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1. First cases of Omicron in France are exhibiting mild symptoms, November 2021-January 2022

Author

A. Maisa, G. Spaccaferri, L. Fournier, J. Schaeffer, J. Deniau, P. Rolland, B. Coignard, A. Andrieu, O. Broustal, S. Chene, S. Chent, E. Fougère, G. Gbaguidi, M. Hamidouche, A. Lamy, Q. Mano, B. Mastrovito, A. Mercier, G. Modenesi, G. Picard, J. Prudhomme, F. Rapilly, A. Riondel, M. Rivière, B. Villegas Ramirez, A. Zhu-Soubise, M. Zurbaran, A. Amzert, L. Andreoletti, A. Bal, R. Beaurepere, S. Behillil, L. Belec, C. Bernard, L. Bocket, L. Bouri, T. Bourlet, C. Bressollette-Bodin, S. Brichler, C. Brugerolles, S. Cado, V. Calvez, N. Capron, S. Castelain, J. Castro-Alvarez, M.-L. Chaix, C. Charpentier, D. Che, C. Chillou, P. Colson, P. Coudene, A. Crinquette, A. De Rougemont, H. Delagrèverie, C. Delamare, T. Denecker-Berardino, D. Descamps, M. Desroches, G. Destras, G. Dos Santos, A. Ducancelle, S. Ducreux, T. Duret, V. Enouf, S. Fafi-Kremer, C. Felici, S. Fourati, P.-E. Fournier, C. Gaudy, H. Germain, V. Giordanengo, O. Gorge, S. Haim-Boukobza, C. Henquell, A. Holstein, L. Houhamdi, J. Izopet, V. Jacomo, A. Jacques, M.-C. Jaffar-Bandjee, M. Jimenez, L. Josset, S. Kemeny, M.-E. Lafon, A. Le Bars, G. Le Corguille, Q. Lepiller, A. Levasseur, N. Leveque, B. Lina, C. Madelaine, C. Malabat, S. Marque-Juillet, T. Martin-Dunavit, P. Mavingui, A. Merens, I. Messak, L. Morand-Joubert, X. Naudot, P. Neybecker, J.-M. Pawlotsky, L. Pilorge, J.-C. Plantier, C. Poggi, M. Pretet, C. Ragot, H. Raoul, S. Rogez, A.-M. Roque-Afonso, B. Roquebert, D. Rousset, F. Rozenberg, C. Sagot, S. Sahnoune, D. Salgado, O. Sand, C. Saudemont, E. Schvoerer, E. Simon-Loriere, R. Stephan, J. Sudour, V. Thibault, E. Tuaillon, A. Vabret, E. Vallee, S. Van Der Werf, J. Van Helden, L. Verdurme, A. Vignola, D. Wilkinson, Y. Yazdanpanah, Santé publique France - French National Public Health Agency [Saint-Maurice, France], EMERGEN consortium, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), NASA Ames Research Center (ARC), Service d'Hépato-Gastro-Entérologie et Nutrition [CHU Limoges], CHU Limoges, Département lmage et Traitement Information (IMT Atlantique - ITI), IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Equipe DECIDE (Lab-STICC_DECIDE), Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT), Institut des Géosciences de l’Environnement (IGE), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Santé publique France, the French national public health agency.Caisse nationale d’assurance maladie (Cnam), the national health insurance funds.'Enhancing Whole Genome Sequencing (WGS) and/or Reverse Transcription Polymerase Chain Reaction (RT-PCR) national infrastructures and capacities to respond to the COVID-19 pandemic in the European Union and European Economic Area' Grant Agreement ECDC/HERA/2021/007 ECD. 12221., Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), and COMBE, Isabelle

Subjects
Adult, Epidemiology, MESH: Hospitalization, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: COVID-19, Humans, MESH: SARS-CoV-2, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Signs and symptoms, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Humans, SARS-CoV-2, Vaccination, COVID-19, MESH: Adult, MESH: Vaccination, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, MESH: France, Hospitalization, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, France, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Surveys and questionnaires, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology
Abstract

International audience; ObjectivesWe aimed to investigate the first Omicron cases detected in France in order to assess case characteristics and provide supporting information on the possible impact of this variant on the healthcare system.MethodsA standardized questionnaire was used to collect information from confirmed and probable Omicron cases.ResultsMedian age of 468 investigated cases was 35 years, 376 were symptomatic (89%); 64% were vaccinated with two doses and 7% had received three doses. Loss of smell and taste were reported by 8.3% and 9% of cases, respectively. Seven cases were hospitalized, three of those were unvaccinated (including two with reported precondition). No admissions to intensive care and no deaths were reported.ConclusionsOur results confirm a mild clinical presentation among the first Omicron cases detected in France and highlight the importance for the national COVID-19 surveillance system to quickly detect and adapt to the emergence of a new variant.

Published
2022

2. Seascape genomics reveals population isolation in the reef-building honeycomb worm, Sabellaria alveolata (L.)

Author

Antony M. Knights, G Le Corguille, Fernando P. Lima, Rui Seabra, Erwan Corre, Anna P. Muir, Stanislas F. Dubois, Louise B. Firth, Flavia L. D. Nunes, Rebecca E. Ross, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Chester, Dynamiques des Écosystèmes Côtiers (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Plymouth University, Institute of Marine Research [Bergen] (IMR), University of Bergen (UiB), Universidade do Porto = University of Porto, ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), FEDER funds through COMPETE POCI-01-0145-FEDER-031088, Portuguese national funds through FCT PTDC/BIA-BMA/31088/2017PTDC/BIA-BMA/31053/2017, FEDER funds through POR Norte NORTE-01-0145-FEDE R-031053, 'Laboratoire d'Excellence' LabexMER ANR-10-LABX-19, ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Dynamiques de l'Environnement Côtier (DYNECO), Universidade do Porto, ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)

Subjects
Gene Flow, 0106 biological sciences, Evolution, Adaptation, Biological, Genomics, Larval dispersal, 010603 evolutionary biology, 01 natural sciences, Sabellaria alveolata, 03 medical and health sciences, QH359-425, Animals, 14. Life underwater, Adaptation, Reef, 030304 developmental biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Seascape, 0303 health sciences, geography, geography.geographical_feature_category, biology, Coral Reefs, Ecology, ACL, [SDV.BA]Life Sciences [q-bio]/Animal biology, fungi, Ocean current, Marine invertebrate, Honeycomb (geometry), RADseq, Marine invertebrates, biology.organism_classification, Genetics, Population, Alveolata, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ocean circulation modelling, Research Article
Abstract

Background Under the threat of climate change populations can disperse, acclimatise or evolve in order to avoid fitness loss. In light of this, it is important to understand neutral gene flow patterns as a measure of dispersal potential, but also adaptive genetic variation as a measure of evolutionary potential. In order to assess genetic variation and how this relates to environment in the honeycomb worm (Sabellaria alveolata (L.)), a reef-building polychaete that supports high biodiversity, we carried out RAD sequencing using individuals from along its complete latitudinal range. Patterns of neutral population genetic structure were compared to larval dispersal as predicted by ocean circulation modelling, and outlier analyses and genotype-environment associations tests were used to attempt to identify loci under selection in relation to local temperature data. Results We genotyped 482 filtered SNPs, from 68 individuals across nine sites, 27 of which were identified as outliers using BAYESCAN and ARLEQUIN. All outlier loci were potentially under balancing selection, despite previous evidence of local adaptation in the system. Limited gene flow was observed among reef-sites (FST = 0.28 ± 0.10), in line with the low dispersal potential identified by the larval dispersal models. The North Atlantic reef emerged as an isolated population and this was linked to high local larval retention and the effect of the North Atlantic Current on dispersal. Conclusions As an isolated population, with limited potential for natural genetic or demographic augmentation from other reefs, the North Atlantic site warrants conservation attention in order to preserve not only this species, but above all the crucial functional ecological roles that are associated with their bioconstructions. Our study highlights the utility of using seascape genomics to identify populations of conservation concern.

Published
2020

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