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

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.