Center for Epidemiology and Animal Health

ABSTRACTAs global temperatures rise and become more variable, the capacity of domestic species to adapt, while maintaining production efficiency, is becoming a pressing concern. In this context, genotype‐by‐environment (GxE) interactions pose a significant challenge for selective breeding, as traits that perform well in one environment may not in another. These interactions complicate the design of breeding programmes that aim to ensure long‐term resilience while optimising short‐term productivity. Genomic Offsets—a metric that can quantify the mismatch between current and future genotype–environment associations, predicting potential genetic mismatch to environmental change—may offer a promising solution. In this perspective piece, we explore potential applications of genomic offsets in agriculture and aquaculture, including their use as tools for risk assessment, selective breeding and cryopreservation. We discuss how genomic offsets can overcome hurdles posed by GxE interactions, addressing practical considerations such as data requirements and methodological frameworks, and needed validation efforts. By predicting genetic mismatches and guiding the selection of individuals best suited for changing environmental conditions, our proposed Adaptive Breeding Framework may help breeders proactively enhance the resilience of farmed populations.

Cattle markets, where livestock producers may buy and sell cattle and calves, act as major hubs in the shipment network that connect cattle populations across the United States (U.S.). Cattle markets can then provide insight into the integration of the U.S. cattle industry, thus informing how regional price fluctuations may influence cattle prices nationally. Despite biosecurity measures and regulatory compliance from livestock markets, commingling and re-distribution of animals from multiple sources may elevate the risk of disease spread and make tracing animal movements more complex, which could pose significant challenges if a transboundary animal disease (TAD) were introduced into the U.S. Therefore, knowing the size and location of cattle markets in the U.S. is critical to understanding cattle industry market dynamics and enhancing pandemic scenario modeling efforts. In this article, we present a list of cattle markets, their locations, and estimated quarterly cattle sales. We compiled a list of 1619 known cattle markets with and without market sales data from 1131 counties across the U.S. from 2012–2016. To estimate unknown market sales data, we fit a spatial autoregressive lag model to annual county-level market sales data and used the fit to predict annual sales in counties that lacked sales information. County-level sales data provide important insight into the structure of the U.S. cattle industry. The dataset can be used to improve national-scale cattle movement models, livestock disease models, and inform TAD surveillance efforts.

Culicoides biting midges adversely impact animal health through transmission of multiple orbiviruses, such as bluetongue virus (BTV). This study used light trapping data collected in the Southeastern United States for three Culicoides midge species that are confirmed or suspected BTV vectors: Culicoides insignis, Culicoides stellifer and Culicoides venustus. Midge presence datasets were combined with meteorological data and ecological data to model habitat suitability for each species. Logistic regression and machine learning models were used to generate individual species distribution models (SDMs). Results for each SDM method were combined in an ensemble model to create a distribution model for each midge species. Based on overlay analyses of livestock populations and midge suitable habitat, there is extensive overlap of cattle and goat populations and suitable habitat for C. insignis in Florida. Suitable habitat for C. stellifer intersects with cattle and goat populations in various counties in Alabama, Arkansas, the Carolinas, Florida, Georgia, Louisiana and Tennessee; and suitable habitat for C. venustus intersects with cattle and goat populations in the same states as C. stellifer, except for Florida. It is critical for orbivirus and midge surveillance to continue in the Southeastern United States as the habitat of all three midge species intersect with livestock populations.

Abstract The introduction of African swine fever virus (ASFV) into uninfected countries can impact economic and animal welfare. Rapid detection and control of the outbreak contribute to successful eradication and promote business continuity. We developed a model to determine the number of samples, sample collectors, laboratory capacity, and processing times following an ASFV introduction into the U.S. We simulated the spread of ASFV in one densely populated swine region, generating a median of 27 (range = 1-68) outbreaks in 150 days, resulting 616 (range = 1-15,011) sampling events with a total of 3,068 barns (range = 7-69,118) sampled. We calculated the total sample collectors needed, considering daily working hours, sampling and driving time, and laboratory capabilities with and without blood sample pooling. Samples included 31 blood samples and five oral fluid samples per barn, which equal 84,830 (range = 52-2,066,831) and 14,195 (range = 10-345,590) blood and oral fluid samples, respectively. The median number of sample collectors needed to prevent sampling delay varied from 136 to 367 and, in the worst epidemic scenarios, from 833 to 3,115. Notably, excluding downtime–which prevented the sampler from visiting additional farms for 24 or 72 hours–reduced the number of sample collectors needed between 28% and 75%, while switching from blood to oral fluid samples reduced this number between 47% and 75%. At a laboratory processing daily capacity of 1,000 samples, the median days for sample processing without pooling were 92 days, with a maximum of 5.7 years. We demonstrated a need to redistribute 10,062 (range = 2-67,940) unprocessed samples daily to other laboratories to prevent processing delays. Our study addresses the challenge of efficiently organizing resources for managing a potential ASFV outbreak, providing information about the number of sample collectors and laboratory capacity needed for one densely populated swine region in the U.S.

Abstract Introductions of foreign animal diseases (FADs) into free-ranging wildlife can be difficult to control and devastating for domestic livestock trade. Combating a new FAD introduction in wildlife with an emergency response requires quickly limiting spread of the disease by intensely removing wild animals and recovering their carcasses for proper disposal. In the case of African swine fever virus (ASFv) in wild pigs (Sus scrofa), which has been spreading in many regions of the world, there is little information on the time- and cost-efficiency of methods for intensively and consistently removing wild pigs and recovering carcasses in an emergency response scenario. We compared the efficiencies of aerial operations, trapping, an experimental toxic bait, and ground shooting in northcentral Texas, USA during two months in 2023. Removing and recovering carcasses of wild pigs averaged a rate of 0.15 wild pigs/person hour and cost an average of $233.04/wild pig ($USD 2023) across all four methods. Aerial operations required the greatest initial investment but subsequently was the most time- and cost-efficient, costing an average of $7,266 to incrementally reduce the population by 10% including recovering carcasses. Aerial operations required a ground crew of ∼7 people/helicopter to recover carcasses. Costs for reducing the population of wild pigs using trapping were similar, although took 13.5 times longer to accomplish. A benefit of trapping was carcass recovery was incorporated. Toxic baiting was less efficient because carcass recovery required substantial time, and we removed very few wild pigs with ground shooting in this landscape. We recommend combining aerial and trapping methodologies to remove wild pigs and their carcasses efficiently and effectively during a FAD response. Overall, our findings can inform the preparation of resources, personnel needs, and deployment readiness for FAD responses involving wild pigs.

Mycoplasma bovis (M. bovis) is an emerging pathogen in North American Bison (Bison bison) characterized by significant mor­bidity and mortality. Herds are reported to experience case fa­tality rates from 10 to 45%, with mature animals being primar­ily affected. To date, there are no published reports regarding the epidemiology of M. bovis within U.S. bison herds; this study serves as the first in-depth analysis of the prevalence, clinical signs and potential risk factors for M. bovis-associated disease in the United States.

African swine fever (ASF) causes significant morbidity and mortality in both domestic and wild suids (Sus scrofa), and disease outbreaks convey profound economic costs to impacted industries due to death loss, the cost of culling exposed/infected animals as the primary disease control measure, and trade restrictions. The co-occurrence of domestic and wild suids significantly complicates ASF management given the potential for wild populations to serve as persistent sources for spillover. We describe the unique threat of African swine fever virus (ASFV) introduction to the United States from epidemiological and ecological perspectives with a specific focus on disease management at the wild-domestic swine interface. The introduction of ASF into domestic herds would require a response focused on containment, culling, and contact tracing. However, detection of ASF among invasive wild pigs would require a far more complex and intensive response given the challenges of detection, containment, and ultimately elimination among wild populations. We describe the state of the science available to inform preparations for an ASF response among invasive wild pigs, describe knowledge gaps and the associated studies needed to fill those gaps, and call for an integrated approach for preparedness that incorporates the best available science and acknowledges sociological attributes and the policy context needed for an integrated disease response.

Development of a foot-and-mouth disease (FMD) carrier state following FMD virus (FMDV) infection is a well-established phenomenon in cattle. However, the proportion of cattle likely to become carriers and the duration of the carrier state at a herd or population-level are incompletely understood. The objective of this study was to examine the epidemiologic and economic impacts of vaccination-to-live strategy in a disease-free region or country. We developed and simulated scenarios of FMD spread and control in the US livestock population, which included depopulation for a limited period, followed by a vaccinate-to-live strategy with strong biosecurity and movement restrictions. Six scenarios of FMD spread and control were simulated in the InterSpread Plus (ISP) modeling tool. Data on the number of infected and depopulated cattle (by operation types) from ISP model runs were used to estimate the monthly number of infected but not depopulated (potential carrier) cattle after the infection. Using available literature data on the FMD carrier state, we estimated the monthly proportion of carrier cattle (from infected but not depopulated cattle) over time following infection. Among the simulated scenarios, the median (25th, 75th percentile) number of infected cattle ranged from 43,217 (42,819, 55,274) head to 148,907 (75,819, 205,350) head, and the epidemic duration ranged from 20 (11, 30) to 76 (38, 136) days. In general, larger outbreaks occurred when depopulation was carried out through longer periods, and the onset of the vaccination was late (p > 0.05). The estimated proportion of surviving cattle, which were infected and not depopulated and had the potential to become persistently infected ranged from 14 to 35% of total infected cattle. Production losses in beef and dairy sectors were higher when outbreaks started in multiple states simultaneously, but production losses were small compared to trade losses and consumer avoidance losses. These results can be used to inform the consideration of a vaccinate-to-live strategy for FMD outbreaks and the development of appropriate post-outbreak management strategies. Furthermore, this output will enable a more detailed examination of the epidemiologic and economic implications of allowing convalescent cattle to survive and remain in production chains after FMD outbreaks in FMD-free regions.