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Remerciements : Institut CARNOT AgriFoodTransition; National audience; To date, host-virus interactions have been studied mainly in cell cultures and/or animal models. These approaches come up against two problems: i) methodological, usually related to using immortalized cell lines, which can differ greatly from the target cells of the virus, and ii) ethical, related to experimenting with animals, which can induce varying degrees of symptoms and cause suffering and death. The recent development of organoids has made it possible to develop ex vivo models whose experimental conditions are significantly closer to physiological conditions. Using organoids makes it possible to plan to decrease animal experimentation greatly, in line with the 3Rs principle (Reduction, Refinement, Replacement), and each animal can potentially produce thousands of organoids from different tissues. The Viral Genetics and Biosafety Unit applies the porcine organoid system developed locally as part of the PigOrg project (of INRAE, ANSES and INSERM, funded by the Carnot Agrifood Transition Institute) to models of enteric coronavirosis in piglets, which has a strong impact on the pig industry. Here, we used the porcine transmissible gastroenteritis virus (TGEv) as a model, for which several strains of varying virulence exist and which can be cultivated on immortalized cells, to establish protocols of infections of different organoids(jejunum, duodenum, and ileum). Infections seem more effective for the jejunum than for the duodenum or ileum, and for viruses isolated on cells than on organ homogenate. This organoid system, which connects in vitro and in vivo conditions, will open novel and original perspectives into understanding the physiopathology of virus infections, especially deciphering host-pathogen interactions, without always needing to rely on extensive animal experiments.

Individual and/or raw data obtained in this study are available on request from the corresponding author.; International audience; In autumn/winter 2016–2017, HPAI-H5N8 viruses belonging to the A/goose/Guandong/1/1996 (Gs/Gd) lineage, clade 2.3.4.4b, were responsible for outbreaks in domestic poultry in Europe, and veterinarians were requested to reinforce surveillance of pigs bred in HPAI-H5Nx confirmed mixed herds. In this context, ten pig herds were visited in southwestern France from December 2016 to May 2017 and serological analyses for influenza A virus (IAV) infections were carried out by ELISA and hemagglutination inhibition assays. In one herd, one backyard pig was shown to have produced antibodies directed against a virus bearing a H5 from clade 2.3.4.4b, suggesting it would have been infected naturally after close contact with HPAI-H5N8 contaminated domestic ducks. Whereas pigs and other mammals, including humans, may have limited sensitivity to HPAI-H5 clade 2.3.4.4b, this information recalls the importance of implementing appropriate biosecurity measures in pig and poultry farms to avoid IAV interspecies transmission, a prerequisite for co-infections and subsequent emergence of new viral genotypes whose impact on both animal and human health cannot be predicted.

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.

Ornithodoros soft ticks are the only known vector and reservoir of the African swine fever virus, a major lethal infectious disease of Suidae. The co-feeding event for virus transmission and maintenance among soft tick populations has been poorly documented. We infected Ornithodoros moubata, a known tick vector in Africa, with an African swine fever virus strain originated in Africa, to test its ability to infect O. moubata through co-feeding on domestic pigs. In our experimental conditions, tick-to-tick virus transmission through co-feeding failed, although pigs became infected through the infectious tick bite.

Additional file 2: Figure S1. Plasmid used for the standard curve for qPCR. Beta-actin primers are shown in cyan and the beta-actin probe in yellow. The ASFV-VP72 gene primers are shown in green and the ASFV-VP72 probe in red.

Additional file 1: Table S1. The number and the stage of ticks used for the study.

Here, we report the coding-complete genome sequence of African swine fever (ASF) virus strain Liv13/33, isolated from experimentally infected pigs and Ornithodoros moubata ticks. The 11 sequences that we obtained harbored no notable differences to each other, and all of them were closely related to the genome sequence of the Mkuzi 1979 strain of genotype I.

African swine fever (ASF) is a lethal viral disease that has spread to Europe and Asia. Infected tick bite is one of the known routes of ASF virus (ASFV) transmission. Some species in the Ornithodoros genus are competent vector for ASFV. However, their role in transmission and maintenance of ASFV currently circulating in Europe remains to be determined. Three Ornithodoros species were selected for transmissions trials: O. moubata (known vector in Africa), O. erraticus (reported vector in Portugal) and O. verrucosus (suspected vector in Ukraine). Four ASFV strains were selected (Liv13/33, OurT88/1, Georgia2007/1 and Ukr12/Zapo) and matched to tick species, which yielded five pairs for vector competence testing: O. moubata-Liv13/33 (OmL), O. moubata-Georgia2007/1 (OmG), O. erraticus-OurT88/1 (OeO), O. erraticus-Georgia2007/1 (OeG) and O. verrucosus-Zapo (OvZ). Tick infection was attempted by feeding on viraemic pigs then re-feeding two to eight months later on healthy pigs to test for virus transmission ability. Only O. moubata was able to transmit ASFV. For other pairs, ticks were crushed and the homogenate of supernatant was injected in naïve pigs. All inoculated pigs developed clinical signs and viremia within a week, confirming ASFV was infectious in these tick-virus pairs. For the first time, the vectorial competence of O. erraticus and O. verrucosus for European strains was tested under experimental conditions and showed the ability of these both ticks to keep the virus infectious after feeding on viraemic pig. These experiments reinforce the importance of studying underlying mechanisms of soft tick vector competence for ASFV.

La Peste Porcine Africaine (PPA) est une maladie historiquement présente en Afrique, mais a été ré-introduite en 2007 en Europe par la Géorgie. Depuis, la PPA s'est propagée en Russie et en Europe de l'Est mais a également atteint en 2018 la Belgique et la Chine. La PPA est une maladie virale infectieuse causée par le virus de la peste porcine africaine qui provoque une forte létalité, pouvant atteindre 100% pour les souches hautement virulentes, et contre laquelle ni vaccin ni traitement thérapeutique existe. Le virus de la PPA infecte uniquement les suidés et les tiques molles du genre Ornithodoros. Une des voies connues de transmission aux porcs est la piqûre de tique infectée. Le rôle des tiques du genre Ornithodoros dans la vectorisation et le maintien de la PPA en Afrique a été démontré, cependant leur rôle en Europe reste encore à déterminer. Dans notre étude, 3 espèces du genre Ornithodoros ont été sélectionnées pour des expériences de transmission : O. moubata (vecteur connu en Afrique), O. erraticus (présente au Portugal) et O. verrucosus (présente en Ukraine). Les 4 souches virales hautement pathogènes étudiées proviennent d'Afrique (Liv13/33), d'Europe de l'Est (Georgia2007/1), du Portugal (OurT88/1) et d'Ukraine (Ukr12/Zapo). Différentes associations tique-virus ont été testées : O. moubata-Liv13/33 (OmL), O. moubata-Georgia2007/1 (OmG), O. erraticus-OurT88/1 (OeO), O. erraticus-Georgia2007/1 (OeG) et O. verrucosus-Zapo (OvZ). Les tiques ont étés infectées sur porc virémique via un repas sanguin puis 2 à 8 mois après infection des tiques, des essais de transmission sur porc ont été réalisés. Pour la première fois, la compétence vectorielle des tiques O. moubata pour les souches virales Liv13/33 et Georgia2007/1 a pu être démontrée expérimentalement. Pour les autres couples n'ayant pas transmis le virus, une injection de broyat de ces tiques a induit la PPA chez les porcs, confirmant ainsi qu'elles étaient infectées et que le virus était bien infectieux. Pour comprendre pourquoi certains couples transmettent et d'autres pas, des titrages viraux à partir des tiques ont été réalisés montrant que certaines souches virales sont plus aptes à se multiplier ou à se maintenir chez certaines espèces de tiques. En complément, des localisations virales ont été réalisées chez les tiques, ce qui a permis de montrer des différences de localisations entre certains couples tique-virus, notamment entre OmG et OeG. Enfin, la capacité des tiques à transmettre le virus à leur descendance et ainsi à construire une colonie de tiques infectées a également été étudiée. Ces résultats montrent que la vectorisation du virus de la PPA semble dépendre de plusieurs facteurs, tant de l'espèce de la tique que de la souche virale, ce qui renforcent l'importance de l'étude des mécanismes sous-jacents de la compétence vectorielle des tiques molles pour la PPA.

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Additional file 1. BALF cell count. Cell concentrations in BALF were counted using a haemocytometer with Trypan blue staining. All data are reported as the mean (±SE) of results obtained for the pigs in the Control or Finistere groups (n = 5 in each group) or the surviving pigs (n = 5–8) in the Lena group. * at 22 dpi, the cell concentrations for Control and Finistere group were underestimated due to the high level of mucus in the BALF for the animals of these groups.