Genetic Analysis

Molecular epidemiology of rubella viruses is an important component for confirming connections between cases or excluding cases during investigations. When combined with global surveillance information and epidemiological data, it can also identify the source of wild-type rubella strains. In addition, genotype determination from clinical samples or virus isolates can distinguish the vaccine strain of rubella virus from wild-type viruses.

WHO Classification

The World Health Organization (WHO) recommends the collection of rubella virus genotype data to support global control and elimination programs. (see Global Measles and Rubella Laboratory Network, January 2004–June 2005). In order to facilitate the use of virologic surveillance in these programs, WHO established a systematic nomenclature for wild-type rubella viruses (see page 338) in 2004.

• Currently, there are two distantly related groups of viruses, called clades, which differ by about 8 to 10% in the nucleotide sequence of 3’ proximal 1/3 of the genome coding for the structural proteins.
  • There are 13 more closely related groups of viruses within the clades called genotypes, one of which is provisional.

Virus Sequencing

The classification of a rubella virus requires sequencing of 739 nucleotides (nt) in the E1 protein coding region (nts 8731-9469) and a phylogenetic comparison of the resulting sequence with 32 well-characterized reference virus sequences that represent the 13 genotypes. In addition, a naming convention exists (see page 339) based on whether the sequence is derived from a virus isolate or directly from a clinical specimen, and the location and date of specimen collection.

Currently, four genotypes of rubella virus are known to be commonly circulating in many regions of the world: 1E, 1G, 1J, and 2B.

See Molecular Epidemiology section on the References and Resources page for additional information.