Genotyping

Genotyping of specimens that are positive for measles virus by RT-PCR.

• Measles
• Subacute sclerosing panencephalitis (SSPE)

Urine, nasopharyngeal (NP) swab, throat swab. All specimens should be collected as soon as possible after rash onset (within 7 days). Viral isolates may also be sent. Specimens should already have been determined to be measles RT-PCR positive. (Specimens referred to the NML for measles detection by RT-PCR will automatically be genotyped if determined to be positive.)

Refer to the information sheet for Measles Molecular Detection (specimens should already have been determined to be measles RT-PCR positive).

Ship a minimum of 0.5 mL of original specimen or viral isolate 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.

Measles cases confirmed by RT-PCR. For cases with recent vaccination, 1 year of age and/or identified as suspected post-vaccine reactions, an RT-qPCR specifically targeting the vaccine virus will be performed.

Completed Measles, Mumps, and Rubella requisition form. Include date of rash onset, date of last measles vaccination (if recent), travel history, case number and/or MARS identifier (from the Measles and Rubella Surveillance application on CNPHI) as available. For suspected post-vaccine reactions select “Genotyping – measles vaccine suspected” on the requisition and provide the vaccination date.

Labs that perform their own measles RT-PCR testing should submit positive samples for genotype surveillance. It is important to provide a complete patient history (including travel). The NML is a WHO/PAHO accredited Measles and Rubella Regional Reference Laboratory and has a mandate to genotype all measles cases. Additional regions or the whole genome may be sequenced for the purposes of enhanced measles surveillance (6). Viral sequences will be deposited in the WHO measles sequence database (MeaNS) (3) and may be published on GenBank (https://www.ncbi.nlm.nih.gov/genbank/). 

Measles genotyping has been standardised by the WHO (2, 3). The entire hemagglutinin (H) gene and/or a portion of the nucleoprotein (N) gene (the N-450) is amplified by conventional RT-PCR and sequenced to determine the genotype of the measles virus (4). For suspected post-vaccine reactions, an RT-qPCR specifically targeting the vaccine virus is used (MeVA) (5) along with the general measles detection RT-qPCR. Positive MeVA result confirms presence of vaccine virus and no further genotyping is necessary. Negative MeVA result, with a positive general RT-qPCR, is consistent with non-vaccine and the genotype is determined by sequencing.

21 calendar days. STAT testing available upon request.

Note: During measles outbreaks, there may be delays in receiving genotyping results. Specimens may be triaged, giving highest priority to cases from new importations and to suspected vaccine cases, and lowest priority to cases from outbreaks of already known genotype.  Please, contact the laboratory for STAT requests.

1. Measles and Rubella Elimination Working Group, Health Canada, Public Health Agency of Canada. Guidelines for the prevention and control of measles outbreaks in Canada. CCDR. 2013; 39:ACS-3. Available at http://www.phac-aspc.gc.ca/publicat/ccdr-rmtc/13vol39/acs-dcc-3/index-eng.php#appa.
2. WHO. Standardization of the nomenclature for describing the genetic characteristics of wild-type measles viruses. WER. 1998;73:265.
3. Mulders M, Rota P, Brown K, Goodson J. Genetic diversity of wild-type measles viruses and the global measles nucleotide surveillance database (MeaNS). WER. 2015;90(30):373.
4. Hiebert J, Severini A. Measles molecular epidemiology: What does it tell us and why is it important? CCDR 2014;40(12):257.
5. Roy F, Mendoza L, Hiebert J, McNall R, Bankamp B, Connolly S, Lüdde A, Friedrich N, Mankertz A, Rota P, Severini A. Rapid identification of measles virus vaccine genotypes by real time PCR. J Clin Microbiol. 2016 Nov 16.
6. WHO. The role of extended and whole genome sequencing for tracking transmission of measles and rubella viruses: report from the Global Measles and Rubella Laboratory Network meeting, 2017. WER. 2018;93(6):55.
7. WHO. Manual for the Laboratory-based Surveillance of Measles, Rubella, and Congenital Rubella Syndrome. Third edition, June 2018. Available at https://www.technet-21.org/en/topics/laboratory-measles-rubella-manual

Pathogen Safety Data Sheets: Infectious Substances – Measles virus

For health professionals: Measles

National case definition: Measles

Measles: Symptoms and treatment

Measles and Rubella Weekly Monitoring Reports