Genomic analysis of diverse rubella virus genotypes

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Abstract
Based on the sequence of the E1 glycoprotein gene, two clades and ten genotypes ofRubella virushave been distinguished; however, genomic sequences have been determined for viruses in only two of these genotypes. In this report, genomic sequences for viruses in an additional six genotypes were determined. The genome was found to be well conserved. The viruses in all eight of these genotypes had the same number of nucleotides in each of the two open reading frames (ORFs) and the untranslated regions (UTRs) at the 5′ and 3′ ends of the genome. Only the UTR between the ORFs (the junction region) exhibited differences in length. Of the nucleotides in the genome, 78 % were invariant. The greatest observed distance between viruses in different genotypes was 8.74 % and the maximum calculated genetic distance was 14.78 substitutions in 100 sites. This degree of variability was similar among regions of the genome with two exceptions, both within the P150 non-structural protein gene: the N-terminal region that encodes the methyl/guanylyltransferase domain was less variable, whereas the hypervariable domain in the middle of the gene was more divergent. Comparative phylogenetic analysis of different regions of the genome was done, using sequences from 43 viruses of the non-structural protease (near the 5′ end of the genome), the junction region (the middle) and the E1 gene (the 3′ end). Phylogenetic segregation of sequences from these three genomic regions was similar with the exception of genotype 1B viruses, among which a recombinational event near the junction region was identified.