Language Selection


Molecular Detection and Genotyping

<<Return to Laboratory

Accredited by the Standards Council of Canada to Laboratory no. 594 (ISO/IEC 17025)

Requisition Forms

Reference Details


Molecular detection of the rubella virus by real-time RT-PCR and genotyping of positive specimens.

Test Category:
Molecular Detection and Genotyping
Rubella virus
Illnesses and Diseases:
  • Rubella (German measles)
  • Congenital rubella infection
  • Congenital rubella syndrome

Nasopharyngeal (NP), throat swabs or urine collected as soon as possible after rash onset (within 7 days). Note: specimens collected later will still be accepted however the assay sensitivity will not be optimal. For CRI/CRS cases, collect urine, NP or throat swabs within the first few months after birth. Viral isolates may also be sent. Other specimen types may be accepted; please contact the Viral Exanthemata laboratory prior to submission.

Collection Method:

Collect 50 mL (minimum 10 mL) of urine in sterile container. For swabs, use sterile swabs approved for virus isolation to swab the throat or nasal passages to collect epithelial cells. Place swabs in 2-3 mL viral transport medium (VTM) for a minimum of 1 hour. For viral isolate, collect infected cells and media and submit 1 mL.

Specimen Processing, Storage and Shipping:

Process urine by centrifuging at 500 x g for 10 minutes, preferably at 4°C. Resuspend the sediment in 2 mL VTM. For small volumes of urine (CRI/CRS cases), resuspend sediment in a minimum of 0.5 mL of VTM.  For swab specimens, remove the swab. For all specimens, store at 4°C and ship on wet ice for arrival at the NML within 48 hours of collection. Otherwise, freeze at -70°C and ship frozen on dry ice. Do not freeze unprocessed urine. Viral Isolates should be shipped frozen (-70°C) on dry ice.

Transportation of Dangerous Goods:

Shipping of specimens shall be done by a TDG certified individual in accordance with TDG regulations. For additional information regarding classification of specimens for the purposes of shipping, consult either Part 2 Appendix 3 of the TDG Regulations or section 3.6.2 of the IATA Dangerous Goods Regulations as applicable.


Patient Criteria:
  1. Suspected cases of rubella (typically with fever, rash and at least one of the following: arthralgia/ arthritis or lymphadenopathy or conjunctivitis) or history of exposure to a confirmed rubella case.
  2. Suspected congenital rubella infection (CRI) / congential rubella syndrome (CRS).
Accompanying Documentation:

Completed Measles, Mumps, and Rubella requisition.  Include date of rash onset, date of last rubella vaccination (if recent), travel history, rubella exposure history, and/or MARS identifier (Measles, Rubella and CRS/CRI Surveillance, CNPHI) as available.


It is important to provide a complete patient history (including travel) for accurate genotype surveillance. Viral sequences (the 739 nucleotides of the E1 glycoprotein) will be submitted to the WHO rubella sequence database (RubeNS, 1) and may be published on GenBank ( Additional regions or the whole genome may also be sequenced for surveillance purposes.  The NML is a WHO/PAHO accredited Measles and Rubella Regional Reference Laboratory.

Methods and Interpretation of Results:

Extracted RNA from samples is amplified by real-time RT-PCR targeting the rubella E1 and p150 genes (4).  A positive rubella RT-PCR result is laboratory confirmation of rubella virus. A portion of the E1 gene of positive samples is amplified by conventional RT-PCR and a WHO standardised region of the E1 glycoprotein (739 nucleotides) is sequenced to determine the genotype of the rubella virus (1-3).

Turnaround Time:

Detection: 7 calendar days. Genotyping: 21 calendar days. Stat testing available upon request.

Phone #: (204) 789-6024 or (204) 789-7055
Fax: (204) 318-2222
  1. World Health Organization. Rubella virus nomenclature update: 2013. WER.  2013;88:337-348.
  2. World Health Organization.  Standardization of the nomenclature for genetic characteristics of wildtype rubella viruses. WER. 2005:80:126-132.
  3. World Health Organization. Manual for the laboratory diagnosis of measles and rubella virus infection. Third edition. 2018. Available at
  4. Schulz H, Neale M, Zubach V, Severini A, Hiebert J. Development of a rapid, internally controlled, two target, real-time RT-PCR for detection of rubella virus. J Virol Methods. 2022 May;303:114500. doi: 10.1016/j.jviromet.2022.114500. Epub 2022 Feb 22. PMID: 35217102.