Identification and genomic characterization of the emerging Senecavirus A in southeast China, 2017

Senecavirus A (SVA) is an emerging non-enveloped virus with a single-stranded, positive-sense RNA genome that belongs to the Senecavirus genus in the Picornaviridae family. Senecavirus A-associated swine idiopathic vesicular disease and epidemic transient neonatal losses have caused substantial economic losses for the swine industry. Here, we describe a case of re-emerging vesicular disease among sows and finishing pigs on a swine farm in Fujian Province of southeast China. Other causative pathogens, including FMDV, SVDV and VSV, were excluded, and a novel SVA strain, CH-FJZZ-2017, was isolated. Sequencing and phylogenetic analysis of the complete genome and individual viral proteins revealed that CH-FJZZ-2017 is closely related to the US strains in 2015. The results further showed that Chinese SVAs have formed two distinct subclades with 2016 as the turning point. Viruses causing outbreaks after late 2016 shared higher nucleotide identities with the US strains in 2015. There is still some evolutionary distance between CH-FJZZ-2017 and other strains isolated in late 2016, suggesting that Chinese SVA isolates have been evolving in different directions. This study provides a basis for the development of effective prevention and control strategies.