Genome and molecular characterization of a CSFV strain isolated from a CSF outbreak in South China

Abstract

In the present study, the full-length nucleotide sequences of the CSFV-GZ-2009 strain of classical swine fever virus (CSFV) isolated from a hog pen in Guangdong province in China was determined. Results demonstrated that the genome of CSFV-GZ-2009 is 12,298 nucleotides (nt) in length, is composed of a 373-nt 5'-untranslated region (UTR), has an 11,697-nt open reading frame encoding a polyprotein of 3,898 amino acids, and has a 228-nt 3'-UTR. Genome comparison of the CSFV-GZ-2009 isolate (GenBank accession No. HQ380231) with other CSFV strains was also analyzed. Gene regions from CSFV-GZ-2009 and other known strains were shown to share 92.7-96.7% identity at the nucleotide level and 94.7-99.2% identity at the amino acid level. Phylogenetic analysis of the full-length genome and the following regions E(rns), E2 and NS5B revealed that the CSFV-GZ-2009 isolate was classified within subgroup 1.1 of group I and closely related to the highly virulent strain JL1 (06), cF114, Shimen and SWH with pairwise distances of 0.0037, 0.0043, 0.0058 and 0.0107, respectively. Analysis of recombination with the SimPlot program demonstrated that strain CSFV-GZ-2009 was not a naturally homologous recombinant. Furthermore, the change of clinical signs of pigs after infection of CSFV-GZ-2009 isolates showed typical symptoms such as diarrhea, persistent fever, and mononuclear lymphocytopenia after CSFV infection. Based on phylogenetic analysis and an animal infection test, we could conclude that the CSFV-GZ-2009 isolate belonged to subgroup 1.1 of group I and was of high virulence.