Contrasting seasonality of African swine fever outbreaks and its drivers.

The seasonality of African swine fever (ASF) outbreaks in domestic pigs differs between temperate and subtropical/tropical regions. We hypothesise that variations in the importance of wild boar-to-farm and farm-to-farm transmission routes shape these contrasting patterns, and we emphasise the implications for effective ASF control.

Measures, Gaps, and Mitigation Strategies in Bangladesh's COVID-19 Response.

The Coronavirus Disease 2019 (COVID-19) spread rapidly from China to most other countries around the world in early 2020 killing millions of people. To prevent virus spread, world governments implemented a variety of response measures. This paper's objectives were to discuss the country's adopted measures to combat the virus through June 2020, identify gaps in the measures' effectiveness, and offer possible mitigations to those gaps. The measures taken included screening device deployment across international air and land ports, flight suspensions and closures from COVID-19 affected countries, and declaration and extension of a national public holiday (equivalent to lockdowns in other countries). Identified gaps were test kit, PPE, ICU beds, and ventilator shortages, limited public awareness, and insufficient coordination and collaboration among national and international partners. Proper and timely risk mapping, preparedness, communication, coordination, and collaboration among governments and organizations, and public awareness and engagement would have provided sufficient COVID-19 mitigation in Bangladesh.

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.

Transmission of highly pathogenic avian influenza in the nomadic free-grazing duck production system in Viet Nam.

The presence of free-grazing ducks (FGD) has consistently been shown to be associated with highly pathogenic avian influenza virus (HPAIV) H5N1 outbreaks in South-East Asia. However, the lack of knowledge about the transmission pathways limits the effectiveness of control efforts. To address this gap, we developed a probabilistic transmission model of HPAIV H5N1 in the nomadic FGD production system in Viet Nam, assuming different scenarios to address parameter uncertainty. Results suggested that HPAIV H5N1 could spread within the nomadic FGD production system, with an estimated flock-level effective reproduction number (re) ranging from 2.16 (95% confidence interval (CI): 1.39-3.49) to 6.10 (95%CI: 3.93-9.85) depending on the scenario. Indirect transmission via boats and trucks was shown to be the main transmission route in all scenarios. Results suggest that re could be reduced below one with 95% confidence if 86% of FGD flocks were vaccinated in the best-case scenario or 95% in the worst-case scenario. If vaccination was combined with cleaning and disinfection of transport vehicles twice a week, vaccination coverage could be lowered to 60% in the best-case scenario. These findings are of particular relevance for prioritising interventions for effective control of HPAIV in nomadic free-grazing duck production systems.

Practising co-production and interdisciplinarity: Challenges and implications for one health research.

We review the nature of interdisciplinary research in relation to One Health, a perspective on human-animal health which would appear to merit close interdisciplinary cooperation to inform public health policy. We discuss the relationship between biological sciences, epidemiology and the social sciences and note that interdisciplinary work demands attention be given to a range of often neglected epistemological and methodological issues. Epidemiologists may sometimes adopt social science techniques as "bolt-ons"1 to their research without having a complete understanding of how the social sciences work. The paper introduces a range of social science concepts and applies them to the challenges of understanding and practicing participatory and local epidemiology. We consider the problem of co-production of knowledge about One Health and zoonotic diseases in relation to funding structures, working in large international teams and explore some of the often-neglected realities of working across disciplines and cultures. We do this in part by applying the concept of value-chain to the research process.

Pastoralist knowledge of sheep and goat disease and implications for peste des petits ruminants virus control in the Afar Region of Ethiopia.

Pastoralist areas of Ethiopia are vulnerable to drought, causing livelihood loss and famine. One approach to increasing pastoralist resilience is the control of livestock disease, but there is limited information from pastoralist areas to inform control strategies. This study aimed to explore pastoralist concepts of small ruminant disease and implications for infectious disease surveillance and control in the pastoralist Afar Region. During 2013-14, qualitative and quantitative methods were applied in two villages of one district in the mid-west of the region. Semi-structured group interviews, incorporating participatory tools, explored pastoralist knowledge of small ruminant diseases and their impact. These were followed by multiple visits in different seasons to 70 households for semi-structured and informal interviews, observation of management practices, clinical examinations, and weekly questionnaires of mortality and morbidity. Thematic analysis was applied to interview transcripts and field notes, and descriptive statistical analysis to quantitative data. Afar concepts of disease causation, terminology and treatment were predominantly naturalistic, related to observable signs and physical causes, rather than personalistic factors (misfortune due to magical or spiritual agents). Disease occurrence was associated with malnutrition and adverse weather, and disease spread with contact between animals during grazing, watering and migration. Disease occurrence varied by season with most syndromes increasing in frequency during the dry season. Names for disease syndromes were related to the main clinical sign or body part affected; 70 terms were recorded for respiratory syndromes, diarrhoea, sheep and goat pox, lameness, skin diseases, ectoparasites, urinary and neurological syndromes and abortion. Some syndromes with pathognomonic signs could be linked to biomedical diagnoses but most were non-specific with several possible diagnoses. The syndromes causing greatest impact were diarrhoea and respiratory disease, due to mortality, reduced milk production, weight loss, abortion, weak offspring and reduced market value. Afar applied a range of traditional methods and modern medicines to prevent or treat disease, based on livestock keeper knowledge, advice of local specialists and occasionally advice from district veterinarians or animal health workers. In relation to surveillance for peste des petits ruminants (PPR), several terms were used for PPR-like syndromes, depending on the predominance of respiratory or diarrhoea signs. Therefore, whenever these terms are encountered during surveillance, the associated disease events should be fully investigated and samples collected for laboratory confirmation. The Afar naturalistic concepts of disease parallel biomedical concepts and provide a good foundation for communication between veterinarians and pastoralists in relation to PPR surveillance and control measures.

Longitudinal Study of Avian Influenza and Newcastle Disease in Village Poultry, Mali, 2009-2011.

Newcastle disease (ND) is endemic in West Africa, which has also experienced outbreaks of highly pathogenic avian influenza (AI) H5N1 since 2006. We aimed to estimate the prevalence and incidence of AI and ND in village poultry in Mali and to identify associated risk factors. A longitudinal serologic study was conducted between November 2009 and February 2011 using ELISA commercial kits to detect antibodies. Sera (5963) were collected from 4890 different poultry. AI was rare, with a seroprevalence of 2.9% (95% confidence interval [CI] 2.3-3.5) and a seroincidence rate of 0.7 birds per 100 bird-months at risk (95% CI 0.4-1.0). AI antibodies were short lived, with a seroreversion rate of 25.4 birds per 100 bird-months at risk (95% CI 19.0-31.7). Risk factors for AI were limited: temporal variation occurred, but proximity to a water body was a risk factor only when large populations of wild waterbirds were present. ND was very common, with seroprevalence of 68.9% (95% CI 61.9-76.0) and a seroincidence rate of 15.9 birds per 100 bird-months at risk (95% CI 11.9-19.8). ND seroreversion rate was 6.2 birds per 100 bird-months at risk (95% CI 3.6-8.9). Regarding risk factors for ND, temporal variations occurred, and ND was more likely to be present in the Sudanian agro-ecological zone than in the Sahelian zone, in chickens than in other species, in flocks with higher numbers of Guinea fowl, and in flocks that had access to a waterbody. Control efforts would benefit from further increasing the ND vaccination coverage of village poultry, although this was already quite high (54.9%) for an African country. Seroconversion seemed satisfactory in vaccinated poultry, since 90.0% (95% CI 87.6-92.4) of these had ND antibodies. Further research should investigate the apparent lack of an epidemiologic role of domestic ducks for AI in Mali (unlike in Southeast Asia) and the potential role of Guinea fowl as a reservoir for ND.

Pig empire under infectious threat: risk of African swine fever introduction into the People's Republic of China.

Pig production and pork consumption are very important to the People's Republic of China for both economic and cultural reasons. The incursion and spread of a disease such as African swine fever (ASF), which emerged in Eastern Europe in 2007, could have devastating socioeconomic consequences for both the Chinese and the global pig industry. The Chinese government consequently attributes a very high priority to ASF and is actively seeking to improve its preparedness. This paper discusses different drivers and pathways of potential emergence of ASF in China in light of the country's specificities, including international movements of people, pigs and pig products, swill feeding practices and wild boar populations. It suggests that effective ASF risk management in China will require a comprehensive and integrated approach linking science and policy and will need to involve all relevant stakeholders to develop realistic policies.

Movement and contact patterns of long-distance free-grazing ducks and avian influenza persistence in Vietnam.

Presence of ducks, and in particular of free-grazing ducks, has consistently been shown to be one of the most important risk factors for highly pathogenic avian influenza outbreaks which has compromised poultry production in South-East Asia since the early 2000s and continues to threaten public health, farmers' livelihood and food security. Although free-grazing duck production has been practised for decades in South-East Asia, there are few published studies describing this production system, which is suspected to play an important role in the maintenance of avian influenza viruses. This study aimed at describing quantitatively the long-distance free-grazing duck production system in South Vietnam, characterising the movement and contact patterns of the duck flocks, and identifying potential associations between farming practices, movement and contact patterns and the circulation of avian influenza viruses. We conducted interviews among stakeholders involved in the free-grazing duck production system (duck farmers, transporters and rice paddy owners) in combination with a virological cross-sectional survey in South Vietnam. Results show that both direct and indirect contacts between free-grazing duck flocks were frequent and diverse. The flocks were transported extensively across district and province boundaries, mainly by boat but also by truck or on foot. A third of the investigated flocks had a positive influenza A virology test, indicating current circulation of avian influenza viruses, but none were positive for H5 subtypes. The age and size of the flock as well as its location at the time of sampling were associated with the risk of influenza A circulation in the flocks. These findings should be considered when developing risk assessment models of influenza virus spread aimed at informing the development of improved biosecurity practices leading to enhanced animal health, sustainable animal production and reliable income for farmers.

English Pig Farmers' Knowledge and Behaviour towards African Swine Fever Suspicion and Reporting.

African swine fever (ASF) is a notifiable, virulent swine disease, and is a major threat to animal health and trade for many European Union (EU) countries. Early detection of the introduction of ASF virus is of paramount importance to be able to limit the potential extent of outbreaks. However, the timely and accurate reporting of ASF primary cases strongly depends on how familiar pig farmers are with the clinical signs, and their motivation to report the disease. Here, an online questionnaire survey was conducted between December 2014 and April 2015 to investigate English pig farmers' knowledge and behaviour towards ASF in terms of clinical suspicion and reporting. Multivariable logistic regression analysis was used to identify factors influencing the two variables of interest: 1) farmers who "would immediately suspect ASF" if they observed clinical signs of fever, lethargy, reduced eating and high mortality on their farm and 2) farmers who "would immediately report ASF" if they suspected ASF on their farm. The questionnaire was completed by 109 pig farmers. Results indicate that pig farmers having poor knowledge about ASF clinical signs and limited concern about ASF compared with other pig diseases are less likely to consider the possibility of an outbreak of ASF on their farm. In addition, pig farmers lacking awareness of outbreaks in other countries, having a perception of the negative impact on them resulting from false positive reporting and the perceived complexity of reporting procedures are less likely to report an ASF suspicion. These findings indicate important areas for educational campaigns targeted at English pig farmers to focus on in an attempt to increase the likelihood of a rapid response in the event of an ASF outbreak.

Live bird markets characterization and trading network analysis in Mali: Implications for the surveillance and control of avian influenza and Newcastle disease.

Live bird markets (LBMs) play an important role in the transmission of avian influenza (AI) and Newcastle disease (ND) viruses in poultry. Our study had two objectives: (1) characterizing LBMs in Mali with a focus on practices influencing the risk of transmission of AI and ND, and (2) identifying which LBMs should be targeted for surveillance and control based on properties of the live poultry trade network. Two surveys were conducted in 2009-2010: a descriptive study in all 96 LBMs of an area encompassing approximately 98% of the Malian poultry population and a network analysis study in Sikasso county, the main poultry supplying county for the capital city Bamako. Regarding LBMs' characteristics, risk factors for the presence of AI and ND viruses (being open every day, more than 2 days before a bird is sold, absence of zoning to segregate poultry-related work flow areas, waste removal or cleaning and disinfecting less frequently than on a daily basis, trash disposal of dead birds and absence of manure processing) were present in 80-100% of the LBMs. Furthermore, LBMs tended to have wide catchment areas because of consumers' preference for village poultry meat, thereby involving a large number of villages in their supply chain. In the poultry trade network from/to Sikasso county, 182 traders were involved and 685 links were recorded among 159 locations. The network had a heterogeneous degree distribution and four hubs were identified based on measures of in-degrees, out-degrees and betweenness: the markets of Medine and Wayerma and the fairs of Farakala and Niena. These results can be used to design biosecurity-improvement interventions and to optimize the prevention, surveillance and control of transmissible poultry diseases in Malian LBMs. Further studies should investigate potential drivers (seasonality, prices) of the poultry trade network and the acceptability of biosecurity and behavior-change recommendations in the Malian socio-cultural context.

Small-scale pig farmers' behavior, silent release of African swine fever virus and consequences for disease spread.

The expanding distribution of African swine fever (ASF) is threatening the pig industry worldwide. Most outbreaks occur in backyard and small-scale herds, where poor farmers often attempt to limit the disease's economic consequences by the emergency sale of their pigs. The risk of African swine fever virus (ASFV) release via this emergency sale was investigated. Simulation modeling was used to study ASFV transmission in backyard and small-scale farms as well as the emergency sale of pigs, and the potential impact of improving farmers and traders' clinical diagnosis ability-its timeliness and/or accuracy-was assessed. The risk of ASFV release was shown to be high, and improving farmers' clinical diagnosis ability does not appear sufficient to effectively reduce this risk. Estimates obtained also showed that the distribution of herd size within the backyard and small-scale sectors influences the relative contribution of these farms to the risk of release of infected pigs. These findings can inform surveillance and control programs.

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.

Characteristics of commercial and traditional village poultry farming in Mali with a focus on practices influencing the risk of transmission of avian influenza and Newcastle disease.

We aimed at characterizing commercial and traditional village poultry farming in Mali, with a focus on practices influencing the risk of transmission of avian influenza and Newcastle disease. Surveys were conducted in 2009-2011 in a study area covering approximately 98% of the Malian poultry population. Among the 282 commercial farms investigated, of which 64 had not been known by the government authorities, 83% were located within a 50km radius from the capitals of the country and regions and 54% had low biosecurity standard. Among the 152 randomly selected village household flocks investigated, characteristics were overall similar to those in other African countries but some differences were notable including a large flock size (median 44 poultry), a low presence of ducks and geese (11% and 1.1% of flocks, respectively), vaccination against Newcastle disease being common (49% of flocks), a low proportion of households selling sick and dead birds (0.7% and 0%, respectively) and limited cohabitation between poultry and humans at night. Our recommendations to limit the risk of disease transmission include (1) for commercial farms, to introduce compulsory farm registration and accreditation, to increase technical proficiency and access to credit for farms with low biosecurity, and to support poultry producer associations; (2) for village poultry, to promote better quarantine and management of sick and dead birds. Such detailed knowledge of country-specific characteristics of poultry production systems is essential to be able to develop more efficient disease risk management policies.

Using risk assessment as part of a systems approach to the control and prevention of HPAIV H5N1.

Since its emergence in China in 1996, highly pathogenic avian influenza virus subtype H5N1 has spread across Asia, Africa, and Europe. Countries had to promptly implement control and prevention measures. Numerous research and capacity building initiatives were conducted in the affected regions to improve the capacity of national animal health services to support the development of risk-based mitigation strategies. This paper reviews and discusses risk assessments initiated in several South-East Asian and African countries under one of these projects. Despite important data gaps, the risk assessment results improved the ability of policy makers to design appropriate risk management policies. Disease risk was strongly influenced by various human behavioral factors. The ongoing circulation of HPAIV H5N1 in several Asian countries and in Egypt, despite major disease control efforts, supports the need for an interdisciplinary approach to development of tailored risk management policies, in accordance with the EcoHealth paradigm and the broad concept of risk governance. In particular, active stakeholders engagement and integration of economic and social studies into the policy making process are needed to optimize compliance and sustainable behavioral changes, thereby increasing the effectiveness of mitigation strategies.

The risk of rinderpest re-introduction in post-eradication era.

In 2011, ten years after the last reported outbreak, the eradication of rinderpest was declared. However, as rinderpest virus stocks still exist, there remains a risk of rinderpest re-introduction. A semi-quantitative risk assessment was conducted to assess this risk, which was defined as the probability of at least one host becoming infected and infectious outside a laboratory anywhere in the world within a one-year period. Pathways leading to rinderpest re-introduction were: deliberate or accidental use of virus in laboratories, deliberate or accidental use of vaccines, host exposure to an environmental source of virus, and use of virus for anti-animal biological warfare. The probability of each pathway step occurring was estimated through expert opinion elicitation. The risk estimate was associated with a high degree of uncertainty. It was estimated to range from negligible to high, with the median being very low. The accidental use of laboratory virus stocks was the highest risk pathway. Reducing the number of virus stocks and restricting their use, as well as upgrading the laboratories to a higher biosafety level, would effectively decrease the maximum and median risks. Likewise, ensuring that remaining vaccine stocks are not used and are instead destroyed or relocated to a limited number of regional repositories would also have a major effect on these estimates. However, these measures are unlikely to eliminate the risk of rinderpest re-introduction so that maintaining response preparedness is essential.

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.

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.

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.