Modelling the global economic consequences of a major African swine fever outbreak in China

A latent class analysis of biosecurity attitudes and decision-making strategies of swine producers in the United States

The 2018 African swine fever (ASF) outbreak highlighted the importance of biosecurity in food production systems. Despite the significant economic impacts, the sociopsychological consequences on decision-making have been overlooked. Previous studies have focused on algebraic models and simulation-based models without considering the complex psychological and social factors that influence farmers' biosecurity behaviors and decision-making processes. This study aims to classify livestock producers into distinct subgroups based on their attitudes towards biosecurity. We conducted a survey presenting producers with three scenarios to assess their willingness to report suspected ASF cases, trust in government agencies, risk perception, biosecurity knowledge, willingness to purchase livestock insurance, motivation to invest in biosecurity, readiness to report suspected infections, and intention to contact a veterinarian. Using latent class analysis, we identified three distinct classes: Biosecurity Sceptics, Biosecurity Compliant, and Biosecurity Ultra-Compliant. Our results show that producer characteristics significantly influence biosecurity attitudes and class membership, with small-scale producers less likely to adopt ultra-compliant biosecurity practices. Attending at least one eradication program encouraged biosecurity compliance. This research informs the design of targeted food policy and risk communication strategies that account for attitudes of livestock producers to encourage biosecurity adoption and reduce the likelihood of Tier 1 disease incursion.

The effect of avian influenza outbreaks on retail price premiums in the United States poultry market

This study analyzes the effect of avian influenza outbreaks on retail price premiums in the US poultry market. We estimate hedonic price models for eggs, chickens, and turkeys, controlling for quality characteristics, unobserved time, and regional factors. To measure the impact of avian influenza outbreaks we use 2 proxies. The first proxy is a measure of the number of new bird infections at the production level. The second proxy measures online search queries related to the outbreak. The results show that, on average, prices increase across product categories, that is, egg, broiler, and turkey markets, during avian influenza outbreaks. Furthermore, we observe price convergence and reduced dispersion within product categories, which is consistent with the economic theory of asymmetric substitutability between conventional and premium products. Our analysis finds that the HPAI outbreak caused a reduction of the price gap between conventional and premium products.

Development of a quantum dots based immunochromatographic strip for rapid and on-site detection of African swine fever virus

African swine fever (ASF) is a lethal disease caused by ASF virus (ASFV), severely impacting the global swine industry. Though nuclear acid-based detection methods are reliable, they are laboratory-dependent. In this study, we developed a device-independent, user friendly and cost-effective quantum dots based immunochromatographic strip (QDs-ICS) with high specificity and sensitivity for the rapid and on-site detection of ASFV antigen. For the preparation of the QDs-ICS, we generated a monoclonal antibody (mAb) mAb-8G8 and polyclonal antibody (pAb) against ASFV-p72 protein. The pAb was labelled with QDs to be used as the detection probe and the mAb-8G8 was coated on the nitrocellulose membrane as the test line. Our results proved that the strip displayed no cross-reactivity with other swine viruses and detection limit of the QDs-ICS was down to 1 ng/mL for the ASFV-p72 protein with great reproducibility. The strip also exhibited high stability with a storage period up to 12 months under room temperature. Twenty blind samples and one hundred clinical samples were examined by the QDs-ICS, conventional PCR and real-time PCR method, respectively. Results showed that the agreement rate between the QDs-ICS and PCR method was 100%, and the agreement rate between the strip and real-time PCR was 94%. The novel QDs-ICS developed here would be an effective tool for on-site detection of ASFV.

Has food security in the EU countries worsened during the COVID-19 pandemic? Analysis of physical and economic access to food

The aim of the paper is to provide an ex-post assessment of the impact of the COVID-19 pandemic on food insecurity in the EU-27 countries expressed by physical and economic food access. We analysed trade and price effects, together with food insecurity and malnutrition indicators. Actual levels of the indicators were compared with their pre-pandemic magnitudes and/or with counterfactual levels derived from predictive models. We also aimed to compare the objective statistics with the subjective consumers' perception of their households' food security. Our research indicates that the EU food trade was more resilient to COVID-19 impacts than the trade in non-food products, while food trade decreases were of a temporary nature. This did not affect the trade balance significantly; however, the import reduction threatened the physical food access in most EU countries. Regarding economic food access, the results indicate that the increase in food prices was offset by the increase in disposable income. It may suggest that the COVID-19 pandemic did not significantly affect the deterioration of economic access to food in the EU countries. However, the prevalence of severe food insecurity in the total population or the proportion of households reporting inability to afford a meal with meat, chicken, fish, or a vegetarian equivalent increased in 2020-2021 compared to 2019. This means that the comparative analysis of the real data on prices and households' income, as well as consumer financial situation and food consumption affordability, does not offer a clear answer concerning the impact of the COVID-19 pandemic on the food security of EU households.

Global antimicrobial use in livestock farming: an estimate for cattle, chickens, and pigs

Livestock farming substantially contributes to the global economy and food security. However, it poses crucial environmental, animal welfare, and public health challenges. The main objective of this study is to quantify the global antimicrobial use (AMU) in cattle, chicken, and pig farming. This information is important for understanding the potential impact of farm AMU on the emergence and spread of antimicrobial resistance among animals and humans. Using the United States Department of Agriculture Production, Supply, and Distribution and the Food and Agriculture Organization databases, we estimated the total supply of cattle (in heads) and its distribution into four weight categories: calves (26%), cows (41%), heifers (4%), and bulls of more than one year (29%). Similarly, we calculated the total supply of pigs (in heads) and divided it into two weight categories: pigs (96%) and sows (4%). For chickens, we considered one weight category. We attributed to each category a standard weight according to the parameters set by the European Medicines Agency (EMA) to determine the animal biomass at risk of antimicrobial treatment, or population correction unit (PCU). Finally, we estimated the global PCUs and then the global AMU based on the average administered to the three species (in mg of active ingredients per kg PCU). With this method, we estimated a global annual AMU of 76 060 tonnes of antimicrobial active ingredients (2019-2021 average), of which 40 697 tonnes (or 53.5%) for cattle, 4 243 tonnes (or 5.6%) for chickens, and 31 120 tonnes (or 40.9%) for pigs. According to our assessment, global AMU leads to almost 20 000 tonnes less than the previous estimates due to a different evaluation of PCUs. In previous studies, PCUs were calculated on the liveweight at slaughtering of animals, while our method considers the age and sex of animals and their average weight at treatment. Our results are consistent with the World Organization for Animal Health (WOAH) estimate of 76 704 tonnes of veterinary antimicrobials globally consumed in 2018 for the total of food-producing animals (the WOAH estimation is based on sales and import data).

Reconstruction and analysis of the transmission network of African swine fever in People's Republic of China, August 2018-September 2019

Introduction of African swine fever (ASF) to China in mid-2018 and the subsequent transboundary spread across Asia devastated regional swine production, affecting live pig and pork product-related markets worldwide. To explore the spatiotemporal spread of ASF in China, we reconstructed possible ASF transmission networks using nearest neighbour, exponential function, equal probability, and spatiotemporal case-distribution algorithms. From these networks, we estimated the reproduction numbers, serial intervals, and transmission distances of the outbreak. The mean serial interval between paired units was around 29 days for all algorithms, while the mean transmission distance ranged 332 -456 km. The reproduction numbers for each algorithm peaked during the first two weeks and steadily declined through the end of 2018 before hovering around the epidemic threshold value of 1 with sporadic increases during 2019. These results suggest that 1) swine husbandry practices and production systems that lend themselves to long-range transmission drove ASF spread; 2) outbreaks went undetected by the surveillance system. Efforts by China and other affected countries to control ASF within their jurisdictions may be aided by the reconstructed spatiotemporal model. Continued support for strict implementation of biosecurity standards and improvements to ASF surveillance is essential for halting transmission in China and spread across Asia.

Decoupling livestock and poultry pollution emissions from industrial development: A step towards reducing environmental emissions

China has implemented policies like Leading areas for Agricultural Green Development (LAGD) to mitigate livestock and poultry farming pollution while promoting industry growth. However, it remains uncertain whether LAGDs have successfully balanced emission reduction with stable development. This study examines 165 LAGDs to analyze changes in emissions, assess the decoupling of emission reduction from output value, and identify influencing factors. Findings reveal that emissions from livestock and poultry in LAGDs initially increased and then decreased between 2010 and 2019. Cattle were responsible for over 40% of fecal emissions, and pigs for more than 20%. Additionally, pigs contributed to over 61% of urine emissions. From 2010 to 2014, increases in chemical oxygen demand were mainly due to pigs and cattle. Total nitrogen levels were significantly impacted by cattle, while pigs were affected by total phosphorus. From 2014 to 2019, reductions in emissions were largely attributed to a decrease in pig-related pollutants. The decoupling status shifted from strong to weak and then back to strong between 2014 and 2019. Production efficiency played a crucial role in reducing emissions, while changes in industrial structure moved from supporting to hindering this reduction. Economic development was a primary factor in driving these changes. Standard emissions in Chinese regions showed a rising and then declining trend from 2010 to 2019. The Northeast and Northwest regions of China demonstrated emission trends that were in sync with the growth in rural income. This study offers insights into the successes and challenges of LAGDs in achieving a balance between reduced emissions and development, using quantitative analysis. The findings are instrumental in informing policies for a sustainable livestock and poultry industry. Recommendations include evaluating coordinated approaches to pollution reduction and industrial growth, setting decoupling goals, designing policies based on influential factors, conducting regional assessments of livestock and poultry demand, and implementing region-specific strategies.

Risk of African swine fever virus transmission among wild boar and domestic pigs in Poland

Introduction

African swine fever (ASF) is a notifiable disease of swine that impacts global pork trade and food security. In several countries across the globe, the disease persists in wild boar (WB) populations sympatric to domestic pig (DP) operations, with continued detections in both sectors. While there is evidence of spillover and spillback between the sectors, the frequency of occurrence and relative importance of different risk factors for transmission at the wildlife-livestock interface remain unclear.

Methods

To address this gap, we leveraged ASF surveillance data from WB and DP across Eastern Poland from 2014-2019 in an analysis that quantified the relative importance of different risk factors for explaining variation in each of the ASF surveillance data from WB and DP.

Results

ASF prevalence exhibited different seasonal trends across the sectors: apparent prevalence was much higher in summer (84% of detections) in DP, but more consistent throughout the year in WB (highest in winter with 45%, lowest in summer at 15%). Only 21.8% of DP-positive surveillance data included surveillance in WB nearby (within 5 km of the grid cell within the last 4 weeks), while 41.9% of WB-positive surveillance samples included any DP surveillance samples nearby. Thus, the surveillance design afforded twice as much opportunity to find DP-positive samples in the recent vicinity of WB-positive samples compared to the opposite, yet the rate of positive WB samples in the recent vicinity of a positive DP sample was 48 times as likely than the rate of positive DP samples in the recent vicinity of a positive WB sample. Our machine learning analyses found that positive samples in WB were predicted by WB-related risk factors, but not to DP-related risk factors. In contrast, WB risk factors were important for predicting detections in DP on a few spatial and temporal scales of data aggregation.

Discussion

Our results highlight that spillover from WB to DP might be more frequent than the reverse, but that the structure of current surveillance systems challenge quantification of spillover frequency and risk factors. Our results emphasize the importance of, and provide guidance for, improving cross-sector surveillance designs.

Origin, genomic diversity and evolution of African swine fever virus in East Asia

Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries have caused a huge impact on the local swine industry, resulting in huge economic losses. However, little is known about the origin, genomic diversity, evolutionary features, and epidemiological history of the genotype II ASFV. Here, 14 high-quality complete genomes of ASFVs were generated via sequencing of samples collected from China over the course of 3 years, followed by phylogenetic and phylodynamic analyses. The strains identified were relatively homogeneous, with a total of 52 SNPs and 11 indels compared with the prototype strain HLJ/2018, among which there were four exceptionally large deletions (620-18,023 nt). Evolutionary analyses revealed that ASFV strains distributed in eastern Asia formed a monophyly and a 'star-like' structure centered around the prototype strain, suggesting a single origin. Additionally, phylogenetic network analysis and ancestral reconstruction of geographic state indicated that genotype II ASFV strains in eastern Asia likely originated from Western Europe. Overall, these results contribute to the understanding of the history and current status of genotype II ASFV strains in eastern Asian, which could be of considerable importance in disease control and prevention.

What can we learn from the five-year African swine fever epidemic in Asia?

Today's global swine industry is exposed to the unprecedented threat of African swine fever (ASF). Asia, the site of the most recent epidemics, could serve as a huge viral reservoir for the rest of the world given the severity of the damage, the huge swine industry, and the high volume of trade with other countries around the world. As the majority of ASF notifications in Asia today originate from pig farms, the movement of live pigs and associated pork products are considered critical control points for disease management. Particularly, small-scale or backyard farms with low biosecurity levels are considered major risk factors. Meanwhile, wild boars account for most notified cases in some countries and regions, which makes the epidemiological scenario different from that in other Asian countries. As such, the current epidemic situation and higher risk factors differ widely between these countries. A variety of studies on ASF control have been conducted and many valuable insights have been obtained in Asia; nevertheless, the overall picture of the epidemic is still unclear. The purpose of this review is to provide an accurate picture of the epidemic situation across Asia, focusing on each subregion to comprehensively explain the disease outbreak. The knowledge gained from the ASF epidemics experienced in Asia over the past 5 years would be useful for disease control in areas that are already infected, such as Europe, as well as for non-affected areas to address preventive measures. To this end, the review includes two aspects: a descriptive analytical review based on publicly available databases showing overall epidemic trends, and an individualized review at the subregional level based on the available literature.

Livestock health and disease economics: a scoping review of selected literature

Animal diseases in production and subsistence environments have the potential to negatively affect consumers, producers, and economies as a whole. A growing global demand for animal sourced food requires safe and efficient production systems. Understanding the burden of animal disease and the distribution of burden throughout a value chain informs policy that promotes safe consumption and efficient markets, as well as providing more effective pathways for investment. This paper surveys existing knowledge on the burden of animal disease across economic categories of production, prevention and treatment, animal welfare, and trade and regulation. Our scoping review covers 192 papers across peer-reviewed journals and reports published by organizations. We find there exists a gap in knowledge in evaluating what the global burdens of animal diseases are and how these burdens are distributed in value chains. We also point to a need for creating an analytical framework based on established methods that guides future evaluation of animal disease burden, which will provide improved access to information on animal health impacts.

African Swine Fever Shock: China's Hog Industry's Resilience and Its Influencing Factors

African swine fever has damaged the foundation of China's hog industry, caused a serious decline in hog production, highlighted the contradiction between supply and demand in the pork market, and led to major economic and social impacts. The industrial resilience of 31 Chinese provinces to African swine fever shock and its spatial and temporal differentiation characteristics from 2018 to 2021 were measured in this study from the two dimensions of resistance and recoverability. Using Geodetector, the key factors influencing the resilience of China's hog industry were explored. The results showed that 2018-2019 and 2020-2021 represented the resistance and recovery periods of the hog industry under African swine fever shock, respectively, with poor resilience characterizing the resistance period and improved resilience characterizing the recovery period. At the early stages of the African swine fever outbreak, the hog industries in Tianjin, Shanxi, Guangxi, and Yunnan had robust resistance due to the slaughter rate, economic level, mortality rate, carcass weight, and culling rate in those areas. At the most severe stage of the outbreak, resistance was generally poor in all provinces due to the slaughter rate, per capita consumption, and scale level at the time. During the period of rapid recovery in hog production, the recoverability of each province was very strong due to the industrial structure, culling rate, economic level, and resource carrying capacity at that time. During the reasonable adjustment period of hog production capacity, the recoverability based on the breeding sow inventory in 13 provinces, including Henan, Shandong, and other large hog-breeding provinces, was negative due to the scale level, slaughter rate, per capita consumption, and resource carrying at that time. Taking measures to enhance the resilience of the hog industry, strengthen the prevention and control of hog epidemics, improve the monitoring and early warning mechanisms, and enhance the ability of the hog industry to cope with major animal epidemics is recommended.

A study on the impact of double external shocks on Chinese wholesale pork prices

Introduction

Fluctuation in pork prices has always been a focus of academic attention. This paper examines the impact of double external shocks on pork prices, to provide reference for the impact of future outbreaks on the pork market.

Methods

This paper constructs a natural experiment based on the time and regional differences in the occurrence of the epidemics. Double difference models and triple difference models are used to identify the impacts of African swine fever and COVID-19 on Chinese pork prices.

Results

The results found that both African swine fever and COVID-19 positively affected pork prices, but African swine fever had a greater degree of impact; before the COVID-19 epidemic, African swine fever caused a more significant increase in pork prices; the impact of a single African swine fever shock was greater than the double shocks.

Discussion

The COVID-19 epidemic may have curbed the further increase in pork prices, due to the decreased market consumption demand caused by the epidemic.

Contacts posing risks of disease introduction in swine breeding herds in Quebec, Canada: Is the frequency of contacts associated with biosecurity measures?

The introduction of pathogens into swine breeding herds can occur through a variety of contacts involving people, animals, vehicle or various supplies. Appropriate biosecurity is critical to mitigate these risks. A retrospective study was conducted to describe contacts with swine breeding sites over a one-month period and to evaluate their association with biosecurity measures and site characteristics. As part of a larger project, sites which had a recent porcine reproductive and respiratory syndrome virus introduction were selected. A questionnaire, logbooks and pig traceability system were used for collecting data relative to persons or supplies entering the breeding unit, live pig transportation, service vehicles, other animal species, neighboring pig sites and manure spreading around the site. The 84 sites investigated had a median sow inventory of 675. A median of 4 farm staff and 2 visitors entered the breeding unit at least once over the one-month period. A total of 73 sites (87%) received visitor(s), mostly from maintenance and technical services. All sites received at least 3 supply deliveries (median of 8) including semen (99% of sites), small material and/or drugs (98% of sites), bags (87% of sites), and/or equipment (61% of sites). Live pig movements were observed in all sites, with a median number of 5 truck entries on the site or exits from the site. For feed mill, rendering and propane trucks, at least one entry was noted in ≥ 61% of sites. For all service vehicle categories except feed mill and manure vacuum trucks, a single service provider was involved in each site. Dogs and cats were banned from all sites, but wild birds were observed in 8% of sites. Manure spreading within a 100 m radius of pig units was noted in 10% of the sites. With a few exceptions, biosecurity measures were not associated with the frequency of contacts. A 100-sow increase in sow inventory was associated with an increase of 0.34 in the cumulated number of staff entering the breeding unit, of 0.30 in the number of visitors and of 0.19 in the number of live pig movements. Live pig movements were also positively associated with vertically integrated farrow-to-wean (vs. independent farrow-to-wean) production and time interval of 4 weeks or more between farrowing (vs. less than 4). Considering the variety and frequency of contacts observed, biosecurity should be meticulously applied in all breeding herds to prevent endemic and exotic disease introduction.

Estimating the effectiveness of control actions on African swine fever transmission in commercial swine populations in the United States

Given the proximity of African swine fever (ASF) to the U.S., there is an urgent need to better understand the possible dissemination pathways of the virus within the U.S. swine industry and to evaluate mitigation strategies. Here, we extended PigSpread, a farm-level spatially-explicit stochastic compartmental transmission model incorporating six transmission routes including between-farm swine movements, vehicle movements, and local spread, to model the dissemination of ASF. We then examined the effectiveness of control actions similar to the ASF national response plan. The average number of secondary infections during the first 60 days of the outbreak was 49 finisher farms, 17 nursery farms, 5 sow farms, and less than one farm in other production types. The between-farm movements of swine were the predominant route of ASF transmission with an average contribution of 71.1%, while local spread and movement of vehicles were less critical with average contributions of 14.6% and 14.4%. We demonstrated that the combination of quarantine, depopulation, movement restrictions, contact tracing, and enhanced surveillance, was the most effective mitigation strategy, resulting in an average reduction of 79.0% of secondary cases by day 140 of the outbreak. Implementing these control actions led to a median of 495,619 depopulated animals, 357,789 diagnostic tests, and 54,522 movement permits. Our results suggest that the successful elimination of an ASF outbreak is likely to require the deployment of all control actions listed in the ASF national response plan for more than 140 days, as well as estimating the resources needed for depopulation, testing, and movement permits under these controls.

Potential reduction of greenhouse gas emissions from pig production in China on the basis of households' pork consumption

In the past decades, the greenhouse gas (GHG) emissions from pig production in China have been increasing rapidly, which has become a huge challenge in fulfilling China's "carbon neutral" commitment. However, few studies have focused on reducing the GHG emissions from pig production in view of households' pork consumption. This study analyzed the temporal and spatial pattern of the GHG emissions from pig production in China in 2001-2020 through geographical information system, optimized the pig production in China, and estimated thepotentialGHG emissions reduction from pig production in China in 2020 through spatial analysis based on pork surplus or deficit. Results show that the temporal and spatial pattern of the GHG emissions from pig production and its proportion in the total GHG emissions from livestock production in China in 2001-2020 varied differently at the province level and conformed to the "Hu Huanyong Line" mode. The largest and smallest GHG emissions from pig production were 108.93 million tons (MT) in 2014 and 78.10 MT in 2020, respectively. The largest and smallest proportions of GHG emissions from pig production in the total GHG emissions from livestock production were 77.52% in Zhejiang in 2013 and 0.13% in Tibet in 2009, respectively. Moreover, a potential optimization scheme of pig production in China in 2020 was provided and a method of GHG emissions reduction from pig production is proposed. The results indicate that the total potentialGHG emissions reduction from pig production on the basis of households' pork consumption could reach 35.21 MT, accounting for 45.09% of the total GHG emissions from pig production and 10.27% of the total GHG emissions from livestock production in China in 2020. These findings areusefulin the spatial layout planning of pig production, agricultural GHG reduction, and global warming mitigation.

The ripple effect of animal disease outbreaks on food systems: The case of African Swine Fever on the Chinese pork market

Research on animal health economics has emphasised the importance of accounting for the indirect economic effects of animal disease outbreaks. Although recent studies have advanced in this direction by assessing consumer and producer welfare losses due to asymmetric price adjustments, potential over-shifting effects along the supply chain and spill-overs to substitute markets have been under-examined. This study contributes to this field of research by assessing the direct and indirect effects of the African swine fever (ASF) outbreak on the pork market in China. We employ impulse response functions estimated by local projection to calculate the price adjustments for consumers and producers, as well as the cross-effect in other meat markets. The results show that the ASF outbreak led to increases in both farmgate and retail prices but the rise in retail prices exceeded the corresponding change in farmgate prices. Furthermore, beef and chicken prices also rose, demonstrating the spill-over impacts of the outbreak to other markets. Overall, the evidence illustrates that a disruption in one part of a food system can have significant ripple effects across other parts of the system.

Complete genome analysis of African swine fever virus genotypes II, IX and XV from domestic pigs in Tanzania

African swine fever (ASF) caused by ASF virus (ASFV) is an infectious transboundary animal disease notifiable to the World Organization for Animal Health causing high mortality in domestic pigs and wild boars threatening the global domestic pig industry. To date, twenty-four ASFV genotypes have been described and currently genotypes II, IX, X, XV and XVI are known to be circulating in Tanzania. Despite the endemic status of ASF in Tanzania, only one complete genome of ASFV from the country has been described. This study describes the first complete genome sequence of ASFV genotype XV. In addition, the first Tanzanian complete genome of ASFV genotype IX and three ASFV strains belonging to genotype II collected during ASF outbreaks in domestic pigs in Tanzania were determined in this study using Illumina sequencing and comparative genomics analysis. The generated ASFV complete genome sequences ranged from 171,004 to 184,521 base pairs in length with an average GC content of 38.53% and encoded 152 to 187 open reading frames. The results of this study provide insights into the genomic structure of ASFV and can be used to monitor changes within the ASFV genome and improve our understanding of ASF transmission dynamics.

Elasticity and substitutability of food demand and emerging disease risk on livestock farms

Disease emergence in livestock is a product of environment, epidemiology and economic forces. The environmental factors contributing to novel pathogen emergence in humans have been studied extensively, but the two-way relationship between farm microeconomics and outbreak risk has received comparably little attention. We introduce a game-theoretic model where farmers produce and sell two goods, one of which (e.g. pigs, poultry) is susceptible to infection by a pathogen. We model market and epidemiological effects at both the individual farm level and the community level. We find that in the case of low demand elasticity for livestock meat, the presence of an animal pathogen causing production losses can lead to a bistable system where two outcomes are possible: (i) successful disease control or (ii) maintained disease circulation, where farmers slaughter their animals at a low rate, face substantial production losses, but maintain large herds because of the appeal of high meat prices. Our observations point to the potentially critical effect of price elasticity of demand for livestock products on the success or failure of livestock disease control policies. We show the potential epidemiological benefits of (i) policies aimed at stabilizing livestock product prices, (ii) subsidies for alternative agricultural activities during epidemics, and (iii) diversifying agricultural production and sources of proteins available to consumers.

Vertical integration selection of Chinese pig industry chain under African swine fever - From the perspective of stable pig supply

Vertical integration is conducive to the realization of complementary interests and sustainable development of pig industry. The outbreak of African swine fever (ASF) in 2018 has disrupted many activities along pig industry chain in China. The production capacity of breeding pigs has dropped rapidly, and the supply of pig is tight. The vertical integration of pig industry chain is the main driving force to ensure food supply. Based on the data of 12 listed pig companies from 2012 to 2019, we examine the ways and reasons for vertical integration of pig companies when external shocks increase by taking ASF as an example, breakpoint regression and Tobit model are used to analyze differences and determinants of the forward and backward integration of pig industry chain under ASF. The empirical results showed that the forward integration of the feed processing link and slaughter circulation link is higher than the backward integration. ASF had different effects on the vertical integration degree of each link. ASF promoted forward integration. The main factors have different influences on the vertical integration of pig industry in China. Forward integration increased mainly depending on previous asset specificity, legal system environment, market demand, and transaction frequency. The findings of the study imply that pig industry chain is taking the forward integration to cope with the ASF shock. The combination of feed link and breeding link reduces feed cost and ensures pig supply. Pig companies tend to reduce transaction costs by strengthening the control of downstream supply.

Identifying Pathogen and Allele Type Simultaneously in a Single Well Using Droplet Digital PCR

In the transmission control of chronic and untreatable livestock diseases such as bovine leukemia virus (BLV) infection, the removal of viral superspreaders is a fundamental approach. On the other hand, selective breeding of cattle with BLV-resistant capacity is also critical for reducing the viral damage to productivity by keeping infected cattle. To provide a way of measuring BLV proviral load (PVL) and identifying susceptible/resistant cattle simply and rapidly, we developed a fourplex droplet digital PCR method targeting the BLV pol gene, BLV-susceptible bovine major histocompatibility complex (BoLA)-DRB3*016:01 allele, resistant DRB3*009:02 allele, and housekeeping RPP30 gene (IPATS-BLV). IPATS-BLV successfully measured the percentage of BLV-infected cells and determined allele types precisely. Furthermore, it discriminated homozygous from heterozygous carriers. Using this method to determine the impact of carrying these alleles on the BLV PVL, we found DRB3*009:02-carrying cattle could suppress the PVL to a low or undetectable level, even with the presence of a susceptible heterozygous allele. Although the population of DRB3*016:01-carrying cattle showed significantly higher PVLs compared with cattle carrying other alleles, their individual PVLs were highly variable. Because of the simplicity and speed of this single-well assay, our method has the potential of being a suitable platform for the combined diagnosis of pathogen level and host biomarkers in other infectious diseases satisfying the two following characteristics of disease outcomes: (i) pathogen level acts as a critical maker of disease progression; and (ii) impactful disease-related host genetic biomarkers are already identified. IMPORTANCE While pathogen-level quantification is an important diagnostic of disease severity and transmissibility, disease-related host biomarkers are also useful in predicting outcomes in infectious diseases. In this study, we demonstrate that combined proviral load (PVL) and host biomarker diagnostics can be used to detect bovine leukemia virus (BLV) infection, which has a negative economic impact on the cattle industry. We developed a fourplex droplet digital PCR assay for PVL of BLV and susceptible and resistant host genes named IPATS-BLV. IPATS-BLV has inherent merits in measuring PVL and identifying susceptible and resistant cattle with superior simplicity and speed because of a single-well assay. Our new laboratory technique contributes to strengthening risk-based herd management used to control within-herd BLV transmission. Furthermore, this assay design potentially improves the diagnostics of other infectious diseases by combining the pathogen level and disease-related host genetic biomarker to predict disease outcomes.

Lower pork consumption and technological change in feed production can reduce the pork supply chain environmental footprint in China

Nearly half of global pork production and consumption occurs in China, but the transition towards intensification is associated with worsening environmental impacts. Here we explore scenarios for implementing structural and technological changes across the pork supply chain to improve environmental sustainability and meet future demand. Following the middle-of-the-road socio-economic pathway (SSP2), we estimate that the environmental footprint from the pork supply chain will increase by ~50% from 2017 to 2050. Utilizing technologies that improve feed crop production and manure management could reduce phosphorus and nitrogen losses by three-quarters and one-third, respectively, with modest reductions in greenhouse gas emissions and cropland area. Reducing pork consumption had substantial mitigation potential. Increased feed and pork imports would decrease domestic environmental footprints and meet demand, but increase footprints elsewhere. We conclude that farm-specific technologies and structural adjustments can support the development of rural, small-scale pig farms near cropland and promote circular economy principles.

CRISPR/Cas-Assisted Colorimetric Biosensor for Point-of-Use Testing for African Swine Fever Virus

African swine fever virus (ASFV) causes a highly contagious and fatal disease affecting both domesticated and wild pigs. Substandard therapies and inadequate vaccinations cause severe economic damages from pig culling and removal of infected carcasses. Therefore, there is an urgent need to develop a rapid point-of-use approach that assists in avoiding the spread of ASFV and reducing economic loss. In this study, we developed a colorimetric sensing platform based on dual enzymatic amplification that combined the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 12a (Cas12a) system and the enzyme urease for accurate and sensitive detection of ASFV. The mechanism of the sensing platform involves a magnetic bead-anchored urease-conjugated single-stranded oligodeoxynucleotide (MB@urODN), which in the presence of ASFV dsDNA is cleaved by activated CRISPR/Cas12a. After magnetically separating the free urease, the presence of virus can be confirmed by measuring the colorimetric change in the solution. The advantage of this method is that it can detect the presence of virus without undergoing a complex target gene duplication process. The established method detected ASFV from three clinical specimens collected from porcine clinical tissue samples. The proposed platform is designed to provide an adequate, simple, robust, highly sensitive and selective analytical technique for rapid zoonotic disease diagnosis while eliminating the need for vast or specialized tools.

Pollinator Deficits, Food Consumption, and Consequences for Human Health: A Modeling Study

BACKGROUND

Animal pollination supports agricultural production for many healthy foods, such as fruits, vegetables, nuts, and legumes, that provide key nutrients and protect against noncommunicable disease. Today, most crops receive suboptimal pollination because of limited abundance and diversity of pollinating insects. Animal pollinators are currently suffering owing to a host of direct and indirect anthropogenic pressures: land-use change, intensive farming techniques, harmful pesticides, nutritional stress, and climate change, among others.

OBJECTIVES

We aimed to model the impacts on current global human health from insufficient pollination via diet.

METHODS

We used a climate zonation approach to estimate current yield gaps for animal-pollinated foods and estimated the proportion of the gap attributable to insufficient pollinators based on existing research. We then simulated closing the "pollinator yield gaps" by eliminating the portion of total yield gaps attributable to insufficient pollination. Next, we used an agriculture-economic model to estimate the impacts of closing the pollinator yield gap on food production, interregional trade, and consumption. Finally, we used a comparative risk assessment to estimate the related changes in dietary risks and mortality by country and globally. In addition, we estimated the lost economic value of crop production for three diverse case-study countries: Honduras, Nepal, and Nigeria.

RESULTS

Globally, we calculated that 3%-5% of fruit, vegetable, and nut production is lost due to inadequate pollination, leading to an estimated 427,000 (95% uncertainty interval: 86,000, 691,000) excess deaths annually from lost healthy food consumption and associated diseases. Modeled impacts were unevenly distributed: Lost food production was concentrated in lower-income countries, whereas impacts on food consumption and mortality attributable to insufficient pollination were greater in middle- and high-income countries with higher rates of noncommunicable disease. Furthermore, in our three case-study countries, we calculated the economic value of crop production to be 12%-31% lower than if pollinators were abundant (due to crop production losses of 3%-19%), mainly due to lost fruit and vegetable production.

DISCUSSION

According to our analysis, insufficient populations of pollinators were responsible for large present-day burdens of disease through lost healthy food consumption. In addition, we calculated that low-income countries lost significant income and crop yields from pollinator deficits. These results underscore the urgent need to promote pollinator-friendly practices for both human health and agricultural livelihoods. https://doi.org/10.1289/EHP10947.

How does imported pork regulate the supply and demand of China's pig market during the epidemic?-based on the analysis of African swine fever and COVID-19

The pig industry is primarily a domestic industry in China is focused on ensuring the domestic pork supply. This paper analyzed changes in Chinese pork imports following the outbreaks of African Swine Fever (ASF) and COVID-19 between January 2017 to November 2020 and evaluated the impact of imported pork on the development of the swine industry in China. The results demonstrated that the shortage of domestic pork supply changed the import volume. ASF transformed imported pork from a complementary product to meet the diversified needs of domestic consumers into a critical substitute required to fill the supply gap. Following the COVID-19 outbreak, the substitution effect of imported pork decreased. ASF, has caused the supply capacity of pork in China to decrease, the price of pork to increase, leading to increased pork import in January 2019. At the end of 2019, pig slaughter decreased, while China cut tariffs on imported pork. The COVID-19 outbreak did not reduce China's pork imports in China, which declined after the global COVID-19 outbreak. Imported pork has made up for the supply gap during COVID-19, not impacting the level of production of the swine industry in China.

Ecological niche modeling based on ensemble algorithms to predicting current and future potential distribution of African swine fever virus in China

African swine fever (ASF) is a tick-borne infectious disease initially described in Shenyang province China in 2018 but is now currently present nationwide. ASF has high infectivity and mortality rates, which often results in transportation and trade bans, and high expenses to prevent and control the, hence causing huge economic losses and a huge negative impact on the Chinese pig farming industry. Ecological niche modeling has long been adopted in the epidemiology of infectious diseases, in particular vector-borne diseases. This study aimed to establish an ecological niche model combined with data from ASF incidence rates in China from August 2018 to December 2021 in order to predict areas for African swine fever virus (ASFV) distribution in China. The model was developed in R software using the biomod2 package and ensemble modeling techniques. Environmental and topographic variables included were mean diurnal range (°C), isothermality, mean temperature of wettest quarter (°C), precipitation seasonality (cv), mean precipitation of warmest quarter(mm), mean precipitation of coldest quarter (mm), normalized difference vegetation index, wind speed (m/s), solar radiation (kJ /day), and elevation/altitude (m). Contribution rates of the variables normalized difference vegetation index, mean temperature of wettest quarter, mean precipitation of coldest quarter, and mean precipitation of warmest quarter were, respectively, 47.61%, 28.85%, 10.85%, and 7.27% (according to CA), which accounted for over 80% of contribution rates related to variables. According to model prediction, most of areas revealed as suitable for ASF distribution are located in the southeast coast or central region of China, wherein environmental conditions are suitable for soft ticks’ survival. In contrast, areas unsuitable for ASFV distribution in China are associated with arid climate and poor vegetation, which are less conducive to soft ticks’ survival, hence to ASFV transmission. In addition, prediction spatial suitability for future ASFV distribution suggests narrower areas for ASFV spread. Thus, the ensemble model designed herein could be used to conceive more efficient prevention and control measure against ASF according to different geographical locations in China.

A global dataset for prevalence of Salmonella Gallinarum between 1945 and 2021

Pullorum disease and fowl typhoid are among the most significant poultry diseases worldwide. However, the global burden of these diseases remains unknown. Most importantly, the parameters contributing to the prevalence of Salmonella Gallinarum variants are not well documented. Therefore, in this study, we present a systematic review and meta-analysis of the global prevalence of Salmonella Gallinarum during 1945–2021. In total, 201 studies were identified for qualitative analysis (>900 million samples). The meta-analysis was subjected to over 183 screened studies. The global prevalence of S. Gallinarum (percentage of positive samples in total samples) was 8.54% (95% CI: 8.43–8.65) and showed a V-shaped recovery over time. Pullorum disease is most common in Asia, particularly in eastern China. Further investigations on chicken origin samples revealed significant differences in S. Gallinarum prevalence by gender, breed, raising mode, economic use, and growth stage, indicating a critical role of vertical transmission. Together, this study offered an updated, evidence-based dataset and knowledge regarding S. Gallinarum epidemics, which might significantly impact decision-making policy with targeted interventions.

Measurement(s)	S. Gallinarum positive samples
Technology Type(s)	Serological test • Molecular method (PCR) • Plate culture and identification • Biochemical test
Factor Type(s)	biovar • time • geographic sampling site • reservoir of bacteria • chicken breed • raising mode • economic use • growth stage • gender
Sample Characteristic - Organism	Animal
Sample Characteristic - Location	world

The Astounding World of Glycans from Giant Viruses

Viruses are a heterogeneous ensemble of entities, all sharing the need for a suitable host to replicate. They are extremely diverse, varying in morphology, size, nature, and complexity of their genomic content. Typically, viruses use host-encoded glycosyltransferases and glycosidases to add and remove sugar residues from their glycoproteins. Thus, the structure of the glycans on the viral proteins have, to date, typically been considered to mimick those of the host. However, the more recently discovered large and giant viruses differ from this paradigm. At least some of these viruses code for an (almost) autonomous glycosylation pathway. These viral genes include those that encode the production of activated sugars, glycosyltransferases, and other enzymes able to manipulate sugars at various levels. This review focuses on large and giant viruses that produce carbohydrate-processing enzymes. A brief description of those harboring these features at the genomic level will be discussed, followed by the achievements reached with regard to the elucidation of the glycan structures, the activity of the proteins able to manipulate sugars, and the organic synthesis of some of these virus-encoded glycans. During this progression, we will also comment on many of the challenging questions on this subject that remain to be addressed.

A Scenario Analysis for Implementing Immunocastration as a Single Solution for Piglet Castration

Simple Summary

The 2010 European Declaration aimed at abandoning surgical castration and switching to alternative methods. With an intention to facilitate the internal trade, the European Union (EU) was initially in favor of a single alternative. Immunocastration, as an active vaccine against the Gonadotropin Releasing Hormone, was proposed as a potential solution. However, its market potential is not yet well understood. This study applied the method of scenario analysis to examine whether and under what conditions immunocastration could be the general solution sought by the EU. Specifically, it developed two extreme scenarios. Both scenarios suggest that it is unlikely that immunocastration will become a single solution for all producers in the EU.

Abstract

Painful castration of male piglets to avoid boar taint can potentially be replaced by three more ethical alternatives: entire male production in combination with a detection method, immunocastration (an active vaccination against the gonadotrophin-releasing factor, GnRF), and castration with pain relief (anesthesia and/or analgesia). With the aim of abandoning piglet castration and facilitating internal trade, the European Union (EU) was initially in favor of a single alternative. Immunocastration was proposed as a potential solution, but it has not yet been sufficiently assessed regarding its market potential. To address this point, this paper uses scenario analysis to examine whether and under what conditions immunocastration could be the general solution sought by the EU. The study constructs two extreme scenarios: one in which all uncertain elements negatively influence the growth of immunocastration; another in which all uncertain elements have positive influences. These scenarios provide insights into the variance in possible futures for the implementation of immunocastration. The results show that it is unlikely that immunocastration will become a single solution for all producers in the EU, because it is not the optimal solution for all types of EU pork production systems (i.e., cost-efficiency oriented, quality oriented, animal-friendly oriented, import dependent). Rather than debating and looking for evidence about which single method is the best for the entire EU, EU authorities are advised to allow the co-existence of all alternatives and to develop protocols for applying them in the pork industry.

Boom and Bust in China’s Pig Sector during 2018–2021: Recent Recovery from the ASF Shocks and Longer-Term Sustainability Considerations

China’s African swine fever (ASF) outbreaks, which started in 2018, severely damaged the country’s pig and sow herds and created serious pork supply shortages. This resulted in high domestic market prices and record amounts of imports in both 2019 and 2020, but also severely impacted its domestic consumers. It casts doubts on whether China’s long-standing self-sufficiency strategy, including its recently communicated 95% self-sufficiency target, can be sustained. Recent data, however, suggest that China is experiencing a rapid recovery in pig production, leading to depressed domestic market prices. This study characterizes the recovery process and analyzes the underlying drivers, such as active responses to the ASF outbreaks, a multiple-prong government initiative towards supporting the pig producers, de facto relaxations of newly introduced environmental regulations, large increases in domestic investment, and a reorganization of the pig sector, featuring more scale operations. However, the rapid recovery has also resulted in decreasing prices, economic losses of producers, and dampened export opportunities for China’s trade partners. This paper, therefore, also analyzes these unintended consequences and explores supply-side measures that may enable the long-run viability of the self-sufficiency goal in the presence of high dependency on imported feed. Through a model-based numerical simulation analysis, we find that supply-side measures, such as yield improvement, can substantially reduce reliance on import feed but can only increase domestic pork production marginally, while technical efficiency improvement in pork production has the largest potential in boosting domestic pork production.

Rapid and sensitive detection of African swine fever virus in pork using recombinase aided amplification combined with QDMs-based test strip

African swine fever virus (ASFV) is the pathogen of African swine fever, a highly contagious and fatal disease of wild boar and domestic pigs. The flow of ASFV through pork products is more concealed, higher risky, and more difficult to prevent and control. Presently, on-site ASFV detection methods in preclinical infected pigs and circulated pork products are lacking. Here, fluorescent test strip-based rapid ASFV detection method in pork was established combined with recombinase aided amplification (RAA) and quantum dot microspheres (QDMs). This method is specific to ASFV with no cross-reactivity to pseudorabies virus (PRV), porcine circovirus type 2 (PCV2), and porcine reproductive and respiratory syndrome virus (PRRSV). The method also showed highly sensitivity with a detection limit of 1 copy for ASFV plasmid templates containing B646L gene and 100 copies/g for DNA extracts from clinical pork samples within a short detection time of less than 25 min. Additionally, the method showed 99.17% consistency with real-time PCR in the ASFV detection of 120 clinical pork samples. Overall, the QDMs-based test strip method provides specific, sensitive, rapid, and simple detection of ASFV in pork, which may contribute to maintain the food safety of pork products, and facilitate ASFV traceability and prevention. Rapid and sensitive detection of African swine fever virus in pork by QDMs based test strip assay.

Determinants of Sick and Dead Pig Waste Recycling—A Case Study of Hebei, Shandong, and Henan Provinces in China

Simple Summary

Proper handling of dead and sick pig carcasses is a significant concern for farmers, the general public, academia, and government. By drawing on the existing literature, the study selects various determinants of sick and dead pig recycling and evaluates the impacts of rewards and punishment mechanisms on farmers’ commitment to proper handling of dead and sick pigs. We utilized face-to-face discussion accompanied by a structured questionnaire to grasp the opinion of the Chinese pig farmers. The article elucidates the moderating effects of reward and punishment mechanisms, which will be crucial for understanding the on-hand experience of the farmers towards dead and sick pig recycling.

Abstract

Improper handling of sick and dead pigs may seriously affect public health, socio-economic conditions, and eventually cause environmental pollution. However, effective promotion of sick and dead pig (SDP) waste recycling has become the prime focus of current rural governance. Therefore, the study explores the impact of commitment, rewards, and punishments to capture the recycling behavior of farmers’ sick and dead pig waste management. The study employs factor analysis, the probit model, and the moderating effect model to craft the findings. The study’s empirical setup comprises the survey data collected from the Hebei, Shandong, and Henan provinces, representing the major pig-producing provinces in China. The study found that the commitment, reward, and punishment mechanisms are essential factors affecting the farmers’ decision-making on recycling sick and dead pig waste. The marginal effect analysis found that the reward and punishment mechanism is more effective than the farmers’ commitment. The study confirmed that in the recycling treatment of sick and dead pig waste, the farmers’ commitment and the government’s reward and punishment policy are the main factors that influence farmers to manage sick and dead pig waste properly. Therefore, the government should highlight the importance of effective waste management, and training facilities should also be extended firmly. The government should impose strict rules and regulations to restrict the irresponsible dumping of farm waste. Monitoring mechanisms should be put in place promptly.

An Analysis of Agricultural Systems Modelling Approaches and Examples to Support Future Policy Development under Disruptive Changes in New Zealand

Agricultural systems have entered a period of significant disruption due to impacts from change drivers, increasingly stringent environmental regulations and the need to reduce unwanted discharges, and emerging technologies and biotechnologies. Governments and industries are developing strategies to respond to the risks and opportunities associated with these disruptors. Modelling is a useful tool for system conceptualisation, understanding, and scenario testing. Today, New Zealand and other nations need integrated modelling tools at the national scale to help industries and stakeholders plan for future disruptive changes. In this paper, following a scoping review process, we analyse modelling approaches and available agricultural systems’ model examples per thematic applications at the regional to national scale to define the best options for the national policy development. Each modelling approach has specificities, such as stakeholder engagement capacity, complex systems reproduction, predictive or prospective scenario testing, and users should consider coupling approaches for greater added value. The efficiency of spatial decision support tools working with a system dynamics approach can help holistically in stakeholders’ participation and understanding, and for improving land planning and policy. This model combination appears to be the most appropriate for the New Zealand national context.

Tradeoff analysis of the pork supply and food security under the influence of African swine fever and the COVID-19 outbreak in China

China is the world's largest consumer of pork and grains. However, African swine fever (ASF) and the COVID-19 outbreak have greatly impacted the pork supply and food security in China. How can food security and the pork supply be ensured under the dual impacts of COVID-19 and ASF? This is a major problem to be urgently solved by the Chinese government. This study indicated that the main pork production and sales areas in China were separated, which reflected the spatial imbalance between the supply and demand. The total area of suitable selected sites for pig farms in China is 21.5 million ha. If only the areas with levels of high and moderate suitability are considered as potential sites for pig farms, the potential pork production can reach 56.1 million tons in China, which is slightly lower than demand. Due to the impact of the ASF epidemic, the food consumed by pigs has been reduced by 34.7 million tons. However, with increasing pork productivity in the future, the self-sufficiency rate of grains may further decline. On the premise that the quality of people's life is not affected, the diversification of meat supply channels should be realized in an orderly and sustainable way, which might alleviate the pressure on food supply. This study provides a theoretical reference for the spatiotemporal layout of the swine industry and addresses the issue of food security in China under the influence of ASF and the COVID-19 outbreak.

Exact Bayesian inference of epidemiological parameters from mortality data: application to African swine fever virus

Pathogens such as African swine fever virus (ASFV) are an increasing threat to global livestock production with implications for economic well-being and food security. Quantification of epidemiological parameters, such as transmission rates and latent and infectious periods, is critical to inform efficient disease control. Parameter estimation for livestock disease systems is often reliant upon transmission experiments, which provide valuable insights in the epidemiology of disease but which may also be unrepresentative of at-risk populations and incur economic and animal welfare costs. Routinely collected mortality data are a potential source of readily available and representative information regarding disease transmission early in outbreaks. We develop methodology to conduct exact Bayesian parameter inference from mortality data using reversible jump Markov chain Monte Carlo incorporating multiple routes of transmission (e.g. within-farm secondary and background transmission from external sources). We use this methodology to infer epidemiological parameters for ASFV using data from outbreaks on nine farms in the Russian Federation. This approach improves inference on transmission rates in comparison with previous methods based on approximate Bayesian computation, allows better estimation of time of introduction and could readily be applied to other outbreaks or pathogens.

Multiple species animal movements: network properties, disease dynamics and the impact of targeted control actions

Infectious diseases in livestock are well-known to infect multiple hosts and persist through a combination of within- and between-host transmission pathways. Uncertainty remains about the epidemic dynamics of diseases being introduced on farms with more than one susceptible host species. Here, we describe multi-host contact networks and elucidate the potential of disease spread through farms with multiple hosts. Four years of between-farm animal movement among all farms of a Brazilian state were described through a static and monthly snapshot of network representations. We developed a stochastic multilevel model to simulate scenarios in which infection was seeded into single host and multi-host farms to quantify disease spread potential, and simulate network-based control actions used to evaluate the reduction of secondarily infected farms. We showed that the swine network was more connected than cattle and small ruminants in both the static and monthly snapshots. The small ruminant network was highly fragmented, however, contributed to interconnecting farms, with other hosts acting as intermediaries throughout the networks. When a single host was initially infected, secondary infections were observed across farms with all other species. Our stochastic multi-host model demonstrated that targeting the top 3.25% of the farms ranked by degree reduced the number of secondarily infected farms. The results of the simulation highlight the importance of considering multi-host dynamics and contact networks while designing surveillance and preparedness control strategies against pathogens known to infect multiple species.

Partitioning, a Novel Approach to Mitigate the Risk and Impact of African Swine Fever in Affected Areas

As African swine fever (ASF) continues to expand geographically, supplementary control strategies are needed to reduce disease risk and impact in affected areas. Full depopulation is central to current ASF control efforts, and its efficacy depends on surveillance and timely disease reporting, while resulting in large losses regardless of the producers' efforts to promptly detect, report, and contain the disease. This disconnect between prompt detection and reporting, and subsequent farm losses, can deter producers to invest in ASF detection and control. Alternative approaches are needed to incentivize individual producers to invest in early detection and reporting. We postulate that commercial swine farms may be effectively partitioned in separate units, or subpopulations, to which biosecurity, surveillance and control can be applied. The suggested Partitioning framework relies on three main components: 1. external and internal biosecurity to reduce the risk of ASF introduction and maintain separate subpopulations; 2. cost-effective on-farm ASF surveillance to enhance early detection; 3. response plans at the unit level, including culling of affected subpopulations, and demonstration of freedom from disease on the remaining ones. With such Partitioning approach, individual producers may reduce ASF risk on a farm and in the region, while also reducing ASF outbreak losses via targeted depopulation of affected units. It requires relevant legislation to incorporate the notion of within-farm subpopulations and provide a regulatory framework for targeted depopulation and substantiation of disease freedom. Its design should be tailored to fit individual farms. Partitioning can be an effective public-private partnership approach for ASF risk reduction. It should be driven by industry, as its benefits are accrued mainly by individual producers, but regulatory oversight is key to ensure proper implementation and avoid further disease spread. Partitioning's value is greatest for producers in ASF-affected regions, but ASF-free areas could also benefit from it for preparedness and early detection. It could also be adapted to other transboundary animal diseases and can be implemented as a stand-alone program or in conjunction with other efforts such as zoning and compartmentalization. Partitioning would contribute to the improved resilience and sustainability of the global pork industry and will benefit consumers and society through improved food security and animal welfare.

Beyond Numbers: Determining the Socioeconomic and Livelihood Impacts of African Swine Fever and Its Control in the Philippines

The impacts of African Swine Fever (ASF) have most frequently been described quantitatively though it is increasingly acknowledged these impacts extend well beyond numbers. During 2020, a multidisciplinary team of researchers developed a framework for Socioeconomic and Livelihood Impact Assessment (SELIA) of livestock diseases in smallholder communities. Two key innovations within this SELIA framework are the integration of sustainable livelihoods concepts to capture rich information beyond financial impacts, and the inclusion of stakeholders across the value chain, beyond farmers. This paper focuses on the findings from one of the first applications of the SELIA framework. In late 2020 the research team applied participatory tools from the SELIA Framework (8 focus group discussions, 14 key informant interviews, and 2 network mapping activities) to gather data to describe the impact of ASF in backyard pig-farming communities and value chains. This was undertaken across two locations in the Philippines, in turn highlighting potential leverage points for intervention. Owing to COVID-19 travel restrictions and risks, modifications to training and field activities were made. Findings from focus groups and interviews revealed the deep, emotional impacts of ASF and the associated control measures. Pigs were considered pets by many farmers and some women described them as being like their children. Animal health-workers (AHWs) also recognised the emotional toll on farmers and were sometimes strongly criticised by community members due to their involvement in depopulation campaigns. Misinformation early in the epidemic also led farmers to hide their animals from AHWs, and to dispose of them inappropriately. While the overall impact of ASF on society was negative, the impacts across different communities, scales of production and different value chain actors varied. The losses experienced by backyard farmers resulted in significant losses to linked value chain actors, such as input suppliers. This trial application of the SELIA framework revealed some complex and varied impacts of ASF. This included significant differences in livelihood and socio-economic impacts amongst different actors within value chains and also among different categories of actors (for example small, medium and large-scale traders). Repeated themes and triangulated findings suggest two leverage points for further consideration. Firstly, it is recommended a One Welfare approach to ASF control in the Philippines is explored. Emphasising careful communication between animal health-workers and farmers, and humane and sensitive pig depopulation practices. Secondly, consideration of ASF support programs tailored to sectoral and specific communities is recommended.

Breeding for disease resilience: opportunities to manage polymicrobial challenge and improve commercial performance in the pig industry

Disease resilience, defined as an animal's ability to maintain productive performance in the face of infection, provides opportunities to manage the polymicrobial challenge common in pig production. Disease resilience can deliver a number of benefits, including more sustainable production as well as improved animal health and the potential for reduced antimicrobial use. However, little progress has been made to date in the application of disease resilience in breeding programs due to a number of factors, including (1) confusion around definitions of disease resilience and its component traits disease resistance and tolerance, and (2) the difficulty in characterizing such a complex trait consisting of multiple biological functions and dynamic elements of rates of response and recovery from infection. Accordingly, this review refines the definitions of disease resistance, tolerance, and resilience based on previous studies to help improve the understanding and application of these breeding goals and traits under different scenarios. We also describe and summarize results from a "natural disease challenge model" designed to provide inputs for selection of disease resilience. The next steps for managing polymicrobial challenges faced by the pig industry will include the development of large-scale multi-omics data, new phenotyping technologies, and mathematical and statistical methods adapted to these data. Genome editing to produce pigs resistant to major diseases may complement selection for disease resilience along with continued efforts in the more traditional areas of biosecurity, vaccination and treatment. Altogether genomic approaches provide exciting opportunities for the pig industry to overcome the challenges provided by hard-to-manage diseases as well as new environmental challenges associated with climate change.

The impact of the epidemic experience on the recovery of production of pig farmers after the outbreak-Evidence from the impact of African swine fever (ASF) in Chinese pig farming

The African swine fever (ASF) has triggered considerable shocks to the pig farming industry, which has become a significant animal disease epidemic. The study explores the effect of epidemic experience on post-outbreak production recovery from resilience and risk perception based on 340 micro-survey data from Sichuan, Henan, and Shandong provinces. Epidemic experience has been shown to impact the degree of post-outbreak production recovery positively, and farmers who have endured epidemics are more likely to recover their production after outbreaks. The mechanistic study indicates that past epidemics in African swine fever shocks can effectively improve farmers' cognitive resilience and management capability, enhance recovery, and reduce risk perception in the aftermath of production recovery. In order to alleviate the endogenous problems caused by selection bias, missing variables, and two-way causality. This paper uses factor analysis to comprehensively measure production recovery capacity and production risk perception, and uses propensity score matching(PSM), instrumental variable method and replacement measurement methods to conduct robustness tests, and find the conclusions are still robust. The empirical analysis shows that the experience of the epidemic will promote the recovery of farmers after the outbreak; the experience of the epidemic will significantly impact the recovery of production after the outbreak for both free-range and professional farmers.

Integrating digital and field surveillance as complementary efforts to manage epidemic diseases of livestock: African swine fever as a case study

SARS-CoV-2 has clearly shown that efficient management of infectious diseases requires a top-down approach which must be complemented with a bottom-up response to be effective. Here we investigate a novel approach to surveillance for transboundary animal diseases using African Swine (ASF) fever as a model. We collected data both at a population level and at the local level on information-seeking behavior respectively through digital data and targeted questionnaire-based surveys to relevant stakeholders such as pig farmers and veterinary authorities. Our study shows how information-seeking behavior and resulting public attention during an epidemic, can be identified through novel data streams from digital platforms such as Wikipedia. Leveraging attention in a critical moment can be key to providing the correct information at the right moment, especially to an interested cohort of people. We also bring evidence on how field surveys aimed at local workers and veterinary authorities remain a crucial tool to assess more in-depth preparedness and awareness among front-line actors. We conclude that these two tools should be used in combination to maximize the outcome of surveillance and prevention activities for selected transboundary animal diseases such as ASF.

Advances in Non-Coding RNA Sequencing

Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.

Different patterns of human activities in nature during Covid-19 pandemic and African swine fever outbreak confirm direct impact on wildlife disruption

Implementation of various restrictions to eradicate viral diseases has globally affected human activity and subsequently nature. But how can the altered routines of human activity (restrictions, lockdowns) affect wildlife behaviour? This study compared the differences between human and wildlife occurrences in the study forest area with acreage of 5430.6 ha in 2018 (African swine fever outbreak, complete entrance ban), 2019 (standard pattern) and 2020 (COVID-19 restrictions) during the breeding season. The number of visitors was lower by 64% in 2018 (non-respecting of the entry ban by forest visitors) compared to standard 2019, while in 2020, the number of visitors increased to 151%. In the COVID-19 period, distinct peaks in the number of visitors were observed between 8-11 AM and 4-7 PM. The peaks of wildlife activity were recorded between 4-7 AM and 9-12 PM. Animals avoided the localities that were visited by humans during the people-influenced time (24 h after people visit), which confirmed the direct negative impact of human activities on wildlife.

Dynamic Variations in Infrared Skin Temperature of Weaned Pigs Experimentally Inoculated with the African Swine Fever Virus: A Pilot Study

African swine fever (ASF) is a devastating viral disease in pigs and is therefore economically important for the swine industry. ASF is characterized by a short incubation period and immediate death, making the early identification of ASF-infected pigs essential. This pilot-scale study evaluates whether the infrared thermography (IRT) technique can be used as a diagnostic tool to detect changes in skin temperature (T_sk) during the early stages of disease development in experimentally ASF-infected pigs. Clinical symptoms and rectal temperatures (T_core) were recorded daily, and IRT readings during the experimental ASF infection were analyzed. All infected pigs died at 5–8 days post inoculation (dpi), and the incubation period was approximately 4 dpi. The average T_core increased from 0 dpi (38.9 ± 0.3 °C) to 7 dpi (41.0 ± 0.5 °C) and decreased by 8 dpi (39.8 ± 0 °C). The maximum T_sk of ASF-infected pigs increased from 2 (35.0 °C) to 3 dpi (38.5 °C). The mean maximum T_sk observed from three regions on the skin (ear, inguinal, and neck) significantly increased from 2 to 3 dpi. This study presents a non-contact method for the early detection of ASF in infected pigs using thermal imaging at 3 days after ASF infection.

African swine fever outbreaks in China led to gross domestic product and economic losses

African swine fever (ASF) is a fatal and highly infectious haemorrhagic disease that has spread to all provinces in China-the world's largest producer and consumer of pork. Here we use an input-output model, partial equilibrium theory and a substitution indicator approach for handling missing data to develop a systematic valuation framework for assessing economic losses caused by ASF outbreaks in China between August 2018 and July 2019. We show that the total economic loss accounts for 0.78% of China's gross domestic product in 2019, with impacts experienced in almost all economic sectors through links to the pork industry and a substantial decrease in consumer surplus. Scenario analyses demonstrate that the worst cases of pig production reduction and price increase would trigger 1.4% and 2.07% declines in gross domestic product, respectively. These findings demonstrate an urgent need for rapid ASF containment and prevention measures to avoid future outbreaks and economic declines.

A stochastic assessment to quantify the risk of introduction of African swine fever virus to Taiwan via illegal pork products carried by international travellers

The current study quantified the risk of releasing African swine fever virus (ASFV) into Taiwan from pork products illegally carried by international travellers from 157 countries or territories through six international airports and three international seaports. The association between various factors and the number of pork products detected by the border control authorities was also examined. The risk was estimated with a stochastic process after modelling the number of undetected illegal pork products, probability of pork product detection at international airports and seaports and probability of ASFV contamination of pork products from various countries. The overall annual probability of ASFV release to Taiwan was estimated to be 1 [95% confidence interval (CI): 1-1] under no enhanced mitigation measures. All the median airport-level risks were higher than .921, and four of them reached 1. The total annual risk was .570 (95% CI: .109-.937) for international seaports. The country or territory level risk was estimated to be 1 for Vietnam, China, Hong Kong, the Philippines and South Korea, .999 (95% CI: .628-1) for Macao and .967 (95% CI: .359-1) for Indonesia. After the total number of travellers was factored in, the number of detected illegal pork products was the highest in January and February, and travellers from Vietnam [risk ratio to Japan (RR): 80.45; 95% CI: 58.68-110.3], the Philippines (RR: 37.67; 95% CI: 26.9-52.74) and Cambodia (RR: 28.39; 95% CI: 12.69-63.51) were most likely to bring pork products to Taiwan. Our study indicated a high risk of ASFV introduction through international travellers and also identified the factors associated with the risk. This information can be used as empirical evidence for cost-effective risk mitigation practices.