Phylogenetic and genome analysis of seven senecavirus A isolates in China

Abstract

Senecavirus A (SVA) is the only member of genus Senecavirus that causes vesicular lesions in pigs. We have characterized seven SVA isolates from different swine farms in Guangdong, China. The most variable isolate, CH-DL-01-2016, contained a single amino acid insertion at position 219-220 and a 16 amino acid insertion at position 250-251. The VP1 protein also had four nucleotide changes when compared to 31 other SVA VP1 sequences obtained from GenBank. These mutations have not been identified before. Phylogenetic trees demonstrated that the new SVA isolates were clustered into two different clades and shared 96.3%-97.1% similarity with US strains and 97.9%-98.3% similarity with Brazilian stains on nucleotide level, respectively. Prediction of antigenic epitope indicated that SVA VP1 protein contained both potential B-cell and potential T-cell epitopes. This report provides information about variation analysis in SVA in southern China.

Emergence of novel Seneca Valley virus strains in China, 2017

“…China has a large pig population with high density; therefore, those pig farms with bad feeding environment may facilitate the spread and mutation of various porcine viruses. Several different isolates have been identified in China in 2016 (Zhao et al., ). Besides, co‐infections of SVV with other porcine viruses may enhance viral pathogenicity and result in more severe clinical symptoms (Zhao et al., ).…”

“…Several different isolates have been identified in China in 2016 (Zhao et al., ). Besides, co‐infections of SVV with other porcine viruses may enhance viral pathogenicity and result in more severe clinical symptoms (Zhao et al., ).…”

“…The total RNA of all the samples was extracted using TRIzol reagent (Invitrogen) according to the instructions provided by the manufacturer. All samples were tested using swine vesicular disease virus (SVDV), vesicular stomatitis virus (VSV), vesicular exanthema of swine virus (VESV), FMDV and SVV specific primers described previously due to that all these viruses can cause vesicular diseases (Fowler et al., ; Zhao et al., ; Zheng et al., ).…”

“…SVV was originally isolated from cell culture media and identified as a cell culture contaminant in the United States (US) in 2002 (Hales et al., ). SVV infection has been reported in the US, Canada, Brazil and China in recent years that was associated with porcine idiopathic vesicular disease (PIVD) in pigs and increased neonatal mortality in piglets ≤7 days of age (Hause, Myers, Duff, & Hesse, ; Leme et al., ; Pasma, Davidson, & Shaw, ; Zhao et al., ).…”

“…In the beginning of 2015, the first case of SVV infection in China was identified in Guangdong province, characterized by vesicular lesions in sows and acute death of neonatal piglets (Wu et al., ), and the causative strain was designated as SVV CH‐01‐2015. Subsequently, six new SVV isolates in six different farms in Guangdong province were identified from May 2015 to January 2016, and phylogenetic analysis grouped them into two different clades (Zhao et al., ). In March 2016, another outbreak of SVV infection occurred in Hubei, Central China.…”