Introduction: In 2014–2015, the epidemic of classical swine fever (CSF) occurred in many large-scale pig farms in different provinces of China, and a subgenotype 2.1d of CSF virus (CSFV) was newly identified.
Material and Methods: The phylogenetic relationship, genetic diversity, and epidemic status of the 2014–2015 CSFV isolates, 18 new CSFV isolates collected in 2015, and 43 other strains isolated in 2014–2015 were fully analysed, together with 163 CSFV reference isolates.
Results: Fifty-two 2014–2015 isolates belonged to subgenotype 2.1d and nine other isolates belonged to subgenotype 2.1b. The two subgenotype isolates showed unique molecular characteristics. Furthermore, the 2.1d isolates were found to possibly diverge from 2.1b isolates.
Conclusion: This study suggests that the Chinese CSFVs will remain pandemic.
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.
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.
The genomic variations of the three isolates will support further analysis of virulence determinants and the evolutionary trend of CSFV.