Characterization of Senecavirus A isolates collected from the environment of U.S. sow slaughter plants

Authors: HOFFMAN, KYLE - Oak Ridge Institute For Science And Education (ORISE); HUMPHREY, NICKI - Animal And Plant Health Inspection Service (APHIS); KORSLUND, JOHN - Animal And Plant Health Inspection Service (APHIS); Anderson, Tavis; FAABERG, KAY - Retired ARS Employee; Lager, Kelly; Buckley, Alexandra

Submitted to: Frontiers in Veterinary Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/16/2022
Publication Date: 6/22/2022
Citation: Hoffman, K., Humphrey, N., Korslund, J., Anderson, T.K., Faaberg, K., Lager, K.M., Devries, A.C. 2022. Characterization of Senecavirus A isolates collected from the environment of U.S. sow slaughter plants. Frontiers in Veterinary Science. 9. Article 923878. https://doi.org/10.3389/fvets.2022.923878.
DOI: https://doi.org/10.3389/fvets.2022.923878

Interpretive Summary: Pigs infected with Senecavirus A (SVA) present with vesicles that are blister-like lesions found on the snout and skin bordering the hooves, which are indistinguishable from vesicular lesions caused by other viral infections of pigs, including foot-and-mouth disease virus (FMDV). FMDV infection is reportable and could have severe economic ramifications if the virus entered an FMDV-free country; therefore, the presence of vesicular lesions in FMDV-free countries prompts a foreign animal disease investigation (FADI) to determine the pathogen responsible for these lesions. These investigations can be time-consuming and expensive and can disrupt swine market chains. Unfortunately, the number of reported SVA cases has been increasing in the U.S. since 2015, prompting more FADIs, particularly at swine slaughter plants. This project sought to better understand the presence of SVA in the environment of U.S. sow slaughter plants reporting high levels of FADIs. In addition, a select number of environmental samples were used to inoculate pigs to determine whether SVA present in the environment was infectious to swine. Finally, six samples were sequenced to compare 2020 sequences to older SVA isolates. Environmental samples demonstrated that SVA was most abundant in warmer months, particularly in August. Of the 450 samples collected, 68.2% were PCR positive for SVA nucleic acids and 23.8% of the samples were virus isolation positive on cell culture. Of the isolates selected for swine bioassay, only a single environmental sample was capable of infecting piglets. Finally, sequencing demonstrated that at least two genetically distinct groups of SVA were in co-circulation at U.S. sow slaughter plants. Results from this study improve our understanding of the ecology of SVA in the swine marketing chain and this information could be used to improve SVA control measures that may help reduce the number of FADIs associated with SVA.

Technical Abstract: Vesicular disease caused by Senecavirus A (SVA) is clinically indistinguishable from foot-and-mouth disease (FMD) and other vesicular diseases of swine. When a vesicle is observed in FMD-free countries, a costly and time-consuming foreign animal disease investigation (FADI) is performed to rule out FMD. Recently, there has been an increase in the number of FADIs and SVA positive samples at slaughter plants in the U.S. The objectives of this investigation were to: 1) describe the environmental burden of SVA in sow slaughter plants; 2) determine whether there was a correlation between PCR diagnostics, virus isolation (VI), and swine bioassay results; and 3) phylogenetically characterize the genetic diversity of contemporary SVA isolates. Environmental swabs were collected from four sow slaughter plants (Plants 1-4) between June to December 2020. Of the 450 samples taken from Plants 1-3, 307 samples were PCR positive and 107 were VI positive. There was no detection of SVA by PCR or VI at Plant 4. SVA positive samples were most frequently found in the summer (78.8% June-August, vs 59.3% September-December), with a peak at 85% in August. Eighteen PCR positive environmental samples with a range of Ct values were selected for a swine bioassay: a single sample infected piglets (n=2). A random subset of the PCR positive samples was sequenced; and phylogenetic analysis demonstrated co-circulation and divergence of two genetically distinct groups of SVA. These data demonstrate that SVA was frequently found in the environment of sow slaughter plants, but environmental persistence and diagnostic detection was not indicative of whether a sampled was infectious to swine. Consequently, we argue that a more detailed understanding of the epidemiology of SVA and its environmental persistence in the marketing chain is necessary to reduce the number of FADIs and aide in the development of control measures to reduce the spread of SVA.