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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in infected patients mainly displays pulmonary and oronasal tropism; however, the presence of the virus has also been demonstrated in the stools of patients and consequently in wastewater treatment plant effluents, raising the question of the potential risk of environmental contamination (such as seawater contamination) through inadequately treated wastewater spillover into surface or coastal waters even if the environmental detection of viral RNA alone does not substantiate risk of infection. Therefore, here, we decided to experimentally evaluate the persistence of the porcine epidemic diarrhea virus (PEDv), considered as a coronavirus representative model, in the coastal environment of France. Coastal seawater was collected, sterile-filtered, and inoculated with PEDv before incubation for 0 to 4 weeks at four temperatures representative of those measured along the French coasts throughout the year (4, 8, 15, and 24°C). The decay rate of PEDv was determined using mathematical modeling and was used to determine the half-life of the virus along the French coast in accordance with temperatures from 2000 to 2021. We experimentally observed an inverse correlation between seawater temperature and the persistence of infectious viruses in seawater and confirm that the risk of transmission of infectious viruses from contaminated stool in wastewater to seawater during recreational practices is very limited. The present work represents a good model to assess the persistence of coronaviruses in coastal environments and contributes to risk evaluation, not only for SARS-CoV-2 persistence, but also for other coronaviruses, specifically enteric coronaviruses from livestock. IMPORTANCE The present work addresses the question of the persistence of coronavirus in marine environments because SARS-CoV-2 is regularly detected in wastewater treatment plants, and the coastal environment, subjected to increasing anthropogenic pressure and the final receiver of surface waters and sometimes insufficiently depurated wastewater, is particularly at risk. The problem also arises in the possibility of soil contamination by CoV from animals, especially livestock, during manure application, where, by soil impregnation and runoff, these viruses can end up in seawater. Our findings are of interest to researchers and authorities seeking to monitor coronaviruses in the environment, either in tourist areas or in regions of the world where centralized systems for wastewater treatment are not implemented, and more broadly, to the scientific community involved in “One Health” approaches.

The control of epidemics requires a thorough understanding of the complex interaction between pathogen transmission, disease impact and population dynamics and management. Mechanistic epidemiological modelling is an effective way to address this issue, but handling highly structured and dynamic systems, remains challenging. We therefore developed a novel approach that combines multi-level agent-based systems with spatial and temporal organization, allowing for a tuned representation of the transmission processes amongst the host population. We applied this method to model the spread of a PRRSv-like virus in pig farms, integrating the clinical consequences (conception and reproduction failures), in terms of animal husbandry practices. the results highlighted the importance to account for spatial and temporal structuring and herd management policies in epidemiological models.Indeed, disease-related abortions, inducing reassignments of sows in different batches, was shown to enhance the transmission process, favouring the persistence of the virus at the herd level. Supported by a domain-specific declarative language, our approach provides flexible and powerful solutions to address the issues of on-farm epidemics and broader public health concerns. The present application based on a simple SEIR model opens the way to the representation of more complex epidemiological systems, including more specific features such as maternally derived antibodies, vaccination, or dual infections, along with their respective clinical consequences on the management procedures.

African swine fever (ASF) is a highly contagious viral disease in domestic pigs and wild boar that causes tremendous socioeconomic damage in related industries. In 2019, the virus emerged in South Korea, which has since reported 21 outbreaks in domestic pig farms and over 2,600 cases in wild boar. In this review, we synthesize the epidemiological knowledge generated on ASF in South Korea during the first three years of the epidemic (2019–2021). We searched four international and one domestic Korean database to identify scientific articles published since 2019 and describing ASF epidemiology in South Korea. Fourteen articles met our selection criteria and were used to synthesize the origin of ASF in South Korea, the risk factors of disease occurrence, the effectiveness of the surveillance and intervention measures that were implemented, and the viral transmission dynamics. We found that timely intensive surveillance and interventions on domestic pig farms successfully blocked between-farm transmission. However, in wild boar, the ASF virus has spread massively towards the south primarily along the mountain ranges despite ongoing fence erection and intensive depopulation efforts, endangering domestic pig farms across the country. The current devastating epidemic is suspected to be the consequence of an ASF control strategy unaligned to the epidemiological context, the challenging implementation of control measures hindered by topological complexities, and inappropriate biosecurity by field workers. To improve our understanding of ASF epidemiology in South Korea and enhance disease management, future research studies should specify the ecological drivers of disease distribution and spread and devise effective control strategies, particularly in relation to Korean topography, and the latent spread of the virus in wild boar populations. Additionally, research studies should explore the psychosocial factors for ASF management, and develop tools to support evidence-based decision-making for managing ASFV in wild boar.

Introduction Increasing demand for animal protein and the diversification of food supply chains are driving foodborne zoonotic diseases responsible for morbidity, mortality, and economic loss worldwide. This trend towards intensive farming requires improved biosecurity to control and prevent zoonotic infections in animals and humans. As part of the One Health European Joint Programme, the "Biosecurity practices for pig farming across Europe" (BIOPIGEE) project aims to establish a protocol of relevant biosecurity measures (BSMs) to reduce the occurrence of Salmonella, Hepatitis E virus (HEV) and pathogenic E. coli in pig production within the EU. While "biosecurity" is well defined, a harmonized definition of a BSM is missing. This, combined with the question of which measures can be counted as BSM, affects their understanding, acceptance, and broad, effective implementation of the concept from the farm to policy level. Therefore, the BIOPIGEE task group i) evaluated potentially relevant in- and exclusion criteria in the context of biosecurity used within BIOPIGEE and ii) screened the scientific literature for existing definitions, with the aim to propose a standard definition for the term BSM. Methodology In- and exclusion criteria related to biosecurity were collected from five BIOPIGEE tasks studying the effectiveness of farm and slaughterhouse biosecurity practices. The significance of each criterion for defining the term BSM was discussed; relevant criteria were summarized to propose a working definition. Concurrently, a literature scoping review was conducted with the search terms "biosecurity measures" AND (swine OR pig) in titles, abstracts, or keywords using Scopus, Pubmed, Web of Science and Google Scholar (GS) databases. As the GS search algorithm does not specify term locations, the first 300 articles sorted by relevance were selected. After removing duplicates, the remainder were processed using R-based bibliometric tools. From each database ≤25 articles explicitly related to BSMs in pig operations were extracted. A bibliometric analysis was performed on the final record subset and full-text articles were extracted by text mining tools. The records containing one of the 100 most frequent terms were included in hierarchical cluster analysis. The outcome identified research clusters among the selected articles, which were modified after an additional full-text reading. Results Inclusion criteria were: association to pathogen occurrence in pig operations; application of procedures (goal, pre/post conditions, timing, physical requirements, rules) or physical processes; primary and secondary biosecurity. Exclusion criteria were: factors requiring major changes of the operation (location of the buildings, size); procedures for the monitoring of, the compliance to or the effectiveness of BSMs; proficiency of personnel; description of pathogen status; tertiary biosecurity. From 926 identified records, 90 articles were retained after removal of duplicates and 34 articles remained due to considerable overlap between the databases. The scoping review did not reveal an existing definition for a BSM. Based on the final paper selection, six specific research themes were identified. We propose the following standard definition for the term BSM: "A biosecurity measure is the active implementation of any standardized segregation, hygiene, or management procedure explicitly aimed at reducing the probability of (i) pathogen introduction into a farm/operation (external biosecurity), (ii) pathogen spread within or out of a farm/operation (internal biosecurity)." Discussion Two key fragments of the proposed definition are "active implementation" and "standardized procedures" (procedure = series of actions conducted in a particular order and way). The latter is linked to various factors such as the geographical region/climate, species of pathogen/animal, production type, policy/law, and farm status (pathogen prevalence, existing biosecurity) as prerequisites. In addition, procedures are shaped by temporal conditions (short vs. long term effects for pathogen reduction), and are affected by human components related to compliance, knowledge and skills. "Active implementation" emphasizes the importance of the action itself. Assessments such as evaluating pathogen prevalence are often considered as BSMs, but whilst indispensable, cannot be considered as BSMs independently as they form part of a procedure. Tertiary biosecurity measures (e.g. vaccination) were excluded in the context of BIOPIGEE, but remain essential biosecurity measures. Although based on expertise and scientific literature from the pig sector, our proposed definition may benefit other species or production types, and improve research and communication of the best BSMs.

This is the deliverable D-JRP21-WP4.11 "Model Output: Number of animal cases with and without biosecurity measures" of the OHEJP BIOPIGEE project produced in WP4.2.

National audience; Hepatitis E is a zoonotic disease that is widespread in pigs and potentially severe in humans. Transmission between pigs occurs via the faecal-oral route, either by direct contact or via the environment. In addition, the main factor of propagation between farms is the transport of live animals. The pig production chain consists of many interconnected actors who form a complex network in space and time. This study aimed to test control scenarios at a national scale by considering the many transmission routes and movements of live animals. Pig movements from 2017-2020 provided by the French national pig traceability database (BDporc) were analysed.Exponential random-graph models were fitted for three subsets defined by the type of animals transported (sows, piglets or growing pigs) to estimate probabilities of contact between farms. The results were validated using cross validation of goodness-of-fit analysis and maps. The estimated contact probabilities and general characteristics of farms were used to build a demographic model that simulated pig movements at three levels − between pens, between production sectors and between farms − according to a deterministic schedule, but with random destinations weighted by the contact probabilities. Finally, the simulated dynamics were used to feed a multi-level stochastic epidemiological model that simulated within- and between-farm transmission. The prevalence of hepatitis E virus -positive pigs shipped to the slaughterhouse was estimated for different control scenarios to evaluate the effectiveness of biosecurity measures implemented at the farm level.; L'hépatite E est une zoonose très répandue chez les porcs et potentiellement grave chez l'homme. La transmission entre porcs se fait par voie fécale-orale, par contact direct ou via l'environnement. Le principal facteur de propagation entre exploitations est le transport d'animaux vivants. La chaîne de production porcine est constituée de nombreux acteurs interconnectés, formant un réseau complexe structuré dans l'espace et le temps. Cette étude vise à tester des scénarios de contrôle à l'échelle nationale en prenant en compte les différentes voies de transmission ainsi que les mouvements d’animaux vivants. Les mouvements de porcs de 2017 à 2020 fournis par la base de données nationale française de traçabilité des porcs (BDporc) ont été analysés. Des modèles de graphes aléatoires exponentiels ont été ajustés pour trois sous-ensembles définis par le type d'animaux transportés (truies, porcelets et porcs en croissance) afin d’évaluer les probabilités de contact entre élevages. Les résultats ont été validés par la validation croisée d’une analyse de la qualité de l'ajustement des modèles et de cartes. Les probabilités de contact estimées ainsi que les caractéristiques générales des systèmes d'élevage en bandes ont permis de construire un modèle démographique simulant les mouvements de porcs à trois niveaux : entre cases, entre secteurs de production et entre élevages selon une horloge déterministe, mais avec des destinations aléatoires pondérées par les probabilités de contact. Enfin, la dynamique simulée a permis d’alimenter un modèle épidémiologique stochastique multi-niveaux simulant la transmission intra- et inter-cases. La prévalence des porcs positifs au virus de l’hépatite E transportés à l'abattoir a été estimée pour différents scénarios de contrôle afin d'évaluer, à terme, l'efficacité de mesures de biosécurité mises en place en élevage.

Selon les termes de la saisine, « Au 3 mars 2022 (14h), 55 foyers d’IAHP ont été confirmés en Vendée et dans les départements limitrophes. 24 suspicions sont également identifiées à cette date.Les foyers sont situés dans une zone à risque de diffusion au sens de l’arrêté du 29/9/2021. Cette zone est stratégique car elle contient aussi de nombreux élevages de reproducteurs et de grands parentaux ainsi que de nombreux couvoirs de toutes les filières avicoles. Les opérateurs de cette zone approvisionnent de nombreux élevages situés en dehors de cette zone.La dynamique de détection des foyers est extrêmement préoccupante et inédite avec une extension dans toute la partie nord de la Vendée, au sud de la Loire Atlantique et dans le département des Deux-Sèvres. Des foyers périphériques sont également présents en Maine et Loire et dans les Deux-Sèvres.Compte tenu de cette diffusion très inquiétante et après échange avec vos équipes il a été décidé de sursoir à tout flux d’œufs à couver (OAC) et de poussins depuis cette zone.Néanmoins en raison de la concentration de la production d’OAC et de poussins dans cette zone la restriction des mouvements d’OAC et de poussins entraine de lourdes difficultés pour les élevages en dehors de la zone et qui vont se retrouver en rupture d’approvisionnement. Pour ces raisons la filière met une forte pression pour maintenir le flux d’OAC et de poussins de ZR [zone réglementée] vers des zones indemnes en mettant en œuvre des dérogations prévues par les textes européens.Les résultats partiels des enquêtes épidémiologiques ne permettent pas à ce jour d’identifier de source majeure de contamination. Cependant, le rôle de réservoir et surtout d’excréteur massif des palmipèdes a été souligné. Parmi les autres facteurs de risque, le rôle possible des sous-produits (épandages de lisiers ou de digestats de méthanisation, tournée d’équarrissage), des mouvements de personnes (vaccinateurs, attrapeurs) a été avancé. Il est à noter que de nombreux épandages sont réalisés actuellement. La réglementation en vigueur (AM biosécurité du 29 septembre 2021) prévoit pour les lisiers la possibilité d’un épandage après assainissement (durée en fonction de la nature du lisier) ou un épandage direct avec enfouissement immédiat.La carte du zonage actuellement mise en place est en annexe. Ce zonage résulte de zones de surveillances et de zones de protection coalescentes qui évoluent quotidiennement avec la confirmation des nouveaux foyers.Compte tenu du caractère clinique avec une forte excrétion pré-symptomatique de la souche virale impliquée, probablement à l’origine de la diffusion rapide observée, une zone réglementée supplémentaire (ZRS) doit être envisagée pour arrêter la diffusion de la maladie. »Objet de la question 3 de la saisine : « Risque de maintenir les dérogations pour sortir des OAC et des poussins (toutes espèces) de ces zonesCompte tenu de la dynamique de la maladie, quel est le niveau de risque lié au maintien de l’activité des couvoirs en ZR pour faire des livraisons en zone indemne ? Selon ce niveau de risque, quelles mesures renforcées de biosécurité doivent être impérativement mises en place par les couvoirs pour leur permettre de poursuivre leur activité et approvisionner des élevages en dehors de la ZRS ? »

Selon les termes de la saisine, « Au 3 mars 2022 (14h), 55 foyers d’IAHP ont été confirmés en Vendée et dans les départements limitrophes. 24 suspicions sont également identifiées à cette date.Les foyers sont situés dans une zone à risque de diffusion au sens de l’arrêté du 29/9/2021. Cette zone est stratégique car elle contient aussi de nombreux élevages de reproducteurs et de grands parentaux ainsi que de nombreux couvoirs de toutes les filières avicoles. Les opérateurs de cette zone approvisionnent de nombreux élevages situés en dehors de cette zone.La dynamique de détection des foyers est extrêmement préoccupante et inédite avec une extension dans toute la partie nord de la Vendée, au sud de la Loire Atlantique et dans le département des Deux-Sèvres. Des foyers périphériques sont également présents en Maine et Loire et dans les Deux-Sèvres.Compte tenu de cette diffusion très inquiétante et après échange avec vos équipes il a été décidé de sursoir à tout flux d’œufs à couver (OAC) et de poussins depuis cette zone.Néanmoins en raison de la concentration de la production d’OAC et de poussins dans cette zone la restriction des mouvements d’OAC et de poussins entraine de lourdes difficultés pour les élevages en dehors de la zone et qui vont se retrouver en rupture d’approvisionnement. Pour ces raisons la filière met une forte pression pour maintenir le flux d’OAC et de poussins de ZR [zone réglementée] vers des zones indemnes en mettant en œuvre des dérogations prévues par les textes européens.Les résultats partiels des enquêtes épidémiologiques ne permettent pas à ce jour d’identifier de source majeure de contamination. Cependant, le rôle de réservoir et surtout d’excréteur massif des palmipèdes a été souligné. Parmi les autres facteurs de risque, le rôle possible des sous-produits (épandages de lisiers ou de digestats de méthanisation, tournée d’équarrissage), des mouvements de personnes (vaccinateurs, attrapeurs) a été avancé. Il est à noter que de nombreux épandages sont réalisés actuellement. La réglementation en vigueur (AM biosécurité du 29 septembre 2021) prévoit pour les lisiers la possibilité d’un épandage après assainissement (durée en fonction de la nature du lisier) ou un épandage direct avec enfouissement immédiat.La carte du zonage actuellement mise en place est en annexe. Ce zonage résulte de zones de surveillances et de zones de protection coalescentes qui évoluent quotidiennement avec la confirmation des nouveaux foyers.Compte tenu du caractère clinique avec une forte excrétion pré-symptomatique de la souche virale impliquée, probablement à l’origine de la diffusion rapide observée, une zone réglementée supplémentaire (ZRS) doit être envisagée pour arrêter la diffusion de la maladie.

Live animal movements generate direct contacts (via the exchange of live animals) and indirect contacts (via the transit of transport vehicles) between farms, which can contribute to the spread of pathogens. However, most analyses focus solely on direct contacts and can therefore underestimate the contribution of live animal movements in the spread of infectious diseases. Here, we used French live duck movement data (2016–2018) from one of the largest transport companies to compare direct and indirect contact patterns between duck farms and evaluate how these patterns were associated with the French 2016–2017 epidemic of highly pathogenic avian influenza H5N8. A total number of 614 farms were included in the study, and two directed networks were generated: the animal introduction network (exchange of live ducks) and the transit network (transit of transport vehicles). Following descriptive analyses, these two networks were scrutinized in relation to farm infection status during the epidemic. Results showed that farms were substantially more connected in the transit network than in the animal introduction network and that the transit of transport vehicles generated more opportunities for transmission than the exchange of live animals. We also showed that animal introduction and transit networks’ statistics decreased substantially during the epidemic (January–March 2017) compared to non-epidemic periods (January–March 2016 and January–March 2018). We estimated a probability of 33.3 % that a farm exposed to the infection through either of the two live duck movement networks (i.e. that was in direct or indirect contact with a farm that was reported as infected in the following seven days) becomes infected within seven days after the contact. However, we also demonstrated that the level of exposure of farms by these two contact patterns was low, leading only to a handful of transmission events through these routes. As a consequence, we showed that live animal movement patterns are efficient transmission routes for HPAI but have been efficiently reduced to limit the spread during the French 2020–2021 epidemic. These results underpin the relevance of studying indirect contacts resulting from the movement of animals to understand their transmission potential and the importance of accounting for both routes when designing disease control strategies., Preventive Veterinary Medicine, 198, ISSN:0167-5877

Following the emergence of highly pathogenic avian influenza (H5N8) in France in early December 2020, we used duck mortality data from the index farm to investigate within-flock transmission dynamics. A stochastic epidemic model was fitted to the daily mortality data and model parameters were estimated using an approximate Bayesian computation sequential Monte Carlo (ABC-SMC) algorithm. The model predicted that the first bird in the flock was infected 5 days (95% credible interval, CI: 3-6) prior to the day of suspicion and that the transmission rate was 4.1 new infections per day (95% CI: 2.8-5.8). On average, ducks became infectious 4.1 h (95% CI: 0.7-9.1) after infection and remained infectious for 4.3 days (95% CI: 2.8-5.7). The model also predicted that 34% (50% prediction interval: 8%-76%) of birds would already be infectious by the day of suspicion, emphasizing the substantial latent threat this virus could pose to other poultry farms and to neighbouring wild birds. This study illustrates how mechanistic models can help provide rapid relevant insights that contribute to the management of infectious disease outbreaks of farmed animals. These methods can be applied to future outbreaks and the resulting parameter estimates made available to veterinary services within a few hours.

All the full-genome sequences listed in this article are gathered into the BioProject No. PRJNA705101; International audience; Modified live vaccines (MLVs) against the porcine reproductive and respiratory syndrome virus (PRRSV) have been regularly associated with safety issues, such as reversion to virulence. In order to characterize the phenotypic and genetic evolution of the PRRSV-1 DV strain from the Porcilis® PRRS MLV after limited passages in pigs, three in vivo experiments were performed. Trial#1 aimed (i) at studying transmission of the vaccine strain from vaccinated to unvaccinated contact pigs. Trial#2 and Trial#3 were designed (ii) to assess the reproducibility of Trial#1, using another vaccine batch, and (iii) to compare the virulence levels of two DV strains isolated from vaccinated (passage one) and diseased contact pigs (passage two) from Trial#1. DV strain isolates from vaccinated and contact pigs from Trial#1 and Trial#2 were submitted to Next-Generation Sequencing (NGS) full-genome sequencing. All contact animals from Trial#1 were infected and showed significantly increased viremia compared to vaccinated pigs, whereas no such change was observed during Trial#2. In Trial#3, viremia and transmission were higher for inoculated pigs with passage two of the DV strain, compared with passage one. In this study, we showed that the re-adaptation of the DV strain to pigs is associated with faster replication and increased transmission of the vaccine strain. Punctually, a decrease of attenuation of the DV vaccine strain associated with clinical signs and increased viremia may occur after limited passages in pigs. Furthermore, we identified three mutations linked to pig re-adaptation and five other mutations as potential virulence determinants.

Hepatitis E virus (HEV) infects pigs and humans. Its spread among pigs occurs within-farm through faecal–oral route including direct and environmental transmission. Live animal movements are known as the major driver of between farms spread. Strongly structured in space and time, the swine production chain is made of various interconnected farms, forming a complex network. We aimed to simulate realistic between-farm movements to feed a multilevel epidemiological model. Swine movements from 2017 to 2019 provided by the National Swine Identification database (BDporc) were analysed using complex network analysis methods. Exponential random graph models (ERGM) were then used to identify the key drivers of trade partner choices and the associated probabilities of contact between farms. In the 36-month period, 2.512.174 loading and unloading events were recorded involving 16.377 premises. Because of the large size of the dataset, analysis was limited to specific subsets of the data, using semestrial data and type of transported animals (breeding sows, piglets and growing pigs). For each data subset, an ERGM was selected using a stepwise forward approach based on AICs comparison and analyzing goodness-of-fit. In all cases, the company, type of farm, free-ranging characteristics, size and batch rearing systems were identified as explanatory variables of the network structure. Network statistics and levels included were subnetwork-specific. ERGM outcomes allow simulating pig trade networks with characteristics similar to the observed one, to prospect on the global impact of the network structure on pathogen transmission. Simulated movements fed a multi-level model developed with SimInf package. This work was done in the frame of the BIOPIGEE OHEJP project.

Selon les termes de la saisine, « cette zone qui s’étend à 20km autour des foyers d’influenza aviaire (IA) déclarés dans ces départements a été mise en place suite à votre avis rendu sur la saisine n° 2020-AST-0179 : Demande d’avis scientifique et technique de l’Anses relative aux mesures de maitrise de l’épizootie d’influenza aviaire dans la région du Sud-Ouest(département 40 et départements mitoyens) », Question n°2. Dans cet avis l’Anses a indiqué “Compte tenu des délais de levée des zones réglementées autour des foyers d’IAHP, le Gecurecommande de lever les restrictions de mises en place d’oiseaux et d’entrées/sorties de la zone tampon à une date au moins égale à celle de la levée de l’APDI du dernier foyer de l’ensemble des zones réglementées qu’encercle la zone tampon (cf. annexe 2 : levée des zones règlementées)".Toutefois nous souhaitons examiner l’opportunité d’une éventuelle levée progressive : il apparaît en effet que certaines zones ne connaissent plus de foyers depuis plusieurs semaines et leur situation épidémiologique pourrait être différenciée d'autres zones qui ont connu des foyers plus récemment. Par ailleurs, alors que dans certaines zones des foyers sont apparus entre 10 et 20km autour des foyers, cela n’est pas le cas, par exemple dans les Pyrénées Atlantiques et le Gers. Du fait des nombreux abattages à titre préventif qui ont été effectués autour des foyers, la densité d'animaux a fortement chuté dans certains territoires, il resterait 35000 canards dans les Landes et 200 000 dans la zone tous départements compris. Cet examen s’intéresse également aux conditions dans lesquelles, après la levée de la zone tampon, des remises en place sont possibles.Aussi les questions que je souhaite vous poser sont les suivantes : - Quelles sont les conditions requises pour envisager la levée de certaines zones stabilisées de la grande zone tampon du sud-ouest ? - Sous quelles modalités peut-il être envisagé cette levée partielle ? - Quelles seraient les conditions pour envisager un repeuplement des élevages dans ces zones ? »