EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks.

The rapid intensification of poultry production raises important concerns about the associated risks of zoonotic infections. Here, we introduce EPINEST (EPIdemic NEtwork Simulation in poultry Transportation systems): an agent-based modelling framework designed to simulate pathogen transmission within realistic poultry production and distribution networks. We provide example applications to broiler production in Bangladesh, but the modular structure of the model allows for easy parameterization to suit specific countries and system configurations. Moreover, the framework enables the replication of a wide range of eco-epidemiological scenarios by incorporating diverse pathogen life-history traits, modes of transmission and interactions between multiple strains and/or pathogens. EPINEST was developed in the context of an interdisciplinary multi-centre study conducted in Bangladesh, India, Vietnam and Sri Lanka, and will facilitate the investigation of the spreading patterns of various health hazards such as avian influenza, Campylobacter, Salmonella and antimicrobial resistance in these countries. Furthermore, this modelling framework holds potential for broader application in veterinary epidemiology and One Health research, extending its relevance beyond poultry to encompass other livestock species and disease systems.

The challenges of pig farming in Hong Kong: a study of farmers' perceptions and attitudes towards a pig health and production management service.

BACKGROUND: Pig farming in Hong Kong differs markedly from other places in the world, with a highly urbanised population, the majority of pigs being imported for slaughter, and limited on-farm veterinary support. Little is known about the barriers and attitudes of pig farmers in Hong Kong and their expectations of a new pig health and production management service provided by veterinarians. We collected qualitative and quantitative data to 1) describe pig farms, 2) identify barriers to pig farming in Hong Kong and 3) describe the perceptions of the new service. Thematic analysis was conducted to identify barriers and attitudes. RESULTS: Eight and nine out of 38 pig farmers agreed to participate in the qualitative and quantitative components, respectively. All farms were farrow-to-finish farms with a median of 2800 (range 950 to 7000) pigs per farm. Three themes were identified during the interview analysis and could be ranked based on their importance to the farmers: the regulatory environment (Theme 1), veterinary support structures (Theme 2), and the sustainability of the pig industry (Theme 3). Farmers expressed dissatisfaction with the regulation of the industry and veterinary services on offer within Hong Kong. However, farmers did note that the provision of a new pig health and production management service was as a positive development. The public perception of pig farming, market forces, and competition from mainland pig farmers have resulted in sustainability challenges for the industry. CONCLUSIONS: Farmers identified very specific local systems and challenges unique to pig farming in Hong Kong. The lack of veterinary support was one of these challenges and although a certain level of scepticism towards the new pig health and production service was expressed, farmers indicated their interest and listed areas where they would benefit from improved veterinary support. Prior experiences of veterinary services clouded farmers perceptions of the usefulness of a new service. To be successful in this environment, clear communication about the goals, role and limitations of the new on farm service is crucial, as is the alignment with the needs of farmers. Despite the small sample size, the qualitative methodology used allows us to assume that these themes give a general idea of what Hong Kong farmers' concerns and attitudes are.

Serological survey of avian metapneumovirus in vaccinated and unvaccinated broiler chickens in Hong Kong.

In chickens, avian metapneumovirus (aMPV) causes the swollen head syndrome, a respiratory disease often associated with a reduction in egg production. The virus' epidemiology in East and Southeast Asia is poorly understood. An aMPV serological survey was conducted on broiler chicken farms of Hong Kong SAR to assess the seroprevalence of aMPV in unvaccinated batches and the serological status of vaccinated batches. Blood samples were collected from 53-93-day-old chickens in 24 chicken farms of Hong Kong SAR and sera were tested for aMPV antibodies by ELISA. Seroprevalence in aMPV unvaccinated birds was 80.6% (95% confidence interval (CI): 78.9-82.2) with a high variation between batches. Batch-level seroprevalence was not significantly different between birds hatched during the rainy season (74.3%, 95% CI: 64.0-84.5) and the ones hatched during the dry season (88.7%, 95% CI: 80.1-97.3, p = 0.5). The high seroprevalence and high antibody titers that are reported in this study indicate repeated exposure of broiler chickens to aMPV in Hong Kong SAR poultry farms. Based on these results, we recommend improving the surveillance of respiratory pathogens and applying appropriate prophylactic measures against aMPV such as vaccination.

Sequestration and Destruction of Rinderpest Virus-Containing Material 10 Years after Eradication.

In 2021, the world marked 10 years free from rinderpest. The United Nations Food and Agriculture Organization and World Organisation for Animal Health have since made great strides in consolidating, sequencing, and destroying stocks of rinderpest virus-containing material, currently kept by only 14 known institutions. This progress must continue.

Transmission Dynamics of African Swine Fever Virus, South Korea, 2019.

African swine fever (ASF) is a substantial concern for global food production and security. However, lack of epidemiologic data in affected areas has limited the knowledge of the main drivers of ASF virus (ASFV) transmission. To assess the role of vehicle movements and wild boar populations in spreading ASFV to pig farms in South Korea, we combined data generated by ASF surveillance on pig farms and of wild boars with nationwide global positioning system-based tracking data for vehicles involved in farming activities. Vehicle movements from infected premises were associated with a higher probability of ASFV incursion into a farm than was geographic proximity to ASFV-infected wild boar populations. Although ASFV can spill over from infected wild boars into domestic pigs, vehicles played a substantial role in spreading infection between farms, despite rapid on-farm detection and culling. This finding highlights the need for interventions targeting farm-to-farm and wildlife-to-farm interfaces.

Estimating effects of intervention measures on COVID-19 outbreak in Wuhan taking account of improving diagnostic capabilities using a modelling approach.

BACKGROUND: Although by late February 2020 the COVID-19 epidemic was effectively controlled in Wuhan, China, estimating the effects of interventions, such as transportation restrictions and quarantine measures, on the early COVID-19 transmission dynamics in Wuhan is critical for guiding future virus containment strategies. Since the exact number of infected cases is unknown, the number of documented cases was used by many disease transmission models to infer epidemiological parameters. This means that it was possible to produce biased estimates of epidemiological parameters and hence of the effects of intervention measures, because the percentage of all cases that were documented changed during the first 2 months of the epidemic, as a consequence of a gradually improving diagnostic capability. METHODS: To overcome these limitations, we constructed a stochastic susceptible-exposed-infected-quarantined-recovered (SEIQR) model, accounting for intervention measures and temporal changes in the proportion of new documented infections out of total new infections, to characterize the transmission dynamics of COVID-19 in Wuhan across different stages of the outbreak. Pre-symptomatic transmission was taken into account in our model, and all epidemiological parameters were estimated using the Particle Markov-chain Monte Carlo (PMCMC) method. RESULTS: Our model captured the local Wuhan epidemic pattern as two-peak transmission dynamics, with one peak on February 4 and the other on February 12, 2020. The impact of intervention measures determined the timing of the first peak, leading to an 86% drop in the Re from 3.23 (95% CI, 2.22 to 4.20) to 0.45 (95% CI, 0.20 to 0.69). The improved diagnostic capability led to the second peak and a higher proportion of documented infections. Our estimated proportion of new documented infections out of the total new infections increased from 11% (95% CI 1-43%) to 28% (95% CI 4-62%) after January 26 when more detection kits were released. After the introduction of a new diagnostic criterion (case definition) on February 12, a higher proportion of daily infected cases were documented (49% (95% CI 7-79%)). CONCLUSIONS: Transportation restrictions and quarantine measures together in Wuhan were able to contain local epidemic growth.

A dynamic model of transmission and elimination of peste des petits ruminants in Ethiopia.

Peste des petits ruminants (PPR), a devastating viral disease of sheep and goats, has been targeted by the global community for eradication within the next 15 years. Although an efficacious attenuated live vaccine is available, the lack of knowledge about the transmission potential of PPR virus (PPRV) may compromise eradication efforts. By fitting a metapopulation model simulating PPRV spread to the results of a nationwide serological survey in Ethiopia, we estimated the level of viral transmission in an endemic setting and the vaccination coverage required for elimination. Results suggest that the pastoral production system as a whole acts as a viral reservoir, from which PPRV spills over into the sedentary production system, where viral persistence is uncertain. Estimated levels of PPRV transmission indicate that viral spread could be prevented if the proportion of immune small ruminants is kept permanently above 37% in at least 71% of pastoral village populations. However, due to the high turnover of these populations, maintaining the fraction of immune animals above this threshold would require high vaccine coverage within villages, and vaccination campaigns to be conducted annually. Adapting vaccination strategies to the specific characteristics of the local epidemiological context and small ruminant population dynamics would result in optimized allocation of limited resources and increase the likelihood of PPR eradication.

The impact of non-pharmaceutical interventions on the prevention and control of COVID-19 in New York City.

The emergence of coronavirus disease 2019 (COVID-19) has infected more than 62 million people worldwide. Control responses varied across countries with different outcomes in terms of epidemic size and social disruption. This study presents an age-specific susceptible-exposed-infected-recovery-death model that considers the unique characteristics of COVID-19 to examine the effectiveness of various non-pharmaceutical interventions (NPIs) in New York City (NYC). Numerical experiments from our model show that the control policies implemented in NYC reduced the number of infections by 72% [interquartile range (IQR) 53-95] and the number of deceased cases by 76% (IQR 58-96) by the end of 2020. Among all the NPIs, social distancing for the entire population and protection for the elderly in public facilities is the most effective control measure in reducing severe infections and deceased cases. School closure policy may not work as effectively as one might expect in terms of reducing the number of deceased cases. Our simulation results provide novel insights into the city-specific implementation of NPIs with minimal social disruption considering the locations and population characteristics.

Demand-driven spreading patterns of African swine fever in China.

African swine fever (ASF) is a highly contagious hemorrhagic viral disease of domestic and wild pigs. ASF has led to major economic losses and adverse impacts on livelihoods of stakeholders involved in the pork food system in many European and Asian countries. While the epidemiology of ASF virus (ASFV) is fairly well understood, there is neither any effective treatment nor vaccine. In this paper, we propose a novel method to model the spread of ASFV in China by integrating the data of pork import/export, transportation networks, and pork distribution centers. We first empirically analyze the overall spatiotemporal patterns of ASFV spread and conduct extensive experiments to evaluate the efficacy of a number of geographic distance measures. These empirical analyses of ASFV spread within China indicate that the first occurrence of ASFV has not been purely dependent on the geographical distance from existing infected regions. Instead, the pork supply-demand patterns have played an important role. Predictions based on a new distance measure achieve better performance in predicting ASFV spread among Chinese provinces and thus have the potential to enable the design of more effective control interventions.

Undetected Circulation of African Swine Fever in Wild Boar, Asia.

African swine fever is a growing threat to the livestock industry. We examined data indicating that in most countries in Asia, most notified events were related to farm outbreaks; meanwhile, only a few wild boar cases were reported. We hypothesize the virus circulates unnoticed in wild boar populations in Asia.

Prevalence of Avian Influenza A(H5) and A(H9) Viruses in Live Bird Markets, Bangladesh.

We conducted a cross-sectional study in live bird markets (LBMs) in Dhaka and Chittagong, Bangladesh, to estimate the prevalence of avian influenza A(H5) and A(H9) viruses in different types of poultry and environmental areas by using Bayesian hierarchical logistic regression models. We detected these viruses in nearly all LBMs. Prevalence of A(H5) virus was higher in waterfowl than in chickens, whereas prevalence of A(H9) virus was higher in chickens than in waterfowl and, among chicken types, in industrial broilers than in cross-breeds and indigenous breeds. LBMs with >1 wholesaler were more frequently contaminated by A(H5) virus than retail-only LBMs. Prevalence of A(H9) virus in poultry and level of environmental contamination were also higher in LBMs with >1 wholesaler. We found a high level of circulation of both avian influenza viruses in surveyed LBMs. Prevalence was influenced by type of poultry, environmental site, and trading.

Social and environmental factors affect tuberculosis related mortality in wild meerkats.

Tuberculosis (TB) is an important and widespread disease of wildlife, livestock and humans world-wide, but long-term empirical datasets describing this condition are rare. A population of meerkats (Suricata suricatta) in South Africa's Kalahari Desert have been diagnosed with Mycobacterium suricattae, a novel strain of TB, causing fatal disease in this group-living species. This study aimed to find characteristics associated with clinical TB in meerkats. These characteristics could subsequently be used to identify 'at-risk' animals within a population, and target these individuals for control measures. We conducted a retrospective study based on a unique, long-term life-history dataset of over 2000 individually identified animals covering a 14-year period after the first confirmatory diagnosis of TB in this population in 2001. Individual- and group-level risk factors were analysed using time-dependent Cox regression to examine their potential influence on the time to development of end-stage TB. Cases of disease involved 144 individuals in 27 of 73 social groups, across 12 of 14 years (an incidence rate of 3·78 cases/100 study years). At the individual level, increasing age had the greatest effect on risk of disease with a hazard ratio of 4·70 (95% CI: 1·92-11·53, P < 0·01) for meerkats aged 24-48 months, and a hazard ratio of 9·36 (3·34-26·25, P < 0·001) for animals aged over 48 months (both age categories compared with animals aged below 24 months). Previous group history of TB increased the hazard by a factor of 4·29 (2·00-9·17, P < 0·01), and an interaction was found between this variable and age. At a group level, immigrations of new group members in the previous year increased hazard by a factor of 3·00 (1·23-7·34, P = 0·016). There was weaker evidence of an environmental effect with a hazard ratio for a low rainfall (<200 mm) year of 2·28 (0·91-5·72, P = 0·079). Our findings identify potential individual characteristics on which to base targeted control measures such as vaccination. Additional data on the dynamics of the infection status of individuals and how this changes over time would complement these findings by enhancing understanding of disease progression and transmission, and thus the implications of potential management measures.

Eco-social processes influencing infectious disease emergence and spread.

The complexity and connectedness of eco-social processes have major influence on the emergence and spread of infectious diseases amongst humans and animals. The disciplinary nature of most research activity has made it difficult to improve our understanding of interactions and feedback loops within the relevant systems. Influenced by the One Health approach, increasing efforts have recently been made to address this knowledge gap. Disease emergence and spread is strongly influenced by host density and contact structures, pathogen characteristics and pathogen population and molecular evolutionary dynamics in different host species, and host response to infection. All these mechanisms are strongly influenced by eco-social processes, such as globalization and urbanization, which lead to changes in global ecosystem dynamics, including patterns of mobility, human population density and contact structures, and food production and consumption. An improved understanding of epidemiological and eco-social processes, including their interdependence, will be essential to be able to manage diseases in these circumstances. The interfaces between wild animals, domestic animals and humans need to be examined to identify the main risk pathways and put in place appropriate mitigation. Some recent examples of emerging infectious disease are described to illustrate eco-social processes that are influencing disease emergence and spread.

Transmission tree of the highly pathogenic avian influenza (H5N1) epidemic in Israel, 2015.

The transmission tree of the Israeli 2015 epidemic of highly pathogenic avian influenza (H5N1) was modelled by combining the spatio-temporal distribution of the outbreaks and the genetic distance between virus isolates. The most likely successions of transmission events were determined and transmission parameters were estimated. It was found that the median infectious pressure exerted at 1 km was 1.59 times (95% CI 1.04, 6.01) and 3.54 times (95% CI 1.09, 131.75) higher than that exerted at 2 and 5 km, respectively, and that three farms were responsible for all seven transmission events.

Interventions for avian influenza A (H5N1) risk management in live bird market networks.

Highly pathogenic avian influenza virus subtype H5N1 is endemic in Asia, with live bird trade as a major disease transmission pathway. A cross-sectional survey was undertaken in northern Vietnam to investigate the structure of the live bird market (LBM) contact network and the implications for virus spread. Based on the movements of traders between LBMs, weighted and directed networks were constructed and used for social network analysis and individual-based modeling. Most LBMs were connected to one another, suggesting that the LBM network may support large-scale disease spread. Because of cross-border trade, it also may promote transboundary virus circulation. However, opportunities for disease control do exist. The implementation of thorough, daily disinfection of the market environment as well as of traders' vehicles and equipment in only a small number of hubs can disconnect the network dramatically, preventing disease spread. These targeted interventions would be an effective alternative to the current policy of a complete ban of LBMs in some areas. Some LBMs that have been banned still are very active, and they likely have a substantial impact on disease dynamics, exhibiting the highest levels of susceptibility and infectiousness. The number of trader visits to markets, information that can be collected quickly and easily, may be used to identify LBMs suitable for implementing interventions. This would not require prior knowledge of the force of infection, for which laboratory-confirmed surveillance would be necessary. These findings are of particular relevance for policy development in resource-scarce settings.

Zoonosis emergence linked to agricultural intensification and environmental change.

A systematic review was conducted by a multidisciplinary team to analyze qualitatively best available scientific evidence on the effect of agricultural intensification and environmental changes on the risk of zoonoses for which there are epidemiological interactions between wildlife and livestock. The study found several examples in which agricultural intensification and/or environmental change were associated with an increased risk of zoonotic disease emergence, driven by the impact of an expanding human population and changing human behavior on the environment. We conclude that the rate of future zoonotic disease emergence or reemergence will be closely linked to the evolution of the agriculture-environment nexus. However, available research inadequately addresses the complexity and interrelatedness of environmental, biological, economic, and social dimensions of zoonotic pathogen emergence, which significantly limits our ability to predict, prevent, and respond to zoonotic disease emergence.

Spatiotemporal trends in the discovery of new swine infectious agents.

A literature review was conducted to assess the spatiotemporal trend and diversity of infectious agents that were newly found in pigs between 1985 and 2010. We identified 173 new variants from 91 species, of which 73 species had not been previously described in pigs. These new species, of which one third was zoonotic, were taxonomically diverse. They were identified throughout the study period, predominantly in the main pork producing countries, with the rate of discovery of new virus variants doubling within the last 10 years of the study period. Whilst infectious agent species newly detected in high-income countries were more likely to be associated with higher virulence, zoonotic agents prevailed in low- and middle-income countries. Although this trend is influenced by factors conditioning infectious agent detection - diagnostic methods, surveillance efforts, research interests -, it may suggest that different scales and types of production systems promote emergence of certain types of infectious agents. Considering the rapid transformation of the swine industry, concerted efforts are needed for improving our understanding of the factors influencing the emergence of infectious agents. This information then needs to inform the design of risk-based surveillance systems and strategies directly mitigating the risk associated with these factors.

The economic value of One Health in relation to the mitigation of zoonotic disease risks.

The essence of One Health is an interdisciplinary approach combined with some degree of intersectoral integration that is aimed at mitigation of human and animal health risks, taking account of environmental, ecological, social and economic factors. While a large number of international stakeholders now consider the One Health approach necessary for more effective protection of the global community against health threats, there is still no systematic allocation of resources to integrated national or multinational programmes, partly due to the inertia of existing sectoral systems and the lack of convincing economic arguments in support of the approach. We propose different degrees of sectoral integration depending on system types and associated economic efficiency gains to be expected from a One Health approach. International and regional organisations have an important role in facilitating the adoption of the approach, since the costs and the benefits are often of a regional or even a global nature, such as in the case of avian influenza.

Dynamics of African swine fever virus shedding and excretion in domestic pigs infected by intramuscular inoculation and contact transmission.

African swine fever virus (ASFV) is a highly virulent swine pathogen that has spread across Eastern Europe since 2007 and for which there is no effective vaccine or treatment available. The dynamics of shedding and excretion is not well known for this currently circulating ASFV strain. Therefore, susceptible pigs were exposed to pigs intramuscularly infected with the Georgia 2007/1 ASFV strain to measure those dynamics through within- and between-pen transmission scenarios. Blood, oral, nasal and rectal fluid samples were tested for the presence of ASFV by virus titration (VT) and quantitative real-time polymerase chain reaction (qPCR). Serum was tested for the presence of ASFV-specific antibodies. Both intramuscular inoculation and contact transmission resulted in development of acute disease in all pigs although the experiments indicated that the pathogenesis of the disease might be different, depending on the route of infection. Infectious ASFV was first isolated in blood among the inoculated pigs by day 3, and then chronologically among the direct and indirect contact pigs, by day 10 and 13, respectively. Close to the onset of clinical signs, higher ASFV titres were found in blood compared with nasal and rectal fluid samples among all pigs. No infectious ASFV was isolated in oral fluid samples although ASFV genome copies were detected. Only one animal developed antibodies starting after 12 days post-inoculation. The results provide quantitative data on shedding and excretion of the Georgia 2007/1 ASFV strain among domestic pigs and suggest a limited potential of this isolate to cause persistent infection.

Spatial multi-criteria decision analysis to predict suitability for African swine fever endemicity in Africa.

BACKGROUND: African swine fever (ASF) is endemic in several countries of Africa and may pose a risk to all pig producing areas on the continent. Official ASF reporting is often rare and there remains limited awareness of the continent-wide distribution of the disease.In the absence of accurate ASF outbreak data and few quantitative studies on the epidemiology of the disease in Africa, we used spatial multi-criteria decision analysis (MCDA) to derive predictions of the continental distribution of suitability for ASF persistence in domestic pig populations as part of sylvatic or domestic transmission cycles. In order to incorporate the uncertainty in the relative importance of different criteria in defining suitability, we modelled decisions within the MCDA framework using a stochastic approach. The predictive performance of suitability estimates was assessed via a partial ROC analysis using ASF outbreak data reported to the OIE since 2005. RESULTS: Outputs from the spatial MCDA indicate that large areas of sub-Saharan Africa may be suitable for ASF persistence as part of either domestic or sylvatic transmission cycles. Areas with high suitability for pig to pig transmission ('domestic cycles') were estimated to occur throughout sub-Saharan Africa, whilst areas with high suitability for introduction from wildlife reservoirs ('sylvatic cycles') were found predominantly in East, Central and Southern Africa. Based on average AUC ratios from the partial ROC analysis, the predictive ability of suitability estimates for domestic cycles alone was considerably higher than suitability estimates for sylvatic cycles alone, or domestic and sylvatic cycles in combination. CONCLUSIONS: This study provides the first standardised estimates of the distribution of suitability for ASF transmission associated with domestic and sylvatic cycles in Africa. We provide further evidence for the utility of knowledge-driven risk mapping in animal health, particularly in data-sparse environments.