The emergence, distribution, and persistence of viral pathogens in swine production systems

Abstract

As swine industries continue to emphasize biosecurity throughout all aspects of swine production, an understanding of viral characteristics is pivotal. Therefore this work aimed to evaluate characteristics of various viruses through different scenarios of swine production. Chapter 1 describes a clinical case where a farrow-to-finish production site was diagnosed with atypical porcine pestivirus (APPV) and an investigation was conducted to understand potential routes of introduction and dissemination within a population of previously-naïve pigs. It was found that litters from both gilts and sows had clinical signs suggestive of APPV, which reduced over time, and that semen doses appeared to be the most likely route of introduction of APPV. Chapter 2 focused on understanding viral pathogen dissemination through production sites and swine production feed mills. Within this investigation, two feed mills and three breed-to-wean facilities were evaluated after suspicion of an epidemiological link for dissemination of porcine deltacoronavirus through feed delivery. The feed mill surfaces that contained detectable porcine enteric viral RNA were associated with feed delivery trucks. Given this knowledge of transportation vehicles contributing to the spread of viral pathogens, chapter 3 was conducted to evaluate the detection and infectivity of viruses within truck cabs after disinfectant application methods. For detection of viral RNA, there was a disinfectant treatment by surface type interaction (P < 0.0001) indicating that how the disinfectant is applied and the surface that the disinfectant is applied to impacts the amount of viral RNA found in environmental samples. When considering the infectivity of these samples from disinfectant application, environmental samples failed to produce infectivity in bioassay analysis. Research using environmental sampling techniques for viral pathogens is still evolving given they are a novel diagnostic tool. The research included in chapter 4 was conducted to evaluate sample processing methods and the presence of organic matter on detection of porcine epidemic diarrhea virus (PEDV) from environmental samples. There was a surface inoculation type by processing method interaction (P < 0.001) indicating material present in environmental samples and sample processing prior to laboratory analysis impacted the sample cycle threshold (Ct) value. Lastly, chapters 5-7 were conducted to understand the potential implications if African swine fever virus (ASFV) were to be introduced into a feed manufacturing facility. Research was conducted using a pilot scale feed mill within BSL3-Ag containment to manufacture ASFV inoculated feed. For environmental samples, sampling zone impacted the log₁₀ p72 genomic copy number/mL (P < 0.0001). When holding environmental samples at room temperature up to 180 days after feed manufacturing, there was no evidence of ASFV degradation across holding times (P = 0.433). For feed samples, the batch of feed when manufactured influenced the log₁₀ genomic copy number/g (P < 0.0001) content of feed samples with greater amounts of ASFV in early batches that decreased with each subsequent batch. When held at room temperature up to 180 days after feed manufacturing, the days held at room temperature and the batch of feed in which feed samples were collected from impacted the amount of ASFV DNA in feed samples (P = 0.023). Thus, viral pathogenesis continues to be a challenge within swine production systems, highlighting the importance of applied research to fully understand the epidemiological implications of viral pathogen emergence, distribution, and persistence.