Truncation of the NS1 protein converts a low pathogenic avian influenza virus into a strong interferon inducer in duck cells

The NS1 protein of influenza A viruses is known as a nonessential virulence factor inhibiting type I interferon (IFN) production in mammals and in chicken cells. Whether NS1 inhibits the induction of type I IFNs in duck cells is currently unknown. In order to investigate this issue, we used reverse genetics to generate a virus expressing a truncated NS1 protein. Using the low pathogenic avian influenza virus A/turkey/Italy/977/1999 (H7N1) as a backbone, we were able to rescue a virus expressing a truncated NS1 protein of 99 amino acids in length. The truncated virus replicated poorly in duck embryonic fibroblasts, but reached high titers in the mammalian IFN-deficient Vero cell line. Using a gene reporter system to measure duck type I IFN production, we showed that the truncated virus is a potent inducer of type I IFN in cell culture. These results show that the NS1 protein functions to prevent the induction of IFN in duck cells and underline the need for a functional NS1 protein in order for the virus to express its full virulence

Analyse moléculaire de la souche atténuée vaccinale SG33 du virus myxomateux : à la recherche des gènes perdus

Le virus myxomateux (VM) est un poxvirus à spectre d'hôte étroit, agent de la myxomatose, une maladie majeure du lapin européen oryctolagus cuniculus. L'analyse informatique des séquences nucléotidiques et protéiques a permis d'émettre des hypothèses fonctionnelles. Deux gènes, serp2 et serp3, codent pour des protéines de la super-famille des Serpines (pour Serine Proteinase INhibitor) qui regroupe des protéines aux fonctions biologiques très variées : coagulation, fibrinolyse, inhibition du complément et inflammation. Trois gènes en tandem codent pour des protéines à répétition ankyrine qui interviennent dans des interactions protéine-protéine et sont présentes dans un grand nombre de protéines de proxvirus et qui réguleraient notamment le spectre tissulaire des virus. Ces facteurs ont été nommés MHR (Myxoma Host Range)-1, -2 et -3. Le dernier gène identifié code pour une protéine comportant un motif zinc finger, appartenant à la classe des motifs LAP (Leukemia Associated Protein) et baptisée MV-LAP. MV-LAP est notamment homologue aux facteurs K3 et K5,codés par l'herpesvirus HHV-8, associé au sarcome de Kaposi. Ces deux facteurs sont impliqués dans la diminution de l'expression du CMH 1 à la surface des cellules infectées. La caractérisation fonctionnelle de chacun de ces facteurs a confirmé leur implication dans le pouvoir pathogène du VM à des degrés divers. Les conséquences sur l'immunogénicité, l'innocuité et la stabilité de la souche vaccinale SG33 sont discutées

Futur campus santé de Sion: vers une collaboration entre services documentaires? : état des lieux et pistes de réflexion

La HES-SO Valais Wallis a pour projet de construire à l’horizon 2020 un nouveau bâtiment regroupant ses formations dans le domaine de la santé (soins infirmiers et physiothérapie) et du social (filières de niveau école supérieure dans l’éducation de l’enfance et l’action socio-professionnelle). Le choix de la localisation de cette nouvelle infrastructure s’est porté sur le site de Champsec à Sion qui regroupe actuellement plusieurs institutions sanitaires valaisannes (Hôpital du Valais, SUVA, Observatoire valaisan de la santé, etc.). Il existe ainsi un potentiel de synergie possible entre partenaires et futurs voisins. Ce travail a pour objectif de déterminer dans un premier temps l’intérêt des différents partenaires à une collaboration sur le plan de la documentation, d’établir un état de la situation actuelle et de proposer des pistes pour une future collaboration institutionnelle

Nucleolar localization of influenza A NS1: striking differences between mammalian and avian cells

In mammalian cells, nucleolar localization of influenza A NS1 requires the presence of a C-terminal nucleolar localization signal. This nucleolar localization signal is present only in certain strains of influenza A viruses. Therefore, only certain NS1 accumulate in the nucleolus of mammalian cells. In contrast, we show that all NS1 tested in this study accumulated in the nucleolus of avian cells even in the absence of the above described C-terminal nucleolar localization signal. Thus, nucleolar localization of NS1 in avian cells appears to rely on a different nucleolar localization signal that is more conserved among influenza virus strains

Whole-genome, deep pyrosequencing analysis of a duck influenza A virus evolution in swine cells.

We studied the sub-population level evolution of a duck influenza A virus isolate during passage in swine tracheal cells. The complete genomes of the A/mallard/Netherlands/10-Nmkt/1999 strain and its swine cell-passaged descendent were analysed by 454 pyrosequencing with coverage depth ranging from several hundred to several thousand reads at any point. This allowed characterization of defined minority sub-populations of gene segments 2, 3, 4, 5, 7, and 8 present in the original isolate. These minority sub-populations ranged between 9.5% (for segment 2) and 46% (for segment 4) of their respective gene segments in the parental stock. They were likely contributed by one or more viruses circulating within the same area, at the same period and in the same or a sympatric host species. The minority sub-populations of segments 3, 4, and 5 became extinct upon viral passage in swine cells, whereas the minority sub-populations of segments 2, 7 and 8 completely replaced their majority counterparts. The swine cell-passaged virus was therefore a three-segment reassortant and also harboured point mutations in segments 3 and 4. The passaged virus was more homogenous than the parental stock, with only 17 minority single nucleotide polymorphisms present above 5% frequency across the whole genome. Though limited here to one sample, this deep sequencing approach highlights the evolutionary versatility of influenza viruses whereby they exploit their genetic diversity, predilection for mixed infection and reassortment to adapt to a new host environmental niche.This work was supported by a grant from DEFRA and HEFCE under the Veterinary Training and Research Initiative to the Cambridge Infectious Diseases Consortium (VB, LT), BBSRC grants BB/H014306/1 and BB/G00479X/1 (LT), and the French Ministry of Agriculture, INRA and the French Région Midi-Pyrénées (GC, J-LG, VB).This is the accepted version of the original version available at: http://dx.doi.org/10.1016/j.meegid.2013.04.03

The poxviral scrapin MV-LAP requires a myxoma viral infection context to efficiently downregulate MHC-I molecules

AbstractDownregulation of MHC class I molecules is a strategy developed by some viruses to escape cellular immune responses. Myxoma virus (MV), a poxvirus causing rabbit myxomatosis, encodes MV-LAP that is known to increase MHC-I endocytosis and degradation through a C4HC3 motif critical for an E3 ubiquitin ligase activity. Here, we performed a functional mapping of MV-LAP and showed that not only the C4HC3 motif is necessary for a marked downregulation of MHC-I but also a conserved region in the C-terminal part of the protein. We also showed that the putative transmembrane domains are responsible for a specific subcellular localization of the protein: they retain MV-LAP in the ER in transfected cells and in the endolysosomal compartments in infected cells. We observed that a specific MV infection context is necessary for a fully efficient downregulation of MHC-I. Our data suggest that the functionality of viral LAP factors, inherited by herpes- and poxviruses from mammalian cells, is more complex than anticipated

Computer-aided screening of autism spectrum disorder: Eye-tracking study using data visualization and deep learning

Background: The early diagnosis of autism spectrum disorder (ASD) is highly desirable but remains a challenging task, which requires a set of cognitive tests and hours of clinical examinations. In addition, variations of such symptoms exist, which can make the identification of ASD even more difficult. Although diagnosis tests are largely developed by experts, they are still subject to human bias. In this respect, computer-assisted technologies can play a key role in supporting the screening process. Objective: This paper follows on the path of using eye tracking as an integrated part of screening assessment in ASD based on the characteristic elements of the eye gaze. This study adds to the mounting efforts in using eye tracking technology to support the process of ASD screening Methods: The proposed approach basically aims to integrate eye tracking with visualization and machine learning. A group of 59 school-aged participants took part in the study. The participants were invited to watch a set of age-appropriate photographs and videos related to social cognition. Initially, eye-tracking scanpaths were transformed into a visual representation as a set of images. Subsequently, a convolutional neural network was trained to perform the image classification task. Results: The experimental results demonstrated that the visual representation could simplify the diagnostic task and also attained high accuracy. Specifically, the convolutional neural network model could achieve a promising classification accuracy. This largely suggests that visualizations could successfully encode the information of gaze motion and its underlying dynamics. Further, we explored possible correlations between the autism severity and the dynamics of eye movement based on the maximal information coefficient. The findings primarily show that the combination of eye tracking, visualization, and machine learning have strong potential in developing an objective tool to assist in the screening of ASD. Conclusions: Broadly speaking, the approach we propose could be transferable to screening for other disorders, particularly neurodevelopmental disorders

An amplicon-based nanopore sequencing workflow for rapid tracking of avian influenza outbreaks, France, 2020-2022

During the recent avian influenza epizootics that occurred in France in 2020/21 and 2021/22, the virus was so contagiousness that it was impossible to control its spread between farms. The preventive slaughter of millions of birds consequently was the only solution available. In an effort to better understand the spread of avian influenza viruses (AIVs) in a rapid and innovative manner, we established an amplicon-based MinION sequencing workflow for the rapid genetic typing of circulating AIV strains. An amplicon-based MinION sequencing workflow based on a set of PCR primers targeting primarily the hemagglutinin gene but also the entire influenza virus genome was developed. Thirty field samples from H5 HPAIV outbreaks in France, including environmental samples, were sequenced using the MinION MK1C. A real-time alignment of the sequences with MinKNOW software allowed the sequencing run to be stopped as soon as enough data were generated. The consensus sequences were then generated and a phylogenetic analysis was conducted to establish links between the outbreaks. The whole sequence of the hemagglutinin gene was obtained for the 30 clinical samples of H5Nx HPAIV belonging to clade 2.3.4.4b. The consensus sequences comparison and the phylogenetic analysis demonstrated links between some outbreaks. While several studies have shown the advantages of MinION for avian influenza virus sequencing, this workflow has been applied exclusively to clinical field samples, without any amplification step on cell cultures or embryonated eggs. As this type of testing pipeline requires only a short amount of time to link outbreaks or demonstrate a new introduction, it could be applied to the real-time management of viral epizootics

Issues and special features of animal health research

In the rapidly changing context of research on animal health, INRA launched a collective discussion on the challenges facing the field, its distinguishing features, and synergies with biomedical research. As has been declared forcibly by the heads of WHO, FAO and OIE, the challenges facing animal health, beyond diseases transmissible to humans, are critically important and involve food security, agriculture economics, and the ensemble of economic activities associated with agriculture. There are in addition issues related to public health (zoonoses, xenobiotics, antimicrobial resistance), the environment, and animal welfare