Molecular Detection of Variola virus

PCR amplification of Variola virus specific genome.

• Smallpox

Lesion fluid and/or crust, scab, skin material; swabs; CSF/serum from encephalitic patients, CSF, other bodily fluids (minimum sample 0.5 mL) and fresh frozen tissues. Formalin-fixed or paraffin-embedded tissues.

Collect lesion or crust material, scabs, and swabs in a sterile 1.5-2.0 mL tube, a dry swab is recommended, transport media will be accepted if indicated on requisition.

CSF and other bodily fluids: Collect in sterile 1.5-2.0 mL screw cap tubes.

Serum: Collect in serum (red top) or serum separator tubes (SST), centrifugation of serum tubes is not needed and should be avoided.

Tissues: Fresh frozen tissues should be placed in plastic containers. Tissues that are formalin-fixed should also be sent in plastic containers and clearly identified as being in formalin. Paraffin-embedded tissues can be sent as entire blocks or four to six 10 uM sections in a plastic tube or vial.

Store samples in refrigerator or frozen until being shipped for testing.  Serum can be shipped refrigerated or frozen. Tissues should be shipped frozen. Ship frozen specimens on dry ice and refrigerated specimens on wet ice. Formalin-fixed samples can be sent at room temperature.

Shipping of samples suspected of containing Risk Group 4 pathogens shall be done by a TDG certified individual in accordance with TDG regulations. If applicable, activate Emergency Response Assistance Plan (ERAP) 24 hours prior to shipping. To activate an ERAP, please click on the link below to access the transport flowchart for Risk Group 4 pathogens or call 204-999-7996 (available 24/7) for assistance.

Patient must be symptomatic with characteristic smallpox papules.

Completed Special Pathogens requisition including sender name, address and telephone number. Patient information including name or identifier, date of birth, and all relevant patient history including clinical diagnosis, underlying diseases, exposure risk and travel history. Indicate type of specimen collected and all specimen information. Select all required tests. If possible, attach lab results that have already been done at local or provincial laboratories.

Variola virus is extinct in nature and an active case would be highly unusual. Contact Special Pathogens prior to submission of sample to ensure appropriate shipping documentation is generated. Generation of request will require activation of Canadian Smallpox Contingency Plan.

PCR test is validated.

For diagnosis of Variola virus infection to be confirmed, one or more of the following diagnostic markers must be positive: (i) Variola virus DNA by PCR, and (ii) isolation of Variola virus.

2 calendar days.

Pathogen Safety Data Sheets: Infectious Substances – Variola virus

National case definition: Smallpox

Smallpox