Genome wide analysis of the evolution of Senecavirus A from swine clinical material and assembly yard environmental samples

Abstract

Senecavirus A (SVA), previously known as Seneca Valley virus, was first isolated in the United States in 2002. SVA was associated with porcine idiopathic vesicular disease in Canada and the USA in 2007 and 2012, respectively. Recent increase in SVA outbreaks resulting in neonatal mortality of piglets and/or vesicular lesions in sows in Brazil, the USA and Canada point to the necessity to study the pathogenicity and molecular epidemiology of the virus. Here, we report the analysis of the complete coding sequences of SVA from 2 clinical cases and 9 assembly yard environmental samples collected in 2015 in Canada, along with 22 previously released complete genomes in the GenBank. With this combined data set, the evolution of the SVA over a 12-month period in 2015/2016 was evaluated. These SVA isolates were characterized by a rapid accumulation of genetic variations driven mainly by a high nucleotide substitution rate and purifying selection. The SVA sequences clustered in clearly defined geographical areas with reported cases of SVA infection. No transmission links were identified between assembly yards, suggesting that point source introductions may have occurred. In addition, 25 fixed non-synonymous mutations were identified across all analyzed strains when compared to the prototype SVA strain (SVV-001). This study highlights the importance of monitoring SVA mutations for their role in increased virulence and impact on SVA diagnostics.

Development and evaluation of a real-time RT-PCR and a field-deployable RT-insulated isothermal PCR for the detection of Seneca Valley virus

“…Foreign animal disease investigations indicated that other vesicular viral pathogens, such as foot-and-mouth disease virus (FMDV), swine vesicular disease virus (SVDV), vesicular stomatitis virus (VSV), and vesicular exanthema of swine virus (VESV), were negative in these cases [10]. Subsequently, SVV detection was reported by other laboratories in the U.S. [11][12][13][14][15][16], China [17][18][19][20][21], Canada [22], Thailand [23], and Colombia [24]. Vesicular lesions were induced in pigs following experimental inoculation with the contemporary U.S. isolates of SVV [25,26], confirming that SVV is a vesicular viral pathogen.…”

Genetic and phylogenetic analysis of reemerged novel Seneca Valley virus strains in Guangdong province, 2017

“…Seneca Valley virus (SVV) was identified from a contaminated PER.C6 cell line in 2002 (Leme, Alfieri, & Alfieri, ; Segales, Barcellos, Alfieri, Burrough, & Marthaler, ), whereas SVV‐associated porcine idiopathic vesicular disease (PIVD) was reported until 2007 in Canada and 2010 in the United States (US) (Leme et al., ; Pasma, Davidson, & Shaw, ; Singh, Corner, Clark, Scherba, & Fredrickson, ). Since the PIVD outbreak in swine herds in Brazil (Leme et al., ), this disease had been reported in the United States (Zhang et al., ), Colombia (Sun, Vannucci, Knutson, Corzo, & Marthaler,), Thailand (Saeng‐Chuto, Rodtian, Temeeyasen, Wegner, & Nilubol, ), Canada (Xu et al., ) and China (Wu et al., ), suggesting a gradually increasing geographic distribution.…”

A new wave of Seneca Valley virus outbreaks in Brazil

“…After the SVV outbreaks in Brazil, the virus infection was also reported in different pig categories/herds of other countries of the Americas (Joshi et al., ; Sun, Vannucci, Knutson, Corzo, & Marthaler, ; Xu et al., ) and Asia (Saeng‐Chuto, Rodtian, Temeeyasen, Wegner, & Nilubol, ; Wu et al., ) during 2015 and 2016. However, the number of field reports on SVV‐suspected cases in piglets and SVV diagnostics has decreased in Brazilian pig herds during 2017, suggesting that the infection became endemic in pig herds, leading to asymptomatic and/or subclinical infections.…”