7.9 Guidelines for reporting a new rubella genotype

Mick Mulders

The following criteria have been developed to standardize the requirements for a recognized genotype of rubella virus:

a. Two reference viruses in the genotype are available and have been submitted to a WHO recognized strain bank.

b. Sequences are available from the entire structural protein open reading frame (SPORF) (coding region for C, E2 and E1 proteins) of the 2 reference viruses in the genotype.

c. Phylogenetic analyses of the reference viruses in the genotype with the reference viruses from all other genotypes show that:

  1. the reference viruses from the genotype cluster together with one another and separately from the reference viruses of all other genotypes with high confidence values (e.g. 80-90% bootstrap values). This clustering should be obtained with at least 2 different analysis methods;
  2. the phylogenetic tree topology obtained with full SP ORF sequences of the reference viruses of the genotype and other reference viruses should be the same when the coding sequences of C, E2 and E1 are analysed individually;
  3. the intragenotype and intergenotype distances for the reference viruses in the genotype are consistent with those for the existing genotypes;
  4. the branching pattern obtained in the phylogenetic analysis versus other reference viruses is consistent with a new genotype.

d. Sequence data for reference viruses in the genotype have been submitted to GenBank with the virus name and associated epidemiological and clinical data