Cross-species transmission potential between wild pigs, livestock, poultry, wildlife, and humans: implications for disease risk management in North America

Snow N.P., Jarzyna M.A., VerCauteren K.C.

Summary The eruption of invasive wild pigs (IWPs) Sus scrofa throughout the world exemplifies the need to understand the influences of exotic and nonnative species expansions. In particular, the continental USA is precariously threatened by a rapid expansion of IWPs, and a better understanding of the rate and process of spread can inform strategies that will limit the expansion. We developed a spatially and temporally dynamic model to examine three decades (1982–2012) of IWP expansion, and predict the spread of IWPs throughout the continental USA, relative to where IWPs previously inhabited. We used the model to predict where IWPs are likely to invade next. The average rate of northward expansion increased from 6·5 to 12·6 km per year, suggesting most counties in the continental USA could be inhabited within the next 3–5 decades. The spread of IWPs was primarily associated with expansion into areas with similar environmental characteristics as their previous range, with the exception of spreading into colder regions. We identified that climate change may assist spread into northern regions by generating milder winters with less snow. Otherwise, the spread of IWPs was not dependent on agriculture, precipitation or biodiversity at the county level. The model correctly predicted 86% of counties that were invaded during 2012, and those predictions indicate that large portions of the USA are in immediate danger of invasion. Synthesis and applications. Anti-invasion efforts should focus along the boundaries of current occupied range to stop natural expansion, and anti-invasion policies should focus on stopping anthropogenic transport and release of invasive wild pigs. Our results demonstrate the utility of a spatio-temporal examination to inform strategies for limiting the spread of invasive wild pigs.

Pérez Rivera C.M., López M.S., Arnaud Franco G., Carreón Nápoles R.

Pedersen K., Miller R.S., Anderson T.D., Pabilonia K.L., Lewis J.R., Mihalco R.L., Gortázar C., Gidlewski T.

Anderson A., Slootmaker C., Harper E., Holderieath J., Shwiff S.A.

We report the results of one of the most comprehensive surveys on feral swine ( Sus scrofa ) damage and control in 11 US states (Alabama, Arkansas, California, Florida, Georgia, Louisiana, Mississippi, Missouri, North Carolina, South Carolina and Texas). The survey was distributed by the USDA National Agricultural Statistical Service in the summer of 2015 to a sample of producers of corn ( Zea mays ), soybeans ( Glycine max ), wheat ( Triticum ), rice ( Oryza sativa ), peanuts ( Arachis hypogaea ), and sorghum ( Sorghum bicolor ) in the 11-state region. Producers that failed to respond to the initial mailing received multiple follow-up phone calls in an attempt to minimize non-response bias, and a total of 4377 responses were obtained. Findings indicate that damage can be substantial. The highest yield loss estimates occur in peanut and corn production in the Southeast and Texas. Control efforts are common, and producers incur considerable costs from shooting and trapping efforts. Extrapolating crop damage estimates to the state-level in 10 states with reportable damage yields an estimated crop loss of $190 million. Though large, this number likely represents only a small fraction of the total damage by feral swine in the 10 states because it only includes crop damage to six crops. We hope findings from this survey will help guide control efforts and research, as well as serve as a benchmark against which the effectiveness of future control efforts can be measured.

Bevins S.N., Dusek R.J., White C.L., Gidlewski T., Bodenstein B., Mansfield K.G., DeBruyn P., Kraege D., Rowan E., Gillin C., Thomas B., Chandler S., Baroch J., Schmit B., Grady M.J., et. al.

A novel highly pathogenic avian influenza virus belonging to the H5 clade 2.3.4.4 variant viruses was detected in North America in late 2014. Motivated by the identification of these viruses in domestic poultry in Canada, an intensive study was initiated to conduct highly pathogenic avian influenza surveillance in wild birds in the Pacific Flyway of the United States. A total of 4,729 hunter-harvested wild birds were sampled and highly pathogenic avian influenza virus was detected in 1.3% (n = 63). Three H5 clade 2.3.4.4 subtypes were isolated from wild birds, H5N2, H5N8, and H5N1, representing the wholly Eurasian lineage H5N8 and two novel reassortant viruses. Testing of 150 additional wild birds during avian morbidity and mortality investigations in Washington yielded 10 (6.7%) additional highly pathogenic avian influenza isolates (H5N8 = 3 and H5N2 = 7). The geographically widespread detection of these viruses in apparently healthy wild waterfowl suggest that the H5 clade 2.3.4.4 variant viruses may behave similarly in this taxonomic group whereby many waterfowl species are susceptible to infection but do not demonstrate obvious clinical disease. Despite these findings in wild waterfowl, mortality has been documented for some wild bird species and losses in US domestic poultry during the first half of 2015 were unprecedented.

Cowie C.E., Hutchings M.R., Barasona J.A., Gortázar C., Vicente J., White P.C.

Livestock diseases such as bovine tuberculosis can have considerable negative effects on human health and economic activity. Wildlife reservoirs often hinder disease eradication in sympatric livestock populations. Therefore, quantifying interactions between wildlife and livestock is an important aspect of understanding disease persistence. This study was conducted on an extensive cattle farm in southwest Spain, where cattle, domestic pigs, wild boar and red deer are considered to be part of a tuberculosis host community. We tested the hypothesis that the frequency of both types of interactions would be greater at food and water sites, due to the aggregation of individuals from multiple species at these locations. We measured direct and indirect interactions between individuals using GPS and proximity loggers. Over 57,000 direct interactions were recorded over a 2-year period, of which 875 (1.5 %) occurred between different species and 216 (0.38 %) occurred between wildlife and livestock. Most direct and indirect interactions occurred at water sites. Over 90 % of indirect interactions between wildlife and livestock took place within the estimated 3-day environmental survival time of Mycobacterium bovis in this habitat. Red deer home ranges and daily activity patterns revealed significant spatial and temporal overlaps with cattle, particularly in autumn. Suids and red deer also cross the farm boundary regularly, introducing a between-farm interaction risk. The infrequent occurrence of direct interactions between individuals from different species suggests that they are unlikely to be the sole mode of disease transmission and that indirect interactions may play an important role.

Luis A.D., O'Shea T.J., Hayman D.T., Wood J.L., Cunningham A.A., Gilbert A.T., Mills J.N., Webb C.T.

Bats are natural reservoirs of several important emerging viruses. Cross-species transmission appears to be quite common among bats, which may contribute to their unique reservoir potential. Therefore, understanding the importance of bats as reservoirs requires examining them in a community context rather than concentrating on individual species. Here, we use a network approach to identify ecological and biological correlates of cross-species virus transmission in bats and rodents, another important host group. We show that given our current knowledge the bat viral sharing network is more connected than the rodent network, suggesting viruses may pass more easily between bat species. We identify host traits associated with important reservoir species: gregarious bats are more likely to share more viruses and bats which migrate regionally are important for spreading viruses through the network. We identify multiple communities of viral sharing within bats and rodents and highlight potential species traits that can help guide studies of novel pathogen emergence.

McClure M.L., Burdett C.L., Farnsworth M.L., Lutman M.W., Theobald D.M., Riggs P.D., Grear D.A., Miller R.S.

Wild pigs (Sus scrofa), also known as wild swine, feral pigs, or feral hogs, are one of the most widespread and successful invasive species around the world. Wild pigs have been linked to extensive and costly agricultural damage and present a serious threat to plant and animal communities due to their rooting behavior and omnivorous diet. We modeled the current distribution of wild pigs in the United States to better understand the physiological and ecological factors that may determine their invasive potential and to guide future study and eradication efforts. Using national-scale wild pig occurrence data reported between 1982 and 2012 by wildlife management professionals, we estimated the probability of wild pig occurrence across the United States using a logistic discrimination function and environmental covariates hypothesized to influence the distribution of the species. Our results suggest the distribution of wild pigs in the U.S. was most strongly limited by cold temperatures and availability of water, and that they were most likely to occur where potential home ranges had higher habitat heterogeneity, providing access to multiple key resources including water, forage, and cover. High probability of occurrence was also associated with frequent high temperatures, up to a high threshold. However, this pattern is driven by pigs’ historic distribution in warm climates of the southern U.S. Further study of pigs’ ability to persist in cold northern climates is needed to better understand whether low temperatures actually limit their distribution. Our model highlights areas at risk of invasion as those with habitat conditions similar to those found in pigs’ current range that are also near current populations. This study provides a macro-scale approach to generalist species distribution modeling that is applicable to other generalist and invasive species.

Wiethoelter A.K., Beltrán-Alcrudo D., Kock R., Mor S.M.

Significance Infectious diseases at the wildlife–livestock interface threaten the health and well-being of wildlife, livestock, and human populations, and contribute to significant economic losses to each sector. No studies have sought to characterize the diseases and animals involved on a global level. Using a scoping review framework we show that 10 diseases—mostly zoonoses—have accounted for half of the published research in this area over the past century. We show that relatively few interfaces can be considered important from a disease ecology perspective. These findings suggest that surveillance and research strategies that target specific wildlife–livestock interfaces may yield the greatest return in investment.

Tompkins D.M., Carver S., Jones M.E., Krkošek M., Skerratt L.F.

We review the literature to distinguish reports of vertebrate wildlife disease emergence with sufficient evidence, enabling a robust assessment of emergence drivers. For potentially emerging agents that cannot be confirmed, sufficient data on prior absence (or a prior difference in disease dynamics) are frequently lacking. Improved surveillance, particularly for neglected host taxa, geographical regions and infectious agents, would enable more effective management should emergence occur. Exposure to domestic sources of infection and human-assisted exposure to wild sources were identified as the two main drivers of emergence across host taxa; the domestic source was primary for fish while the wild source was primary for other taxa. There was generally insufficient evidence for major roles of other hypothesized drivers of emergence.

Pilosof S., Morand S., Krasnov B.R., Nunn C.L.

Epidemiological networks are commonly used to explore dynamics of parasite transmission among individuals in a population of a given host species. However, many parasites infect multiple host species, and thus multi-host networks may offer a better framework for investigating parasite dynamics. We investigated the factors that influence parasite sharing – and thus potential transmission pathways – among rodent hosts in Southeast Asia. We focused on differences between networks of a single host species and networks that involve multiple host species. In host-parasite networks, modularity (the extent to which the network is divided into subgroups of rodents that interact with similar parasites) was higher in the multi-species than in the single-species networks. This suggests that phylogeny affects patterns of parasite sharing, which was confirmed in analyses showing that it predicted affiliation of individuals to modules. We then constructed “potential transmission networks” based on the host-parasite networks, in which edges depict the similarity between a pair of individuals in the parasites they share. The centrality of individuals in these networks differed between multi- and single-species networks, with species identity and individual characteristics influencing their position in the networks. Simulations further revealed that parasite dynamics differed between multi- and single-species networks. We conclude that multi-host networks based on parasite sharing can provide new insights into the potential for transmission among hosts in an ecological community. In addition, the factors that determine the nature of parasite sharing (i.e. structure of the host-parasite network) may impact transmission patterns.

Barasona J.A., Latham M.C., Acevedo P., Armenteros J.A., Latham A.D., Gortazar C., Carro F., Soriguer R.C., Vicente J.

Controlling infectious diseases at the wildlife/livestock interface is often difficult because the ecological processes driving transmission between wildlife reservoirs and sympatric livestock populations are poorly understood. Thus, assessing how animals use their environment and how this affects interspecific interactions is an important factor in determining the local risk for disease transmission and maintenance. We used data from concurrently monitored GPS-collared domestic cattle and wild boar (Sus scrofa) to assess spatiotemporal interactions and associated implications for bovine tuberculosis (TB) transmission in a complex ecological and epidemiological system, Doñana National Park (DNP, South Spain). We found that fine-scale spatial overlap of cattle and wild boar was seasonally high in some habitats. In general, spatial interactions between the two species were highest in the marsh-shrub ecotone and at permanent water sources, whereas shrub-woodlands and seasonal grass-marshlands were areas with lower predicted relative interactions. Wild boar and cattle generally used different resources during winter and spring in DNP. Conversely, limited differences in resource selection during summer and autumn, when food and water availability were limiting, resulted in negligible spatial segregation and thus probably high encounter rates. The spatial gradient in potential overlap between the two species across DNP corresponded well with the spatial variation in the observed incidence of TB in cattle and prevalence of TB in wild boar. We suggest that the marsh-shrub ecotone and permanent water sources act as important points of TB transmission in our system, particularly during summer and autumn. Targeted management actions are suggested to reduce potential interactions between cattle and wild boar in order to prevent disease transmission and design effective control strategies.

Holzbauer S.M., Agger W.A., Hall R.L., Johnson G.M., Schmitt D., Garvey A., Bishop H.S., Rivera H., de Almeida M.E., Hill D., Stromberg B.E., Lynfield R., Smith K.E.

Rates of trichinellosis have declined significantly in the United States due to improved pork production practices and public awareness of the danger of eating raw or undercooked pork. In April 2011, the Minnesota Department of Health received a report of presumptive trichinellosis in a 50-year-old man with a history of wild boar consumption. A public health investigation was initiated.Medical record reviews and patient and family interviews were conducted. Trichinella species serology was performed on patient and family serum samples, and larval identification was attempted on clinical specimens and meat samples.The index patient harvested a wild boar from an Iowa game farm; he processed the meat after returning home and developed gastrointestinal symptoms 2 days later. Four days after his illness onset, all 5 family members consumed a roast from the boar. The index patient sought healthcare 4 times after illness onset before being definitively diagnosed with trichinellosis. Following initiation of albendazole therapy, the index patient developed atrial fibrillation. One additional family member who processed the raw meat was diagnosed with trichinellosis. Trichinella spiralis larvae were identified in wild boar meat samples.Trichinellosis has long been recognized as a potential hazard of consuming undercooked wild carnivore meat, and historically has been associated with consumption of pork from domestic swine, but may be unfamiliar to practicing clinicians in the United States. Education of hunters and the broader population on the potential for trichinellosis and the importance of proper handling and cooking meat from wild or free-range animals needs to be reinforced.

Brook R.K., van Beest F.M.

Feral wild boar (Sus scrofa) are rapidly expanding their distribution and abundance globally and causing considerable socio-economic impacts. Prior to this study, the spatial distribution of feral boar on the Canada prairies was largely unknown. We surveyed all 296 rural municipalities in Saskatchewan, Canada, to determine the distribution of feral boar in the province and characterize community leader perceptions of risk. Of the respondents, over the past 3 years 48% never saw feral boar, 48% saw them at least occasionally, and 3% responded “I don't know,” indicating a few respondents were not confident in saying feral boar were present or absent. Feral boar were observed across a range of habitats, in all months, and at all times of day. Variables that best predicted the distribution of feral boar included % farmland (β = 6.46), % flaxseed crop (β = −8.63), density of paved roads (β = −1.92), % deciduous forest (β = 5.93), and % mustard seed crop (β = −12.63). Mapping the resource selection probability function (RSPF) across the landscape of rural Saskatchewan predicted 70% of municipalities had RSPF >0.7 (high probability of boar presence) and 12% had RSPF

Bevins S.N., Pedersen K., Lutman M.W., Gidlewski T., Deliberto T.J.

Khan T.U., Nabi G., Iqbal A., Ullah K., Hu H.

Human–wildlife conflict poses significant ecological and socio-economic challenges, particularly in rural communities where agriculture and livestock rearing form the backbone of livelihoods. Despite the growing importance of this issue, District Lakki Marwat remains an unexplored area of northwest Pakistan. This study aims to fill this gap by systematically assessing the status, economic impacts, and community perceptions of five wildlife species: wild boar (Sus scrofa), grey wolf (Canis lupus), golden jackal (Canis aureus), striped hyena (Hyaena hyaena), and red fox (Vulpes vulpes). Using semi-structured surveys with 117 respondents, we analyzed species prevalence, perceived danger levels, crop damage patterns, and predation impacts on livestock and poultry. The findings revealed that wild boars were identified as the primary contributors to agricultural damage, with total annual crop losses surpassing the economic impacts attributed to the studied carnivores. On average, each surveyed household experienced an annual loss of PKR 4510.38. For the 39% of households reporting crop damage, the annual loss per reported household was PKR 11,727, which was higher than the average annual loss across all households, underscoring the severity of the impact on those specifically affected by the wild boar-related crop damage. Notably, community attitudes were most negative toward wild boars, a pattern driven by the economic burden of crop losses, challenging the conventional focus on carnivores as the primary conflict species. A Pearson’s X2 test confirmed strong associations between species and perceived danger levels, while regression analysis demonstrated an association between crop damage and negative attitudes. Traditional deterrents like thorn fences were found ineffective against wild boars. More advanced methods, including game-proof fencing, trenches, bio-fencing, crop rotation, audio and visual deterrents, taste and order repellents, and watchtowers combined with group vigilance, are recommended to reduce crop damage. Integrating these approaches with community-based education, habitat management, and government-supported compensation schemes can mitigate wild boar impacts. This study contributes new insights into multi-species HWC dynamics, demonstrating that community perceptions are primarily shaped by the economic impact of a species, regardless of whether it is a carnivore or an omnivore. The attitudes of local communities are driven by the financial losses incurred, rather than the species' behavior or ecological role. This study underscores the need for collaborative efforts to reduce human–wildlife conflict, foster coexistence, and ensure ecological balance in vulnerable rural areas.

Paintsil E.K., Adu-Asiamah C.K., Boahen K.G., Akenten C.W., Kwarteng A., Berg S., Obiri-Danso K., May J., Dekker D., Ofori L.A.

AbstractBackgroundCampylobacter fetuscauses reproductive diseases in livestock and zoonotic infections in humans, especially in immunocompromised individuals. Despite its significance, its genomic characteristics are poorly understood. This study analyzed 114 publicly availableC. fetusgenomes to provide global insights into its genetic diversity, antimicrobial resistance (AMR) patterns, and zoonotic risk.ResultsA total of 32 distinct sequence types (STs), ranging from ST-1 to ST-74, were identified across 111 of the 114C. fetusgenomes, spanning six continents and diverse hosts (cattle, humans, sheep, and reptiles). ST-4 was the most prevalent (n = 45), followed by ST-3 (n = 8). A significant proportion (90.9%; n/N=40/44) ofC. fetussubsp.venerealis(Cfv) and its biovar intermedius (Cfvi) were assigned to ST-4. Despite being isolated from five continents, Cfv and Cfvi genomes clustered closely, forming distinct branches at the biovar level; however, six Cfv genomes were located within Cfvi clades, suggesting a shared evolutionary lineage. In contrast,C. fetussubsp.testudinum(Cft) genomes, exhibiting 20 distinct STs, formed distinct clades from Cfv, Cfvi, andC. fetussubsp.fetus(Cff). While Cfv genomes from North America and Cfvi genomes from South America formed distinct geographic clusters, Cff genomes displayed no clear geographical patterns, with branches containing strains from multiple continents, indicating a globally dispersed distribution. Pangenomic analysis revealed pronounced clustering within Cft, characterized by unique gene presence/absence patterns. Five distinct AMR genes were detected, withtet(O)(n = 3) being the most common. Horizontal gene transfer analysis identified 140 genomic islands across 41 genomes, and virulence factor analysis revealedcheYas the sole conserved virulence gene across 35 genomes.ConclusionThese findings provide critical insights into the genomic diversity, zoonotic potential, and global distribution ofC. fetus, emphasizing the need for integrated genomic and epidemiological strategies to assess its impact on human and animal health.

Bradley E.A., Lockaby B.G., Madere S., Bolds S., Kalin L., Ditchkoff S.S., Brown V.R.

AbstractThe range and density of one of North America's most destructive and invasive mammalian species, wild pigs (Sus scrofa), has expanded rapidly over the past several decades. Alongside this growth, their fecal contamination of surface waters has impaired water quality through significantly increased levels of pathogenic bacteria, raising concerns over the potential for zoonotic disease transmission. Significant remediation of these water quality impacts has been shown as a result of reductions in wild pig populations due to control efforts; however, the duration of these remediation effects as populations rebound remains unclear. Our study sought to determine the longevity of water quality remediation resulting from wild pig population control efforts. We found that median concentrations of Escherichia coli and fecal coliform (CFU/100 mL) increased by 746% and 159% in the year following the conclusion of removal efforts, resulting in median concentrations of 79% and 159% greater than those observed prior. We also found increased public health risk, with samples exceeding E. coli and fecal coliform guidelines 10% and 12% more often than pre‐removal, respectively. While further research into wild pig population dynamics and fecal contamination is necessary, we conclude that ongoing population control efforts may be necessary to remediate water quality impacts and public health risks associated with invasive wild pigs.

Coelho I.M., Paiva M.T., da Costa A.J., Nicolino R.R.

Walker H.L., Miller R.S., Pomeroy L.W., Arruda A.G.

Gaya H.E., D’Angelo G.J., Vukovich M., Youngmann J.L., Lance S.L., Kilgo J.C.

Context Control of invasive wild pigs (Sus scrofa) is a growing management concern throughout their invaded range. In the United States, control programs often leave wild pig carcasses on the landscape where they are freely available for consumption by scavengers such as coyotes (Canis latrans). Coyotes consume wild pigs, but no studies have investigated the importance of pig carcasses for maintaining coyote abundance. Aims We tested the hypothesis that coyote populations may be bolstered by wild pig carcasses created by control programs. Methods From July 2014 to July 2017, we surveyed road transects for scat to monitor coyote abundance in response to changing levels of pig carcass availability. From June 2015 to July 2017, wild pigs were removed from the eastern half of the study area and placed at one of four carcass dump sites on the western side. We analysed the scat data using an open population spatially-explicit capture–mark recapture model to estimate seasonal abundance and movement of coyotes in response to the carcass treatment. Results Coyote density across the entire study area declined from 95 coyotes/100 km2 in July 2014 to 65 coyotes/100 km2 by July 2016, but declines were unrelated to the carcass availability treatment. Additional analysis on non-genotyped scat data showed no apparent effect of carcass availability on coyote density. Coyote activity centers moved fewer than 100 m towards the nearest carcass dump site in response to the carcass treatment. Conclusions Wild pig carcass availability is not likely to be a primary driver of coyote abundance or territory selection at the study location. Implications We conclude that the availability of wild pig carcasses has little effect on coyote abundance and thus wild pig carcass removal will not be an effective coyote management strategy.

Masocha W., Ssempijja F., Kasozi K.I., Tesoriero C., Del Gallo F., Abah S., Seke Etet P.F., Welburn S.C., Kennedy P.G.

Chalkowski K., Pepin K., Lavelle M., Miller R., Fischer J., Brown V., Glow M., Smith B., Cook S., Kohen K., Sherburne S., Smith H., Leland B., VerCauteren K., Snow N.

Sinn Kay Chan O., Surendran-Nair M., Lam T.

The relationship among microbes, animals, and humans often manifests as zoonotic, anthropo-zoonotic, or sylvatic infections. Infections transmitted from animals to humans are considered zoonotic and often cause outbreaks of diseases, epidemics, or even pandemics. The battle for survival between microbes and mammalian species has been occurring throughout all documented human history. The control, de-escalation, or deceleration of the spread of these diseases often hinges upon the detection of infectious agents. The diagnostic tests to detect and monitor infectious agents have evolved throughout human biomedical history. Infectious disease diagnosis in the past decades has improved by combining physical examination, microbiology, immunology, and molecular tests. This chapter highlights the characteristics of diseases by their clinical presentation, laboratory tests, use of multi-omics, and other attributes of diagnostics.

Tarasiuk G., Giménez-Lirola L.G., Rotolo M.L., Zimmerman J.J.

A highly invasive species, free-ranging Sus scrofa often negatively impact the ecosystem and are capable of spreading a number of impactful pathogens to domestic livestock. Measures taken to ameliorate these impacts and/or control population size are based on the delivery of oral baits containing bioactive chemicals or vaccines, e.g., classical swine fever vaccine. The efficacy of these methods depends on the rate at which inoculated baits are consumed by the pigs. Rhodamine B, tetracycline, and iophenoxic acid are commonly used to quantitate bait uptake in free-ranging pig population studies. All three are effective in this application but differ in fundamental characteristics. When used as a tracer, the effective dose of rhodamine B was established at 15 mg/kg to ensure a 12-week window of detection based on evaluation of hair samples using fluorescent microscopy. Tetracyclines are likewise effective tracers in free-ranging pigs, but the process of detection is highly invasive, i.e., requires euthanasia, and extraction of bone or teeth, followed by examination by fluorescence microscopy. Iophenoxic acid and its derivatives also highly suitable tracers and may be detected in serum for ≥9 months after exposure. Notably tracers used in free-ranging pigs are not suitable for behavioral studies in farm-raised pigs either because the detection method is highly invasive (tetracyclines) or because they are unapproved for use in meat destined for human consumption.

Martins J.A., Hisano Higuti A.Y., Pellegrin A.O., Juliano R.S., Araújo A.M., Pellegrin L.A., Liesenberg V., Ramos A.P., Gonçalves W.N., Sant’Ana D.A., Pistori H., Junior J.M.

Crop segmentation, the process of identifying and delineating agricultural fields or specific crops within an image, plays a crucial role in precision agriculture, enabling farmers and public managers to make informed decisions regarding crop health, yield estimation, and resource allocation in Midwest Brazil. The crops (corn) in this region are being damaged by wild pigs and other diseases. For the quantification of corn fields, this paper applies novel computer-vision techniques and a new dataset of corn imagery composed of 1416 256 × 256 images and corresponding labels. We flew nine drone missions and classified wild pig damage in ten orthomosaics in different stages of growth using semi-automatic digitizing and deep-learning techniques. The period of crop-development analysis will range from early sprouting to the start of the drying phase. The objective of segmentation is to transform or simplify the representation of an image, making it more meaningful and easier to interpret. For the objective class, corn achieved an IoU of 77.92%, and for background 83.25%, using DeepLabV3+ architecture, 78.81% for corn, and 83.73% for background using SegFormer architecture. For the objective class, the accuracy metrics were achieved at 86.88% and for background 91.41% using DeepLabV3+, 88.14% for the objective, and 91.15% for background using SegFormer.

Shwiff S.A., Auweloa C.L., Caires K., Friel G., Katayama L., Munoz Z., Price M.R., Risch D., Shartaj M., Steensma K., Thorne M., Zifko R.

AbstractBACKGROUNDInvasive ungulates (hoofed mammals), including deer, feral pigs, feral goats, and feral sheep, are known to cause damage to agriculture, property, natural resources, and many other commodities. Most of the information regarding the economic impacts of wild ungulates is from North America, where some of these species are native. To evaluate invasive ungulate damage to livestock producers in the Hawaiian Islands, which have no native ungulates, a survey was distributed to livestock producers across the state.RESULTSSurvey results described how total annual costs are distributed among damage, control, and repairs for survey respondents, who represented a significant percentage of total ranchland acreage across the islands. The estimates, excluding fixed fence installation, revealed an annual cost to livestock producers who responded to the survey of US$1.42 million, which ranged from $3.6 million to $7.5 million when extrapolated to the entire state. The large cost contributors included damage to property, pastureland repair, control costs (excluding fencing), supplemental feed, and predation of calves by wild pigs. Additionally, producers reported spending more than $2 million in upfront fence installation costs. Most of these costs were reported by respondents on the islands of Hawai'i and Moloka'i.CONCLUSIONStudy results revealed substantial damage to state livestock producers due to wild ungulates and are useful in determining an invasive ungulate management strategy that can appropriately aid the most impacted sectors of Hawai'i. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Alberts F., Berke O., Rocha L., Keay S., Maboni G., Poljak Z.

IntroductionPredicting which species are susceptible to viruses (i.e., host range) is important for understanding and developing effective strategies to control viral outbreaks in both humans and animals. The use of machine learning and bioinformatic approaches to predict viral hosts has been expanded with advancements in in-silico techniques. We conducted a scoping review to identify the breadth of machine learning methods applied to influenza and coronavirus genome data for the identification of susceptible host species.MethodsThe protocol for this scoping review is available at https://hdl.handle.net/10214/26112. Five online databases were searched, and 1,217 citations, published between January 2000 and May 2022, were obtained, and screened in duplicate for English language and in-silico research, covering the use of machine learning to identify susceptible species to viruses.ResultsFifty-three relevant publications were identified for data charting. The breadth of research was extensive including 32 different machine learning algorithms used in combination with 29 different feature selection methods and 43 different genome data input formats. There were 20 different methods used by authors to assess accuracy. Authors mostly used influenza viruses (n = 31/53 publications, 58.5%), however, more recent publications focused on coronaviruses and other viruses in combination with influenza viruses (n = 22/53, 41.5%). The susceptible animal groups authors most used were humans (n = 57/77 analyses, 74.0%), avian (n = 35/77 45.4%), and swine (n = 28/77, 36.4%). In total, 53 different hosts were used and, in most publications, data from multiple hosts was used.DiscussionThe main gaps in research were a lack of standardized reporting of methodology and the use of broad host categories for classification. Overall, approaches to viral host identification using machine learning were diverse and extensive.

Zhao J., Wan W., Yu K., Lemey P., Pettersson J.H., Bi Y., Lu M., Li X., Chen Z., Zheng M., Yan G., Dai J., Li Y., Haerheng A., He N., et. al.

Animals such as raccoon dogs, mink and muskrats are farmed for fur and are sometimes used as food or medicinal products1,2, yet they are also potential reservoirs of emerging pathogens3. Here we performed single-sample metatranscriptomic sequencing of internal tissues from 461 individual fur animals that were found dead due to disease. We characterized 125 virus species, including 36 that were novel and 39 at potentially high risk of cross-species transmission, including zoonotic spillover. Notably, we identified seven species of coronaviruses, expanding their known host range, and documented the cross-species transmission of a novel canine respiratory coronavirus to raccoon dogs and of bat HKU5-like coronaviruses to mink, present at a high abundance in lung tissues. Three subtypes of influenza A virus—H1N2, H5N6 and H6N2—were detected in the lungs of guinea pig, mink and muskrat, respectively. Multiple known zoonotic viruses, such as Japanese encephalitis virus and mammalian orthoreovirus4,5, were detected in guinea pigs. Raccoon dogs and mink carried the highest number of potentially high-risk viruses, while viruses from the Coronaviridae, Paramyxoviridae and Sedoreoviridae families commonly infected multiple hosts. These data also reveal potential virus transmission between farmed animals and wild animals, and from humans to farmed animals, indicating that fur farming represents an important transmission hub for viral zoonoses. Fur farming represents an important hub of cross-species transmission for viral zoonoses.

Li X., Parker B.M., Boughton R.K., Beasley J.C., Smyser T.J., Austin J.D., Pepin K.M., Miller R.S., Vercauteren K.C., Wisely S.M.

Understanding the epidemiology and transmission dynamics of transboundary animal diseases (TADs) among wild pigs (Sus scrofa) will aid in preventing the introduction or containment of TADs among wild populations. Given the challenges associated with studying TADs in free-ranging populations, a surrogate pathogen system may predict how pathogens may circulate and be maintained within wild free-ranging swine populations, how they may spill over into domestic populations, and how management actions may impact transmission. We assessed the suitability of Torque teno sus virus 1 (TTSuV1) to serve as a surrogate pathogen for molecular epidemiological studies in wild pigs by investigating the prevalence, persistence, correlation with host health status and genetic variability at two study areas: Archbold’s Buck Island Ranch in Florida and Savannah River Site in South Carolina. We then conducted a molecular epidemiological case study within Archbold’s Buck Island Ranch site to determine how analysis of this pathogen could inform transmission dynamics of a directly transmitted virus. Prevalence was high in both study areas (40%, n = 190), and phylogenetic analyses revealed high levels of genetic variability within and between study areas. Our case study showed that pairwise host relatedness and geographic distance were highly correlated to pairwise viral genetic similarity. Molecular epidemiological analyses revealed a distinct pattern of direct transmission from pig to pig occurring within and between family groups. Our results suggest that TTSuV1 is highly suitable for molecular epidemiological analyses and will be useful for future studies of transmission dynamics in wild free-ranging pigs.