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

Zhen Zhu,Shujie Zhou,Yan Wang,Min-Hsin Chen,Haiyun Chen,Wenbo Xu,Changyin Wang,Joseph Icenogle,Yuan Si,Emily Abernathy,Chunfang Zhao

doi:10.1038/srep39025

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.

Highlights

Phylogenic analysis of the nucleic acid sequences of a 739-nt region in E1 gene of wild-type RVs [corresponding to nts 8731–9469 in the RV reference strain (NC_001545.2)] showed two distinct groups, clade 1 and clade 2
Selected viruses from each cluster found in China from 2000 to 2013 consisted of four representative viruses from 1E viruses as the subgroup (1E-A), two from 1E-B, one from 2B-C and two from a cluster of pre-2009 viruses designated as 2B-D (Table 1)
Genotype 1E viruses have been found in Europe, Southeast Asia, and northern Africa with sporadic cases or outbreaks occurring in other regions such as the Americas[10,29]

Summary

Introduction

Phylogenic analysis of the nucleic acid sequences of a 739-nt region in E1 gene of wild-type RVs [corresponding to nts 8731–9469 in the RV reference strain (NC_001545.2)] showed two distinct groups, clade 1 and clade 2. The sequences in these two clades differ by ~8%. Genotype 2B viruses found in China since 2011, not distinct from those collected in other countries, were found to belong to two distinct lineages. We performed genomic sequencing of genotypes 1E and 2B viruses isolated in China. The results reported here add whole genome data to the as yet unexplained observation of changes in the predominant circulating RV(s) in rubella endemic countries[12]

Methods

Results

Conclusion