Biosecurity Insights from the United States Swine Health Improvement Plan: Analyzing Data to Enhance Industry Practices

Biosecurity practices aim to reduce the frequency of disease outbreaks in a farm, region, or country and play a pivotal role in fortifying the country's pork industry against emerging threats, particularly foreign animal diseases (FADs). This article addresses the current biosecurity landscape of the US swine industry by summarizing the biosecurity practices reported by the producers through the United States Swine Health Improvement Plan (US SHIP) enrollment surveys, and it provides a general assessment of practices implemented. US SHIP is a voluntary, collaborative effort between industry, state, and federal entities regarding health certification programs for the swine industry. With 12,195 sites surveyed across 31 states, the study provides a comprehensive snapshot of current biosecurity practices. Key findings include variability by site types that have completed Secure Pork Supply plans, variability in outdoor access and presence of perimeter fencing, and diverse farm entry protocols for visitors. The data also reflect the industry's response to the threat of FADs, exemplified by the implementation of the US SHIP in 2020. As the US SHIP program advances, these insights will guide industry stakeholders in refining biosecurity practices, fostering endemic re-emerging and FAD preparedness, and ensuring the sustainability of the swine industry in the face of evolving challenges.

Novel influenza A viruses in pigs with zoonotic potential, Chile

Novel H1N2 and H3N2 swine influenza A viruses (IAVs) have recently been identified in Chile. The objective of this study was to evaluate their zoonotic potential. We perform phylogenetic analyses to determine the genetic origin and evolution of these viruses, and a serological analysis to determine the level of cross-protective antibodies in the human population. Eight genotypes were identified, all with pandemic H1N1 2009-like internal genes. H1N1 and H1N2 were the subtypes more commonly detected. Swine H1N2 and H3N2 IAVs had hemagglutinin and neuraminidase lineages genetically divergent from IAVs reported worldwide, including human vaccine strains. These genes originated from human seasonal viruses were introduced into the swine population since the mid-1980s. Serological data indicate that the general population is susceptible to the H3N2 virus and that elderly and young children also lack protective antibodies against the H1N2 strains, suggesting that these viruses could be potential zoonotic threats. Continuous IAV surveillance and monitoring of the swine and human populations is strongly recommended.IMPORTANCEIn the global context, where swine serve as crucial intermediate hosts for influenza A viruses (IAVs), this study addresses the pressing concern of the zoonotic potential of novel reassortant strains. Conducted on a large scale in Chile, it presents a comprehensive account of swine influenza A virus diversity, covering 93.8% of the country's industrialized swine farms. The findings reveal eight distinct swine IAV genotypes, all carrying a complete internal gene cassette of pandemic H1N1 2009 origin, emphasizing potential increased replication and transmission fitness. Genetic divergence of H1N2 and H3N2 IAVs from globally reported strains raises alarms, with evidence suggesting introductions from human seasonal viruses since the mid-1980s. A detailed serological analysis underscores the zoonotic threat, indicating susceptibility in the general population to swine H3N2 and a lack of protective antibodies in vulnerable demographics. These data highlight the importance of continuous surveillance, providing crucial insights for global health organizations.

Control technologies to prevent aerosol-based disease transmission in animal agriculture production settings: a review of established and emerging approaches

Transmission of infectious agents via aerosols is an ever-present concern in animal agriculture production settings, as the aerosol route to disease transmission can lead to difficult-to-control and costly diseases, such as porcine respiratory and reproductive syndrome virus and influenza A virus. It is increasingly necessary to implement control technologies to mitigate aerosol-based disease transmission. Here, we review currently utilized and prospective future aerosol control technologies to collect and potentially inactivate pathogens in aerosols, with an emphasis on technologies that can be incorporated into mechanically driven (forced air) ventilation systems to prevent aerosol-based disease spread from facility to facility. Broadly, we find that control technologies can be grouped into three categories: (1) currently implemented technologies; (2) scaled technologies used in industrial and medical settings; and (3) emerging technologies. Category (1) solely consists of fibrous filter media, which have been demonstrated to reduce the spread of PRRSV between swine production facilities. We review the mechanisms by which filters function and are rated (minimum efficiency reporting values). Category (2) consists of electrostatic precipitators (ESPs), used industrially to collect aerosol particles in higher flow rate systems, and ultraviolet C (UV-C) systems, used in medical settings to inactivate pathogens. Finally, category (3) consists of a variety of technologies, including ionization-based systems, microwaves, and those generating reactive oxygen species, often with the goal of pathogen inactivation in aerosols. As such technologies are typically first tested through varied means at the laboratory scale, we additionally review control technology testing techniques at various stages of development, from laboratory studies to field demonstration, and in doing so, suggest uniform testing and report standards are needed. Testing standards should consider the cost-benefit of implementing the technologies applicable to the livestock species of interest. Finally, we examine economic models for implementing aerosol control technologies, defining the collected infectious particles per unit energy demand.

Infection dynamics and incidence of wild-type porcine reproductive and respiratory syndrome virus in growing pig herds in the U.S. Midwest

Porcine reproductive and respiratory syndrome virus (PRRSV) infections greatly impact the health and productivity of growing pigs. The introduction and persistence of wild-type PRRSV (WT-PRRSV) strains in growing pig populations is poorly understood. In an observational prospective cohort study, we monitored and surveyed 63 wean-to-finish (WTF) herds across 10 companies located in medium to high pig dense areas in the U.S. Midwest. All herds received weaned pigs from PRRSV-negative or positive-stable breeding herds. Herds were monitored monthly using oral fluids collected following a fixed spatial sampling regime and samples were tested by PRRSV ELISA, RT-PCR and ORF5 sequencing. In most (90%) of the herds, pigs were vaccinated with PRRSV modified-live vaccines either at processing, weaning or shortly after weaning. Wild type PRRSV (WT-PRRSV) infections were defined by the criterion of having more than 2% nucleotide differences in the ORF-5 region compared with reference vaccine strain sequences. Wild type PRRSV was detected in 42% of the herds with infections being more prevalent in the mid to late growing period, with a mean of 20 weeks post placement. Nineteen distinct WT-PRRSV were identified in seven out of 10 production companies with an average of 3 distinct WT-PRRSV strains per company. Vaccinated WTF herds with and without WT-PRRSV detection were compared to each other showing different PCR and ELISA infection patterns. Close-out mortality in vaccinated herds with WT-PRRSV was numerically higher (6.5%) than mortality in those sites where WT-PRRSV was not detected (5.0%) (p = 0.07). Mortality was also higher (10.5%) when WT-PRRSV was detected earlier at eight weeks post-placement compared to late finishing at 20 and 25 weeks post-placement, 2.9% and 4.5% respectively (p = 0.017). Overall, this study sheds light on WT-PRRSV infection dynamics in vaccinated populations of growing pigs, reinforces the importance of biosecurity practices in this phase of production and calls for better understanding of risk factors associated with PRRSV introductions in growing pig sites.

Farm management practices associated with influenza A virus contamination of people working in Midwestern United States swine farms

Indirect transmission of influenza A virus (IAV) contributes to virus spread in pigs. To identify farm management activities with the ability to contaminate farmworkers' hands and clothing that then could be a source of virus spread to other pigs, we conducted a within-farm, prospective IAV surveillance study. Hands and clothes from farmworkers performing the activities of piglet processing, vaccination, or weaning were sampled before and after the activities were performed. Samples were tested by IAV rRT-PCR and virus viability was assessed by cell culture. A multivariate generalized linear model was used to detect associations of the activities with IAV contamination. Of the samples collected for IAV rRT-PCR testing, there were 16% (12/76) collected immediately after processing, 96% (45/48) collected after vaccination, and 94% (29/31) collected after weaning that tested positive. Samples collected immediately after vaccination and weaning, i.e., activities that took place during the peri-weaning period when pigs were about 3 weeks of age, had almost 6 times higher risk of IAV detection and had more samples IAV positive (p-value < 0.0001) than samples collected after processing, i.e., an activity that took place in the first few days of life. Both, hands and clothes had similar contamination rates (46% and 55% respectively, p-value = 0.42) and viable virus was isolated from both. Our results indicate that activities that involve the handling of infected piglets close to weaning age represent a significant risk for IAV dissemination due to the high level of IAV contamination found in farmworkers' hands and coveralls involved in the activities. Biosecurity protocols that include hand sanitation and changing clothing after performing activities with a high-risk of influenza contamination should be recommended to farmworkers to control and limit the mechanical spread of IAV between pigs.

Evaluation of internal farm biosecurity measures combined with sow vaccination to prevent influenza A virus infection in groups of due-to-wean pigs

Background

Influenza A virus (IAV) is an important respiratory pathogen of pigs that affects pig health, well-being and productivity, has zoonotic potential, and has significant economic impact for producers. The ultimate goal is to maintain herds free from IAV. Due to the probability of IAV introduction into the herds, it is also desirable for herds to have some immunity to the virus. In this study, we evaluated a protocol that combined sow vaccination with the implementation of internal biosecurity practices during the pre-weaning period with the goal to wean IAV negative pigs.

Five IAV positive breeding herds were vaccinated twice, 3 weeks apart with a herd-specific autogenous vaccine. For the subsequent 8 weeks, a biosecurity protocol was maintained, consisting of no pig movements after 3 days of age, no use of nurse sows, workers changing disposable gloves between litters, workers not stepping into farrowing crates, and daily disinfection of tools and materials used to handle pigs.

Results

Following these interventions, four of the five treatment farms had significant reductions in IAV detection (p value < 0.05). Three of the farms tested negative at all sampling points post-intervention and one farm had a 21% reduction in IAV positivity.

Conclusions

This study indicates that a protocol that combines sow vaccination and enhanced biosecurity practices may limit IAV transmission among piglets and enable the weaning of groups of pigs free from the virus.

Evaluation of dam parity and internal biosecurity practices in influenza infections in piglets prior to weaning

Influenza is an important respiratory disease of pigs and humans. Controlling influenza in pigs is challenging due to the substantial genetic diversity of influenza A virus (IAV). In this study, we assessed the impact of internal biosecurity practices directed at limiting exposure of piglets to IAV before weaning; evaluated the association of sow parity with IAV prevalence in piglets and the levels of maternally derived antibodies (MDA), and documented the frequency of detection of IAV on farmworkers' hands and the instruments used when handling pigs. The control group included litters in rooms where no specific changes were made to standard farm procedures. The treatment group included litters in rooms where no cross-fostering or nurse sows use was allowed, and where farmworkers were required to change gloves between litters when handling pigs. Both, younger (≤ Parity 3) and older parity sows (>Parity 3) were represented in all rooms included in the study. Overall, litters in the treatment group had lower IAV prevalence (29.9 %) than litters in the control group (44.2 %) (p < 0.001), and at day 8 of age the litters from the control group had 7.5 times higher IAV prevalence than the litters from the treatment group. However, at weaning differences were not found (77.2 % vs. 81 % for treatment vs. control, respectively, p = 0.41). There were no differences in IAV detection between parity groups at any of the sampling points (p = 0.86) and incidence of detection in sows from farrowing to weaning was 29 %. Piglets that tested ELISA negative were 1.3 times more likely to test IAV positive than piglets that were ELISA positive for IAV antibody test, suggesting that effective colostrum intake may reduce the likelihood of infection. IAV was detected on 46 % of the instruments used when handling piglets and on 58 % of farmworkers' hands, indicating the potential risk for mechanical transmission of IAV in pigs. Overall, we showed that the implementation of internal biosecurity practices that limit IAV exposure to newborn piglets helped delay IAV infections but were not sufficient to reduce the prevalence of IAV infection in litters at weaning.

Vaccination decreases the risk of influenza A virus reassortment but not genetic variation in pigs

Although vaccination is broadly used in North American swine breeding herds, managing swine influenza is challenging primarily due to the continuous evolution of influenza A virus (IAV) and the ability of the virus to transmit among vaccinated pigs. Studies that have simultaneously assessed the impact of vaccination on the emergence of IAV reassortment and genetic variation in pigs are limited. Here, we directly sequenced 28 bronchoalveolar lavage fluid (BALF) samples collected from vaccinated and unvaccinated pigs co-infected with H1N1 and H3N2 IAV strains, and characterized 202 individual viral plaques recovered from 13 BALF samples. We identified 54 reassortant viruses that were grouped in 17 single and 16 mixed genotypes. Notably, we found that prime-boost vaccinated pigs had less reassortant viruses than nonvaccinated pigs, likely due to a reduction in the number of days pigs were co-infected with both challenge viruses. However, direct sequencing from BALF samples revealed limited impact of vaccination on viral variant frequency, evolutionary rates, and nucleotide diversity in any IAV coding regions. Overall, our results highlight the value of IAV vaccination not only at limiting virus replication in pigs but also at protecting public health by restricting the generation of novel reassortants with zoonotic and/or pandemic potential.

Swine influenza A viruses cause severe illness among pigs and financial losses on pig farms worldwide. These viruses can also infect humans and have caused deadly human pandemics in the past. Influenza A viruses are dangerous because viruses can be transferred between humans, birds and pigs. These co-infections can allow the viruses to swap genetic material. Viral genetic exchanges can result in new virus strains that are more dangerous or that can infect other types of animals more easily.

Farmers vaccinate their pigs to control the swine influenza A virus. The vaccines are regularly updated to match circulating virus strains. But the virus evolves rapidly to escape vaccine-induced immunity, and infections are common even in vaccinated pigs. Learning about how vaccination affects the evolution of influenza A viruses in pigs could help scientists prevent outbreaks on pig farms and avoid spillover pandemics in humans.

Li et al. show that influenza A viruses are less likely to swap genetic material in vaccinated and boosted pigs than in unvaccinated animals. In the experiments, Li et al. collected swine influenza A samples from the lungs of pigs that had received different vaccination protocols. Next, Li et al. used next-generation sequencing to identify new mutations in the virus or genetic swaps among different strains. In pigs infected with both the H1N1 and H3N2 strains of influenza, the two viruses began trading genes within a week. But less genetic mixing occurred in vaccinated and boosted pigs because they spent less time infected with both viruses than in unvaccinated pigs. The vaccination status of the pig did not have much effect on how many new mutations occurred in the viruses.

The experiments show that vaccinating and boosting pigs against influenza A viruses may protect against genetic swapping among influenza viruses. If future studies on pig farms confirm the results, the information gleaned from the study could help scientists improve farm vaccine protocols to further reduce influenza risks to animals and people.

Evidence of influenza A infection and risk of transmission between pigs and farmworkers

Interspecies transmission of influenza A virus (IAV) between pigs and people represents a threat to both animal and public health. To better understand the risks of influenza transmission at the human–animal interface, we evaluated 1) the rate of IAV detection in swine farmworkers before and after work during two human influenza seasons, 2) assessed risk factors associated with IAV detection in farmworkers and 3) characterized the genetic sequences of IAV detected in both workers and pigs. Of 58 workers providing nasal passage samples during 8‐week periods during the 2017/18 and 2018/19 influenza seasons, 33 (57%) tested positive by rRT‐PCR at least once. Sixteen (27%) workers tested positive before work and 24 (41%) after work. At the sample level, 58 of 1,785 nasal swabs (3.2%) tested rRT‐PCR positive, of which 20 of 898 (2.2%) were collected prior to work and 38 of 887 (4.3%) after work. Although farmworkers were more likely to test positive at the end of the working day (OR = 1.98, 95% CI 1.14–3.41), there were no influenza‐like illness (ILI) symptoms, or other risk indicators, associated with IAV detection before or after reporting to work. Direct whole‐genome sequencing from samples obtained from worker nasal passages indicated evidence of infection of a worker with pandemic 2009 H1N1 of human‐origin IAV (H1‐pdm 1A 3.3.2) when reporting to work, and exposure of several workers to a swine‐origin IAV (H1‐alpha 1A 1.1) circulating in the pigs on the farm where they were employed. Our study provides evidence of 1) risk of IAV transmission between pigs and people, 2) pandemic H1N1 IAV infected workers reporting to work and 3) workers exposed to swine harbouring swine‐origin IAV in their nasal passages temporarily. Overall, our results emphasize the need to implement surveillance and transmission preventive protocols at the pig/human interface.

Wind tunnel-based testing of a photoelectrochemical oxidative filter-based air purification unit in coronavirus and influenza aerosol removal and inactivation

Recirculating air purification technologies are employed as potential means of reducing exposure to aerosol particles and airborne viruses. Toward improved testing of recirculating air purification units, we developed and applied a medium-scale single-pass wind tunnel test to examine the size-dependent collection of particles and the collection and inactivation of viable bovine coronavirus (BCoV, a betacoronavirus), porcine respiratory coronavirus (PRCV, an alphacoronavirus), and influenza A virus (IAV), by a commercial air purification unit. The tested unit, the Molekule Air Mini, incorporates a MERV 16 filter as well as a photoelectrochemical oxidating layer. It was found to have a collection efficiency above 95.8% for all tested particle diameters and flow rates, with collection efficiencies above 99% for supermicrometer particles with the minimum collection efficiency for particles smaller than 100 nm. For all three tested viruses, the physical tracer-based log reduction was near 2.0 (99% removal). Conversely, the viable virus log reductions were found to be near 4.0 for IAV, 3.0 for BCoV, and 2.5 for PRCV, suggesting additional inactivation in a virus family- and genus-specific manner. In total, this work describes a suite of test methods which can be used to rigorously evaluate the efficacy of recirculating air purification technologies.

Effect of pooling udder skin wipes on the detection of influenza A virus in preweaning pigs

Influenza A virus (IAV) active surveillance in pigs prior to weaning is commonly conducted by collecting individual samples, mostly nasal swabs. Recently, the use of udder skin wipes collected from lactating sows was identified as an effective sampling method to indicate IAV status of suckling piglets prior to weaning. However, there is limited information on the effect of pooling multiple udder wipes on the ability to detect IAV. We evaluated the effect of pooling 3, 5, or 10 udder wipes on the sensitivity of detecting IAV and compared the results with testing the wipes individually. The likelihood of detecting positive udder wipes decreased with pooling when the initial positive cycle threshold value was ≥31.5; pooling of up to 3 samples could be performed without affecting sensitivity significantly. Our results support pooling of udder skin wipes to conduct surveillance of IAV in pigs prior to weaning.

Greater than 3-Log Reduction in Viable Coronavirus Aerosol Concentration in Ducted Ultraviolet-C (UV-C) Systems

Control technologies to inactivate airborne viruses effectively are needed during the ongoing SARS-CoV-2 pandemic, and to guard against airborne transmitted diseases. We demonstrate that sealed UV-C flow reactors operating with fluences near 253 ± 1 nm of 13.9-49.6 mJ cm-2 efficiently inactivate coronaviruses in an aerosol. For measurements, porcine respiratory coronavirus (PRCV) was nebulized in a custom-built, 3.86 m wind tunnel housed in a biosafety level class II facility. The single pass log10 reduction of active coronavirus was in excess of 2.2 at a flow rate of 2439 L min-1 (13.9 mJ cm-2) and in excess of 3.7 (99.98% removal efficiency) at 684 L min-1 (49.6 mJ cm-2). Because virus titers resulting from sampling downstream of the UV-C reactor were below the limit of detection, the true log reduction is likely even higher than measured. Comparison of virus titration results to reverse transcriptase quantitative PCR and measurement of fluorescein concentrations (doped into the nebulized aerosol) reveals that the reduction in viable PRCV is primarily due to UV-C based inactivation, as opposed to physical collection of virus. The results confirm that UV-C flow reactors can efficiently inactivate coronaviruses through incorporation into HVAC ducts or recirculating air purifiers.

Shedding and transmission of a live attenuated influenza A virus vaccine in pre-weaned pigs under field conditions

Influenza A virus (IAV) is one of the most important respiratory viruses affecting pig health and vaccination is the most common strategy to control influenza infections. In this field study we assessed the onset and duration of shedding of a live attenuated influenza virus (LAIV) vaccine, its ability to transmit to non-vaccinated pigs and whether the LAIV could be aerosolized and detected in the environment. Thirty-three litters (n = 33) of a farm using the LAIV vaccine were selected for the study, a subset of them (n = 12) were left unvaccinated and a subset of piglets (n = 3) in vaccinated litters were also left unvaccinated to serve as sentinels. Selected piglets from the litters were sampled multiple days post vaccination (DPV) by collecting nasal swabs and blood, and were tested using a LAIV vaccine specific RT-PCR assay and hemagglutination inhibition assay against the LAIV strains respectively. Environmental specimens consisting of air and surface wipes were also collected. One hundred percent (21/21) of the vaccinated litters tested LAIV positive 1 DPV and until 6 DPV. In contrast, only five (5/33) of the thirty-three non-vaccinated pigs tested positive during the course of the study. Viable LAIV was confirmed in vaccinated pigs by cell culture and whole genome sequencing. In addition, low levels of LAIV RNA (RT-PCR Ct values ranging between 33 and 38) were detected in all air specimens collected on the day of vaccination and until 6 DPV (3/10). Pigs had maternally derived antibodies reactive against the LAIV strains which may have influenced the degree of shedding observed. Under the conditions of this study, shedding of the LAIV from vaccinated pigs was limited in time, resulted in minimal transmission to non-vaccinated pigs and was detected in low levels in aerosols collected in the vaccinated rooms likely influenced by the presence of maternally derived antibodies against the LAIV strains.

Comparison of samplers collecting airborne influenza viruses: 1. Primarily impingers and cyclones

Researchers must be able to measure concentrations, sizes, and infectivity of virus-containing particles in animal agriculture facilities to know how far infectious virus-containing particles may travel through air, where they may deposit in the human or animal respiratory tract, and the most effective ways to limit exposures to them. The objective of this study was to evaluate a variety of impinger and cyclone aerosol or bioaerosol samplers to determine approaches most suitable for detecting and measuring concentrations of virus-containing particles in air. Six impinger/cyclone air samplers, a filter-based sampler, and a cascade impactor were used in separate tests to collect artificially generated aerosols of MS2 bacteriophage and swine and avian influenza viruses. Quantification of infectious MS2 coliphage was carried out using a double agar layer procedure. The influenza viruses were titrated in cell cultures to determine quantities of infectious virus. Viral RNA was extracted and used for quantitative real time RT-PCR, to provide total virus concentrations for all three viruses. The amounts of virus recovered and the measured airborne virus concentrations were calculated and compared among the samplers. Not surprisingly, high flow rate samplers generally collected greater quantities of virus than low flow samplers. However, low flow rate samplers generally measured higher, and likely more accurate, airborne concentrations of Infectious virus and viral RNA than high flow samplers. To assess airborne viruses in the field, a two-sampler approach may work well. A suitable high flow sampler may provide low limits of detection to determine if any virus is present in the air. If virus is detected, a suitable lower flow sampler may measure airborne virus concentrations accurately.

Effect of influenza A virus sow vaccination on infection in pigs at weaning: A prospective longitudinal study

Although vaccination is the main measure to control influenza A virus (IAV) in swine, there is limited information on the efficacy of sow vaccination on reducing IAV infections in pigs at weaning. We assessed the effect of sow vaccination on IAV infection in pigs at weaning in a cohort of 52 breeding herds studied prospectively. Herds were voluntarily enrolled according to their IAV history, sow vaccination protocol and monitored during six months (prospective longitudinal study). On each herd, nasal swabs were collected monthly from 30 pigs at weaning and tested for IAV by RT-PCR. IAV was detected in 25% (75/305) of sampling events. Of 9,150 nasal swab pools (3 individual nasal swabs/pool), 15% (458/3050) of pools tested IAV positive. IAV infections in pigs at weaning were lower in vaccinated herds compared to non-vaccinated ones. Moreover, no significant differences were seen between prefarrow and whole herd protocols, or the use of commercial versus autogenous IAV vaccines. Prefarrow and whole herd vaccination protocols reduced the odds of groups testing IAV positive at weaning in comparison with no vaccination. Our results are relevant when considering implementation of sow vaccination to control influenza infections in pigs at weaning and, hence, minimize transmission to growing pigs and other farms.

Exploring heterologous prime-boost vaccination approaches to enhance influenza control in pigs

Influenza A viruses evolve rapidly to escape host immunity. In swine, this viral evolution has resulted in the emergence of multiple H1 and H3 influenza A virus (IAV) lineages in the United States (US) pig populations. The heterologous prime-boost vaccination strategy is a promising way to deal with diverse IAV infection in multiple animal models. However, whether or not this vaccination strategy is applicable to US swine to impart immunity against infection from North American strains of IAV is still unknown. We performed a vaccination-challenge study to evaluate the protective efficacy of using multivalent inactivated vaccine and/or a live attenuated IAV vaccine (LAIV) in pigs following multiple prime-boost vaccination protocols against a simultaneous H1N1 and H3N2 IAV infection. Our data show that pigs in the heterologous prime-boost vaccination group had more favorable outcomes consistent with a better response against virus challenge than non-vaccinated pigs. Additionally, delivering a multivalent heterologous inactivated vaccine boost to pigs following a single LAIV administration was also beneficial. We concluded the heterologous prime boost vaccination strategy may potentiate responses to suboptimal immunogens and holds the potential applicability to control IAV in the North American swine industry. However, more studies are needed to validate the application of this vaccination approach under field conditions.

Inactivation of airborne porcine reproductive and respiratory syndrome virus (PRRSv) by a packed bed dielectric barrier discharge non-thermal plasma

Porcine reproductive and respiratory syndrome virus (PRRSv) is one of the most significant airborne viruses impacting the pork industry in the US. Non-thermal plasmas (NTPs) are electrical discharges comprised of reactive radicals and excited species that inactivate viruses and bacteria. Our previous experiments using a packed bed NTP reactor demonstrated effective inactivation of bacteriophage MS2 as a function of applied voltage and power. The present study examined the effectiveness of the same reactor in inactivating aerosolized PRRSv. A PRRSv solution containing ∼10⁵ TCID₅₀/ml of PRRSv VR2332 strain was aerosolized at 3 ml/min by an air-jet nebulizer and introduced into 5 or 12 cfm air flow followed by NTP exposure in the reactor. Twin impingers upstream and downstream of the reactor collected samples of the virus-laden air flow for subsequent TCID₅₀ assay and qPCR analyses. An optical particle sizer measured upstream and downstream aerosol size distributions, giving estimates of aerosol filtration by the reactor. The results showed that PRRSv was inactivated to a similar degree as MS2 at the same conditions, with the maximum 1.3-log inactivation of PRRSv achieved at 20 kV and 12 cfm air flow rate. The results demonstrate the potential of properly optimized NTPs in controlling PRRSv transmission.

Immune responses to porcine epidemic diarrhea virus (PEDV) in swine and protection against subsequent infection

Understanding the immune responses against Porcine epidemic diarrhea virus (PEDV) is important to prevent infection and to design control strategies. We evaluated both systemic and mucosal immune responses to PEDV in pigs and assessed if prior exposure to virus protects against re-infection. Three-week-old pigs were infected with PEDV and immune response in blood, intestine, and mesenteric lymph node (MLN) was evaluated. At 30 dpi, virus exposed pigs were challenged with a field isolate of PEDV and immune response at 5 d post challenge was evaluated. We found that PEDV RNA persists in the intestine even after fecal shedding of the virus was stopped at 28 dpi and pigs previously exposed to PEDV are protected from virus shedding after re-infection. PEDV infection induced both humoral and cell mediated immune response with an increase in PEDV specific IgA and IgG antibodies in intestine and serum. Flow cytometry analysis showed a significantly higher frequency of B cells and lower frequency of T cells at 4 dpi. The frequency of CD4/CD8 double positive (DP) memory T cells was significantly increased in the MLN of challenged animals. These studies may provide further insights into understanding the mucosal immune response to PEDV and its role in protection against disease.

Animal Disease Surveillance in the 21st Century: Applications and Robustness of Phylodynamic Methods in Recent U.S. Human-Like H3 Swine Influenza Outbreaks

Emerging and endemic animal viral diseases continue to impose substantial impacts on animal and human health. Most current and past molecular surveillance studies of animal diseases investigated spatio-temporal and evolutionary dynamics of the viruses in a disjointed analytical framework, ignoring many uncertainties and made joint conclusions from both analytical approaches. Phylodynamic methods offer a uniquely integrated platform capable of inferring complex epidemiological and evolutionary processes from the phylogeny of viruses in populations using a single Bayesian statistical framework. In this study, we reviewed and outlined basic concepts and aspects of phylodynamic methods and attempted to summarize essential components of the methodology in one analytical pipeline to facilitate the proper use of the methods by animal health researchers. Also, we challenged the robustness of the posterior evolutionary parameters, inferred by the commonly used phylodynamic models, using hemagglutinin (HA) and polymerase basic 2 (PB2) segments of the currently circulating human-like H3 swine influenza (SI) viruses isolated in the United States and multiple priors. Subsequently, we compared similarities and differences between the posterior parameters inferred from sequence data using multiple phylodynamic models. Our suggested phylodynamic approach attempts to reduce the impact of its inherent limitations to offer less biased and biologically plausible inferences about the pathogen evolutionary characteristics to properly guide intervention activities. We also pinpointed requirements and challenges for integrating phylodynamic methods in routine animal disease surveillance activities.

Genetic variability of influenza A virus in pigs at weaning in Midwestern United States swine farms

Suckling piglets play an important role at maintaining influenza A virus (IAV) infections in breeding herds and disseminating them to other farms at weaning. However, the role they play at weaning to support and promote genetic variability of IAV is not fully understood. The objective here was to evaluate the genetic diversity of IAV in pigs at weaning in farms located in the Midwestern USA. Nasal swabs (n = 9,090) collected from piglets in breed-to-wean farms (n = 52) over a six-month period across seasons were evaluated for the presence of IAV. Nasal swabs (n = 391) from 23 IAV-positive farms were whole-genome sequenced. Multiple lineages of HA (n = 7) and NA (n = 3) were identified in 96% (22/23) and 61% (237/391) of the investigated farms and individual piglets, respectively. Co-circulation of multiple types of functional HA and NA was identified in most (83%) farms. Whole IAV genomes were completed for 126 individual piglet samples and 25 distinct and 23 mixed genotypes were identified, highlighting significant genetic variability of IAV in piglets. Co-circulation of IAV in the farms and co-infection of individual piglets at weaning was observed at multiple time points over the investigation period and appears to be common in the investigated farms. Statistically significant genetic variability was estimated within and between farms by AMOVA, and varying levels of diversity between farms were detected using the Shannon-Weiner Index. Results reported here demonstrate previously unreported levels of molecular complexity and genetic variability among IAV at the farm and piglet levels at weaning. Movement of such piglets infected at weaning may result in emergence of new strains and maintenance of endemic IAV infection in the US swine herds. Results presented here highlight the need for developing and implementing novel, effective strategies to prevent or control the introduction and transmission of IAV within and between farms in the country.

Transmission of influenza A virus and porcine reproductive and respiratory syndrome virus using a novel nurse sow model: a proof of concept

The mechanisms of transmission of influenza A virus (IAV) and porcine reproductive and respiratory syndrome virus (PRRSV) in pigs during the pre-weaning period are not fully elucidated. Since viable IAV and PRRSV can be found on the udder skin of lactating sows and the use of nurse sows is a common management practice, we developed a novel nurse sow model to evaluate the transmission of IAV and PRRSV from lactating sows to their adopted piglets. In two studies, we infected pigs with either IAV or PRRSV who then contaminated the udder skin of lactating dams with their nasal and oral secretions while suckling. Once the skin was confirmed virus positive for IAV and PRRSV, the sows were moved to separate empty clean rooms to adopt IAV and PRRSV negative suckling piglets. After adoption, 1 out of eight (12.5%) piglets tested IAV positive 1-day post-adoption (dpa) and the entire litter (8 out of 8) became positive by 4 dpa. In the case of PRRSV, 3 out of 11 (27.3%) pigs tested rRT-PCR positive 2 dpa and there were 7 out of 11 (63.6%) pigs positive at the termination of the study at 7 dpa. This study documented the transmission of IAV and PRRSV between litters of piglets by nurse sows and highlights the importance of the nurse sow-piglet as a unit that contributes to the maintenance of endemic infections in breeding herds. The use of nurse sows in pig farms, though beneficial for minimizing pre-weaning mortality and maximizing farm productivity, is seemingly detrimental as this practice may facilitate the transmission of IAV and PRRSV to piglets prior to weaning.

Antigenic characterization of novel H1 influenza A viruses in swine

Novel H1N2 influenza A viruses (IAVs) in swine have been identified in Chile co-circulating with pandemic H1N1 2009-like (A(H1N1)pdm09-like) viruses. The objective of this study was to characterize antigenically the swine H1 IAVs circulating in Chile. Genetic analysis based on the HA1 domain and antigenic analysis by hemagglutination inhibition assay were carried out. Three antigenic clusters were identified, named Chilean H1 A (ChH1A), Chilean H1 B (ChH1B), and A(H1N1)pdm09-like. The antigenic sites of ChH1A and ChH1B strains were 10–60% distant from those of commercial vaccine strains at the amino acid sequence level. Antigenic variants were identified within the clusters ChH1A and A(H1N1)pdm09-like. Substitutions in the main antigenic sites (E153G in Sa, Q193H in Sb, D168N in Ca1, P137S in Ca2, and F71L in Cb) were detected in variants from the ChH1A cluster, whereas only a single substitution in antigenic site Sa (G155E) was detected in variants from A(H1N1)pdm09-like cluster, which confirms the importance to carrying out antigenic analyses in addition to genetic analyses to evaluate control measures such as vaccination. These results highlight the need to update vaccines for swine in Chile and the importance of continued surveillance to determine the onward transmission of antigenic variants in Chilean pig populations.

Evaluation of potential risk of transmission of avian influenza A viruses at live bird markets in response to unusual crow die-offs in Bangladesh

In response to unusual crow die‐offs from avian influenza A(H5N1) virus infection during January‐February 2017 in Dhaka, Bangladesh, a One Health team assessed potential infection risks in live bird markets (LBMs). Evidence of aerosolized avian influenza A viruses was detected in LBMs and in the respiratory tracts of market workers, indicating exposure and potential for infection. This study highlighted the importance of surveillance platforms with a coordinated One Health strategy to investigate and mitigate zoonotic risk.

Genetic diversity of influenza A viruses circulating in pigs between winter and summer in a Minnesota live animal market

There has been little surveillance of influenza A viruses (IAVs) circulating in swine at live animal markets, particularly in the United States. To address this gap, we conducted active surveillance of IAVs in pigs, the air, and the environment during a summer and winter season in a live animal market in St. Paul, Minnesota, that had been epidemiologically associated with swine-origin influenza cases in humans previously. High rates of IAV were detected by PCR in swine lungs and oral fluids during both summer and winter seasons. Rates of IAV detection by PCR in the air were similar during summer and winter, although rates of successful virus isolation in the air were lower during summer than in winter (26% and 67%, respectively). H3N2 was the most prevalent subtype in both seasons, followed by H1N2. Genetically diverse viruses with multiple gene constellations were isolated from both winter and summer, with a total of 19 distinct genotypes identified. Comparative phylogenetic analysis of all eight segments of 40 virus isolates from summer and 122 isolates from winter revealed that the summer and winter isolates were genetically distinct, indicating IAVs are not maintained in the market, but rather are re-introduced, likely from commercial swine. These findings highlight the extent of IAV genetic diversity circulating in swine in live animal markets, even during summer months, and the ongoing risk to humans.

Indirect assessment of porcine reproductive and respiratory syndrome virus status in pigs prior to weaning by sampling sows and the environment

There is a need to develop cost effective approaches to sample large populations in particular to determine the disease status of pigs prior to weaning. In this study we assessed the presence of the porcine reproductive and respiratory syndrome virus (PRRSV) in the environment (surfaces and air) of farrowing rooms, and udder skin of lactating sows as an indirect measure of piglet PRRSV status. Samples were collected at processing and weaning every three weeks for 23 weeks after a PRRSV outbreak was diagnosed in a swine breeding herd. PRRSV was detected at processing in udder skin wipes, environmental wipes and airborne deposited particle samples up to 14 weeks post outbreak and at weaning in udder skin wipes up to 17 weeks post outbreak. Similar sensitivities were observed for udder skin wipes (43% [95% CI: 23%-66%]) and surface wipes (57% [95% CI: 34%-77%]) when compared to serum at the litter level from piglets at processing. PRRSV was detected in the environment and the udder skin of lactating sows, which indicates that aggregate samples of the environment or lactating sows may be used to evaluate the PRRSV status of the herd in pigs prior to weaning. However, the use of environmental samples to detect PRRSV by RT-PCR should not be used as the single method to assess the PRRSV status at the litter level. Furthermore, our findings also highlight potential sources of PRRSV infection for piglets in breeding herds.

Individual or Common Good? Voluntary Data Sharing to Inform Disease Surveillance Systems in Food Animals

Livestock producers have traditionally been reluctant to share information related to their business, including data on health status of their animals, which, sometimes, has impaired the ability to implement surveillance programs. However, during the last decade, swine producers in the United States (US) and other countries have voluntarily begun to share data for the control and elimination of specific infectious diseases, such as the porcine reproductive and respiratory syndrome virus (PRRSv). Those surveillance programs have played a pivotal role in bringing producers and veterinarians together for the benefit of the industry. Examples of situations in which producers have decided to voluntarily share data for extended periods of time to support applied research and, ultimately, disease control in the absence of a regulatory framework have rarely been documented in the peer-reviewed literature. Here, we provide evidence of a national program for voluntary sharing of disease status data that has helped the implementation of surveillance activities that, ultimately, allowed the generation of critically important scientific information to better support disease control activities. Altogether, this effort has supported, and is supporting, the design and implementation of prevention and control approaches for the most economically devastating swine disease affecting the US. The program, which has been voluntarily sustained and supported over an extended period of time by the swine industry in the absence of any regulatory framework and that includes data on approximately 50% of the sow population in the US, represents a unique example of a livestock industry self-organized surveillance program to generate scientific-driven solutions for emerging swine health issues in North America.

Human-Origin Influenza A(H3N2) Reassortant Viruses in Swine, Southeast Mexico

The genetic diversity of influenza A viruses circulating in swine in Mexico complicates control efforts in animals and presents a threat to humans, as shown by influenza A(H1N1)pdm09 virus. To describe evolution of swine influenza A viruses in Mexico and evaluate strains for vaccine development, we sequenced the genomes of 59 viruses and performed antigenic cartography on strains from 5 regions. We found that genetic and antigenic diversity were particularly high in southeast Mexico because of repeated introductions of viruses from humans and swine in other regions in Mexico. We identified novel reassortant H3N2 viruses with genome segments derived from 2 different viruses that were independently introduced from humans into swine: pandemic H1N1 viruses and seasonal H3N2 viruses. The Mexico swine viruses are antigenically distinct from US swine lineages. Protection against these viruses is unlikely to be afforded by US virus vaccines and would require development of new vaccines specifically targeting these diverse strains.

Comparison of individual, group and environmental sampling strategies to conduct influenza surveillance in pigs

BACKGROUND

Influenza A virus (IAV) is an important pathogen in pigs that affects productivity and has important public health implications because of its zoonotic nature. Surveillance is central to the control of influenza, however, detection of IAV infections can be challenging in endemically infected herds with low prevalence of infection.

METHODS

In groups of suckling (18-21 days of age) and growing (35-45 days of age) pigs, we compared various sampling approaches to detect, isolate and sequence IAV using individual (nasal swabs, nasal wipes and oropharyngeal swabs), group (oral fluids, surface wipes and sow udder skin wipes) and environmental (airborne particles deposited on surfaces and air samples) sampling approaches. All samples were tested by IAV rRT-PCR and a subset was used for virus isolation and direct sequencing.

RESULTS

In general, environmental and group samples resulted in higher odd ratios (range = 3.87-16.5, p-value < 0.05) of detecting a positive sample by rRT-PCR compared to individual pooled samples, except for oropharyngeal swabs (OR = 8.07, p-value < 0.05). In contrast, individual samples were most likely to yield a viral isolate by cell culture. Oropharyngeal swabs in suckling pigs (78.4%), and nasal swabs (47.6%) or nasal wipes (45%) in growing pigs, and udder wipes in lactating sows (75%) were the preferred samples to obtain an isolate.

CONCLUSIONS

Our findings indicate that group and environmental sampling strategies should be considered in influenza surveillance programs in particular if the goal is just to detect infection. This study provides new information on sampling approaches to conduct effective influenza surveillance in pigs and identifies udder wipes from lactating sows as a novel sample type that offers a convenient, cheap and sensitive manner to monitor IAV in litters prior to weaning.

Effect of strain-specific maternally-derived antibodies on influenza A virus infection dynamics in nursery pigs

Reducing the number of influenza A virus (IAV) infected pigs at weaning is critical to minimize IAV spread to other farms. Sow vaccination is a common measure to reduce influenza levels at weaning. However, the impact of maternally-derived antibodies on IAV infection dynamics in growing pigs is poorly understood. We evaluated the effect of maternally-derived antibodies at weaning on IAV prevalence at weaning, time of influenza infection, number of weeks that pigs tested IAV positive, and estimated quantity of IAV in nursery pigs. We evaluated 301 pigs within 10 cohorts for their influenza serological (seroprevalence estimated by hemagglutination inhibition (HI) test) and virological (prevalence) status. Nasal swabs were collected weekly and pigs were bled 3 times throughout the nursery period. There was significant variability in influenza seroprevalence, HI titers and influenza prevalence after weaning. Increase in influenza seroprevalence at weaning was associated with low influenza prevalence at weaning and delayed time to IAV infection throughout the nursery. Piglets with IAV HI titers of 40 or higher at weaning were also less likely to test IAV positive at weaning, took longer to become infected, tested IAV RT-PCR positive for fewer weeks, and had higher IAV RT-PCR cycle threshold values compared to piglets with HI titers less than 40. Our findings suggest that sow vaccination or infection status that results in high levels of IAV strain-specific maternally-derived antibodies may help to reduce IAV circulation in both suckling and nursery pigs.

Breed-to-wean farm factors associated with influenza A virus infection in piglets at weaning

Breed-to-wean pig farms play an important role in spreading influenza A virus (IAV) because suckling piglets maintain, diversify and transmit IAV at weaning to other farms. Understanding the nature and extent of which farm factors drive IAV infection in piglets is a prerequisite to reduce the burden of influenza in swine. We evaluated the association between IAV infection in piglets at weaning and farm factors including farm features, herd management practices and gilt- and piglet-specific management procedures performed at the farm. Voluntarily enrolled breed-to-wean farms (n = 83) agreed to share IAV diagnostic testing and farm data from July 2011 through March 2017 including data obtained via the administration of a survey. There were 23% IAV RT-PCR positive samples of the 12,814 samples submitted for IAV testing within 2989 diagnostic submissions with 30% positive submissions. Among all the factors evaluated (n = 24), and considering the season-adjusted multivariable analysis, only sow IAV vaccination and gilt IAV status at entry significantly reduced (p-value<0.05) IAV infections in piglets at weaning. Results from this study indicate that veterinarians and producers could manage these identified factors to reduce the burden of influenza in piglets prior to wean and perhaps, reduce the spread of IAV to other farms and people.

Use of processing fluids and serum samples to characterize porcine reproductive and respiratory syndrome virus dynamics in 3 day-old pigs

Collection of serum samples of pigs at weaning to monitor for porcine reproductive and respiratory syndrome virus (PRRSV) has become a common practice to determine PRRSV herd infection status. Diagnostic sensitivity of this practice is low in herds undergoing PRRSV elimination once prevalence of infection is near zero. Thus, the goal of this study was to characterize the dynamics of PRRSV infection in 3 day-old pigs overtime using serum and serosanguineous fluids obtained as part of castration and tail docking practices (processing fluids (PF)). Secondary goal was to estimate sensitivity and specificity of PF in the 3 day old population. A 6000 breed-to-wean sow herd was monitored every three weeks for 23 weeks after a PRRSV outbreak by collecting both PF and individual serum samples from all pigs in the selected litters. Out of the 77 litters tested, 23 (29.8%) were identified as positive using the PF and the serum samples, with a Cohen's kappa statistic of 0.81 (95% CI: 0.59-1) between the results obtained in each sample type. The sensitivity and specificity of the PF relative to the results in serum was 87% (95% CI: 66%-97%) and 94% (95% CI: 85%-99%) respectively. The percentage of PRRSV positive litters decreased over time and litters from gilts were more likely to test positive than those from older sows. Overall, the study demonstrates that PF can be a convenient and reliable specimen to monitor PRRSV infection in breeding herds.

Detection of influenza A virus in aerosols of vaccinated and non-vaccinated pigs in a warm environment

The 2009 influenza pandemic, the variant H3N2v viruses in agricultural fairs and the zoonotic poultry H5N9 infections in China have highlighted the constant threat that influenza A viruses (IAV) present to people and animals. In this study we evaluated the effect of IAV vaccination on aerosol shedding in pigs housed in warm environmental conditions. Thirty-six, three-week old weaned pigs were obtained from an IAV negative herd and were randomly allocated to one of 4 groups: 1) a homologous vaccine group, 2) a heterologous multivalent vaccine group, 3) a heterologous monovalent group and, 4) a non-vaccinated group. After vaccination pigs were challenged with the triple reassortant A/Sw/IA/00239/04 H1N1 virus. Environmental temperature and relative humidity were recorded throughout the study. Nasal swabs, oral fluids and air samples were collected daily. All samples were tested by RRT-PCR and virus isolation was attempted on positive samples. Average temperature and relative humidity throughout the study were 27°C (80°F) and 53%, respectively. A significantly higher proportion of infected pigs was detected in the non-vaccinated than in the vaccinated group. Lower levels of nasal virus shedding were found in vaccinated groups compared to non-vaccinated group and IAV was not detected in air samples of any of the vaccinated groups. In contrast, positive air samples were detected in the non-vaccinated group at 1, 2 and 3 days post infection although the overall levels were considered low most likely due to the elevated environmental temperature. In conclusion, both the decrease in shedding and the increase in environmental temperature may have contributed to the inability to detect airborne IAV in vaccinated pigs.

Influenza Herd-Level Prevalence and Seasonality in Breed-to-Wean Pig Farms in the Midwestern United States

Influenza is a costly disease for pig producers and understanding its epidemiology is critical to control it. In this study, we aimed to estimate the herd-level prevalence and seasonality of influenza in breed-to-wean pig farms, evaluate the correlation between influenza herd-level prevalence and meteorological conditions, and characterize influenza genetic diversity over time. A cohort of 34 breed-to-wean farms with monthly influenza status obtained over a 5-year period in piglets prior to wean was selected. A farm was considered positive in a given month if at least one oral fluid tested influenza positive by reverse transcriptase polymerase chain reaction. Influenza seasonality was assessed combining autoregressive integrated moving average (ARIMA) models with trigonometric functions as covariates. Meteorological conditions were gathered from local land-based weather stations, monthly aggregated and correlated with influenza herd-level prevalence. Influenza herd-level prevalence had a median of 28% with a range from 7 to 57% and followed a cyclical pattern with levels increasing during fall, peaking in both early winter (December) and late spring (May), and decreasing in summer. Influenza herd-level prevalence was correlated with mean outdoor air absolute humidity (AH) and temperature. Influenza genetic diversity was substantial over time with influenza isolates belonging to 10 distinct clades from which H1 delta 1 and H1 gamma 1 were the most common. Twenty-one percent of farms had three different clades co-circulating over time, 18% of farms had two clades, and 41% of farms had one clade. In summary, our study showed that influenza had a cyclical pattern explained in part by air AH and temperature changes over time, and highlighted the importance of active surveillance to identify high-risk periods when strategic control measures for influenza could be implemented.

Multiple Genome Constellations of Similar and Distinct Influenza A Viruses Co-Circulate in Pigs During Epidemic Events

Swine play a key role in the ecology and transmission of influenza A viruses (IAVs) between species. However, the epidemiology and diversity of swine IAVs is not completely understood. In this cohort study, we sampled on a weekly basis 132 3-week old pigs for 15 weeks. We found two overlapping epidemic events of infection in which most pigs (98.4%) tested PCR positive for IAVs. The prevalence rate of infection ranged between 0 and 86% per week and the incidence density ranged between 0 and 71 cases per 100 pigs-week. Three distinct influenza viral groups (VGs) replicating as a "swarm" of viruses were identified (swine H1-gamma, H1-beta, and H3-cluster-IV IAVs) and co-circulated at different proportions over time suggesting differential allele fitness. Furthermore, using deep genome sequencing 13 distinct viral genome constellations were differentiated. Moreover, 78% of the pigs had recurrent infections with IAVs closely related to each other or IAVs clearly distinct. Our results demonstrated the molecular complexity of swine IAVs during natural infection of pigs in which novel strains of IAVs with zoonotic and pandemic potential can emerge. These are key findings to design better health interventions to reduce the transmission of swine IAVs and minimize the public health risk.

Investigation into the Airborne Dissemination of H5N2 Highly Pathogenic Avian Influenza Virus During the 2015 Spring Outbreaks in the Midwestern United States

We investigated the plausibility of aerosol transmission of H5N2 highly pathogenic avian influenza (HPAI) virus during the 2015 spring outbreaks that occurred in the U.S. midwest. Air samples were collected inside and outside of infected turkey and layer facilities. Samples were tested to assess HPAI virus concentration (RNA copies/m(3) of air), virus viability, and virus distribution by particle size. HPAI virus RNA was detected inside and up to 1000 m from infected facilities. HPAI virus was isolated from air samples collected inside, immediately outside, up to 70 m from infected facilities, and in aerosol particles larger than 2.1 μm. Direct exposure to exhausted aerosols proved to be a significant source of environmental contamination. These findings demonstrate HPAI virus aerosolization from infected flocks, and that both the transport of infectious aerosolized particles and the deposition of particles on surfaces around infected premises represent a potential risk for the spread of HPAI.

The Use of Bioaerosol Sampling for Airborne Virus Surveillance in Swine Production Facilities: A Mini Review

Modern swine production facilities typically house dense populations of pigs and may harbor a variety of potentially zoonotic viruses that can pass from one pig generation to another and periodically infect human caretakers. Bioaerosol sampling is a common technique that has been used to conduct microbial risk assessments in swine production, and other similar settings, for a number of years. However, much of this work seems to have been focused on the detection of non-viral microbial agents (i.e., bacteria, fungi, endotoxins, etc.), and efforts to detect viral aerosols in pig farms seem sparse. Data generated by such studies would be particularly useful for assessments of virus transmission and ecology. Here, we summarize the results of a literature review conducted to identify published articles related to bioaerosol generation and detection within swine production facilities, with a focus on airborne viruses. We identified 73 scientific reports, published between 1991 and 2017, which were included in this review. Of these, 19 (26.7%) used sampling methodology for the detection of viruses. Our findings show that bioaerosol sampling methodologies in swine production settings have predominately focused on the detection of bacteria and fungi, with no apparent standardization between different approaches. Information, specifically regarding virus aerosol burden in swine production settings, appears to be limited. However, the number of viral aerosol studies has markedly increased in the past 5 years. With the advent of new sampling technologies and improved diagnostics, viral bioaerosol sampling could be a promising way to conduct non-invasive viral surveillance among swine farms.

Evaluation of biosecurity measures to prevent indirect transmission of porcine epidemic diarrhea virus

Background

The effectiveness of biosecurity methods to mitigate the transmission of porcine epidemic diarrhea virus (PEDV) via farm personnel or contaminated fomites is poorly understood. This study was undertaken to evaluate the effectiveness of biosecurity procedures directed at minimizing transmission via personnel following different biosecurity protocols using a controlled experimental setting.

Results

PEDV RNA was detected from rectal swabs of experimentally infected (INF) and sentinel pigs by real-time reverse transcription polymerase chain reaction (rRT-PCR). Virus shedding in INF pigs peaked at 1 day post infection (dpi) and viral RNA levels remained elevated through 19 dpi. Sentinel pigs in the low biosecurity group (LB) became PEDV positive after the first movement of study personnel from the INF group. However, rectal swabs from pigs in the medium biosecurity (MB) and high biosecurity (HB) groups were negative during the 10 consecutive days of movements and remained negative through 24 days post movement (dpm) when the first trial was terminated.

Viral RNA was detected at 1 dpm through 3 dpm from the personal protective equipment (PPE) of LB personnel. In addition, at 1 dpm, 2 hair/face swabs from MB personnel were positive; however, transmission of virus was not detected. All swabs of fomite from the HB study personnel were negative.

Conclusions

These results indicate that indirect PEDV transmission through contaminated PPE occurs rapidly (within 24 h) under modeled conditions. Biosecurity procedures such as changing PPE, washing exposed skin areas, or taking a shower are recommended for pig production systems and appear to be an effective option for lowering the risk of PEDV transmission between groups of pigs.

Influenza A virus in swine breeding herds: Combination of vaccination and biosecurity practices can reduce likelihood of endemic piglet reservoir

Recent modelling and empirical work on influenza A virus (IAV) suggests that piglets play an important role as an endemic reservoir. The objective of this study is to test intervention strategies aimed at reducing the incidence of IAV in piglets and ideally, preventing piglets from becoming exposed in the first place. These interventions include biosecurity measures, vaccination, and management options that swine producers may employ individually or jointly to control IAV in their herds. We have developed a stochastic Susceptible-Exposed-Infectious-Recovered-Vaccinated (SEIRV) model that reflects the spatial organization of a standard breeding herd and accounts for the different production classes of pigs therein. Notably, this model allows for loss of immunity for vaccinated and recovered animals, and for vaccinated animals to have different latency and infectious periods from unvaccinated animals as suggested by the literature. The interventions tested include: (1) varied timing of gilt introductions to the breeding herd, (2) gilt separation (no indirect transmission to or from the gilt development unit), (3) gilt vaccination upon arrival to the farm, (4) early weaning, and (5) vaccination strategies of sows with different timing (mass and pre-farrow) and efficacy (homologous vs. heterologous). We conducted a Latin Hypercube Sampling and Partial Rank Correlation Coefficient (LHS-PRCC) analysis combined with a random forest analysis to assess the relative importance of each epidemiological parameter in determining epidemic outcomes. In concert, mass vaccination, early weaning of piglets (removal 0-7days after birth), gilt separation, gilt vaccination, and longer periods between introductions of gilts (6 months) were the most effective at reducing prevalence. Endemic prevalence overall was reduced by 51% relative to the null case; endemic prevalence in piglets was reduced by 74%; and IAV was eliminated completely from the herd in 23% of all simulations. Importantly, elimination of IAV was most likely to occur within the first few days of an epidemic. The latency period, infectious period, duration of immunity, and transmission rate for piglets with maternal immunity had the highest correlation with three separate measures of IAV prevalence; therefore, these are parameters that warrant increased attention for obtaining empirical estimates. Our findings support other studies suggesting that piglets play a key role in maintaining IAV in breeding herds. We recommend biosecurity measures in combination with targeted homologous vaccination or vaccines that provide wider cross-protective immunity to prevent incursions of virus to the farm and subsequent establishment of an infected piglet reservoir.

Modeling risk of occupational zoonotic influenza infection in swine workers

Zoonotic transmission of influenza A virus (IAV) between swine and workers in swine production facilities may play a role in the emergence of novel influenza strains with pandemic potential. Guidelines to prevent transmission of influenza to swine workers have been developed but there is a need for evidence-based decision-making about protective measures such as respiratory protection. A mathematical model was applied to estimate the risk of occupational IAV exposure to swine workers by contact and airborne transmission, and to evaluate the use of respirators to reduce transmission.  The Markov model was used to simulate the transport and exposure of workers to IAV in a swine facility. A dose-response function was used to estimate the risk of infection. This approach is similar to methods previously used to estimate the risk of infection in human health care settings. This study uses concentration of virus in air from field measurements collected during outbreaks of influenza in commercial swine facilities, and analyzed by polymerase chain reaction.  It was found that spending 25 min working in a barn during an influenza outbreak in a swine herd could be sufficient to cause zoonotic infection in a worker. However, this risk estimate was sensitive to estimates of viral infectivity to humans. Wearing an excellent fitting N95 respirator reduced this risk, but with high aerosol levels the predicted risk of infection remained high under certain assumptions.  The results of this analysis indicate that under the conditions studied, swine workers are at risk of zoonotic influenza infection. The use of an N95 respirator could reduce such risk. These findings have implications for risk assessment and preventive programs targeting swine workers. The exact level of risk remains uncertain, since our model may have overestimated the viability or infectivity of IAV. Additionally, the potential for partial immunity in swine workers associated with repeated low-dose exposures or from previous infection with other influenza strains was not considered. Further studies should explore these uncertainties.

Swine Worker Precautions During Suspected Outbreaks of Influenza in Swine

To assess the behavior and precautions that swine workers take during suspected influenza outbreaks in swine, six commercial swine farms in the Midwest U.S. region were visited when influenza outbreaks were suspected in herds during the fall/winter of 2012-2013. Use of personal protective equipment (PPE) and type of task performed by swine workers were recorded based on farm representative reports. Between one to two workers were working on the day of each visit and spent approximately 25 minutes performing work-related tasks that placed them in close contact with the swine. The most common tasks reported were walking the aisles (27%), handling pigs (21%), and handling equipment (21%). The most common PPE were boots (100%), heavy rubber gloves (75%), and dedicated nondisposable clothing (74%). Use of N95 respirators was reported at three farms. Hand hygiene practices were common in most of the farms, but reportedly performed for only 20% to 25% of tasks.

Evaluation of an electrostatic particle ionization technology for decreasing airborne pathogens in pigs

Influenza A virus (IAV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV) and Staphylococcus aureus are important swine pathogens capable of being transmitted via aerosols. The electrostatic particle ionization system (EPI) consists of a conductive line that emits negative ions that charge particles electrically resulting in the settling of airborne particles onto surfaces and potentially decreasing the risk of pathogen dissemination. The objectives of this study were to determine the effect of the EPI system on the quantity and viability of IAV, PRRSV, PEDV and S. aureus in experimentally generated aerosols and in aerosols generated by infected animals. Efficiency at removing airborne particles was evaluated as a function of particle size (ranging from 0.4 to 10 µm), distance from the source of ions (1, 2 and 3 m) and relative air humidity (RH 30 vs. 70 %). Aerosols were sampled with the EPI system "off" and "on." Removal efficiency was significantly greater for all pathogens when the EPI line was the closest to the source of aerosols. There was a greater reduction for larger particles ranging between 3.3 and 9 µm, which varied by pathogen. Overall airborne pathogen reduction ranged between 0.5 and 1.9 logs. Viable pathogens were detected with the EPI system "on," but there was a trend to reducing the quantity of viable PRRSV and IAV. There was not a significant effect on the pathogens removal efficiency based on the RH conditions tested. In summary, distance to the source of ions, type of pathogen and particle size influenced the removal efficiency of the EPI system. The reduction in infectious agents in the air by the EPI technology could potentially decrease the microbial exposure for pigs and people in confinement livestock facilities.

Haemophilus parasuis: infection, immunity and enrofloxacin

Haemophilus parasuis is an early colonizer of the porcine upper respiratory tract and is the etiological agent of Glasser’s disease. The factors responsible for H. parasuis colonization and systemic infection are not yet well understood, while prevention and control of Glasser’s disease continues to be challenging. Recent studies on innate immunity to H. parasuis have demonstrated that porcine alveolar macrophages (PAMs) are able to differentially up-regulate several genes related to inflammation and phagocytosis, and several pro-inflammatory cytokines are produced by porcine cells upon exposure to H. parasuis. The susceptibility of H. parasuis strains to phagocytosis by PAMs and the bactericidal effect of complement are influenced by the virulent phenotype of the strains. While non-virulent strains are susceptible to phagocytosis and complement, virulent strains are resistant to both. However, in the presence of specific antibodies against H. parasuis, virulent strains become susceptible to phagocytosis. More information is still needed, though, in order to better understand the host immune responses to H. parasuis. Antimicrobials are commonly used in the swine industry to help treat and control Glasser’s disease. Some of the common antimicrobials have been shown to reduce colonization by H. parasuis, which may have implications for disease dynamics, development of effective immune responses and immunomodulation. Here, we provide the current state of research on innate and adaptive immune responses to H. parasuis and discuss the potential effect of enrofloxacin on the development of a protective immune response against H. parasuis infection.

Concentration, Size Distribution, and Infectivity of Airborne Particles Carrying Swine Viruses

When pathogens become airborne, they travel associated with particles of different size and composition. Particle size determines the distance across which pathogens can be transported, as well as the site of deposition and the survivability of the pathogen. Despite the importance of this information, the size distribution of particles bearing viruses emitted by infectious animals remains unknown. In this study we characterized the concentration and size distribution of inhalable particles that transport influenza A virus (IAV), porcine reproductive and respiratory syndrome virus (PRRSV), and porcine epidemic diarrhea virus (PEDV) generated by acutely infected pigs and assessed virus viability for each particle size range. Aerosols from experimentally infected pigs were sampled for 24 days using an Andersen cascade impactor able to separate particles by size (ranging from 0.4 to 10 micrometer (μm) in diameter). Air samples collected for the first 9, 20 and the last 3 days of the study were analyzed for IAV, PRRSV and PEDV, respectively, using quantitative reverse transcription polymerase chain reaction (RT-PCR) and quantified as geometric mean copies/m³ within each size range. IAV was detected in all particle size ranges in quantities ranging from 5.5x10² (in particles ranging from 1.1 to 2.1μm) to 4.3x10⁵ RNA copies/m³ in the largest particles (9.0–10.0μm). PRRSV was detected in all size ranges except particles between 0.7 and 2.1μm in quantities ranging from 6x10² (0.4–0.7μm) to 5.1x10⁴ RNA copies/m³ (9.0–10.0μm). PEDV, an enteric virus, was detected in all particle sizes and in higher quantities than IAV and PRRSV (p < 0.0001) ranging from 1.3x10⁶ (0.4–0.7μm) to 3.5x10⁸ RNA copies/m³ (9.0–10.0μm). Infectious status was demonstrated for the 3 viruses, and in the case of IAV and PRRSV, viruses were isolated from particles larger than 2.1μm. In summary, our results indicated that airborne PEDV, IAV and PRRSV can be found in a wide range of particle sizes. However, virus viability is particle size dependent.

Novel Human-like Influenza A Viruses Circulate in Swine in Mexico and Chile

INTRODUCTION

Further understanding of the genetic diversity and evolution of influenza A viruses circulating in swine (IAV-S) is important for the development of effective vaccines and our knowledge of pandemic threats. Until recently, very little was known of IAV-S diversity in Latin America, owing to a lack of surveillance.

METHODS

To address this gap, we sequenced and conducted a phylogenetic analysis of 69 hemagglutinin (HA) sequences from IAV-S isolates collected in swine in Mexico and Chile during 2010-2014, including the H1N1, H1N2, and H3N2 subtypes.

RESULTS

Our analysis identified multiple IAV-S lineages that appear to have been circulating undetected in swine for decades, including four novel IAV-S lineages of human seasonal virus origin that have not been previously identified in any swine populations globally. We also found evidence of repeated introductions of pandemic H1N1 viruses from humans into swine in Mexico and Chile since 2009, and incursions of H1 and H3 viruses from North American swine into Mexico.

DISCUSSION

Overall, our findings indicate that at least 12 genetically distinct HA lineages circulate in Latin American swine herds, only two of which have been found in North American swine herds. Human-to-swine transmission, spatial migration via swine movements, and genomic reassortment are the key evolutionary mechanisms that generate this viral diversity. Additional antigenic characterization and whole-genome sequencing is greatly needed to understand the diversity and independent evolution of IAV-S in Latin America.

Genome plasticity of triple-reassortant H1N1 influenza A virus during infection of vaccinated pigs

To gain insight into the evolution of influenza A viruses (IAVs) during infection of vaccinated pigs, we experimentally infected a 3-week-old naive pig with a triple-reassortant H1N1 IAV and placed the seeder pig in direct contact with a group of age-matched vaccinated pigs (n = 10). We indexed the genetic diversity and evolution of the virus at an intra-host level by deep sequencing the entire genome directly from nasal swabs collected at two separate samplings during infection. We obtained 13 IAV metagenomes from 13 samples, which included the virus inoculum and two samples from each of the six pigs that tested positive for IAV during the study. The infection produced a population of heterogeneous alleles (sequence variants) that was dynamic over time. Overall, 794 polymorphisms were identified amongst all samples, which yielded 327 alleles, 214 of which were unique sequences. A total of 43 distinct haemagglutinin proteins were translated, two of which were observed in multiple pigs, whereas the neuraminidase (NA) was conserved and only one dominant NA was found throughout the study. The genetic diversity of IAVs changed dynamically within and between pigs. However, most of the substitutions observed in the internal gene segments were synonymous. Our results demonstrated remarkable IAV diversity, and the complex, rapid and dynamic evolution of IAV during infection of vaccinated pigs that can only be appreciated with repeated sampling of individual animals and deep sequence analysis.

Live Animal Markets in Minnesota: A Potential Source for Emergence of Novel Influenza A Viruses and Interspecies Transmission

BACKGROUND

Live animal markets have been implicated in transmission of influenza A viruses (IAVs) from animals to people. We sought to characterize IAVs at 2 live animal markets in Minnesota to assess potential routes of occupational exposure and risk for interspecies transmission.

METHODS

We implemented surveillance for IAVs among employees, swine, and environment (air and surfaces) during a 12-week period (October 2012-January 2013) at 2 markets epidemiologically associated with persons with swine-origin IAV (variant) infections. Real-time reverse transcription polymerase chain reaction (rRT-PCR), viral culture, and whole-genome sequencing were performed on respiratory and environmental specimens, and serology on sera from employees at beginning and end of surveillance.

RESULTS

Nasal swabs from 11 of 17 (65%) employees tested positive for IAVs by rRT-PCR; 7 employees tested positive on multiple occasions and 1 employee reported influenza-like illness. Eleven of 15 (73%) employees had baseline hemagglutination inhibition antibody titers ≥40 to swine-origin IAVs, but only 1 demonstrated a 4-fold titer increase to both swine-origin and pandemic A/Mexico/4108/2009 IAVs. IAVs were isolated from swine (72/84), air (30/45), and pen railings (5/21). Whole-genome sequencing of 122 IAVs isolated from swine and environmental specimens revealed multiple strains and subtype codetections. Multiple gene segment exchanges among and within subtypes were observed, resulting in new genetic constellations and reassortant viruses. Genetic sequence similarities of 99%-100% among IAVs of 1 market customer and swine indicated interspecies transmission.

CONCLUSIONS

At markets where swine and persons are in close contact, swine-origin IAVs are prevalent and potentially provide conditions for novel IAV emergence.

Association between Influenza A Virus Infection and Pigs Subpopulations in Endemically Infected Breeding Herds

Influenza A viruses (IAVs) are distributed worldwide in birds, pigs and humans, and cause important endemic disease affecting hosts in all countries. Although pigs play a key role in the ecology of IAVs, the epidemiology of IAVs within swine herds is poorly understood. In this longitudinal study we describe the prevalence of IAVs infection in three subpopulations of pigs in 5 breeding herds in the Midwestern USA. Each herd was sampled monthly for a year and, at each visit, 30 individual nasal swabs were collected from the three subpopulations, namely, a) replacement females, resident on-farm for less than 4 weeks (new gilts), b) replacement females, resident on-farm for more than 4 weeks (gilts), and c) neonatal pigs less than 21 days of age (piglets). Real time reverse transcriptase polymerase chain reaction (RRT-PCR) was used to detect IAVs, and the association between IAVs infection and pig subpopulation was measured using a mixed logistic regression model. Nasal swabs (n = 4,190) were collected from 141 groups of pigs. At least, one IAV-positive nasal swab was found in 19.9% (n = 28) of the sampled groups, and 7.7% (n = 324) of all nasal swabs tested positive. After adjusting by annual quarter and sampling event, the odds of testing IAV positive were 7.9 (95% CI 1.4, 43.9) and 4.4 (95% CI 1.1, 17.1) times higher in groups of new gilts and piglets compared to groups of gilts, respectively. Results indicate that new gilts and piglets had higher odds of testing IAV positive than gilts in swine breeding herds and that season influences IAV infection in pigs. Based on these findings, we recommend that IAV control strategies be aimed at preventing infection before gilts are introduced into the farm, and in pigs prior to weaning.

The effect of anatomic site and age on detection of Staphylococcus aureus in pigs

Despite active research into methicillin-resistant Staphylococcus aureus (MRSA) in pigs since 2004, the ecology of the susceptible ancestral organism has been neglected. A longitudinal study of pigs in 2 intensive production systems was conducted to investigate the effects of age and anatomical site on detection of S. aureus. Sampling was replicated in 2 cohorts per farm, with swabs collected from the nares, tonsils, skin (axilla), and rectum in lactating sows, suckling, weaned, and market-age pigs, plus the vagina of sows. No MRSA were isolated, but S. aureus was detected in a least 1 site in 175 (91.1%) out of 192 pigs. Pig-level prevalence did not differ among the age groups, but the proportion of positive samples (all sites) was higher in market-age pigs (75.2%) and nursery-age pigs (63.2%) than in sows (40.7%) and suckling piglets (38%). Prevalence did not differ among nasal (67.9%), skin (62.3%), and tonsil (61.7%) swabs, but was lower in rectal (42%) and vaginal swabs (39.6%). Multiple multilocus sequence typing (MLST) and spa types were found in both production systems, but all isolates were of ST398, ST9, or ST5. These MLST lineages have been variably predominant among reports of MRSA in pigs on 3 continents, and the presence of methicillin-sensitive variants in several countries raises the likelihood that MRSA in pigs has likely resulted from independent acquisition of the mecA gene by multiple S. aureus lineages that have been adapted to swine over the long term, rather than recent introduction of novel clones into swine populations.