Genomic analysis of diverse rubella virus genotypes

Abstract

Based on the sequence of the E1 glycoprotein gene, two clades and ten genotypes of Rubella virus have 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.

Limits and patterns of cytomegalovirus genomic diversity in humans

“…These values differ from those estimated for other species. The number of conserved sites in the human genome is ∼8% (48), and, in other viruses, the proportion is much higher, including 66% for HIV (49), 63% for influenza A virus (50), and 78% for rubella virus (51). These trends suggest that the number of invariant sites is inversely correlated with genome size.…”

Identification of a Ca 2+ -Binding Domain in the Rubella Virus Nonstructural Protease

“…Prediction of the secondary structure elements revealed that the RUB NS protease Ca 2ϩ -binding loop was flanked by two helices, as observed in most EF-hand CaBPs (47). The predicted Ca 2ϩ -binding motif is highly conserved among the eight genotypes of RUB for which sequence of this region is available (72), including all of the Ca 2ϩ -binding coordination ligands (Fig. 1B).…”

Calibration of Multiple Poliovirus Molecular Clocks Covering an Extended Evolutionary Range

“…Understanding of past transmission pathways may contribute to a better understanding of current risks of poliovirus spread from the remaining foci of endemicity. Similar analyses of other rapidly evolving RNA viruses, especially agents of vaccine-preventable diseases known to have significant transition biases (13,71,97), may aid in the development of improved strategies for their control.…”