Analysis of complete genomes of the rubella virus genotypes 1E and 2B which circulated in China, 2000–2013

Abstract

Rubella viruses of genotypes 1E and 2B are currently the most frequently detected wild-type viruses in the world. Genotype 1E viruses from China have been genetically distinct from genotype 1E viruses found elsewhere, while genotype 2B viruses found in China are not distinguishable from genotype 2B viruses from other areas. Genetic clusters of viruses of both genotypes were defined previously using sequences of the 739-nt genotyping window. Here we report phylogenic analysis using whole genomic sequences from seven genotype 1E and three genotype 2B viruses which were isolated in China between 2000 and 2013 and confirm the subgrouping of current circulating genotypes 1E and 2B viruses. In addition, the whole genomic characterization of Chinese rubella viruses was clarified. The results indicated that the Chinese rubella viruses were highly conserved at the genomic level, and no predicted amino acid variations were found at positions where functional domains of the proteins were identified. Therefore, it gives us the idea that the rubella control and elimination goal should be achieved if vaccine immunization coverage continues maintaining at the high level.

Infectious vaccine-derived rubella viruses emerge, persist, and evolve in cutaneous granulomas of children with primary immunodeficiencies

“…Whole genome sequencing revealed that each of the recovered viruses contained multiple predominantly virus-specific nucleotide and amino acid substitutions with respect to RA27/3, which gives a molecular basis for the differences in their biological properties from each other and vaccine virus. Our estimate of the overall evolutionary rate of iVDRV (1.8 x 10 −3 subs/site/year) based on the whole genome sequences is consistent with evolutionary rates reported for other small RNA viruses [51] and somewhat higher that those reported for wtRV (genotype 1E: 9.16 × 10 −4 –1.04 × 10 −3 subs/site/year) in populations with person-to-person transmission [52]. Higher iVDRV evolution rates may be due to continuous viral replication and selection during chronic infection in a single individual as opposed to intermittent replication and selection during disease outbreaks.…”

Phylogeography of rubella virus in Asia: Vaccination and demography shape synchronous outbreaks

“…Clade 1, a large clade of primarily Chinese sequences, corresponds to the previously identified Chinese 1E lineage (Zhu et al, 2015, 2012; Zhu et al, 2016). In line with previous estimates, we identified a divergence time of 2000.4 (HPDI: 1999.53–2001.04).…”

Potential neuroinvasive and neurotrophic properties of SARS-CoV-2 in pediatric patients: comparison of SARS-CoV-2 with non-segmented RNA viruses

“…The reliability of phylogenetic inference at each branch node was estimated by the Bootstrap test with 1000 replications (Felsenstein 1985 ). Bootstrap values greater than 80% were considered statistically significant for grouping (Zhu et al 2016 ). The trees were visualized by Dendroscope-3 (University of Tübingen, Baden-Württemberg, Germany) (Huson and Scornavacca 2012 ).…”