Molecular Detection and Genotyping<<Return to Laboratory
Accredited by the Standards Council of Canada to Laboratory no. 594 - CAN-P-4E (ISO/IEC 17025)
Molecular detection of the rubella virus by real-time RT-PCR and genotyping of positive specimens.
- Rubella (German measles)
- Congenital rubella infection
- Congenital rubella syndrome
Nasopharyngeal (NP), throat swabs or urine collected as soon as possible after rash onset (within 5 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 for research purposes; please contact the Viral Exanthemata laboratory prior to submission.
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.
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.
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.
For additional guidance on the transport of infectious substances in other languages, please click on the link below.
- 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.
- Suspected congenital rubella infection (CRI) / congential rubella syndrome (CRS).
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 (https://www.ncbi.nlm.nih.gov/genbank/). The NML is a WHO/PAHO accredited Measles and Rubella Regional Reference Laboratory.
Extracted RNA from samples is amplified by for the rubella E1 and p150 genes (4,5,6). 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 (739 nucleotides) is sequenced to determine the genotype of the rubella virus (1,2).
Detection: 7 calendar days. Genotyping: 21 calendar days. Stat testing available upon request.
- World Health Organization. Rubella virus nomenclature update: 2013. WER. 2013;88:337-348.
- World Health Organization. Standardization of the nomenclature for genetic characteristics of wildtype rubella viruses. WER. 2005:80:126-132.
- World Health Organization. Manual for the laboratory diagnosis of measles and rubella virus infection. Third edition. 2018. Available at https://www.who.int/immunization/monitoring_surveillance/burden/laboratory/manual/en/.
- WHO manual for the laboratory diagnosis of measles and rubella virus infection, Annex B12. Available at https://www.who.int/immunization/monitoring_surveillance/burden/laboratory/AnnexB12_Rubella_Realtime_RTPCR.pdf?ua=1 Accessed 2020-03-10.
- Namuwulya P, Abernathy E, Bukenya H, Bwogi J, Tushabe P, Birungi M, Seguya R, Kabaliisa T, Alibu VP, Kayondo JK, Rivailler P, Icenogle J, Bakamutumaho B. Phylogenetic analysis of rubella viruses identified in Uganda, 2003-2012. J Med Virol. 2014 Dec;86(12):2107-13.
- Zhu Z, Xu W, Abernathy ES, Chen MH, Zheng Q, Wang T, Zhang Z, Li C, Wang C, He W, Zhou S, Icenogle J. Comparison of four methods using throat swabs to confirm rubella virus infection. J Clin Microbiol. 2007 Sep;45(9):2847-52.