Epidemic intelligence in Europe: a user needs perspective to foster innovation in digital health surveillance.

BACKGROUND: European epidemic intelligence (EI) systems receive vast amounts of information and data on disease outbreaks and potential health threats. The quantity and variety of available data sources for EI, as well as the available methods to manage and analyse these data sources, are constantly increasing. Our aim was to identify the difficulties encountered in this context and which innovations, according to EI practitioners, could improve the detection, monitoring and analysis of disease outbreaks and the emergence of new pathogens. METHODS: We conducted a qualitative study to identify the need for innovation expressed by 33 EI practitioners of national public health and animal health agencies in five European countries and at the European Centre for Disease Prevention and Control (ECDC). We adopted a stepwise approach to identify the EI stakeholders, to understand the problems they faced concerning their EI activities, and to validate and further define with practitioners the problems to address and the most adapted solutions to their work conditions. We characterized their EI activities, professional logics, and desired changes in their activities using NvivoⓇ software. RESULTS: Our analysis highlights that EI practitioners wished to collectively review their EI strategy to enhance their preparedness for emerging infectious diseases, adapt their routines to manage an increasing amount of data and have methodological support for cross-sectoral analysis. Practitioners were in demand of timely, validated and standardized data acquisition processes by text mining of various sources; better validated dataflows respecting the data protection rules; and more interoperable data with homogeneous quality levels and standardized covariate sets for epidemiological assessments of national EI. The set of solutions identified to facilitate risk detection and risk assessment included visualization, text mining, and predefined analytical tools combined with methodological guidance. Practitioners also highlighted their preference for partial rather than full automation of analyses to maintain control over the data and inputs and to adapt parameters to versatile objectives and characteristics. CONCLUSIONS: The study showed that the set of solutions needed by practitioners had to be based on holistic and integrated approaches for monitoring zoonosis and antimicrobial resistance and on harmonization between agencies and sectors while maintaining flexibility in the choice of tools and methods. The technical requirements should be defined in detail by iterative exchanges with EI practitioners and decision-makers.

A combined methodological approach to characterize pig farming and its influence on the occurrence of interactions between wild boars and domestic pigs in Corsican micro-regions.

The pig sector in Corsica is based by a wide range of farming systems, mainly characterized on traditional extensive practices, which favor contacts between domestic and wild individuals. These contacts are suspected to influence the maintenance and the transmission of shared infectious diseases between both populations. Therefore, it is important to develop methods that allow to understand and anticipate their occurrence. Modeling these interactions requires accurate data on the presence, location and use of land on pig farms and farming practices, but such data are often unavailable, incomplete or outdated. In this study, we suggest a method to collect and analyze pig farming information that combines approaches from social sciences and epidemiology and enables a spatial representation of an index of potential interaction (IPI) between wild and domestic pigs at municipality level in the Corsican territory. As a first step of the process, interviews were conducted to gather information from 103 pig farms. Then, using hierarchical clustering, we identified five different clusters of pig farming practices which were evaluated and validated by local experts using participatory tools. The five pig farming clusters with their respective estimated levels of direct and indirect interactions with wild boars were combined in a linear equation with pig density to estimate a hypothetical index of potential interaction (IPI) in 155 municipalities. Our results revealed the diversity of pig farming practices across the island of Corsica and pointed out potential hotspots of interaction. Our method proved to be an effective way to collect and update information on the presence and typology of pig farms which has the potential to update official livestock production statistics. The spatial representation of an IPI between wild boars and domestic pigs in the Corsican territory could help design regional disease management strategies and policies to improve the control of certain shared pig pathogens in pig farms from Corsica.

An Updated Review of Ornithodoros Ticks as Reservoirs of African Swine Fever in Sub-Saharan Africa and Madagascar.

This updated review provides an overview of the available information on Ornithodoros ticks as reservoirs and biological vectors of the ASF virus in Africa and Indian Ocean islands in order to update the current knowledge in this field, inclusive of an overview of available methods to investigate the presence of ticks in the natural environment and in domestic pig premises. In addition, it highlights the major areas of research that require attention in order to guide future investigations and fill knowledge gaps. The available information suggests that current knowledge is clearly insufficient to develop risk-based control and prevention strategies, which should be based on a sound understanding of genotype distribution and the potential for spillover from the source population. Studies on tick biology in the natural and domestic cycle, including genetics and systematics, represent another important knowledge gap. Considering the rapidly changing dynamics affecting the African continent (demographic growth, agricultural expansion, habitat transformation), anthropogenic factors influencing tick population distribution and ASF virus (ASFV) evolution in Africa are anticipated and have been recorded in southern Africa. This dynamic context, together with the current global trends of ASFV dissemination, highlights the need to prioritize further investigation on the acarological aspects linked with ASF ecology and evolution.

A questionnaire survey for the assessment of wild-domestic pig interactions in a context oedema disease outbreaks among wild boars (Sus scrofa) in South-Eastern France.

Pig outdoor farming is gaining popularity and commercial success in the European Union, and its expansion, together with an increasing wild boar population, facilitates interactions between domestic and wild suids. In the Southern French Department of Ardèche, several episodes of mass mortalities due to infection with an enteropathogenic strain of Escherichia coli causing oedema disease (OD) were reported in wild boar populations between 2013 and 2016. In order to investigate a potential link between those events and the frequency of interactions between wild boar and domestic pig, we analyzed regional vegetation and hunting bag data and implemented a semi-structured questionnaire survey among a total of 30 outdoor pig farmers and 30 hunters distributed inside and outside the identified area of OD emergence. One third of interviewed farmers (11/30) had experienced intrusions of wild boars in domestic pig premises during the previous year. Similarly, 23% of interviewed hunters reported interactions between wild boar and feral free-ranging pigs in recent years, and 60% reported the observation of free-ranging pigs with a phenotypic feature of Vietnamese pot-bellied pigs (55%). Our analysis identified that in the OD emergence area, several factors could facilitate the transmission of pathogens between wild and domestic suids including a predominance of forested vegetation, a higher estimated wild boar density, weaker levels of farm biosecurity, a higher level of reported wild boar intrusions in pig farms and several reports of feral pot-bellied pig presence. Although our sample was limited, our study suggested a widespread occurrence of situations facilitating the transmission of pathogens between wild and domestic suids. Similar studies in other rural regions in the European Union are recommended, in order to promote preparedness for the emergence and circulation of shared swine pathogens.

The African swine fever modelling challenge: Model comparison and lessons learnt.

Robust epidemiological knowledge and predictive modelling tools are needed to address challenging objectives, such as: understanding epidemic drivers; forecasting epidemics; and prioritising control measures. Often, multiple modelling approaches can be used during an epidemic to support effective decision making in a timely manner. Modelling challenges contribute to understanding the pros and cons of different approaches and to fostering technical dialogue between modellers. In this paper, we present the results of the first modelling challenge in animal health - the ASF Challenge - which focused on a synthetic epidemic of African swine fever (ASF) on an island. The modelling approaches proposed by five independent international teams were compared. We assessed their ability to predict temporal and spatial epidemic expansion at the interface between domestic pigs and wild boar, and to prioritise a limited number of alternative interventions. We also compared their qualitative and quantitative spatio-temporal predictions over the first two one-month projection phases of the challenge. Top-performing models in predicting the ASF epidemic differed according to the challenge phase, host species, and in predicting spatial or temporal dynamics. Ensemble models built using all team-predictions outperformed any individual model in at least one phase. The ASF Challenge demonstrated that accounting for the interface between livestock and wildlife is key to increasing our effectiveness in controlling emerging animal diseases, and contributed to improving the readiness of the scientific community to face future ASF epidemics. Finally, we discuss the lessons learnt from model comparison to guide decision making.

Systematic Review on Crimean-Congo Hemorrhagic Fever Enzootic Cycle and Factors Favoring Virus Transmission: Special Focus on France, an Apparently Free-Disease Area in Europe.

Crimean-Congo hemorrhagic fever (CCHF) is a viral zoonotic disease resulting in hemorrhagic syndrome in humans. Its causative agent is naturally transmitted by ticks to non-human vertebrate hosts within an enzootic sylvatic cycle. Ticks are considered biological vectors, as well as reservoirs for CCHF virus (CCHFV), as they are able to maintain the virus for several months or even years and to transmit CCHFV to other ticks. Although animals are not symptomatic, some of them can sufficiently replicate the virus, becoming a source of infection for ticks as well as humans through direct contact with contaminated body fluids. The recent emergence of CCHF in Spain indicates that tick-human interaction rates promoting virus transmission are changing and lead to the emergence of CCHF. In other European countries such as France, the presence of one of its main tick vectors and the detection of antibodies targeting CCHFV in animals, at least in Corsica and in the absence of human cases, suggest that CCHFV could be spreading silently. In this review, we study the CCHFV epidemiological cycle as hypothesized in the French local context and select the most likely parameters that may influence virus transmission among tick vectors and non-human vertebrate hosts. For this, a total of 1,035 articles dating from 1957 to 2021 were selected for data extraction. This study made it possible to identify the tick species that seem to be the best candidate vectors of CCHFV in France, but also to highlight the importance of the abundance and composition of local host communities on vectors' infection prevalence. Regarding the presumed transmission cycle involving Hyalomma marginatum, as it might exist in France, at least in Corsica, it is assumed that tick vectors are still weakly infected and the probability of disease emergence in humans remains low. The likelihood of factors that may modify this equilibrium is discussed.

A combination of probabilistic and mechanistic approaches for predicting the spread of African swine fever on Merry Island.

Over the last decade African swine fever virus, one of the most virulent pathogens known to affect pigs, has devastated pork industries and wild pig populations throughout the world. Despite a growing literature on specific aspects of African swine fever transmission dynamics, it remains unclear which methods and approaches are most effective for controlling the disease during a crisis. As a consequence, an international modelling challenge was organized in which teams analyzed and responded to a stream of data from an in silico outbreak in the fictive country of Merry Island. In response to this outbreak, we developed a modelling approach that aimed to predict the evolution of the epidemic and evaluate the impact of potential control measures. Two independent models were developed: a stochastic mechanistic space-time compartmental model for characterizing the dissemination of the virus among wild boar; and a deterministic probabilistic risk model for quantifying infection probabilities in domestic pig herds. The combined results of these two models provided valuable information for anticipating the main risks of dissemination and maintenance of the virus (speed and direction of African swine fever spread among wild boar populations, pig herds at greatest risk of infection, the size of the epidemic in the short and long terms), for evaluating the impact of different control measures and for providing specific recommendations concerning control interventions.

Low prevalence of hepatitis E virus in the liver of Corsican pigs slaughtered after 12 months despite high antibody seroprevalence.

Hepatitis E virus (HEV) infection can be acute and benign or evolve to chronic hepatitis with rapid progression toward cirrhosis or liver failure in humans. Hence, hepatitis E (HE) disease is a major public health concern. In countries where pig populations are highly contaminated with HEV, human cases of HE are mainly foodborne, occurring frequently after consumption of raw or undercooked pork products or liver. Among factors associated to the presence of HEV in pork livers from intensive rearing systems, early slaughter (≤6 months) seems to be major. In Corsica, local pigs are raised in extensive farming systems and slaughtered after 12 months. To evaluate if slaughter of pigs over 12 months reduces the risk of HEV presence in livers, 1197 liver samples were randomly collected in 2 Corsican slaughterhouses. Presence of HEV RNA was detected in liver and HEV seroprevalence was determined in paired serum. The sampling included 1083 livers from animals between 12 and 48 months and 114 livers from animals <12 months. The samples were predominantly from semi-extensive and extensive farms (n = 1154). Estimated HEV seroprevalence was high, that is, >88%, and HEV RNA prevalence in adult pig livers (>12 months old) was low, that is, 0.18%. However, in livers from younger animals (<12 months), including piglets below 6 months old, 5.3% (6/114) of the samples were positive for HEV RNA. Sequences recovered from positive livers belonged to HEV genotype 3c and 3f. The presence of infectious HEV was confirmed in two livers by the detection of HEV replication in HepaRG cell cultures. Thus, this study demonstrates the low prevalence of HEV in livers of pigs over 12 months, even in farms with high HEV circulation. This observation may open new perspectives on the preferential use of livers from animals older than 12 months in raw pork liver products.

Spatial-Temporal Movements of Free Ranging Pigs at the Wildlife-Livestock Interface of Murchison Falls National Park, Uganda: Potential of Disease Control at a Local Scale.

In many Ugandan rural communities, pigs are generally kept under traditional smallholder systems without basic biosecurity measures in place. In some instances, these systems are at the livestock-wildlife interface, as it is the case in Nwoya district, which is bordered by Murchison Falls National Park (MFNP). This pig system has potential for the maintenance and transmission of pathogens like African swine fever (ASF) between different herds, and also with wild pigs (warthogs and bushpigs). In this paper, we describe the spatial and temporal pattern of the movements of free ranging domestic pigs in a rural setting in Northern Uganda where ASF is endemic. We also determine their use of habitat to highlight the potential interaction hotspots between domestic pigs and between domestic and wild pig populations. We fitted 10 free-ranging domestic pigs owned by different homesteads with GPS harnesses during rainy and dry seasons. The pig home range, daily distance, activity pattern and habitat use were calculated. Our results show that the maximum area covered (MCP 100%) by the pigs varied between 35,965 and 475,077 m2. The core area varied from 1,317 to 50,769 m2. The pigs' home ranges were significantly bigger during the dry season than during the rainy season (Wilcoxon test, W = 22, p = 0.04). The mean full day (24 h) distance was longer in the dry season than in the rainy season (Student test, t = 2.7, p = 0.03). The pigs were mostly located within their own homestead, but they also used other homesteads, grass and crop fields. This study highlights that free-ranging domestic pigs may cover a wide area, especially during the dry season. Interestingly, the home range of pigs from different herds may overlap with areas used by wild pigs which share crops and other resources in this area. This study provides insights into a better understanding of the potential for spread of diseases such as ASF at small-scale and can be used to raise awareness of such risks and to better target implementation of preventive measures.

Do wild suids from Ndumo Game Reserve, South Africa, play a role in the maintenance and transmission of African swine fever to domestic pigs?

Warthogs (Phacochoerus africanus) and bushpigs (Potamochoerus larvatus) are considered as the wild reservoirs of ASF. They are both present in Ndumo Game Reserve (NGR), located in the Northern South African Province of KwaZulu on the border with Mozambique. In that area, the occurrence of tick-warthog sylvatic cycle of ASF has been suspected for years. To assess if wild suids represent a risk of ASF virus spillover to domestic pigs, wild suid abundance and incursions outside NGR boundaries were estimated using transect counts, fence patrols and camera traps. Also, the presence of Ornithodoros ticks was explored in 35 warthog burrows within NGR. In addition, blood samples were taken from 67 domestic pig farms located outside NGR to be tested for ASF antibodies. Information on interactions between domestic and wild suids and ASF occurrence was gathered using interviews with pig farmers (n = 254) in the study area. In conclusion, the bushpigs and warthog's population estimates in NGR are 5 and 3-5 individuals/km2 , respectively. Both species move out of the reserve regularly (15.4 warthogs/day and 6.35 bushpigs/day), with movements significantly increasing in the dry season. Some farmers observed warthogs and bushpigs as far as 8 and 19 km from NGR, respectively, but no reports of direct wild-domestic suids interactions or ASF outbreaks. Also, no soft ticks were detected in all warthog burrows and all the pig blood samples were negative for ASF antibodies. The absence of ticks in warthog burrows, the absence of antibodies in pigs sampled, the absence of reported outbreaks, and no familiarity with ASF in the study area, suggest that a sylvatic cycle of ASF is, at present, unlikely in NGR. This conclusion must be confirmed by a larger survey of warthog burrows and monitoring potential antibodies in warthogs from NGR.

An expert opinion assessment of blood-feeding arthropods based on their capacity to transmit African swine fever virus in Metropolitan France.

To deal with the limited literature data on the vectorial capacity of blood-feeding arthropods (BFAs) and their role in the transmission of African swine fever virus (ASFV) in Metropolitan France, a dedicated working group of the French Agency for Food, Environmental and Occupational Health & Safety performed an expert knowledge elicitation. In total, 15 different BFAs were selected as potential vectors by the ad hoc working group involved. Ten criteria were considered to define the vectorial capacity: vectorial competence, current abundance, expected temporal abundance, spatial distribution, longevity, biting rate, active dispersal capacity, trophic preferences for Suidae, probability of contact with domestic pigs and probability of contact with wild boar. Fourteen experts participated to the elicitation. For each BFA, experts proposed a score (between 0 and 3) for each of the above criteria with an index of uncertainty (between 1 and 4). Overall, all experts gave a weight for all criteria (by distributing 100 marbles). A global weighted sum of score per BFA was calculated permitting to rank the different BFAs in decreasing order. Finally, a regression tree analysis was used to group those BFAs with comparable likelihood to play a role in ASF transmission. Out of the ten considered criteria, the experts indicated vectorial competence, abundance and biting rate as the most important criteria. In the context of Metropolitan France, the stable fly (Stomoxys calcitrans) was ranked as the most probable BFA to be a vector of ASFV, followed by lice (Haematopinus suis), mosquitoes (Aedes, Culex and Anopheles), Culicoides and Tabanidea. Since scientific knowledge on their vectorial competence for ASF is scarce and associated uncertainty on expert elicitation moderate to high, more studies are however requested to investigate the potential vector role of these BFAs could have in ASFV spread, starting with Stomoxys calcitrans.

Mechanical transmission of African swine fever virus by Stomoxys calcitrans: Insights from a mechanistic model.

African swine fever (ASF) represents a global threat with huge economic consequences for the swine industry. Even though direct contact is likely to be the main transmission route from infected to susceptible hosts, recent epidemiological investigations have raised questions regarding the role of haematophagous arthropods, in particular the stable fly (Stomoxys calcitrans). In this study, we developed a mechanistic vector-borne transmission model for ASF virus (ASFV) within an outdoor domestic pig farm in order to assess the relative contribution of stable flies to the spread of the virus. The model was fitted to the ecology of the vector, its blood-feeding behaviour and pig-to-pig transmission dynamic. Model outputs suggested that in a context of low abundance (<5 flies per pig), stable flies would play a minor role in the spread of ASFV, as they are expected to be responsible for around 10% of transmission events. However, with abundances of 20 and 50 stable flies per pig, the vector-borne transmission would likely be responsible for almost 30% and 50% of transmission events, respectively. In these situations, time to reach a pig mortality of 10% would be reduced by around 26% and 40%, respectively. The sensitivity analysis emphasized that the expected relative contribution of stable flies was strongly dependent on the volume of blood they regurgitated and the infectious dose for pigs. This study identified crucial knowledge gaps that need to be filled in order to assess more precisely the potential contribution of stable flies to the spread of ASFV, including a quantitative description of the populations of haematophagous arthropods that could be found in pig farms, a better understanding of blood-feeding behaviours of stable flies and the quantification of the probability that stable flies partially fed with infectious blood transmit the virus to a susceptible pig during a subsequent blood-feeding attempt.

Silent Circulation of Rift Valley Fever in Humans, Botswana, 2013-2014.

We evaluated the prevalence of Rift Valley fever virus IgG and IgM in human serum samples (n = 1,276) collected in 2013-2014 in northern Botswana. Our findings provide evidence of active circulation of this virus in humans in the absence of clinical disease in this region.

Putative Role of Arthropod Vectors in African Swine Fever Virus Transmission in Relation to Their Bio-Ecological Properties.

African swine fever (ASF) is one of the most important diseases in Suidae due to its significant health and socioeconomic consequences and represents a major threat to the European pig industry, especially in the absence of any available treatment or vaccine. In fact, with its high mortality rate and the subsequent trade restrictions imposed on affected countries, ASF can dramatically disrupt the pig industry in afflicted countries. In September 2018, ASF was unexpectedly identified in wild boars from southern Belgium in the province of Luxembourg, not far from the Franco-Belgian border. The French authorities rapidly commissioned an expert opinion on the risk of ASF introduction and dissemination into metropolitan France. In Europe, the main transmission routes of the virus comprise direct contact between infected and susceptible animals and indirect transmission through contaminated material or feed. However, the seasonality of the disease in some pig farms in Baltic countries, including outbreaks in farms with high biosecurity levels, have led to questions on the possible involvement of arthropods in the transmission of the virus. This review explores the current body of knowledge on the most common arthropod families present in metropolitan France. We examine their potential role in spreading ASF-by active biological or mechanical transmission or by passive transport or ingestion-in relation to their bio-ecological properties. It also highlights the existence of significant gaps in our knowledge on vector ecology in domestic and wild boar environments and in vector competence for ASFV transmission. Filling these gaps is essential to further understanding ASF transmission in order to thus implement appropriate management measures.

Seroprevalence of Selected Tick Borne Pathogens and Diversity and Abundance of Ixodid Ticks (Acari: Ixodidae) at the Wildlife-Livestock Interface in Northern Botswana.

Ticks and tick borne diseases (TBDs) undermine livestock production with considerable economic losses to livestock producers in endemic areas worldwide. Despite the impact of ticks and TBDs in livestock production, there is a paucity of information on ticks and diseases they transmit in Botswana. To address this gap, a cross-sectional study was conducted to determine (i) the seroprevalence of selected tick borne (TB) pathogens and (ii) the diversity and abundance of ixodid ticks among 301 cattle foraging around two protected areas in northern Botswana, differing by the presence or absence of a physical barrier (fence) separating wildlife and livestock. Competitive inhibition enzyme linked immuno-sorbent assay (cELISA) was used to test for Anaplasma spp. infection and Indirect Fluorescence Antibody Test (IFAT) was used to test for Theileria parva, Babesia bovis, and B. bigemina. Ticks were identified morphologically at either genus or species level. Seroprevalence of cattle was found to be 90% for Anaplasma spp., followed by 38.6% for Babesia spp. and 2.4% for T. parva. Except for Babesia spp., comparisons of the seroprevalence of the selected haemoparasites between the two wildlife-livestock interface areas were not significantly different. The overall prevalence of ticks was found to be 73.4% with Amblyomma variegatum being the most abundant (53.1%) followed by Rhipicephalus evertsi evertsi (31.7%) and R. (B.) decoloratus (7.7%). Except for Babesia spp., comparisons of the seroprevalence of the selected haemoparasites between the two study areas were not significantly different while comparisons of the burden of tick infestation between the study sites revealed significant difference for A. variegatum and R. evertsi evertsi with both tick infestations higher where there is no barrier. Our work provided baseline data on TBD pathogens and tick infestation in cattle populations exposed to different levels of contact with adjacent buffalo populations. The presence of a veterinary fence did not significantly influence the seroprevalence of the selected TBD pathogens (except for Babesia spp.) but seemed to reduce tick burdens in cattle. Findings from this study can be used for guiding future epidemiological study designs to improve our understanding of ticks and TBDs dynamics in northern Botswana.

African Swine Fever Epidemiology and Control.

African swine fever is a devastating disease that can result in death in almost all infected pigs. The continuing spread of African swine fever from Africa to Europe and recently to the high-pig production countries of China and others in Southeast Asia threatens global pork production and food security. The African swine fever virus is an unusual complex DNA virus and is not related to other viruses. This has presented challenges for vaccine development, and currently none is available. The virus is extremely well adapted to replicate in its hosts in the sylvatic cycle in East and South Africa. Its spread to other regions, with different wildlife hosts, climatic conditions, and pig production systems, has revealed unexpected epidemiological scenarios and different challenges for control. Here we review the epidemiology of African swine fever in these different scenarios and methods used for control. We also discuss progress toward vaccine development and research priorities to better understand this complex disease and improve control.