Genomic regions associated with pseudorabies virus infection status in naturally infected feral swine (Sus scrofa)

Courtney F Bowden; Jennifer N Kiser; Ryan S Miller; Alexandra C Buckley; Paola M Boggiatto; Rachael M Giglio; Vienna R Brown; Dorian Garrick; Holly L Neibergs; Antoinette J Piaggio; Scott E Speidel; Timothy J Smyser

doi:10.3389/fgene.2023.1292671

Genomic regions associated with pseudorabies virus infection status in naturally infected feral swine (Sus scrofa)

Front Genet. 2023 Nov 23:14:1292671. doi: 10.3389/fgene.2023.1292671. eCollection 2023.

Affiliations

¹ National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, CO, United States.
² Department of Animal Sciences, College of Agricultural, Human, and Natural Resource Sciences, Washington State University, Pullman, WA, United States.
³ Center for Epidemiology and Animal Health, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, CO, United States.
⁴ Virus and Prion Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States.
⁵ Infectious Bacterial Diseases Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States.
⁶ National Feral Swine Damage Management Program, Wildlife Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, CO, United States.
⁷ AL Rae Centre for Genetics and Breeding, Massey University, Palmerston North, New Zealand.
⁸ Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, United States.

Abstract

Pseudorabies virus (PRV)-the causative agent of Aujeszky's disease-was eliminated from commercial pig production herds in the United States (US) in 2004; however, PRV remains endemic among invasive feral swine (Sus scrofa). The circulation of PRV among abundant, widespread feral swine populations poses a sustained risk for disease spillover to production herds. Risk-based surveillance has been successfully implemented for PRV in feral swine populations in the US. However, understanding the role of host genetics in infection status may offer new insights into the epidemiology and disease dynamics of PRV that can be applied to management strategies. Genetic mechanisms underlying host susceptibility to PRV are relatively unknown; therefore, we sought to identify genomic regions associated with PRV infection status among naturally infected feral swine using genome-wide association studies (GWAS) and gene set enrichment analysis of single nucleotide polymorphism data (GSEA-SNP). Paired serological and genotypic data were collected from 6,081 feral swine distributed across the invaded range within the contiguous US. Three complementary study populations were developed for GWAS: 1) comprehensive population consisting of feral swine throughout the invaded range within the contiguous US; 2) population of feral swine under high, but temporally variable PRV infection pressure; and 3) population of feral swine under temporally stable, high PRV infection pressure. We identified one intronic SNP associated with PRV infection status within candidate gene AKAP6 on autosome 7. Various gene sets linked to metabolic pathways were enriched in the GSEA-SNP. Ultimately, improving disease surveillance efforts in feral swine will be critical to further understanding of the role host genetics play in PRV infection status, helping secure the health of commercial pork production.

Keywords: Aujeszky’s disease; GSEA-SNP; GWAS; disease spillover; feral swine; pseudo-heritability; pseudorabies virus (PRV).

Associated data

Dryad/10.5061/dryad.zgmsbccjh

Grants and funding

The authors declare financial support was received for the research, authorship, and/or publication of this article. This research was supported by the U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services.