Genetic Analysis of Wild-type Measles Viruses

Utility of Molecular Epidemiology

The combination of molecular epidemiologic techniques and standard case classification and reporting provides a very sensitive means to track the transmission pathways of measles.

Sequence data has proven useful to:

• confirm the source of virus
• indicate a likely source or narrow the possibilities for "unknown source" cases
• establish links, or lack thereof, between various cases and outbreaks

Virologic surveillance is especially beneficial when it is possible to observe the change in viral genotypes over time in a particular country or region. This information, when analyzed in conjunction with standard epidemiologic data, has helped to document the interruption of transmission of endemic measles.

Molecular characterization of measles viruses has provided a valuable tool for measuring the effectiveness of measles control programs.

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Distinguishing Vaccine Reactions from Wild-type Infections

Virologic surveillance can also help to classify suspected cases as vaccine reactions. A small proportion of measles vaccine recipients experience rash and fever 10-14 days following vaccination. During outbreaks, measles vaccine is administered to help control the outbreak, and in these situations, vaccine reactions may be mistakenly classified as measles cases. Since serologic methods cannot distinguish between a vaccine-induced antibody response and antibodies derived from natural disease, molecular characterization of viral isolates provides a method to confirm whether vaccine or wild-type measles virus caused the rash and fever.

Surveillance guidelines recommend that countries involved in measles elimination collect appropriate specimens for virus isolation from every chain of transmission, while countries involved in outbreak control activities and mortality reduction obtain representative specimens from measles outbreaks(1).

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Standard Methods for Molecular Epidemiology of Measles

In 1998, the World Health Organization (WHO) made recommendations for a standard nomenclature for naming strains, describing genotypes, and conducting sequence analysis so that genetic data would be directly comparable between laboratories. These recommendations have been updated periodically since 1998.

Consult the list of standard methods for molecular epidemiology of measles.

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Analysis of Measles Virus Sequences

The minimum amount of sequence data (as recommended by the WHO) for genotype determination is the 450 nucleotides that code for the carboxy-terminal 150 amino acids of the nucleoprotein (N) gene. Complete sequences of the hemagglutinin (H) gene should be obtained if a new genotype is suspected.

For molecular epidemiologic purposes, the genotype designations are considered the operational taxonomic unit, while related genotypes are grouped by clades.

WHO currently recognizes 8 clades designated A, B, C, D, E, F, G, and H.

Within these clades, there are 23 recognized genotypes, designated A, B1, B2, B3, C1, C2, D1, D2, D3, D4, D5, D6, D7, D8, D9, D10, E, F, G1, G2, G3, H1, and H2.

Sequences from recent viral isolates are then compared to the set of WHO reference sequences, which are available from GenBank and the WHO Strain Banks, to determine the genotype.

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Data Reporting and Surveillance Guidelines

Through the efforts of the WHO Measles and Rubella Laboratory Network, virologic surveillance has expanded on a global scale. Information on circulating genotypes has been reported from almost every country with endemic or widespread measles.

WHO maintains a database of genotype information that is reported from national and regional laboratories within the WHO Measles and Rubella Laboratory Network. Comparison of the sequence information is as important as having the genotype designation. Many genotypes contain multiple co-circulating lineages and assignment of a viral sequence to one of these lineages allows for more accurate mapping of transmission pathways. For this reason, rapid exchange of both genotype and sequence information on a global scale is critical.

Measles sequences are reported to National Center for Biotechnology Information (NCBI) GenBank. Provision of sequences to GenBank does not constitute prior publication.

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Guidelines for Naming Measles Strains or Sequences

The strain names will provide information that is essential for interpretation of the molecular data. Since sequence data may be derived from viruses isolated in cell culture or from RNA extracted directly from clinical material, strains or sequences will be designated as either

1. MVi: measles virus isolate in cell culture; or
2. MVs: measles virus sequence derived from RNA extracted from clinical material.

Other information to be included in the strain/sequence name:

• city/province where case of measles was diagnosed, write full name or abbreviation(required);
• country, use WHO 3-letter (exit) designation (required);
• date of specimen collection by epidemic week (1-52) and year (required);
• isolate number if more than 1 per week in the same location (optional);
• genotype (optional initially, required after sequencing of at least 450 nucleotides of the N gene (text-only) is completed);
• special designation for sequences derived from measles inclusion body encephalitis (MIBE) or subacute sclerosing panencephalitis (SSPE) cases (optional).

The following examples illustrate the proposed nomenclature:

• MVi/NewYork.USA/03.98/2 [D2]
• MVs/London.UNK/17.97 [G3] SSPE

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Measles Strain Banks

In order to maintain reference stocks of viruses and provide facilities capable of conducting viral sequencing, two global Measles Strain Banks have been established. The Measles Virus Section laboratory of the Centers for Disease Control and Prevention (CDC) in Atlanta, Georgia, USA, and Central Public Health Laboratory (CPHL) in London, UK, were selected to serve this purpose.

Upon request, viral sequencing, sequence analysis, and assistance with data reporting can be provided by the CDC Measles Strain Bank.

Laboratorians are requested to consult with the CDC Measles Strain Bank before reporting a new measles genotype. To report a possible new genotype of measles, contact prota@cdc.gov

Contact:

Reference

1. PubMed PMID: 18621499. Rota PA, Featherstone DA, Bellini WJ. 2009. Molecular epidemiology of measles virus. Curr Top Microbiol Immunol 330:129-150.

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