title: Genetic diversity and positive selection analysis of classical swine fever virus isolates in south China.
abstract: Classical swine fever virus (CSFV) causes a highly contagious disease that leads to significant economic losses in the pig industry worldwide. However, there is a paucity of knowledge on the accurate genotyping of CSFV isolates in south China. This study genotyped the E2 gene of 14 CSFV strains isolated during 2008-2010 from domestic pigs in different districts of south China. Phylogenetic analyses revealed that all of the 14 CSFV isolates were clustered into genetic subgroup 1.1. This contrasts with most parts of China, where group 2 isolates are predominant. Furthermore, the positive selection pressures acting on the E(rns) and E2 envelope protein genes of CSFV were assessed and a site-by-site analysis of the dN/dS ratio was performed to identify specific codons that undergo diversification under positive selection. While no significant evidence for positive selection was observed in E(rns), two positively selected sites at amino acid residues 49 and 72 in the E2 encoding region were identified. Our results revealed that a predominance of subgroup 1.1 CSFV isolates is currently circulating in some districts of south China, which appear to be unrelated to the Chinese C-strain vaccine. Moreover, the envelope protein gene, E2, has undergone positive selection in 14 CSFV strains and two positively selected sites have been identified in this study. Understanding the molecular epidemiology and functional importance of these positively selected amino acid positions could help to predict possible changes in virulence, the development of vaccines and disease control.
authors.affiliation: College of Veterinary Medicine, South China Agricultural University, No. 483 Wushan Road, Tianhe, Guangzhou 510640, People's Republic of China.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Shen
authors.forename: Jingjing
authors.initials: J
authors.lastname: Pei
authors.forename: Jialin
authors.initials: J
authors.lastname: Bai
authors.forename: Mingqiu
authors.initials: M
authors.lastname: Zhao
authors.forename: Chunmei
authors.initials: C
authors.lastname: Ju
authors.forename: Lin
authors.initials: L
authors.lastname: Yi
authors.forename: Yanmei
authors.initials: Y
authors.lastname: Kang
authors.forename: Xuetao
authors.initials: X
authors.lastname: Zhang
authors.forename: Lijun
authors.initials: L
authors.lastname: Chen
authors.forename: Yinguang
authors.initials: Y
authors.lastname: Li
authors.forename: Jiaying
authors.initials: J
authors.lastname: Wang
authors.forename: Jinding
authors.initials: J
authors.lastname: Chen
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002681:China; D006691:Classical Swine Fever / Q000453:epidemiology; D006692:Classical Swine Fever Virus / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010802:Phylogeny; D012641:Selection, Genetic; D016415:Sequence Alignment; D034421:Sus scrofa; D013552:Swine; D014759:Viral Envelope Proteins / Q000235:genetics
chemical_list: D014759:Viral Envelope Proteins