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Complete genome sequence of a novel sub-subgenotype 2.1g isolate of classical swine fever virus from China

Gong, Wenjie, Zhang, Li, Lu, Zongji, Jia, Junjie, Wang, Meng, Peng, Zhicheng, Guo, Huancheng, Shi, Jishu, Tu, Changchun
Archives of virology 2016 v.161 no.9 pp. 2613-2617
3' untranslated regions, 5' untranslated regions, Classical swine fever virus, amino acid sequences, amino acid substitution, genome, kidneys, nucleotides, open reading frames, phylogeny, polyproteins, sequence analysis, topology, virulence, viruses, China
Current subgenotype 2.1 isolates of classical swine fever virus (CSFV) play a dominant role in CSF outbreaks in China, and a novel sub-subgenotype 2.1g of CSFV was recently identified, but the complete genome sequence of this new sub-subgenotype has not been reported. In this study, complete genome of 2.1g isolate GD19/2011 collected from Guangdong province of China in 2011 was sequenced. It was found to be 12,298 nucleotides (nt) in length, including a 375-nt 5’UTR, a 11,697-nt opening reading frame (ORF), and a 227-nt 3’UTR. GD19/2011 shared 91.0-93.7 % and 95.6-97.5 % nt and amino acid sequence identity, respectively, with other subgenotype 2.1 isolates. The topology of a phylogenetic tree constructed based on complete genome sequences of GD19/2011 and other CSFV isolates was identical to that obtained with full-length E2 gene sequences, but it was significantly different from those obtained with the 5’UTR and core sequences. Serial passages of GD9/2011 in PK-15 cells generated a highly cell-adapted virus stock with an infectious titer of 10⁷.⁸ TCID₅₀/ml at the 12ᵗʰ passage in which two amino acid substitutions, S476R and N2494S, were observed in comparison with the complete polyprotein sequence of the original isolate from kidney tissue, GD19/2011. This is the first report of the complete genome sequence of a 2.1g isolate, and the GD19/2011 isolate will be useful for further analysis of the evolution and virulence of CSFV isolates.