Complete genome sequences of three sub-genotype 2.1b isolates of classical swine fever virus in China

Liu, Chunxiao; Li, Mingliang; Yin, Xingwang; Zhang, Hongliang; Xiang, Lirun; Zhai, Hongyue; Wang, Congcong; Kan, Yunchao; Yao, Lunguang; Tian, Zhijun; Leng, Chaoliang

doi:10.2478/jvetres-2018-0002

Abstract

Introduction

Classical swine fever (CSF) has caused severe economic losses in pig production in many countries. Recent CSF outbreaks in China are mainly associated with sub-genotype 2.1 of CSF virus (CSFV). Although there is abundant information regarding 2.1 isolates, few data are available on whole-genome analysis.

Material and Methods

The biological and genome characteristics of three recently emerged Chinese CSFV isolates, i.e. SD2014-1, SD2014-2, and SD2014-3, were fully analysed.

Results

Sequence analysis showed that the isolates shared 83.4%–95.0% nucleotide identity with eight other CSFV isolates. In addition, the 5′ untranslated region (5′UTR) and the non-structural (NS) proteins NS3, NS4A, and NS4B were more conserved than other regions of the genome. Phylogenetic analysis based on the complete genome sequences or full-length structural protein E2 gene sequences revealed that the three isolates belonged to sub-genotype 2.1b. In addition, several unique molecular characteristics of the 5′UTR, 3′UTR, and E2 were identified.

Conclusion

The genomic variations of the three isolates will support further analysis of virulence determinants and the evolutionary trend of CSFV.

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