Modeling between-farm transmission dynamics of porcine epidemic diarrhea virus: Characterizing the dominant transmission routes

A network evaluation of human and animal movement data across multiple swine farm systems in North America

INTRODUCTION

The U.S. swine industry is vulnerable to the rapid spread of disease due to systemic structural issues. While animal movement networks are used to identify disease spread risks and design response plans, human movement between farms were rarely accounted for. Human movements, when integrated with animal movement models, create a different, more inclusive, and accurate network structure when compared to animal movements alone.

METHODS

One year of propriety farm visit data was analyzed and consisted of anonymized property IDs, location, and user/truck IDs, along with visit dates, property, vehicle, and entry types from three swine management companies. A static directed network was created using the igraph package in R for all movements, with separate sub-networks for each entry type (animal, human, and subsets of vehicle types). Network statistics for each sub-network were compared.

RESULTS

The full network included 455 properties, 11 property types, 9 vehicle types, 12 entry types, and 320001 edges (trips between properties). The longest path length was 10 in the animal movement network but decreased to 5 for the full and human movement network, while the average path length decreased from 3.2 to 2.2. Edge density increased from 0.03 to 0.09 for the human network and 0.1 for the full network. For all network properties examined, the full and human movement networks demonstrated higher connectivity than the animal network. A heavy right skew in the degree distributions indicates a 'hub' structure (scale-free-like network) and the shorter path lengths indicates a small-world network topology.

DISCUSSION

The full network is very well connected, more so than expected based on animal movement alone. Hubs may indicate points of disease susceptibility and 'super-spreader' properties. The high connectivity shows that swine farm networks may be more susceptible to spread of an introduced disease than expected from previous analyses.

CONCLUSIONS

Monitoring human, as well as animal movement, provides for a more complete and accurate understanding of swine farm biosecurity risks.

Analyzing the intrastate and interstate swine movement network in the United States

Identifying and restricting animal movements is a common approach used to mitigate the spread of diseases between premises in livestock systems. Therefore, it is essential to uncover between-premises movement dynamics, including shipment distances and network-based control strategies. Here, we analyzed three years of between-premises pig movements, which include 197,022 unique animal shipments, 3973 premises, and 391,625,374 pigs shipped across 20 U.S. states. We constructed unweighted, directed, temporal networks at 180-day intervals to calculate premises-to-premises movement distances, the size of connected components, network loyalty, and degree distributions, and, based on the out-going contact chains, identified network-based control actions. Our results show that the median distance between premises pig movements was 74.37 km, with median intrastate and interstate movements of 52.71 km and 328.76 km, respectively. On average, 2842 premises were connected via 6705 edges, resulting in a weak giant connected component that included 91 % of the premises. The premises-level network exhibited loyalty, with a median of 0.65 (IQR: 0.45 - 0.77). Results highlight the effectiveness of node targeting to reduce the risk of disease spread; we demonstrated that targeting 25 % of farms with the highest degree or betweenness limited spread to 1.23 % and 1.7 % of premises, respectively. While there is no complete shipment data for the entire U.S., our multi-state movement analysis demonstrated the value and the needs of such data for enhancing the design and implementation of proactive- disease control tactics.

The role of vehicle movement in swine disease dissemination: Novel method accounting for pathogen stability and vehicle cleaning effectiveness uncertainties

Several propagation routes drive animal disease dissemination, and among these routes, contaminated vehicles traveling between farms have been associated with indirect disease transmission. In this study, we used near-real-time vehicle movement data and vehicle cleaning efficacy to reconstruct the between-farm dissemination of the African swine fever virus (ASFV). We collected one year of Global Positioning System data of 823 vehicles transporting feed, pigs, and people to 6363 swine production farms in two regions in the U.S. Without cleaning, vehicles connected up to 2157 farms in region one and 437 farms in region two. Individually, in region one vehicles transporting feed connected 2151 farms, pigs to farms 2089 farms, pigs to market 1507 farms, undefined vehicles 1760 farm, and personnel three farms. The simulation results indicated that the contact networks were reduced the most for crew transport vehicles with a 66% reduction, followed by vehicles carrying pigs to market and farms, with reductions of 43% and 26%, respectively, when 100% cleaning efficacy was achieved. The results of this study showed that even when vehicle cleaning and disinfection are 100% effective, vehicles are still connected to numerous farms. This emphasizes the importance of better understanding transmission risks posed by vehicles to the swine industry and regulatory agencies.

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.

Emergent Molecular Techniques Applied to the Detection of Porcine Viruses

Molecular diagnostic tests have evolved very rapidly in the field of human health, especially with the arrival of the recent pandemic caused by the SARS-CoV-2 virus. However, the animal sector is constantly neglected, even though accurate detection by molecular tools could represent economic advantages by preventing the spread of viruses. In this regard, the swine industry is of great interest. The main viruses that affect the swine industry are described in this review, including African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV), and porcine circovirus (PCV), which have been effectively detected by different molecular tools in recent times. Here, we describe the rationale of molecular techniques such as multiplex PCR, isothermal methods (LAMP, NASBA, RPA, and PSR) and novel methods such as CRISPR-Cas and microfluidics platforms. Successful molecular diagnostic developments are presented by highlighting their most important findings. Finally, we describe the barriers that hinder the large-scale development of affordable, accessible, rapid, and easy-to-use molecular diagnostic tests. The evolution of diagnostic techniques is critical to prevent the spread of viruses and the development of viral reservoirs in the swine industry that impact the possible development of future pandemics and the world economy.

Fractal and fractional SIS model for syphilis data

This work studies the SIS model extended by fractional and fractal derivatives. We obtain explicit solutions for the standard and fractal formulations; for the fractional case, we study numerical solutions. As a real data example, we consider the Brazilian syphilis data from 2011 to 2021. We fit the data by considering the three variations of the model. Our fit suggests a recovery period of 11.6 days and a reproduction ratio (R0) equal to 6.5. By calculating the correlation coefficient (r) between the real data and the theoretical points, our results suggest that the fractal model presents a higher r compared to the standard or fractional case. The fractal formulation is improved when two different fractal orders with distinguishing weights are considered. This modification in the model provides a better description of the data and improves the correlation coefficient.

Effectiveness of gilt acclimatization - improvement procedures in a farm with recurrent outbreaks of porcine epidemic diarrhea

Background and Aim

Porcine epidemic diarrhea (PED) is a severe infectious disease that causes very high mortality in newborn piglets up to 2-3 weeks age. The main cause of repeated outbreaks of PED in infected farms is the continuing circulation of the PED virus (PEDV). Improper gilt management, including inappropriate gut feedback, commingling, and inadequate immunization, causes a prolonged virus circulation in breeding herds. Moreover, insufficient transfer of passive immunity through the colostrum to newborn piglets can also increase infection risk. Therefore, a gilt management program that controls infection should focus on infection monitoring and acclimatization. We investigated the source of recurrent PEDV outbreaks and examined how the effect of immunization methods, specifically using gut feedback mechanism and vaccination, can reduce PEDV circulation and improve immune responses in replacement gilts.

Materials and Methods

The study site was a segregated commercial production farm with endemic PEDV. The acclimatization methods included gut feedback and vaccination. This longitudinal study evaluated two strategies of gilt acclimatization against PEDV: Program 1 (routine farm management) and Program 2 (early feedback program and all-in-all-out system). Levels of PED RNA in fecal samples were measured using quantitative reverse transcription-polymerase chain reaction, and the PEDV S gene was sequenced. Porcine epidemic diarrhea-specific immune responses were assessed using enzyme-linked immunosorbent assay and the serum neutralization test.

Results

Porcine epidemic diarrhea outbreaks occurred in the farrowing, nursery, and finishing units and farrowed litters 5-10 days old were symptomatic of PED. Phylogenetic analyses of the S gene showed PEDV sequence divergence between PEDV field strains and vaccine strain, which may contribute to periodic outbreaks and continued persistence of PEDV in the farm. After gut feedback and acclimatization, replacement gilts from Program 1 continued to shed PEDV before being introduced to sow herds, while those from Program 2 did not shed PEDV before being introduced to sow herds. However, the components of the immune response against PEDV in serum samples, including specific immunoglobulin (Ig)G, specific IgA, and neutralizing antibodies were lower in gilts of Program 2 than those in Program 1.

Conclusion

We speculate that implementing the appropriate gilt acclimatization program can control PEDV circulation in farm. However, the acclimatization methods in Program 2 did not induce a strong and adequate immune response in replacement gilts. Therefore, maternal immunity levels and the degree of protection against PEDV require further study.