Introgressive hybridisation between domestic pigs (Sus scrofa domesticus) and endemic Corsican wild boars (S. s. meridionalis): effects of human-mediated interventions.

Owing to the intensified domestication process with artificial trait selection, introgressive hybridisation between domestic and wild species poses a management problem. Traditional free-range livestock husbandry, as practiced in Corsica and Sardinia, is known to facilitate hybridisation between wild boars and domestic pigs (Sus scrofa). Here, we assessed the genetic distinctness and genome-wide domestic pig ancestry levels of the Corsican wild boar subspecies S. s. meridionalis, with reference to its Sardinian conspecifics, employing a genome-wide single nucleotide polymorphism (SNP) assay and mitochondrial control region (mtCR) haplotypes. We also assessed the reliance of morphological criteria and the melanocortin-1 receptor (MC1R) coat colour gene to identify individuals with domestic introgression. While Corsican wild boars showed closest affinity to Sardinian and Italian wild boars compared to other European populations based on principal component analysis, the observation of previously undescribed mtCR haplotypes and high levels of nuclear divergence (Weir's θ > 0.14) highlighted the genetic distinctness of Corsican S. s. meridionalis. Across three complementary analyses of mixed ancestry (i.e., STRUCTURE, PCADMIX, and ELAI), proportions of domestic pig ancestry were estimated at 9.5% in Corsican wild boars, which was significantly higher than in wild boars in Sardinia, where free-range pig keeping was banned in 2012. Comparison of morphologically pure- and hybrid-looking Corsican wild boars suggested a weak correlation between morphological criteria and genome-wide domestic pig ancestry. The study highlights the usefulness of molecular markers to assess the direct impacts of management practices on gene flow between domestic and wild species.

Identification and molecular characterization of Echinococcus canadensis G6/7 in dogs from Corsica, France.

Recent surveys at slaughterhouses confirmed the presence of three different species of Echinococcus granulosus sensu lato in France: E. granulosus sensu stricto, E. ortleppi, and E. canadensis G6/7. The latter species was only identified on the French Mediterranean island of Corsica, with a high prevalence in pigs and wild boar. In order to investigate the life cycle of E. canadensis in this region, dog feces were collected in 31 municipalities, mainly from individual kennels. The analysis of fecal samples from 259 dogs by multiplex real-time PCR shows no infection by E. granulosus sensu stricto, but three dogs were infected by E. canadensis G6/7. Genetic analyses of mitochondrial genes (cox1, nad1, nad3, atp6) revealed in two dogs a haplotype previously identified in pigs. The third dog was infected by a new haplotype differing only from the two others from dogs by two mutations in the nad3 gene. This latter haplotype is genetically closer to those identified in pigs rather than those from wild boars. Analysis of questionnaires completed by the owners revealed that the sampled dog population was almost exclusively composed of hunting dogs that had been infrequently dewormed. Most of the owners (78%) leave carcasses of hunter-harvested wild boar in close proximity to their dogs. Nevertheless, genetic results seem to indicate that the three dogs were infected due to their consumption of a pig's infected viscera following home slaughtering. This study confirms the role of dogs as definitive hosts of E. canadensis G6/7 in Corsica. Further molecular studies, notably in human cases, are needed to assess the zoonotic impact of E. canadensis G6/7 in this region.

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.

Detection of porcine enteric viruses (Kobuvirus, Mamastrovirus and Sapelovirus) in domestic pigs in Corsica, France.

Many enteric viruses are found in pig farms around the world and can cause death of animals or important production losses for breeders. Among the wide spectrum of enteric viral species, porcine Sapelovirus (PSV), porcine Kobuvirus (PKoV) and porcine Astrovirus (PAstV) are frequently found in pig feces. In this study we investigated sixteen pig farms in Corsica, France, to evaluate the circulation of three enteric viruses (PKoV, PAstV-1 and PSV). In addition to the three viruses studied by RT-qPCR (908 pig feces samples), 26 stool samples were tested using the Next Generation Sequencing method (NGS). Our results showed viral RNA detection rates (i) of 62.0% [58.7-65.1] (n = 563/908) for PSV, (ii) of 44.8% [41.5-48.1] (n = 407/908) for PKoV and (iii) of 8.6% [6.8-10.6] (n = 78/908) for PAstV-1. Significant differences were observed for all three viruses according to age (P-value = 2.4e-13 for PAstV-1; 2.4e-12 for PKoV and 0.005 for PSV). The type of breeding was significantly associated with RNA detection only for PAstV-1 (P-value = 9.6e-6). Among the 26 samples tested with NGS method, consensus sequences corresponding to 10 different species of virus were detected. This study provides first insight on the presence of three common porcine enteric viruses in France. We also showed that they are frequently encountered in pigs born and bred in Corsica, which demonstrates endemic local circulation.

Tuberculosis in the wild boar: Frequentist and Bayesian estimations of diagnostic test parameters when Mycobacterium bovis is present in wild boars but at low prevalence.

The Eurasian wild boar (Sus scrofa) is increasingly considered as a relevant actor in the epidemiology of animal tuberculosis (TB). Therefore, monitoring TB in this species is key when establishing comprehensive control schemes for this disease still present in Europe. No data are available on direct and indirect TB diagnostic methods in wild boars in epidemiological contexts where TB is endemic in cattle and detected in wild boars at low prevalence. We aimed to estimate and compare sensitivity and specificity values for bacterial culture, PCR and three commercial ELISAs, i.e. the TB ELISA-VK (using the bPPD antigen), INgezim TB Porcine and IDEXX M. bovis Ab Test (both using the MPB83 and MPB70 antigens), under field conditions in France. We used frequentist methods, with bacteriology as the gold standard, and a Bayesian formulation of the latent class analysis (LCA), without using a gold standard. Submandibular lymph nodes and sera from 495 wild boars hunter-harvested in three endemic areas (Aquitaine region, Côte d'Or region, and Corsica region) were collected between 2014 and 2016. Only eight individuals were positive for M. bovis by bacteriology (1.61%; CI95% 0.70-3.51%). The LCA method provided high specificities (99.2%; CI95% 98.2-99.8% for INgezim TB Porcine and 99.7%; CI95% 98.8-100% for IDEXX M. bovis Ab Test) and sensitivities (78.5%; CI95% 65.1-88.8% for INgezim TB Porcine and 83.9%; CI95% 58.9-97.2% for IDEXX M. bovis Ab Test) for both ELISAs using the MPB83 and MPB70 antigens. Bacterial culture showed limited sensitivity (42.8%; CI95% 19.0-70.6%), estimated as the probability of a positive result in an animal exposed to M. bovis. PCR and ELISA using the bPPD antigens demonstrated high specificities, and sensitivities intermediates between culture and the ELISAs using the MPB83 and MPB70 antigens. These results suggest that ELISA tests using the MPB83 and MPB70 antigens are useful to detect and monitor TB exposure of wild boar populations in field conditions in France.

Drastic decline of hepatitis E virus detection in domestic pigs after the age of 6 months, Corsica, France.

Suidae is an important reservoir of hepatitis E virus (HEV) and a source of transmission to humans (direct contact or via consumption of meat products). Our goal was to characterize the epidemiology of HEV infecting domestic pigs in Corsica Island, a French region hyperendemic for HEV. In Corsica, traditional extensive (or semi-extensive) outdoor pig farming system is common. Sixteen farms were selected according to location and breeding system. Individual pig faeces samples were collected and qRT-PCR for detecting HEV RNA was performed. Nucleic acids from HEV-positive samples were amplified using specific ORF2 genotyping system. The genotype and subtype of the Corsican HEV sequences were determined by phylogenetic analysis. Among the 919 porcine faeces samples tested 9.2% (n = 85) were positive. The presence of viral RNA was correlated with (a) age (>6 months) Adjusted Odd Ratio (AOR) 0.25 [0.068-0.90] p = .032; 3-4 months AOR = 4.94 [2.30-10.62] p = .000043) with the logistic regression model with a random effect at the farm level. Among the 85 positive samples, 83 belonged to genotype 3c and two to genotype 3f. The highest prevalence was observed in the 3-4 months age group and older age (>6 months) was negatively related to HEV infection and this suggests that traditional breeding with a late slaughter age may limit the risk of transmission to humans. A kinetic study of pigs from birth to slaughtering would allow to ensure that the type of traditional breeding reported here is very favourable to the absence of the virus in slaughtered pigs and in pork products.

Serological survey of influenza A viruses in domestic and wild Suidae in Corsica (France), a Mediterranean island environment.

Corsica is a mountainous French island in the north-western Mediterranean Sea. It is a rural area, where pig farming is a major economic activity. Although no acute respiratory outbreaks due to swine influenza A viruses (swIAVs) have ever been reported in this free-ranging pig breeding system, influenza A viruses (IAVs) could be circulating within this pig population. A serological study was conducted as a first approach to domestic pigs and wild boars. Serum samples from 543 pigs raised on 91 different farms were collected during the 2013-2014 slaughtering season, and 279 sera from wild boars were obtained over four hunting seasons (between 2009 and 2014). They were first analysed by ELISA and then IAV positive and doubtful sera were subjected to haemagglutination inhibition tests using antigens representative of the four major enzootic swIAV lineages in Europe, i.e. avian-like swine H1N1 (H1avN1), pandemic-like swine H1N1 (H1N1pdm), H1N2 and H3N2. According to the ELISA results, 26.4% (CI95%: 17.7-36.7%) of herds had at least one positive animal (positive or doubtful by ELISA) and 12.4% (CI95%: 7.8-19.8%) of the pigs tested positive. Using the test characteristics (sensitivity and specificity), the true seroprevalence among Corsican pigs was estimated to be 16.4% (95% CI: 9.9-26.3). Antibodies directed against two different viral lineages were identified: H1N1pdm (in 66.2% and 45.8% of the IAV positive pigs and farms respectively) and H1avN1 (15.0% and 20.8% respectively). Evidence of exposure to viruses from two distinct lineages were detected on a single farm but in two different animals. Among the wild boars, 1.4% (CI95%: 0.4-3.6%) tested positive by ELISA and antibodies against the same two viruses were detected. Altogether, these results suggest that swIAVs from at least two different lineages are circulating among Corsican pigs, i.e. the H1N1pdm virus, probably introduced during the 2009 pandemic, and the H1avN1 virus, which is the most frequent swIAV in Europe. The low frequency of positive results observed in the Corsican wild boars hunted suggests that they would not play a major role in IAV dispersion dynamics on the island.

First Identification and Genomic Characterization of a Porcine Sapelovirus from Corsica, France, 2017.

We report the isolation and genomic characterization of a Sapelovirus A strain, or porcine sapelovirus (PSV), from a diarrheic Corsican piglet in France. It shares 87% nucleotide identity with a 2014 German isolate.

Aujeszky's Disease and Hepatitis E Viruses Transmission between Domestic Pigs and Wild Boars in Corsica: Evaluating the Importance of Wild/Domestic Interactions and the Efficacy of Management Measures.

Wildlife species as reservoirs of infectious pathogens represent a serious constraint in the implementation of disease management strategies. In the Mediterranean island of Corsica, the dynamics of hepatitis E virus (HEV) and Aujeszky's disease virus (ADV) are suspected to be influenced by interactions between wild and domestic pigs. To improve our understanding of these influences, we first compared the seroprevalences of both viruses in domestic pig populations from different locations with contrasted levels of wild-domestic interactions, ADV vaccination, biosafety, and farm husbandry. Second, we performed an analysis at a more restricted geographical scale, to assess the matching of ADV or HEV prevalence between sympatric wild boar and outdoor pig farms most exposed to interactions with wildlife. Logistic models were adjusted to the observed data. A high seroprevalence of HEV (>80%) and ADV (40%) in pigs, with no significant difference according to the region, confirms that both pathogens are enzootic in Corsica. Vaccination against ADV had a strong protective effect, even when performed voluntarily by farmers. Farm biosafety had an additional effect on pigs' exposure, suggesting that contact between wild boars and pigs were involved in disease transmission. A strong correlation in HEV seroprevalence was observed between pigs and wild boars that were in close contact, and significantly lower seroprevalence was observed in pigs when they had little contact with wild boars due to spatial segregation. These results suggest a regular HEV circulation between sympatric wild boar and domestic pigs. The high HEV seroprevalence observed in domestic pigs (>80%) suggests a spillover of the virus from domestic to wild populations through environmental contamination, but this hypothesis has to be confirmed. Conversely, even though avoiding sows' release on pasture during estrus showed some protecting effect in the free ranging pig farms regarding ADV, ADV seroprevalence was not dependent on the swine populations (wild or domestic) or on the wild-domestic spatial overlap, suggesting two quasi-separate enzootic cycles. This information will prove useful for designing more efficient disease management strategies in Corsica and similar contexts.

Questionnaire-Based Assessment of Wild Boar/Domestic Pig Interactions and Implications for Disease Risk Management in Corsica.

Wild boars and domestic pigs belong to the same species (Sus scrofa). When sympatric populations of wild boars, feral pigs, and domestic pigs share the same environment, interactions between domestic and wild suids (IDWS) are suspected to facilitate the spread and maintenance of several pig pathogens which can impact on public health and pig production. However, information on the nature and factors facilitating those IDWS are rarely described in the literature. In order to understand the occurrence, nature, and the factors facilitating IDWS, a total of 85 semi-structured interviews were implemented face to face among 25 strict farmers, 20 strict hunters, and 40 hunting farmers in the main traditional pig-farming regions of Corsica, where IDWS are suspected to be common and widespread. Different forms of IDWS were described: those linked with sexual attraction of wild boars by domestic sows (including sexual interactions and fights between wild and domestic boars) were most frequently reported (by 61 and 44% of the respondents, respectively) in the autumn months and early winter. Foraging around common food or water was equally frequent (reported by 60% of the respondents) but spread all along the year except in winter. Spatially, IDWS were more frequent in higher altitude pastures were pig herds remain unattended during summer and autumn months with limited human presence. Abandonment of carcasses and carcass offal in the forest were equally frequent and efficient form of IDWS reported by 70% of the respondents. Certain traditional practices already implemented by hunters and farmers had the potential to mitigate IDWS in the local context. This study provided quantitative evidence of the nature of different IDWS in the context of extensive commercial outdoor pig farming in Corsica and identified their spatial and temporal trends. The identification of those trends is useful to target suitable times and locations to develop further ecological investigations of IDWS at a finer scale in order to better understand diseases transmission patterns between populations and promote adapted management strategies.

Assessment of Domestic Pigs, Wild Boars and Feral Hybrid Pigs as Reservoirs of Hepatitis E Virus in Corsica, France.

In Corsica, extensive pig breeding systems allow frequent interactions between wild boars and domestic pigs, which are suspected to act as reservoirs of several zoonotic diseases including hepatitis E virus (HEV). In this context, 370 sera and 166 liver samples were collected from phenotypically characterized as pure or hybrid wild boars, between 2009 and 2012. In addition, serum and liver from 208 domestic pigs belonging to 30 farms were collected at the abattoir during the end of 2013. Anti-HEV antibodies were detected in 26% (21%-31.6%) of the pure wild boar, 43.5% (31%-56.7%) of hybrid wild boar and 88% (82.6%-91.9%) of the domestic pig sera. In addition, HEV RNA was detected in five wild boars, three hybrid wild boars and two domestic pig livers tested. Our findings provide evidence that both domestic pig and wild boar (pure and hybrid) act as reservoirs of HEV in Corsica, representing an important zoonotic risk for Corsican hunters and farmers but also for the large population of consumers of raw pig liver specialties produced in Corsica. In addition, hybrid wild boars seem to play an important ecological role in the dissemination of HEV between domestic pig and wild boar populations, unnoticed to date, that deserves further investigation.

Ticks (Acari: Ixodidae) infesting cattle and some other domestic and wild hosts on the French Mediterranean island of Corsica.

BACKGROUND: Corsica is a mountainous French island in the north-western Mediterranean presenting a large diversity of natural environments where many interactions between domestic animals and wild fauna occur. Despite a favourable context for ticks and tick-borne diseases (TBDs), the tick fauna of Corsica has not systematically been investigated. METHODS: For one year (May 2014-May 2015), a survey of ticks infesting cattle was performed in the three Corsican cattle slaughterhouses. Two of these were visited monthly and one quarterly; the ticks were manually collected, just after flaying. Ticks were identified on their morphology; when necessary, some specimens were also molecularly identified by sequencing mitochondrial cox1 (cytochrome c oxidase subunit 1) and 16S ribosomal RNA genes and ITS2 (internal transcribed spacer 2). During the same period, ticks from other domestic animals (small ruminants, horses, domestic carnivores) and wild animals (wild boars, mouflons, deer) were occasionally collected. RESULTS: A total of 1,938 ticks was collected from 264 of 418 cattle examined, reared in 86 different localities. Eight tick species were found infesting cattle: Rhipicephalus bursa (56.1 %), Hyalomma marginatum (21.5 %), Hy. scupense (8.7 %), Ixodes ricinus (5.7 %), Haemaphysalis punctata (4.8 %), Rh. sanguineus (sensu lato) (2.3 %), Rh. (Boophilus) annulatus (0.7 %) and Dermacentor marginatus (0.2 %). The cattle infestation rate remained high all year (more than 50 %). Several tick species showed seasonal variation of their activity. From other Corsican animals 1,196 ticks were collected. Comparing ticks collected from cattle with those found on other animals, several host preferences were shown. A noteworthy record is that of a few Ha. sulcata on mouflons which were mainly infested by Rh. bursa. CONCLUSION: The Corsican tick fauna is characterized by typical Mediterranean species (Rh. bursa and Hy. marginatum), but the mild climate and diversified environment provide satisfactory habitats both for species usually found in dry areas (Hy. scupense) and species usually collected in humid areas (I. ricinus).