lesion material that can be submitted for testing (e.g. scab). Skin lesions usually have higher viral loads, therefore skin swabs or lesion material are more sensitive (approximately 90%) for Monkeypox virus detection. However, blood should always be submitted along with a nasopharyngeal (NP) swab or throat swab on patients suspected of Monkeypox virus infection who do not have a skin rash (e.g. a close contact of a case with a febrile illness but no rash), or their skin rash can’t be reliably swabbed (e.g. macular or papular rash only).


Testing for herpesviruses (e.g. Herpes simplex, Varicella) and Enterovirus may be ordered on the same specimens being tested for Monkeypox – these will be performed once Monkeypox testing is completed. If any other tests are required, submit additional specimens, as specimens submitted for Monkeypox virus testing will not be routinely processed for additional tests besides herpesviruses and Enterovirus.
Note: all other tests ordered for a patient being investigated for monkeypox, including those already received at PHO, will be put on hold until Monkeypox virus testing is completed.


Swabs from lesions and nasopharyngeal specimens submitted from pediatric patients (<18 years of age) will be tested for Enterovirus in addition to Monkeypox. Enterovirus PCR may be ordered on the requisition for adult patients when submitting swabs from skin, lesions and nasopharyngeal specimens.


Swab samples can be collected as a dry swab or added to a minimum volume of viral transport media (e.g. 1ml) to avoid excessive dilution of the sample. In situations where this collection method is not possible, utilization of currently available virus culture collection kits is accepted.


Extracted nucleic acid (minimum volume 50 ul) may be submitted for Monkeypox testing provided that the specimen was heat inactivated for 60 minutes at 60°C prior to off-board lysis. Please indicate (i) the heat treatment duration and temperature and (ii) the extraction method/kit used on the requisition when extracted nucleic acid is submitted.


All specimens from a patient being investigated for monkeypox, including specimens submitted for other tests, should indicate on the requisition that this patient is suspected of having monkeypox.


Urine is not considered a routine specimen for Monkeypox testing but may be considered for collection. Performance characteristics for this specimen type are not well understood at this time.

Preparation Prior to Transport

Label the specimen with the patient’s full name, date of collection and one other unique identifier such as the patient’s date of birth or Health Card Number. 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.

Specimens should be stored at 2-8°C following collection and shipped to the PHO’s Laboratory on ice packs. If transport will be delayed more than 72 hours, specimens should be frozen at -70°C or below and shipped on dry ice. Formalin-fixed specimens can be transported and stored at room temperature.

Effective June 2, 2022, clinical specimens from patients undergoing Monkeypox testing have been temporarily reclassified as UN3373 Biological Substance, Category B for land transport. The exemption applies to transportation by land (in a road vehicle, railway vehicle, vessel, between two points in Canada). In addition to the routine Category B requirement, the outer packaging must be marked, on a contrasting background, with “TU 0886”, “Temporary Certificate – TU 0886” or “Certificat Temporaire – TU 0886”. For full details on packaging and transporting, see the Temporary Certificate TU 0886.

Note: At this time, specimens requiring air transport still require Category A packaging and transportation.

Special Instructions

Complete all fields of the General Test Requisition, including:

  • Requesting health care provider (CPSO number)
  • Complete mailing address
  • Telephone and fax number
  • Patient’s full name, date of birth, and health card number where applicable (must match specimen label)
  • Test(s) requested and indication for testing
  • Clinical information including symptom onset date or if asymptomatic
  • Specimen type and collection

If available please also provide

  • Travel history (if applicable)
  • Exposure history and details (include smallpox vaccination history if applicable)

Failure to complete all requisition fields appropriately may result in rejection or testing delay.

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Testing is performed daily Monday to Sunday.

Monkeypox virus PCR results will be issued up to 2 days from receipt at PHO’s Laboratory testing site in Toronto.  


Results are reported to the ordering physician or health care provider as indicated on the requisition. At this time all Monkeypox-related testing results are reported to the Medical Officer of Health.

Test Methods

Monkeypox virus PCR testing at PHO’s Laboratory is a nucleic acid amplification test (NAAT) that uses a real-time multiplex PCR assay to detect 2 targets - a generic Monkeypox virus (panmonkeypox) target that detects both Monkeypox virus clades [West African and Congo Basin (Central African)] and a target which only detects the West African clade. This is a laboratory developed test endorsed by the World Health Organization, which has been verified at PHO’s Laboratory for clinical testing.

Orthopoxvirus testing at PHO’s Laboratory is based on molecular nucleic acid amplification testing (NAAT) using real-time PCR for detection of viruses in the Orthopoxvirus genus (e.g. Monkeypox, Cowpox, Vaccinia, Camelpox, Smallpox).  This test uses a Canadian Laboratory Response Network protocol originally developed for environmental testing which has been validated at PHO’s Laboratory for clinical testing, and final reporting of all results.

Note: Monkeypox serology and antigen testing are not being offered, nor are they currently available or recommended in Canada.


As of June 23, 2022, PHO’s Laboratory routinely tests all specimens requesting Monkeypox testing using the Monkeypox PCR assay. Orthopoxvirus PCR will only be used in circumstances when the Monkeypox PCR assay results require further clarification. All Monkeypox virus-related PCR results from PHO’s Laboratory will be considered final. Specimens for which only a SINGLE Monkeypox target is detected and indeterminate/not detected for the second target, or indeterminate for both targets will undergo review and further investigation unless they occur in patients for whom there were other specimens submitted and in which Monkeypox virus was detected.

Invalid Monkeypox PCR results from testing conducted at PHO’s Laboratory are also reported as final, in which case submission of another specimen is recommended if clinically indicated.

Note: Monkeypox virus is the only virus belonging to the Orthopoxvirus genus recently detected in Canada. Other Orthopoxvirus known to infect humans butnot currently circulating in Canada include Variola (eradicated worldwide), Vaccinia (component of the smallpox vaccine, rare post-vaccine transmission), Cowpox (rare zoonotic infection), and Camelpox (rare zoonotic infection).


Monkeypox virus PCR Test Result Interpretation

Monkeypox virus (panmonkeypox)@ West African Clade Monkeypox virus Interpretation on report Comments
Not detected Not detected Monkeypox virus DNA NOT detected by real-time PCR Monkeypox virus is not detected.
Detected Detected Monkeypox virus (West African clade) DNA DETECTED by real-time PCR. Monkeypox virus is detected.
Detected Not detected Monkeypox virus (panmonkeypox) DNA target DETECTED; West African clade Monkeypox virus DNA target NOT DETECTED by real-time PCR Monkeypox virus is detected.
Not detected Detected Monkeypox virus (panmonkeypox) DNA target NOT DETECTED; West African clade Monkeypox virus DNA target DETECTED by real-time PCR See footnote.*
Detected Indeterminate# Monkeypox virus (panmonkeypox) DNA target DETECTED; West African clade Monkeypox virus DNA target INDETERMINATE by real-time PCR Monkeypox virus is detected. See footnote.*
Indeterminate# Detected Monkeypox virus (panmonkeypox) DNA target INDETERMINATE; West African clade Monkeypox virus DNA target DETECTED by real-time PCR See footnote.*
Indeterminate# Not detected Monkeypox virus (panmonkeypox) DNA target INDETERMINATE; West African clade Monkeypox virus DNA target NOT DETECTED by real-time PCR See footnote.*
Not detected Indeterminate# Monkeypox virus (panmonkeypox) DNA target NOT DETECTED; West African clade Monkeypox virus DNA target INDETERMINATE by real-time PCR See footnote.*
Indeterminate# Indeterminate# Monkeypox virus (panmonkeypox) DNA target INDETERMINATE; West African clade Monkeypox virus DNA target INDETERMINATE by real-time PCR See footnote.*
Invalid Invalid Monkeypox virus DNA PCR test INVALID Invalid

@Detection of the generic Monkeypox virus (panmonkeypox) PCR target is sufficient for laboratory confirmation of Monkeypox virus infection.

*Patients who have specimen(s) with one of the two Monkeypox virus targets detected, or one or both targets indeterminate, and no other specimens with Monkeypox virus detected, will have further testing done by either Orthopoxvirus PCR or gene sequencing to confirm the presence of Monkeypox virus.

#The indeterminate range for this assay includes cycle threshold (Ct) values from 38.01 to 39.99.

In cases where Orthopoxvirus PCR test is performed after Monkeypox virus PCR testing is complete, result interpretation is outlined in the table below.

Orthopoxvirus Target Gene Cycle Threshold (Ct)# Result Interpretation Additional Notes
Ct ≤ 40 Detected Detection of Orthopoxvirus by real-time PCR. Monkeypox virus is the only virus belonging to the Orthopoxvirus genus recently detected in Canada.
Ct between 40.01 and 44.99 Indeterminate Orthopoxvirus DNA indeterminate by real-time PCR. An indeterminate result may be due to 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.
Ct ≥ 45 with valid internal control gene amplification Not Detected Orthopoxvirus DNA NOT DETECTED by real-time PCR Negative Orthopoxvirus PCR results are Monkeypox virus negative and final.
Ct ≥ 45 with no detection of internal control gene amplification Invalid Orthopoxvirus real-time PCR result is invalid. Test is invalid due to failed amplification of the extraction control. Amplification failure may be due to inadequate specimen content, extraction failure, or PCR inhibition. Submit another specimen for testing if clinically indicated.

For an explanation of cycle threshold values, see An Overview of Cycle Threshold Values and their Role in SARS-CoV-2 Real-Time PCR Test Interpretation.

Updated 23 June 2022