Nicolas Rose

Background: Swine influenza A viruses (swIAV) are highly contagious zoonotic pathogens that cause an acute respiratory infection in pigs, presenting substantial economic and health risks for animals and farmers. This drives the pig industry and stakeholders in animal health to monitor swIAV in livestock. In the 10 years prior to the 2009 flu pandemic, H1 _av N1 (HA-1C.2.1) and H1 _hu N2 (HA-1B.1.2.3) circulated in pig herds in France while H3N2 was not detected. The H1N1 _pdm (HA-1A.3.3.2) lineage became enzootic after its introduction. In 2020, a new H1 _av N2 genotype (HA-1C.2.4) emerged, altering the frequencies of enzootic swIAV lineages. To support our knowledge built on event-based surveillance and gain information on swIAV infections, serological studies were conducted. Three independent surveys were performed nationally in 2008 and in 2018 (before and after the A/H1N1pdm09 pandemic, respectively), and in North West in 2022 (after the H1 _av N2 emergence in Brittany area). These surveys aimed to estimate swIAV prevalence in livestock using ELISA on fattening pigs and hemagglutination inhibition (HI) tests to determine the relative frequencies of different swIAV lineages. Results: The national seroprevalence estimated by ELISA was 91% [83–96] _CI95 in 2008, and 87% [81–92] _CI95 in 2018. In 2022, seroprevalence in the North West reached 91% [73–97] _CI95 . In each survey, antibodies against several swIAV subtypes were detected simultaneously by HI tests in approximately 25% of ELISA-positives batches. In 2008, anti-HA-1C.2.1 antibodies were widespread, while anti-HA-1B.1.2.3 antibodies were found in most regions except for the South West. In contrast, H3N2 seroprevalence was very low, restricted to the North East. By 2018, anti-HA-1C.2.1 antibodies remained the most prevalent and anti-H3 antibodies the weakest, but anti-HA-1B.1.2.3 prevalence had strongly decreased, while anti-HA-1A.3.3.2 antibodies were detected nationwide. In 2022, the North West showed the highest seroprevalence for H1 _av N1 (HA-1C.2.1), followed by H1 _av N2 (HA-1C.2.4), H1N1 _pdm and finally H1 _hu N2. Conclusions: These surveys revealed a high and sustained swIAV seroprevalence, particularly in areas with a high density of pigs. They also highlighted changes in the relative frequencies of anti-HA antibodies, reflecting viral emergence and dynamics. Despite challenges in interpreting HI test results, the surveys provided valuable data, uncovering rare events (e.g. H3N2), potential undiagnosed asymptomatic cases (e.g. H1N1 _pdm ), and co-circulating viruses, which may lead to genomic reassortments and the emergence of new reassortant viruses.

African swine fever (ASF) has devastating effects on swine production, farmer livelihood, animal welfare, and biodiversity. Extremely difficult to control, epidemic management is further complicated when spillover between domestic pig and wild boar populations is suspected. To quantify ASF viral transmission between domestic pigs and wild boar, a spatially-explicit stochastic mechanistic model was constructed using village centroids to represent aggregated backyard pig herds and a hexagonal raster of forest coverage to represent wild boar abundance. The model was parameterized to the initial six months of the ongoing Romanian epidemic through approximate Bayesian computation. It was estimated that a median of 69.4% (interquartile range: 53.0–80.0%) of domestic pig herd cases came from other infected domestic pig herds while 20.4% (11.2–33.8%) originated from infected wild boar sources, and 8.4% (4.7–14.2%) stemmed from external sources not explicitly represented. Also, 31.9% of infected wild boar habitat (16.7–56.2%) originated from domestic pig herds and 68.1% (43.8–83.3%) came from neighboring infected wild boar populations. Furthermore, it was found that habitats with a forest coverage greater than 15% were 2.6 times more infectious and 5.3 times more susceptible than other habitats. All alternative control scenarios, including culling domestic pig herds upon local domestic pig or wild boar case detection, improved epidemic outcomes, with the greatest decrease in final epidemic size being observed from the reactive culling of entire villages following case detection. These results can be used to further inform policy recommendations in ASF-epidemic regions. Significance Statement The current African swine fever (ASF) pandemic is devastating to affected nations, and quantifying transmission parameters is critical to informing control strategies. Disease spillover between wild and domestic hosts further complicates control efforts, yet the influence of spillover events on epidemic propagation remains unknown. Using the context of Romania—one of the European nations with the most severe epidemic and where spillover transmission is strongly suspected—we show that targeting spillover mechanisms is critical for achieving holistic disease control, and then demonstrate the impact of alternative control scenarios had they been enacted. These results can inform control strategy policy decisions in the many nations at-risk for or actively experiencing ASF epidemics.

Background: The seroprevalence of SARS-CoV-2 infection in the French population was estimated with a representative, repeated cross-sectional survey based on residual sera from routine blood testing. These data contained no information on infection or vaccination status, thus limiting the ability to detail changes observed in the immunity level of the population over time. Objective: Our aim is to predict the infected or vaccinated status of individuals in the French serosurveillance survey based only on the results of serological assays. Reference data on longitudinal serological profiles of seronegative, infected, and vaccinated individuals from another French cohort were used to build the predictive model. Methods: A model of individual vaccination or infection status with respect to SARS-CoV-2 obtained from a machine learning procedure was proposed based on 3 complementary serological assays. This model was applied to the French nationwide serosurveillance survey from March 2020 to March 2022 to estimate the proportions of the population that were negative, infected, vaccinated, or infected and vaccinated. Results: From February 2021 to March 2022, the estimated percentage of infected and unvaccinated individuals in France increased from 7.5% to 16.8%. During this period, the estimated percentage increased from 3.6% to 45.2% for vaccinated and uninfected individuals and from 2.1% to 29.1% for vaccinated and infected individuals. The decrease in the seronegative population can be largely attributed to vaccination. Conclusions: Combining results from the serosurveillance survey with more complete data from another longitudinal cohort completes the information retrieved from serosurveillance while keeping its protocol simple and easy to implement.

BACKGROUND The seroprevalence of SARS-CoV-2 infection in the French population was estimated with a representative, repeated cross-sectional survey based on residual sera from routine blood testing. These data contained no information on infection or vaccination status, thus limiting the ability to detail changes observed in the immunity level of the population over time. OBJECTIVE Our aim is to predict the infected or vaccinated status of individuals in the French serosurveillance survey based only on the results of serological assays. Reference data on longitudinal serological profiles of seronegative, infected, and vaccinated individuals from another French cohort were used to build the predictive model. METHODS A model of individual vaccination or infection status with respect to SARS-CoV-2 obtained from a machine learning procedure was proposed based on 3 complementary serological assays. This model was applied to the French nationwide serosurveillance survey from March 2020 to March 2022 to estimate the proportions of the population that were negative, infected, vaccinated, or infected and vaccinated. RESULTS From February 2021 to March 2022, the estimated percentage of infected and unvaccinated individuals in France increased from 7.5% to 16.8%. During this period, the estimated percentage increased from 3.6% to 45.2% for vaccinated and uninfected individuals and from 2.1% to 29.1% for vaccinated and infected individuals. The decrease in the seronegative population can be largely attributed to vaccination. CONCLUSIONS Combining results from the serosurveillance survey with more complete data from another longitudinal cohort completes the information retrieved from serosurveillance while keeping its protocol simple and easy to implement.

The circulation of livestock pathogens in the pig industry is strongly related to animal movements. Epidemiological models developed to understand the circulation of pathogens within the industry should include the probability of transmission via between-farm contacts. The pig industry presents a structured network in time and space, whose composition changes over time. Therefore, to improve the predictive capabilities of epidemiological models, it is important to identify the drivers of farmers’ choices in terms of trade partnerships. Combining complex network analysis approaches and exponential random graph models, this study aims to analyze patterns of the swine industry network and identify key factors responsible for between-farm contacts at the French scale. The analysis confirms the topological stability of the network over time while highlighting the important roles of companies, types of farm, farm sizes, outdoor housing systems and batch-rearing systems. Both approaches revealed to be complementary and very effective to understand the drivers of the network. Results of this study are promising for future developments of epidemiological models for livestock diseases. This study is part of the One Health European Joint Programme: BIOPIGEE.

Lameness and foot disorders are major health and welfare issues in intensive swine production systems. They are exacerbated when sows are housed in large groups on slatted concrete floors during gestation. Our study aimed to assess the effect of rubber mats in the lying area of the gestation pen on lameness and leg health in gestating sows housed in large pens in commercial conditions. The study was conducted on three commercial farms over two successive gestations. A total of 582 Large White × Landrace sows, housed in 10 static groups, were enrolled: 5 groups in pens with rubber mats and 5 groups on slatted concrete floors. Lameness, bursitis, leg injuries, claw growth defects and claw lesions were measured at the beginning, middle and end of each gestation period. The rubber mats decreased the risk of suffering from bursitis, but had no effect on the risk of lameness, leg injuries, claw growth defects or claw lesions. Sows housed on rubber mats were heavily soiled compared with those on slatted concrete floors because the mats were not perforated for slurry evacuation. Locomotion disorders and foot lesions remained prevalent despite the rubber mats in the lying area of the gestation pens, but adding rubber mats in service rooms and farrowing crates may produce better results.

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.