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Xavier Rossello, Jannick AN Dorresteijn, Arne Janssen, Ekaterini Lambrinou, Martijn Scherrenberg, Eric Bonnefoy-Cudraz, Mark Cobain, Massimo F Piepoli, Frank LJ Visseren, Paul Dendale, null This paper is a co-publication betw, Centro Nacional de Investigaciones Cardiovasculares Carlos III [Madrid, Spain] (CNIC), Instituto de Salud Carlos III [Madrid] (ISC), Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), University Medical Center [Utrecht], Jessa Ziekenhuis [Hasselt], Cyprus University of Technology, Hasselt University (UHasselt), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hospices Civils de Lyon (HCL), Service de Cardiologie Lyon (Hôpital Louis Pradel [CHU - HCL]), Hôpital Louis Pradel [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Imperial College London, University of Southern California (USC), Rossello, Xavier/0000-0001-6783-8463, Rossello, Xavier, Dorresteijn, Jannick A. N., JANSSEN, Arne, Lambrinou, Ekaterini, SCHERRENBERG, Martijn, Bonnefoy-Cudraz, Eric, Cobain, Mark, Piepoli, Massimo F., Visseren, Frank L. J., DENDALE, Paul, CarMeN, laboratoire, Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Emma Partiot, Nilda Vanesa Ayala-Nunez, Jacky G. Goetz, Gautier Follain, Judith R.E. Roels, Anita Eckly, Béatrice Uring-Lambert, Maxime Chazal, Raphael Gaudin, Gillian Hale, Frank M. J. Jacobs, Sandrine Bourdoulous, Orestis Faklaris, Sherif R. Zaki, Aurélie Hirschler, Nolwenn Jouvenet, Margot Carocci, Florian Bakoa, Sarah Cianférani, Christine Carapito, Frédéric Doussau, Brigid C. Bollweg, François Delalande, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), Institut National de la Santé et de la Recherche Médicale (INSERM), Immuno-Rhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Strasbourg (UNISTRA), Fédération de Médecine Translationnelle de Strasbourg (FMTS), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Swammerdam Institute for Life Sciences, University of Amsterdam [Amsterdam] (UvA)-Center for Neurosciences, Génomique virale et vaccination, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université Paris Descartes - Paris 5 (UPD5), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), BioCampus Montpellier (BCM), Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Biologie et pharmacologie des plaquettes sanguines: hémostase, thrombose, transfusion, Université de Strasbourg (UNISTRA)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Les Hôpitaux Universitaires de Strasbourg (HUS), Institut des Neurosciences Cellulaires et Intégratives (INCI), Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), This work has received funding from the French State via the French National Research Agency (ANR) as part of the program Investissements d’avenir (IdEx Université de Strasbourg) to RG. This work was supported by an ATIP-AVENIR starting grant to RG. The research leading to these results has received funding from the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Program (FP7/2007–2013) under REA grant agreement no. PCOFUND-GA-2013-609102, through the PRESTIGE program coordinated by Campus France, and from the French Agency for Research on AIDS and Viral Hepatitis (ANRS), both attributed to NVAN. Experiments conducted by G.F. and J.G.G. were funded by Plan Cancer (OptoMetaTrap), Ligue contre le Cancer, Idex Attractivités (University of Strasbourg), and by institutional funds from INSERM and University of Strasbourg. G.F. was supported by a doctoral fellowship from Ligue Contre le Cancer. Mass spectrometry experiments were supported by the French Proteomic Infrastructure (ProFI, ANR-10-INBS-08-03). F.B. is a recipient of a PhD grant provided by ANRT (Association Nationale de la Recherche et de la Technologie). N.J. is funded by Agence Nationale pour la Recherche (ANR-16-CE15-0025-01), Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur. CDC contributions to this paper written and edited by G.L.H. and B.C.B. in their private capacity. No official support or endorsement by the Centers for Disease Control and Prevention, Department of Health and Human Services is intended, nor should be inferred. All authors read, provided feedback, and approved the paper. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention. The following reagent was obtained through the NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: HIV-1 NL4-3 AD8 Infectious Molecular Clone (pNL(AD8)) from Dr. Eric O. Freed (cat# 11346)., ANR-16-CE15-0025,Viro-Storm,Mécanismes de production incontrôlée de cytokines au cours de l'infection virale(2016), European Project: 609102,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,PRESTIGE(2014), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), EFS-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), jouvenet, nolwenn, Mécanismes de production incontrôlée de cytokines au cours de l'infection virale - - Viro-Storm2016 - ANR-16-CE15-0025 - AAPG2016 - VALID, PRES Towards International Gain of Excellence - PRESTIGE - - EC:FP7:PEOPLE2014-09-01 - 2019-08-31 - 609102 - VALID, Equipe Direction scientifique, Sciences et Technologies de la Musique et du Son (STMS), Université Pierre et Marie Curie - Paris 6 (UPMC)-IRCAM-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-IRCAM-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Neuro-Immunologie Virale, Virologie UMR1161 (VIRO), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Photonique Quantique et Moléculaire (LPQM), Centre National de la Recherche Scientifique (CNRS)-CentraleSupélec-École normale supérieure - Cachan (ENS Cachan), Biologie et pharmacologie des plaquettes sanguines: hémostase, thrombose, transfusion (http://www.u949.inserm.fr/), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-EFS, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Spectrométrie de Masse BioOrganique, Département des Sciences Analytiques, Institut Pluridisciplinaire Hubert Curien, Strasbourg, France (LSMBO-DSA-IPHC), Centre National de la Recherche Scientifique (CNRS), Immunorhumathologie moléculaire, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Molecular Neuroscience (SILS, FNWI)

Morgane Bourmaud, Anda Huna, Ikrame Naciri, Marthe Laisné, Pierre-Antoine Defossez, Selene Di Carlo, Nikhil Gupta, David Bernard, Lucie Peduto, Laure Ferry, Olivier Kirsh, Nadine Martin, Centre épigénétique et destin cellulaire (EDC), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Biologie de l'Os et du Cartilage : Régulations et Ciblages Thérapeutiques (BIOSCAR (UMR_S_1132 / U1132)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Stroma, inflammation et réparation tissulaire - Stroma, Inflammation and Tissue Repair, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Institutes of Health [EpiCALC 2013 to P.A.D. and D.B.], Institut National du Cancer [PLBio15–013 to P.A.D. and D.B.], Labex ‘Who am I?’ [ANR-11-LABX-0071 under ANR-11-IDEX-005–02, to P.A.D.], European Research Council [ERC648428-PERIF to L.P.], Fondation ARC [4th-year PhD scholarship to I.N., Programme Labellisé PGA1/RF20180206807 to P.A.D.], Fondation pour la Recherche Médicale [postdoctoral fellowship to A.H.]. The open access publication charge for this paper has been waived by Oxford University Press - NAR Editorial Board members are entitled to one free paper per year in recognition of their work on behalf of the journal., The authors thanks the Genomics Platform of Institut Curie for Nanostring analysis. The Nanostring platform of Institut Curie was initiated with the support of French grants (LabEx and EquipEx): ANR-10-IDEX-0001–02 PSL, ANR-11-LBX-0044 and « INCa-DGOS- 4654 » SIRIC11–002. We thank Valérie Doye, Stéphanie Bolhy, and Philippe Girard at Institut Jacques Monod for help with the Incucyte. Concerning the lentiviral vector production, we acknowledge Christophe Huret and the Paris Diderot Vectorology Platform of Paris Diderot University, Sorbonne Paris Cité, CNRS UMR 7216, Paris, France. We acknowledge the kind help of Elisabeth Brambilla with some experiments that do not appear in the submitted version of the manuscript. For the gift of reagents we acknowledge the kind contribution of Katrin Chua, Philippe Chavrier, Annabelle Decottignies, Sébastien Jauliac and Michael Kracht. Finally, we thank the following colleagues for useful discussions: Jean-Marc Vanacker, Robert Dante, Nathalie Théret, Saadi Khochbin, Céline Prunier, Céline Vallot, Claire Rougeulle, Isabelle Bernard-Pierrot, Slimane Ait-si-ali, Jonathan Weitzman, Valérie Lallemand-Mezger, ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011), European Project: 648428,H2020,ERC-2014-CoG,PERIF(2015), Centre épigénétique et destin cellulaire (EDC (UMR_7216)), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Jacques Monod (IJM), Biologie du Développement et Reproduction (BDR), Institut National de la Recherche Agronomique (INRA), École pratique des hautes études (EPHE), Centre de Recherche en Cancérologie de Lyon (CRCL), Stroma, inflammation et réparation tissulaire, ATMEL [Rousset], Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), TOMASSO DEVERGE, Carina, Université Sorbonne Paris Cité - - USPC2011 - ANR-11-IDEX-0005 - IDEX - VALID, and Perivascular cells at the crossroads of inflammation, regeneration and fibrosis - PERIF - - H20202015-11-01 - 2020-10-31 - 648428 - VALID

Atle Mysterud, Nicolas Morellet, Stefano Focardi, Ferdinando Urbano, Marco Heurich, Derek B. Spitz, Wibke Peters, Francesca Cagnacci, John D. C. Linnell, Mark Hebblewhite, Petter Kjellander, Department of Ecosystem and Conservation Science, Wildlife Biology Program, University of Montana, Research and Innovation Centre, Biodiversity and Molecular Ecology Department, Edmund Mach Foundation (FEM), Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique (INRA), Department of Conservation and Research, Bavarian Forest National Park, Faculty of Environment and Natural Resources, Wildlife Ecology and Management, University of Freiburg, Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), Norwegian Institute for Nature Research (NINA), Organismic and Evolutionary Biology Department, Harvard University [Cambridge], This paper was conceived and written within the collaborative EURODEER project (paper no. 006 of the EURODEER series, Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences (SLU), and Peters, Wibke

Teresa Barreneche, Rémy J. Petit, Clément Larue, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie du fruit et pathologie (BFP), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Bordeaux (UB), and This paper is part of the PhD of CL. This work was supported by ANRt funding under CIFRE PhD program to CL. Financial support to Invenio for this project was provided by the Conseil Regional d'Aquitaine for CL PhD work, and as part of the REGINA project to RJP. The PGTB facility where part of the work was conducted benefits from grants from the Conseil Regional d'Aquitaine no. 20030304002FA and 20040305003FA, from the European Union FEDER no. 2003227 and from Investissements d'Avenir (ANR-10-EQPX-16-01).

Samantha J. Green, Daria Valente, Zarin P. Machanda, Erica van de Waal, Joan B. Silk, Christopher Young, Daniela Hedwig, Klaus Zuberbühler, Oliver Schülke, Lindsey Hagberg, Sally E. Street, Anna Zanoli, Mary S. M. Pavelka, Martha M. Robbins, Martin N. Muller, Chloe Chen-Kraus, Roberta Salmi, Barbara Fruth, Cristina Giacoma, Isaac Schamberg, Michelle Brown, Louise Peckre, Fredy Quintero, Richard W. Wrangham, Andrew J. J. MacIntosh, Shreejata Gupta, Gillian King-Bailey, Felix O. Angwela, Eithne Kavanagh, Stuart Semple, Zanna Clay, Melissa Emery Thompson, Claudia Wilke, Camille Coye, Julia Ostner, Cyril C. Grueter, Marco Gamba, Raffaella Ventura, Margarita Briseño-Jaramillo, Hugh Notman, Sophie Marshall, Jérôme Micheletta, Thore J. Bergman, Bonaventura Majolo, Anna H. Weyher, Megan Petersdorf, Valérie A. M. Schoof, Gabriel Ramos-Fernández, Maryjka B. Blaszczyk, Kirsty E. Graham, Adriano R. Lameira, Morgan L. Gustison, Alban Lemasson, Karim Ouattara, Alejandro Estrada, Laura M. Bolt, David Macgregor Inglis, Peter M. Kappeler, Valeria Torti, Claudia Fichtel, Barbora Kuběnová, Stéphanie Mercier, J. Roberto Sosa-López, Katharine M. Jack, Katie E. Slocombe, University of York [York, UK], Nottingham Trent University, Durham University, University of Michigan [Ann Arbor], University of Michigan System, University of Texas at Austin [Austin], University of Waterloo [Waterloo], Universidad Nacional Autónoma de México (UNAM), University of California [Santa Barbara] (UCSB), University of California, Yale University [New Haven], University of Exeter, Ethologie animale et humaine (EthoS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), No funding was provided specifically for the current paper, but funding which supported data collection at field sites is acknowledged in electronic supplementary material, S11., University of St Andrews. School of Psychology and Neuroscience, University of St Andrews. Institute of Behavioural and Neural Sciences, University of St Andrews. Centre for Social Learning & Cognitive Evolution, Mountains of the Moon University, Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), University of California [Santa Barbara] (UC Santa Barbara), University of California (UC), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), The University of New Mexico [Albuquerque], German Primate Center - Deutsches Primatenzentrum -- Leibniz Insitute for Primate Research -- [Göttingen, Allemagne] (GPC - DPZ), Liverpool John Moores University (LJMU), Max Planck Institute of Animal Behavior, Università degli studi di Torino = University of Turin (UNITO), School of Psychology and Neuroscience [University of St. Andrews], University of St Andrews [Scotland], The University of Western Australia (UWA), Harvard University, Cornell University [New York], Tulane University, Kyoto University, University of Roehampton, United Kingdom, Tufts University [Medford], University of Lincoln, Université de Neufchätel (UNIME), University of Portsmouth, Athabasca University (AU), Centre Suisse de Recherches Scientifiques en Cote d'Ivoire [Abidjan] (CSRS-CI), University of Calgary, New York University [New York] (NYU), NYU System (NYU), Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, University of Georgia [USA], Arizona State University [Tempe] (ASU), Instituto Politecnico Nacional [Mexico] (IPN), Abertay University (Abertay University), Université de Lausanne = University of Lausanne (UNIL), University of Massachusetts [Amherst] (UMass Amherst), University of Massachusetts System (UMASS), University of Pretoria [South Africa], and University of Lethbridge

Julia Baudry, Denis Lairon, Alison Dussiot, Philippe Pointereau, Brigitte Langevin, Benjamin Allès, Pauline Rebouillat, Emmanuelle Kesse-Guyot, Mathilde Touvier, Joséphine Brunin, Serge Hercberg, François Mariotti, Hélène Fouillet, Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle (CRESS - U1153), Université Sorbonne Paris Nord-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Physiologie de la Nutrition et du Comportement Alimentaire (PNCA (UMR 0914)), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), SOLAGRO, Solagro, Agence de l'Environnement et de la Maîtrise de l'Energie (ADEME), Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Association Solagro (Solagro), The NutriNet-Sante study is funded by FrenchMinistry of Health and Social Affairs, Sante Publique France, Institut National de la Sante et de la Recherche Medicale, Institut National de la Recherche Agronomique, Conservatoire National des Arts et Metiers, and Sorbonne Paris Nord University. The BioNutriNet project was supported by the French National Research Agency (Agence Nationale de la Recherche) in the context of the 2013 Programme de Recherche Systemes Alimentaires Durables (ANR-13-ALID-0001). The funders had no role in the study design, data collection, analysis, interpretation of data, preparation of the manuscript, and decision to submit the paper., ANR-13-ALID-0001,BioNutriNet,Consommation d'aliments issus de l'agriculture biologique: déterminants et motivation vis-à-vis de la durabilité, impact nutritionnel, économique, environnemental et toxicologique(2013), Kesse-guyot, Emmanuelle, and Systèmes Alimentaires Durables - Consommation d'aliments issus de l'agriculture biologique: déterminants et motivation vis-à-vis de la durabilité, impact nutritionnel, économique, environnemental et toxicologique - - BioNutriNet2013 - ANR-13-ALID-0001 - ALID - VALID

Koussay Dellagi, Patrick Mavingui, Pablo Tortosa, Yann Gomard, Steve Michael Goodman, Processus Infectieux en Milieu Insulaire Tropical (PIMIT), Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IRD-Centre National de la Recherche Scientifique (CNRS), Direction Internationale de l'Institut Pasteur, Institut Pasteur [Paris] (IP), Association Vahatra [Antananarivo, Madagascar], Field Museum of Natural History [Chicago, USA], The sampling of Mormopterus acetabulosus on Mauritius was supported by a grant from European Research Development Fund (ERDF) 'Pathogènes associés à la Faune Sauvage Océan Indien' #31189. Original serological data presented in this paper were obtained under a grant from ERDF known as InterregV ECOSPIR 'Eco-épidemiologie des leptospires endémiques de l’Océan Indien: des bactéries à risque pour les populations humaines?' (number RE6875)., Tortosa, Pablo, Centre National de la Recherche Scientifique (CNRS)-IRD-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de La Réunion (UR), and Institut Pasteur [Paris]

Elisabeth Sanchez-Padilla, Nazir Ahmed Ismail, Thomas Kohl, Christian Utpatel, Patrick Beckert, Stefan Niemann, Claudio U. Köser, Harald Hoffmann, Sönke Andres, Robin M. Warren, Bouke C. de Jong, Marisa Klopper, Matthias Merker, Florian P. Maurer, Shaheed V. Omar, Katharina Kranzer, Maryline Bonnet, Bernhard Kerschberger, Viola Dreyer, Ivan Barilar, Elisa Ardizzoni, Birgit Schramm, Gugu Maphalala, Forschungszentrum Borstel - Research Center Borstel, German Center for Infection Research (DZIF), Heidelberg University, Epicentre [Paris] [Médecins Sans Frontières], University of Cambridge [UK] (CAM), National Institute for Communicable Diseases [Johannesburg] (NICD), University of Pretoria [South Africa], University of the Witwatersrand [Johannesburg] (WITS), Stellenbosch University, Institute of Tropical Medicine [Antwerp] (ITM), London School of Hygiene and Tropical Medicine (LSHTM), Universitaetsklinikum Hamburg-Eppendorf = University Medical Center Hamburg-Eppendorf [Hamburg] (UKE), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM), Infectious and Tropical Diseases Department [Montpellier], Institut de Recherche pour le Développement (IRD)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Namibia (UNAM), Parts of this work have been supported by the European Union TB-PAN-NET (FP7-223681) project, by Médecins Sans Frontières-Switzerland, and by German Center for Infection Research, Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germanys Excellence Strategy – EXC 2167, and Leibniz Science Campus Evolutionary Medicine of the LUNG (EvoLUNG). The funders had no role in the study design, in the collection, analysis, and interpretation of the data, in the writing of the report, and in the decision to submit the paper for publication., European Project: 223681,EC:FP7:HEALTH,FP7-HEALTH-2007-B,TB PAN-NET(2009), Niemann, Stefan [0000-0002-6604-0684], and Apollo - University of Cambridge Repository

Robert M. Hubbard, Marco Aurélio Figura, Gabriela Gonçalves Moreira, Clayton Alcarde Alvares, Rafaela Lorenzato Carneiro, Otávio Camargo Campoe, Rocky Mountain Research Station, Forestry Science and Research Institute (IPEF), Universidade Federal de Lavras (UFLA), Universidade Estadual Paulista (Unesp), Klabin SA, and International Paper

Wirulda Pootakham, Kanchana Sittikankaew, Frédéric Tangy, Piroon Jenjaroenpun, Jasper J. Koehorst, Intawat Nookaew, Tanaporn Uengwetwanit, Wanilada Rungrassamee, Peter J. Schaap, Pacharaporn Angthong, Jutatip Khudet, Sopacha Arayamethakorn, Rungnapa Leelatanawit, Duangjai Sangsrakru, Vitor A. P. Martins dos Santos, Thidathip Wongsurawat, Chutima Sonthirod, Nitsara Karoonuthaisiri, National Center for Genetic Engineering and Biotechnology [Thailand] (BIOTEC), National Science and Technology Development Agency [Bangkok] (NSTDA), University of Arkansas for Medical Sciences (UAMS), Shrimp Genetic Improvement Center [Thani, Thailand] (SGIC), National Science and Technology Development Agency [Bangkok] (NSTDA)-National Science and Technology Development Agency [Bangkok] (NSTDA), Department of Agrotechnology and Food Sciences [Wageningen], Wageningen University and Research [Wageningen] (WUR), Génomique virale et vaccination, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), This project was funded by National Center for Genetic Engineering and Biotechnology (BIOTEC Platform No. P1651718), TDG Food and Feed program, National Science and Technology Development Agency (No. P1950419) and partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 734486 (SAFE-Aqua)., Visiting Professor Program 2019 was awarded to Dr. Intawat Nookaew by the National Science and Technology Development Agency, Thailand., The authors acknowledge NSTDA Supercomputer Center (ThaiSC) for providing HPC resources that have contributed to the research results reported within this paper. We thank Ms. Somjai Wongtripop, Mr. Kaidtisak kaewlok and Shrimp Genetic Improvement Center (SGIC) members, as well as Ms. Sudtida Phuengwas (BIOTEC) for the shrimp sample collection., We acknowledge Zulema Dominguez (University of Arkansas for Medical Sciences, USA) for technical assistance on comparative genome. We are grateful to Prof. Morakot Tanticharoen (NSTDA), Dr. Kanyawim Kirtikara (BIOTEC), Dr. Wonnop Visessanguan (BIOTEC) and Assoc Prof. Skorn Koonawootrittriron (Kasetsart University, Thailand) for their mentorship on the shrimp research programs., and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Gayetri Ramachandran, Rachel Golub, Marie Cherrier, Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Lymphocytes et Immunité - Lymphocytes and Immunity, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), M.C. is supported by INSERM and Association François Aupetit dedicated to patients suffering from IBD. R.G. work is supported by Institut Pasteur, Institut National de la Santé et de la Recherche Médicale, Université de Paris, and ANR project NASHILCCD8 (#18-CE15-0024-01)., We thank Serge van de Pavert for critical discussions and for review of the paper., ANR-18-CE15-0024,NASHILCCD8,Contribution des ILC et des cellules T CD8 à la stéatose hépatique non alcoolique et à sa progression vers l'hépatocarcinome.(2018), Vougny, Marie-Christine, APPEL À PROJETS GÉNÉRIQUE 2018 - Contribution des ILC et des cellules T CD8 à la stéatose hépatique non alcoolique et à sa progression vers l'hépatocarcinome. - - NASHILCCD82018 - ANR-18-CE15-0024 - AAPG2018 - VALID, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)

Emilie Giraud, Evie Melanitou, Interactions Virus-Insectes - Insect-Virus Interactions (IVI), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Département Parasites et Insectes vecteurs - Department of Parasites and Insect Vectors, Institut Pasteur [Paris], This work was supported by institutional funding from the Institut Pasteur., We are grateful to the members of the Immunophysiology and Parasitism Unit for their recommendations for these experimental procedures and their participation to the original work described in the published paper from where this protocol is derived (Giraud et al. al., 2019b, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)

Philippe Archambault, Laurent Chauvaud, Pierre Poitevin, Pascal Lazure, Julien Thébault, Justine Doré, Gwénaëlle Chaillou, André Poirier, 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 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), Institut des Sciences de la MER de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Centre de recherche sur la dynamique du système Terre (GEOTOP), Université de Montréal (UdeM)-McGill University = Université McGill [Montréal, Canada]-École Polytechnique de Montréal (EPM)-Concordia University [Montreal]-Université du Québec à Rimouski (UQAR)-Université du Québec à Montréal = University of Québec in Montréal (UQAM)-Université du Québec en Abitibi-Témiscamingue (UQAT), Departement de Biologie [Québec], Université Laval [Québec] (ULaval), This research is a contribution of LIA-BeBEST, an international collaboration between French (IUEM-UBO, LEMAR - Brest) and Canadian (ISMER-UQAR, Rimouski) academic institutions. We thank the LEMAR and the DFO for their help. We are sincerely grateful to Dr. Virginie Roy (MLI, Quebec-Canada) for her relevant advice and her kindness. In addition, we express our sincere gratitude to Dr. Simon B.elanger (UQAR) and Dr. Peter Galbraith (MLI) for their help to disentangle the information and Herl.e Goraguer (Ifremer delegate in SPM) for his commitment to the preparation and sending of a part of the samples. We show our appreciation to Laure Devine and Hannah Whitby for their useful comments. We also thank Eric Dabas for his technical assistance in the sclerochronology process. Finally, we would like to thank the two anonymous reviewers for their valuable comments and suggestions in a previous version of the manuscript. This research was supported by a grant from the Natural Sciences and Engineering Research Council of Canada (to G.C.) and the Canada Research Chair Program (to G.C.) as well as the Region Bretagne and the Cluster of Excellence LabexMER. This research was carried out as part of the Ph.D. thesis of Justine Dore for the University of Western Brittany. All the data used to produce the results of this paper may be obtained by contacting the corresponding author., 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 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), and École Polytechnique de Montréal (EPM)-McGill University = Université McGill [Montréal, Canada]-Université de Montréal (UdeM)-Université du Québec en Abitibi-Témiscamingue (UQAT)-Université du Québec à Rimouski (UQAR)-Concordia University [Montreal]-Université du Québec à Montréal = University of Québec in Montréal (UQAM)

Uwe Maskos, Neurobiologie intégrative des Systèmes cholinergiques / Integrative Neurobiology of Cholinergic Systems (NISC), Sorbonne Université (SU)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), he author has received funding to carry out the work of his laboratory described in the Review article, as indicated in the published papers. No funding has been received that is directly relevant to this Review article. The author has no conflict of interest to declare., and Institut Pasteur [Paris] (IP)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)

Bernard Faye, Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Al-Farabi Kazakh National University [Almaty] (KazNU), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and This paper is supported by the PRIMA programme under grant agreement No1832, project 'Boost the production, processing and consumption of camel milk in the Mediterranean basin (CAMELMILK)'. The PRIMA programme is supported by the European Union. We acknowledge also Mrs. Mohammed Bengoumi and Thomas Schultze for proofreading the English version.

Leonardo Rodrigues Barbosa, Pedro José Ferreira-Filho, Carlos Frederico Wilcken, Wagner de Souza Tavares, Jacyr Mesquita Alves, José Cola Zanuncio, Marcus Vinicius Masson, Bracell Ltd., PT. Riau Andalan Pulp and Paper (RAPP), Universidade Federal de São Carlos (UFSCar), Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Universidade Estadual Paulista (UNESP), and Universidade Federal de Viçosa (UFV)

Martin Hommes, Dominique Mazzi, Michael Gaffney, Tor J. Johansen, Richard Meadow, Quentin Schorpp, Annette Schjøll, Nicolai V. Meyling, Gunda Thöming, Rosemary Collier, Ute Vogler, Anne-Marie Cortesero, University of Warwick [Coventry], Agroscope, Norwegian Institute of Bioeconomy Research (NIBIO), Julius Kühn-Institut (JKI), ‎ Norwegian Univ Life Sci, University of Copenhagen = Københavns Universitet (KU), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Teagasc - The Agriculture and Food Development Authority (Teagasc), This paper has arisen from a European ERA-NET C-IPM project called FlyIPM (integrated control of root-feeding fly larvae infesting vegetable crops). Participation was funded nationally. National funders were the Danish Environmental Protection Agency (grant no. MST-667-00280), the UK Department for Environment, Food and Rural Affairs (DEFRA), the Research Council of Norway (RCN), project No. 273179/E50, the Swiss Federal Office for Agriculture (FOAG). Ireland through Teagasc, The Agriculture and Food Authority, project No. 0336 and Department of Agriculture, Food and the Marine Stimulus project 14/s/879 and Agence Française pour la Biodiversité (AFB)., Norsk institutt for bioøkonomi=Norwegian Institute of Bioeconomy Research (NIBIO), University of Copenhagen = Københavns Universitet (UCPH), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Alessandro Cescatti, Alessio Collalti, Andreas Ibrom, Giorgio Matteucci, Marcos Fernández-Martínez, Ramdane Alkama, Daniel S. Goll, Julia Pongratz, Philippe Ciais, Anders Stockmarr, Vanessa Haverd, Stephen Sitch, Julia E. M. S. Nabel, Iain Colin Prentice, Pierre Friedlingstein, Almut Arneth, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), FOE-2019 College of Natural Resources, University of California Berkeley, CNR: DTA.AD003.474, We thank R.H. Waring, S. Vicca, M. Campioli, F. Pagani and E. Grieco for early constructive comments and thoughtful suggestions, S. Noce for the map of data points. We thank efforts from all site investigators and their funding agencies. This paper contributes to the AXA Chair Programme in Biosphere and Climate Impacts and the Imperial College initiative Grand Challenges in Ecosystems and the Environment. A.C. and G.M. are partially supported by resources available from the Ministry of University and Research (FOE-2019), under the project 'Climate Change' (CNR DTA.AD003.474), M.F.-M. is a postdoctoral fellow of the Research Foundation—Flanders (FWO), AXA Research Fund, and Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)

Basile Kamgang, Aurelie P. Yougang, Theodel A. Wilson-Bahun, Armel N. Tedjou, Charles S. Wondji, Laurence Mousson, Anna-Bella Failloux, Marie Vazeille, Centre for Research in Infectious Diseases [Yaoundé] (CRID), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP), Université de Yaoundé I, University Marien Ngouabi of Brazzaville (umng), Liverpool School of Tropical Medicine (LSTM), This study was supported by a Wellcome Trust Training Fellowship in Public Health and Tropical Medicine [grant number 204862/Z/16/Z] awarded to BK., We would like to thank the populations of different collection sites for their collaboration during the field works. BK, CSW and ABF designed the experiments. BK performed the research. MV and LM provided a technical help. ANT, APY, TAWB helped in mosquito collections, BK, CSW and ABF wrote the paper with contribution from all other authors., and Institut Pasteur [Paris]

José Cola Zanuncio, Jonas Pereira Pontes, Germano Leão Demolin Leite, Carlos Frederico Wilcken, Wagner de Souza Tavares, Edilson Paulo Rodrigues Bispo, Claubert Wagner Guimarães de Menezes, Universidade Federal de Minas Gerais (UFMG), Asia Pacific Resources Int Holdings Ltd APRIL, Inst Fed Norte Minas Gerais, Universidade Estadual Paulista (Unesp), Universidade Federal de Viçosa (UFV), PT. Riau Andalan Pulp and Paper (RAPP), Instituto Federal do Norte de Minas Gerais, and Universidade Estadual Paulista (UNESP)

Lewandowska-Sabat, Anna Monika, Solberg, Trygve Roger, Lewandowska-Sabat, Anna, Kirsanova, Elena, Klopp, Christophe, Solberg, Trygve, Heringstad, Bjørg, Østerås, Olav, Boysen, Preben, Olsaker, Ingrid, Norwegian University of Life Sciences (NMBU), Geno Breeding & AI Assoc, Hamar, Norway, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Norwegian Cattle Hlth Serv, As, Norway, TINE Extens Serv, As, Norway, and This paper is a part of the 'Multimast' project (no. 233778) funded by the Research Council of Norway, Tine and Geno.

Philippe Faure, Jean-Christophe Olivo-Marin, Fabrice de Chaumont, Nicolas Torquet, Albane Imbert, Stephane Dallongeville, Anne-Marie Le Sourd, Thomas Bourgeron, Elodie Ey, Thierry Legou, Thibault Lagache, Analyse d'images biologiques - Biological Image Analysis (BIA), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique humaine et fonctions cognitives - Human Genetics and Cognitive Functions (GHFC (UMR_3571 / U-Pasteur_1)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Neurosciences Paris Seine (NPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche et Innovation Technologique (CITECH), Institut Pasteur [Paris], Laboratoire Parole et Langage (LPL), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), This work was partially funded by the Institut Pasteur, the Bettencourt-Schueller Foundation, the Cognacq–Jay Foundation, the Conny–Maeva Foundation, the ERANET–NEURON SYNPATHY program, the Agence Nationale de la Recherche through grant number ANR-10-LABX-62-IBEID, France-BioImaging infrastructure through grant number ANR-10-INBS-04 and the INCEPTION program through grant number ANR-16-CONV-0005, the Centre National de la Recherche Scientifique, the University Paris Diderot, the BioPsy Labex, the Institut National du Cancer through grant number TABAC-16–022, the Foundation for Medical Research (Equipe DEQ20130326488), the Innovative Medicines Initiative Joint Undertaking through grant agreement number 115300, resources of which are composed of financial contributions from the European Union’s Seventh Framework Program (FP7/2007–2013) and EFPIA companies in kind contribution., The authors thank Y. Archambeau and P. Ollivon at the workshop of the Institut Pasteur for building the first 12 setups and advising on hardware, W. Meiniel for the mathematical proof for decisions of head/tail probability, Microsoft France for their technical support, P. Spinicelli for optical engineering and reading of the paper, R. Marée for machine learning support, B. König for advice and reading of biological experiments, J. N. Crawley for reading and providing comments on the manuscript, A. Barmpoutis for providing us with the early Kinect 2 driver and support, N. Chenouard for driving the use of the machine learning solution, P. Dugast for drawing the mice in the different behavioural events, A. Engelberg for checking the English, S. Wagner and R. Accardi for RFID advice, M. Marim for website development, and X. Montagutelli and M. Bérard for animal facility support., Analyse d'images biologiques - BioImage Analysis (AIQ), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Institut Pasteur [Paris], Neuroscience Paris Seine (NPS), Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Orzenil B. Silva-Junior, Bruno Marco de Lima, Shawn D. Mansfield, Carla Garcia, Dario Grattapaglia, Eduardo P. Cappa, BRUNO MARCO DE LIMA, USP, EDUARDO P. CAPPA, INSTITUTO NACIONAL DE TECNOLOGI´A AGROPECUARIA (INTA), ARGENTINA, ORZENIL BONFIM DA SILVA JUNIOR, Cenargen, CARLA GARCIA, INTERNATIONAL PAPER DO BRASIL ROD, SHAWN D. MANSFIELD, UNIVERSITY OF BRITISH COLUMBIA, CANADA, and DARIO GRATTAPAGLIA, Cenargen.

Florence Tardy, Jean-Pierre Bouillet, Jean-Paul Laclau, Marcelo Zacharias Moreira, D.R.M. Caldeira, José Leonardo de Moraes Gonçalves, Fernando Palha Leite, Carolina B. Brandani, Maureen Voigtlaender, Ranieri Ribeiro Paula, Didier Brunet, Universidade de São Paulo (USP), Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA), Centro de Energia Nuclear na Agricultura (CENA ), University of São Paulo (USP), Celulose Nipo-Brasileira SA (CENIBRA), Universidade Federal do Espirito Santo (UFES), Cenibra, International Paper, Suzano Papel e Celulose, SOERE F-ORE-T network, which is supported annually by Ecofor, Allenvi and the French National Research Infrastructure ANAEE-F, Universidade Estadual Paulista (Unesp), UMR Eco&Sols, University of Montpellier, Coordenação de Pesquisa Florestal, UFES, Universidade de São Paulo = University of São Paulo (USP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Jelena Melesina, Wolfgang Sippl, Tino Heimburg, Christophe Romier, Martin Marek, Karin Schmidtkunz, E. Ramos-Morales, Julien Lancelot, C. Da Veiga, Manfred Jung, Takayoshi Suzuki, Dina Robaa, Eric Ennifar, Dmitrii V. Kalinin, T.B. Shaik, Raymond J. Pierce, Alokta Chakrabarti, Ralph Holl, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Martin-Luther-Universität Halle Wittenberg (MLU), Albert-Ludwigs-Universität Freiburg, Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Institut de biologie moléculaire et cellulaire (IBMC), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), University of Münster, Kyoto Prefectural University of Medicine [Kyoto, Japon], Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), University of Hamburg, This work and the authors of this paper have been supported by funding from the European Union’s Seventh Framework Programme for research, technological development, and demonstration under grant agreements nos. 241865 (SEtTReND) and 602080 (A-ParaDDisE) as well as the German Research Foundation (DFG) to W.S. (Si868/13-1) and M.J. (Ju295/13-1). This study was supported by the grant ANR-10-LABX-0030-INRT, a French State fund managed by the Agence Nationale de la Recherche under the frame program Investissements d’Avenir ANR-10-IDEX-0002-02. C.R., M.M., T.B.S., E.R.M., and R.J.P. are supported by institutional funds from the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé et de la Recherche Médicale (INSERM), the Université de Strasbourg, the Institut Pasteur de Lille and the Université de Lille. W.S. was supported by the European Regional Development Fund of the European Commission. We acknowledge the support and the use of resources of the French Infrastructure for Integrated Structural Biology FRISBI ANR-10-INBS-05 and of Instruct-ERIC, We thank members of the ESRF-EMBL joint structural biology groups, the SOLEIL, and the Swiss Light Source (SLS) synchrotrons for the use of their beamline facilities and for help during data collection. We are grateful to Alastair McEwen (IGBMC) for his kind assistance during X-ray data collections., ANR-10-IDEX-0002,UNISTRA,Par-delà les frontières, l'Université de Strasbourg(2010), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), European Project: 241865,EC:FP7:HEALTH,FP7-HEALTH-2009-single-stage,SETTREND(2010), European Project: 602080,EC:FP7:HEALTH,FP7-HEALTH-2013-INNOVATION-1,A-PARADDISE(2014), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), and Westfälische Wilhelms-Universität Münster = University of Münster (WWU)

Aissata Basse, Inès Vigan-Womas, Alioune Dieye, Cheikh Loucoubar, Babacar Mbengue, Marie Louise Varela, Ronald Perraut, Aissatou Touré, Institut Pasteur de Dakar, Réseau International des Instituts Pasteur (RIIP), Institut Pasteur de Madagascar, Département Parasites et Insectes vecteurs - Department of Parasites and Insect Vectors, Institut Pasteur [Paris], This study was supported by grants from Institut Pasteur Fondation, from Rotary International, ACIP (Institut Pasteur, N°25_2012) and EDCTP—European & Developing Countries Clinical Trials Partnership., We thank Dr Odile Mercereau-Puijalon and Dr Shirley Longacre for constant support and providing antigens, we are grateful to Dr Shirley Longacre for revising this paper. We thank Drs Marc Jouan and Jérôme Salomon from Division International (Institut Pasteur, Paris) for their help to initiate this work in the very early steps. We are grateful to the villagers of Dielmo and Ndiop for their active participation and continuing collaboration in the project and Pr Bacary Diatta for help providing hospital samples., and Institut Pasteur [Paris] (IP)

Adriaenssens, Evelien M, Wittmann, Johannes, Kuhn, Jens H, Turner, Dann, Sullivan, Matthew B., Dutilh, Bas E, Jang, Ho Bin, van Zyl, Leonardo J, Klumpp, Jochen, Lobocka, Malgorzata, Moreno Switt, Andrea I, Rumnieks, Janis, Edwards, Robert A, Uchiyama, Jumpei, Alfenas-Zerbini, Poliane, Petty, Nicola K, Kropinski, Andrew M, Barylski, Jakub, Gillis, Annika, Clokie, Martha R C, Prangishvili, David, Lavigne, Rob, Aziz, Ramy Karam, Duffy, Siobain, Krupovic, Mart, Poranen, Minna M., Knezevic, Petar, Enault, Francois, Tong, Yigang, Oksanen, Hanna M., Rodney Brister, J, Sub Bioinformatics, Theoretical Biology and Bioinformatics, University of Liverpool, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), University of the West of England [Bristol] (UWE Bristol), Ohio State University [Columbus] (OSU), Utrecht University [Utrecht], Radboud University Medical Center [Nijmegen], University of the Western Cape, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Polish Academy of Sciences (PAN), Universidad Andrés Bello - UNAB (CHILE), Latvian Biomedical Research and Study Centre [Rīga], San Diego State University (SDSU), Azabu University, Universidade Federal de Vicosa (UFV), iThree Institute, University of Technology Sydney (UTS), University of Guelph, Adam Mickiewicz University in Poznań (UAM), Université Catholique de Louvain = Catholic University of Louvain (UCL), University of Leicester, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Cairo University, University of Warwick [Coventry], University of Helsinki, University of Novi Sad, Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Beijing Institute of Microbiology and Epidemiology, This work was funded in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I (J.H.K.). B.E.D. was supported by the Netherlands Organization for Scientific Research (NWO), Vidi Grant 864.14.004. R.A.E was supported by grant MCB-1330800 from the National Science Foundation. J.R.B. was supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine. R.L. is a member of the phagebiotics research community, supported by FWO Vlaanderen. M.M.P. was supported by the Academy of Finland (272507). A.G. was supported by the National Fund for Scientific Research (FNRS). H.M.O. was supported by University of Helsinki funding for Instruct-F1 research infrastructure., The committee would like to thank Dr. Graham Hatfull (University of Pittsburgh) for permitting us to use Actinobacteriophage Database electron micrographs in 2017’s taxonomy proposals. The authors thank Laura Bollinger (National Institutes of Health/National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Frederick, MD, USA) for editing this paper., University of the Western Cape (UWC), Universidad Andrés Bello [Santiago] (UNAB), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Institut Pasteur [Paris] (IP), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), UCL - SST/ELI/ELIM - Applied Microbiology, Sub Bioinformatics, and Theoretical Biology and Bioinformatics

Victor Carocha, Raphael Ployet, Jacqueline Grima-Pettenati, Marçal Soler, Nathalie Ladouce, Ana Alves, Luc Harvengt, José-Carlos Rodrigues, Christiane Marque, Chantal Teulières, Fabien Mounet, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), RAIZ – Forestry & Paper Research Institut, Régulation et Dynamique de la Formation du Bois, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Centro de Estudos Florestais, Technical University of Lisbon-Instituto Superior de Agronomia, Laboratoire de Biotechnologie, Institut Technologique Forêt Cellulose Bois-construction Ameublement (FCBA), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and FCBA

Madiha Bou Ali, Youssef Gargouri, Saoussen Ben Ayed, Aymen Bali, Yassine Ben Ali, Dhafer Laouini, École Nationale d'Ingénieurs de Sfax | National School of Engineers of Sfax (ENIS), Université de Sfax - University of Sfax, Laboratoire de Transmission, Contrôle et Immunobiologie des Infections - Laboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), and The authors would like to thank Mr. Anouar Fendri, Professor of English, who kindly proofread this paper.

Panagiotis S. Adam, Simonetta Gribaldo, Guillaume Borrel, Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP), Université Paris Diderot - Paris 7 (UPD7), P.S.A. is supported by a PhD fellowship from Paris Diderot University and by funds from the PhD Programme 'Frontières du Vivant (FdV)–Programme Bettencourt.' G.B. is a recipient of a Roux-Cantarini fellowship from the Institut Pasteur. S.G. acknowledges funding from the French National Agency for Research Grant ArchEvol (ANR-16-CE02-0005-01)., We thank Alexander Probst for feedback on an earlier version of the paper, and two anonymous reviewers whose comments helped improve clarity and correctness of the manuscript., ANR-16-CE02-0005,Arch-Evol,Approches phylogenomiques pour étudier l'origine et évolution des Archées(2016), and Institut Pasteur [Paris]

Johannes Charlier, Ward Bryssinckx, Valérie De Waele, Frédéric Simard, Evans Buliva, Abdulhafid Hussain, Nhu Nguyen Tran Minh, Muhammad Mukhtar, David Roiz, Nabil Haddad, Ali Bouattour, Guy Hendrickx, Els Ducheyne, Osama Mahmoud, Mamunur Rahman Malik, Avia-GIS [Zoersel], WHO - Regional Office for the Eastern Mediterranean [Cairo, Egypt] (EMRO), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Université Libanaise, Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Ministry of Health Oman, Directorate of Malaria Control [Islamabad] (DoMC), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP), Ministry of Health and Human Services [Somalia], Vector Control Group (MIVEGEC-VCG), This work was supported by the WHO Regional Office for the Eastern Mediterranean. The work was supported partially by the project InvaCosts (ANR-14-CE02-0021-01). Field work in Lebanon was supported by the WHO National Bureau (LEB1409860)., We thank the numerous entomologists and health officers of the EMR who shared data with the WHO Regional Office for the Eastern Mediterranean. Ms. Barwa and Dr. Zayed are gratefully acknowledged for their technical assistance. We gratefully acknowledge the valuable input of the anonymous reviewers on the first version of this paper., ANR-14-CE02-0021,InvaCosts,Insectes envahissants et leurs couts pour la biodiversité, l'économie et la santé humaine(2014), and Regional Office for the Eastern Mediterranean [Cairo] (EMRO)

Muhindo Mavoko, Htee Khu Naw, Estrella Lasry, Nicholas J. White, Sodiomon B. Sirima, Melissa C. Kapulu, Mores Loolpapit, Marie Claire Henry, Thomas N. Williams, Alfred Ngwa Amambua, Claude Rwagacondo, Rick M. Fairhurst, Nicholas P. J. Day, Joseph Okebe, Umberto D'Alessandro, Mahamadou Diakite, Rindra Randremanana, Mavuto Mukaka, James A. Berkley, Jean-Pierre Van Geertruyden, Charles O Obonyo, Malcolm E. Molyneux, Muna Affara, Philipe Brasseur, Peter G. Kremsner, Pascal Lutumba, Endalamaw Gadisa, Abraham Aseffa, Grace Malenga, Caterina I. Fanello, Grant Dorsey, Karen I. Barnes, Zolia Yah, Jane Achan, Patrice Piola, Kathryn Maitland, Chandy C. John, Davis Nwakanma, Joel J. Jones, W. Robert Taylor, Birgit Schramm, Marie A. Onyamboko, Junior Matangila, Philip Bejon, Geneva University Hospital (HUG), Mahidol Oxford Tropical Medicine Research Unit (MORU), Wellcome Trust-Mahidol University [Bangkok]-University of Oxford [Oxford], KEMRI-Wellcome Trust Research Programme (KWTRP), Imperial College London, University of Oxford [Oxford], Medical Research Council Unit The Gambia (MRC), University of Antwerp (UA), University of Kinshasa (UNIKIN), Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), Epicentre [Paris] [Médecins Sans Frontières], Kinshasa Mahidol Oxford Research Unit (KIMORU), Wellcome Trust-Mahidol University [Bangkok]-University of Oxford [Oxford]-Wellcome Trust-Mahidol University [Bangkok]-University of Oxford [Oxford], Ecole de Santé Publique de Kinshasa (KSPH ou ESP), National Malaria Control Programme, Ministry of Health and Social Welfare, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Malaria Research and Training Center [Bamako, Mali], Université de Bamako, Queen Elizabeth Hospital, University of Liverpool, Kenya Medical Research Institute (KEMRI), Armauer Hansen Research Institute (AHRI), Amref Health Africa [Kenya], African Medical and Research Foundation (AMREF), Centre de Recherche Entomologique de Cotonou (CREC), Ministère de la Santé, University of California [San Francisco] (UCSF), University of California, Indiana University - Purdue University Indianapolis (IUPUI), Indiana University System, Centre National de Recherche et de Formation sur le Paludisme [Ouagadougou, Burkina Faso] (CNRFP), Groupe de recherche action en santé (GRAS), University of Cape Town, University of Tübingen, TNW is supported by a Fellowship from the Wellcome Trust (202800). The KEMRI–Wellcome Trust Research Programme in Kenya is funded through a Strategic Award from the KEMRI–Wellcome Trust Research Programme (203077). RMF was supported by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, US National Institutes of Health. NJW is a Wellcome Trust Principal Fellow., We acknowledge with gratitude the Demographic Health Survey of USAID for permission to download data from their website. This paper is published with permission from the Director of KEMRI., University of Oxford-Mahidol University [Bangkok]-Wellcome Trust, University of Oxford, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Oxford-Mahidol University [Bangkok]-Wellcome Trust-University of Oxford-Mahidol University [Bangkok]-Wellcome Trust, University of California [San Francisco] (UC San Francisco), University of California (UC), RANDRIAMANANTSOA, Volatiana Manohisoa, and Wellcome Trust

Patrick Weber, Nadia Benaroudj, Frederick Saul, Sarah Dubrac, Annie Landier, Bénédicte Beaudeau, Raléb Taher, Mounira Kebouchi, Ahmed Haouz, Mathieu Picardeau, Biologie des Spirochètes / Biology of Spirochetes, Institut Pasteur [Paris], Cristallographie (Plateforme) - Crystallography (Platform), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Biologie des Bactéries pathogènes à Gram-positif, This work was supported by the Institut Pasteur and Agence National de la Recherche Grant ANR-08-MIE-018., M. K., R. T., A. L., B. B., and P. W. performed experiments. F. S., A. H., S. D., M. P., and N. B. conceived, performed, and analyzed experiments. N. B. conceived and coordinated the study and wrote the paper. All authors approved the final version of the manuscript.We acknowledge SOLEIL for provision of synchrotron radiation facilities, and we thank the staff of beamline PROXIMA 1 for assistance. We are grateful to Gerald Murray and Ben Adler for providing the perR mutant. We thank Gouzel Karimova, Isabelle Michaud-Soret, and Victor Duarte for critically reading the manuscript and for helpful discussions., ANR-08-MIEN-0018,LEPTOVIR,Les leptospires : de la génétique à la pathogénèse(2008), Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Giada Rossini, Rémi N. Charrel, Vittorio Sambri, Silvia Morini, P. Cenni, Caterina Vocale, Nazli Ayhan, M. P. Landini, Anna Pierro, Paolo Gaibani, Stefania Varani, Michele Bartoletti, Antonio Mastroianni, F. Prati, Luigi Raumer, S. Schivazappa, Russell E. Lewis, S. Ficarelli, CRREM Laboratory [Bologna, Italy] (Unit of Microbiology), University hospital - Policlinico S.Orsola-Malpighi [Bologna, Italy], Unit of Microbiology [Pievesestina, Italy] (The Romagna Hub Laboratory), The Romagna Hub Laboratory [Pievesestina, Italy], Emergence des Pathologies Virales (EPV), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Medical and Surgical Science [Bologna, Italy] (Infectious Disease Unit), University of Bologna/Università di Bologna, Infectious Disease Unit [Forlì, Italy], G.B. Morgagni-Pierantoni Hospital [Forlì, Italy], Infectious Disease Division [Reggio Emilia, Italy], Reggio Emilia Hospital [Italy], Emergency Department [Imola, Italy], Imola Hospital S. Maria della Scaletta [Imola, Italy], Department of Experimental, Diagnostic and Specialty Medicine [Bologna, Italy] (DIMES), Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), This work was supported by the University of Bologna (RFO2013e2015 to SV, MPL) and by the Emilia-Romagna Region (Lab P3 funds). This work was also supported in part by the European Virus Archive goes Global (EVAg) project that has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 653316 (to RNC), the EDENext FP7- n261504 EU project (to RNC) and this paper is catalogued by the EDENext Steering Committee (http://www.edenext.eu) as EDENext467. The work of RNC was done under the frame of EurNegVec COST Action TD1303., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011), University of Bologna, BUISINE, Soline, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, Biology and control of vector-borne infections in Europe - EDENEXT - - EC:FP7:HEALTH2011-01-01 - 2015-06-30 - 261504 - VALID, Pierro, A., Ficarelli, S., Ayhan, N., Morini, S., Raumer, L., Bartoletti, M., Mastroianni, A., Prati, F., Schivazappa, S., Cenni, P., Vocale, C., Rossini, G., Gaibani, P., Sambri, V., Landini, M.P., Lewis, R.E., Charrel, R.N., and Varani, S.

Laetitia Petit-Jentreau, Ludovic Tailleux, Janine L. Coombes, University of Liverpool, Pathogénomique mycobactérienne intégrée, Institut Pasteur [Paris] (IP), Génétique mycobactérienne - Mycobacterial genetics, The present work was supported by the University of Liverpool. JLC is a lecturer at the University of Liverpool, UK, LT is a researcher at Institut Pasteur, France, and LP-J is a postdoctoral researcher on the JLC's Biotechnology and Biological Sciences Research Council (BBSRC) grant (BB/M023540/1) at the University of Liverpool, UK., LP-J wrote the paper with input from LT and JLC. All authors revised the manuscript, and approved it for publication., and Institut Pasteur [Paris]

Kurtesh Sherifi, Rémi N. Charrel, Kristaq Berxholi, Arber Taraku, Nazli Ayhan, Emergence des Pathologies Virales (EPV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), University of Prishtina, Agricultural University of Tirana, This work was supported in part by the European Virus Archive Goes Global project, which has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement no. 653316, the EDENext FP7-no. 261504 European Union project and this paper is catalogued by the EDENext Steering Committee as EDENext469 (http://www.edenext.eu). The work of N.A. and R.N.C. was conducted under the frame of EurNegVec COST Action TD1303. N.A. is supported by the Fondation Mediterranee Infection., European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011), BUISINE, Soline, European Virus Archive goes global - EVAg - - H20202015-04-01 - 2019-03-31 - 653316 - VALID, and Biology and control of vector-borne infections in Europe - EDENEXT - - EC:FP7:HEALTH2011-01-01 - 2015-06-30 - 261504 - VALID

Pierre Garneret, Patrick Tabeling, Beatrice Jacquelin, Fabrice Monti, Anavaj Sakuntabhai, Pierre Lafaye, Laura Magro, Aurélia Kwasiborski, Camille Escadafal, Jessica Vanhomwegen, Jean-Claude Manuguerra, Laboratoire Microfluidique, MEMS, Nanostructures (MMN), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Cellule d'Intervention Biologique d'Urgence - Laboratory for Urgent Response to Biological Threats (CIBU), Institut Pasteur [Paris], HIV, Inflammation et persistance, Génétique fonctionnelle des Maladies infectieuses - Functional Genetics of Infectious Diseases, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Ingénierie des Anticorps (plate-forme) - Antibody Engineering (Platform), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], P. T., J. C. M. and P. L. initiated the collaboration. L. M., P. G., B. J. and C. E. prepared the manuscript with the assistance of P. T. L. M., F. M. and P. T. brought expertise on paper microfluidics and technological developments. J. C. M., A. S., C. E., A. K., J. V. and P. L. helped on more biological points of view: isothermal amplifications and sample preparations., Institut Pasteur [Paris] (IP), HIV, Inflammation et persistance - HIV, Inflammation and Persistence, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Verena Königer, D. Scott Merrell, Roman Andriiovych Moskalenko, Rainer Haas, Thomas Borén, Sara Henriksson, Jafar Mahdavi, Abhijit Chowdhury, Johan Ögren, Anders Hofer, Jay V. Solnick, Dan Danielsson, Sara K. Lindén, Dag Ilver, Konstantinos S. Papadakos, Susanne Vikström, Jörgen Ådén, Jan Holgersson, Gerhard Gröbner, Alexej Schmidt, Jeanna Bugaytsova, Oscar Björnham, Göran O. Bylund, Rolf Sjöström, Stefan Oscarson, Dionyssios N. Sgouras, Lori M. Hansen, Yevgen A Chernov, Anders Esberg, Kristof Moonens, Christopher Aisenbrey, Charles Kelly, Ludmilla A. Morozova-Roche, Jeannette M. Whitmire, Beatriz Martinez-Gonzalez, Asish K. Mukhopadhyay, Angela Eldridge, Nicklas Strömberg, Robert H. Gilman, Andre Dubois, Lars Engstrand, Staffan Schedin, Brett A. Chromy, Justine Younson, Matthew Goldman, Anna Shevtsova, Macarena P. Quintana-Hayashi, Hui Liu, Magnus Unemo, Lena Rakhimova, Anna Åberg, Sebastian Suerbaum, Anna Arnqvist, Pär Gideonsson, Maréne Landström, Douglas E. Berg, Kristoffer Brännström, Anders Olofsson, Melissa Mendez, G. Balakrish Nair, Han Remaut, Umeå University, School of Life Sciences, University of Nottingham, UK (UON), Sahlgrenska Academy at University of Gothenburg [Göteborg], Université libre de Bruxelles (ULB), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Sumy State University, Max Von Pettenkofer Institute (MVP), Ludwig-Maximilians-Universität München (LMU), Uniformed Services University of the Health Sciences (USUHS), King‘s College London, Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), School of Digestive and Liver Diseases [Kolkata] (SDLD), National Institute of Cholera and Enteric Diseases, Translational Health Science and Technology Institute [Faridabad] (THSTI), Institut Pasteur Hellénique, Réseau International des Instituts Pasteur (RIIP), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Karolinska Institutet [Stockholm], Örebro University Hospital [Örebro, Sweden], Hannover Medical School [Hannover] (MHH), German Center for Infection Research - partner site Hannover-Braunschweig (DZIF), School of Chemistry and Chemical Biology (UCD), University College Dublin [Dublin] (UCD), University of California [Davis] (UC Davis), University of California, German Center for Infection Research, Partnersite Munich (DZIF), Département d'Informatique [Bruxelles] (ULB), Faculté des Sciences [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), University of California [San Diego] (UC San Diego), This work was supported by grants from Vetenskapsrådet (VR/M) to T.B. and S.K.L., Cancerfonden to T.B. and A.A., VR/NT to A.A. and S. Schedin, Formas to S.K.L., the J.C. Kempe and Seth M. Kempe Memorial Foundation, the Knut and Alice Wallenberg Foundation (2012.0090) to T.B. and M.L., European Union Seventh Framework Program GastricGlycoExplorer ITN grant number 316929 to T.B. and Y.A.C., Magn. Bergvall’s Foundation to S. Schedin, DFG (SFB 900/A1) to S. Suerbaum, DFG (HA2697/16-1) to R.H., FP6 ANR-06-PATHO-00701 ERA-NET and Actions Concertées Inter-Pasteuriennes (ACIP) (2006) to D.N.S., NIH R01DK063041 to D.E.B., NIH CA082312 to D.S.M., NIH AI070803 and AI081037 to J.V.S., CSIR project, India (No. 37(1640)/14/EMR –II) to A.K.M., and VIB and FWO (grants: G033717N and 12H8416N) to K.M. and H.R., This paper is dedicated to the memory of our friend, collaborator, and co-author Dr. Andre Dubois, a great scientist who contributed importantly both intellectually and materially to this project. We thank S. Michopoulos and G. Mantzaris for H. pylori clinical isolates and Ö. Furberg (NoPolo.se), N. Ulander (softplanbangkok.com), S. Lindström, and M. Borén for the digital movie, tech, art, and figure work, respectively., Vrije Universiteit Brussel, Basic (bio-) Medical Sciences, Structural Biology Brussels, and Department of Bio-engineering Sciences

Francois Lamoureux, Marta Tellez-Gabriel, Benjamin Ory, Dominique Heymann, Marie-Françoise Heymann, Laboratorio Hematologia Oncologica y de Transplantes [Barcelona, Spain], Institut Investigacions Biomèdiques (IBB) Sant Pau [Barcelona, Spain]-Hospital de la Santa Creu i Sant Pau, Equipe LIGUE Nationale Contre le Cancer 2012, Physiopathologie des Adaptations Nutritionnelles (PhAN), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Oncology and Metabolism [Sheffield, UK], The University of Sheffield [Sheffield, U.K.], European Associated Laboratory [Sheffield, UK] (Sarcoma Research Unit), This paper was written as a part of a research project which received funding from the Seventh Framework Programme ([FP7/2007-2013]) under grant agreement n 264817—BONE-NET. This work was supported by the Bone Cancer Research Trust (UK, research project number 144681)., European Project: 264817,EC:FP7:PEOPLE,FP7-PEOPLE-2010-ITN,BONE-NET(2011), Heymann, Dominique, and European Training Network on Cancer-Induced Bone Diseases - BONE-NET - - EC:FP7:PEOPLE2011-02-01 - 2015-01-31 - 264817 - VALID

Thierry Lefèvre, Amélie Vantaux, Anna Cohuet, Olivier Roux, Benjamin Roche, Kounbobr Roch Dabiré, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche en Sciences de la Santé (IRSS), CNRST, Transmission-Interactions-Adaptations hôtes/vecteurs/pathogènes (MIVEGEC-TRIAD), Evolution des Systèmes Vectoriels (ESV), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche en Sciences de la Santé (IRSS) / Centre Muraz, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), This study was funded by the ANR grant 11-PDOC-006-01 to TL., We would like to thank all of the children and their parents who participated in this study, as well as the local authorities for their support, and Andrea Yockey-Dejean for proofreading the paper. We are very grateful to the IRSS staff in Burkina Faso for technical assistance., and Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA)

Stéphanie Petrella, Alexandra Aubry, Nicolas Veziris, Hélène Ferrand, Claudine Mayer, Aurélie Bouige, Alix Pantel, Stéphanie Matrat, Wladimir Sougakoff, Université Pierre et Marie Curie - Paris 6 (UPMC), Microbiologie structurale - Structural Microbiology (Microb. Struc. (UMR_3528 / U-Pasteur_5)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie et de Maladies Infectieuses (CIMI), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Parts of this paper were presented at the ‘International Conference on Antimicrobial Agents and Chemotherapy’, USA, 2011 (C1-626), and at the EMBO Conference ‘Tuberculosis 2012’, France, 2012 (TUBERCULOSIS2012/000269)., Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence des Mycobactéries et de la Résistance aux Antituberculeux [CHU Pitié-Salpêtrière], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Bactériologie-Hygiène [CHU Pitié-Salpêtrière] ], and CHU Pitié-Salpêtrière [APHP]

Annelise Tran, Vladimir Grosbois, Jean-Pierre Ravalohery, Fanjasoa Rakotomanana, Jean-Michel Heraud, Soa Fy Andriamandimby, Christophe Rogier, Seta Andriamamonjy, Véronique Chevalier, Benoit Durand, Marie-Marie Olive, Animal et gestion intégrée des risques (UPR AGIRs), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Unité de Virologie [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Réseau International des Instituts Pasteur (RIIP), This study was supported in part by funds raised by (i) CIRAD (ii) the Centre National d'Etudes Spatiales (CNES, grant # 131163/00) (iii) the Institut Pasteur de Madagascar. Human field work was funded by the Institut Pasteur of Madagascar (Internal Project through the ZORA (ZOonoses, Rodent and Arboviruses) project and the Centers for Disease Control and Prevention (CDC, and Cooperative Agreement #U51/IP000327). Moreover, this material is based upon work supported by the U. S. Department of Homeland Security under the Center of Excellence of Emerging and Zoonotic Animal Diseases Grant Award Number 2010-ST061-AG0001. Cattle study was supported in part by funds raised by World Health Organization (WHO) and the Food and Agriculture Organization of the United Nations (FAO) through the Central Emergency Response Fund of the United Nations. The views and conclusions contained in this paper are those of the authors and should not be interpreted as necessarily representing the official policies, either explicit or implicit, of the U. S. Department of Homeland Security. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Antoine Chalopin, Benjamin Ory, Lidia Rodriguez Calleja, Marta Tellez Gabriel, Dominique Heymann, Equipe LIGUE Nationale Contre le Cancer 2012, Physiopathologie des Adaptations Nutritionnelles (PhAN), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre hospitalier universitaire de Nantes (CHU Nantes), Department of Oncology and Metabolism [Sheffield, UK], The University of Sheffield [Sheffield, U.K.], This paper was written as a part of research project which received funding from the Seventh Framework Program [(FP7/2007-2013) under grant agreement no. 264817—BONE-NET and this work was supported by the Fondation de France (Engt no. 16390)]., European Project: 264817,EC:FP7:PEOPLE,FP7-PEOPLE-2010-ITN,BONE-NET(2011), Heymann, Dominique, and European Training Network on Cancer-Induced Bone Diseases - BONE-NET - - EC:FP7:PEOPLE2011-02-01 - 2015-01-31 - 264817 - VALID

Alexandra Magro, Artur Gil, A.J.M. Loomans, Cang Hui, Katie M. Murray, Sandra Viglášová, Paul S. van Wielink, Axel Vandereycken, Arnaud Estoup, Susana Clusella-Trullas, Benoit Facon, Annette Herz, May-Guri Saethre, Zdenka Martinkova, Richard Comont, Isabel Borges, Dirk Maes, Sergey K. Ryndevich, Thomas Guillemaud, Helen E. Roy, António O. Soares, Marina J. Orlova-Bienkowskaja, Mary M. Gardiner, Alexander Ok Lukashuk, Tim Adriaens, William D. Hutchison, Ingrid A. Minnaar, Patrick De Clercq, John J. Sloggett, Peter M. J. Brown, Alois Honek, Marc Kenis, Audrey A. Grez, Hans Peter Ravn, Tania Zaviezo, Nick Berkvens, Wolfgang Rabitsch, Danny Haelewaters, Riaan Stals, Zihua Zhao, Ján Kulfan, John E. Losey, Peter Zach, Andy G. Howe, Eric Lombaert, I. A. Zakharov, Lori Lawson Handley, Oldrich Nedved, Robert L. Koch, Steph L. Rorke, Matthew C. Tinsley, Gabriele Rondoni, René Eschen, Naoya Osawa, Edward W. Evans, Gilles San Martin, Centre for Ecology and Hydrology [Wallingford] (CEH), Natural Environment Research Council (NERC), Anglia Ruskin University (ARU), Research Institute for Nature and Forest (INBO), Research Institute for Agricultural, Fisheries and Food (ILVO), University of the Azores, Centre for Ecology, Evolution and Environmental Changes (cE3c) / Azorean Biodiversity Group and Universidade dos Açores, Departamento de Ciências e Engenharia do Ambiente, Açores, Stellenbosch University, Centre for Invasion Biology, Department of Botany and Zoology, Bumblebee Conservation Trust, Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Crop Protection, Centre for Agricultural and Biosciences International Europe - Switzerland (CABI Europe - Switzerland), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Utah State University (USU), Ohio State University [Columbus] (OSU), Ohio Agricultural Research and Development Center, Universidad de Chile = University of Chile [Santiago] (UCHILE), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Crop Res Inst, Div Crop Genet & Breeding, Prague, Czech Republic, Partenaires INRAE, Department of Geosciences and Natural Resource Management [Copenhagen] (IGN), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Centre for Invasion Biology, Department of Mathematical Sciences, Stellenbosch University, University of Minnesota System, Institute of Forest Ecology - SAS, University of Hull [United Kingdom], National Plant Protection Organization (NPPO), Cornell University [New York], Berezinskiy Biosphere Reserve, Belarus, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Stirling, Department of Biological and Environmental Sciences, University of Stirling, Walloon Agricultural Research Centre, Department of Botany and Zoology, Centre of Excellence for Invasion Biology, University of South Bohemia, Institute of Entomology [České Budějovice] (BIOLOGY CENTRE CAS), Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Kyoto University [Kyoto], Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Environment Agency Austria, Department of Agricultural, Food and Environmental Sciences, University of Perugia (DSA3), Università degli Studi di Perugia (UNIPG), The paper had its origin at a workshop on 'Drivers, impacts, mechanisms and adaptation in insect invasions' hosted by the DST-NRF Centre of Excellence for Invasion Biology in Stellenbosch, South Africa, in November 2014. Additional financial support was provided by HortGro, the National Research Foundation of South Africa, Stellenbosch University, and SubTrop. We thank all our collaborators, and particularly the volunteer community, who have contributed to research around the world on H. axyridis. The number of references included reflects the range of inspiring studies on H. axyridis from so many people-we look forward to new and continued collaborations in the future. We are grateful to the editors of this special issue for inviting this review and providing an opportunity to explore ideas through the 'Invasive Insects Workshop funding (NRF South Africa, CIB)'. We also thank the anonymous reviewers for all their useful comments and reflections. The UK Ladybird Survey and associated coauthors are supported by the Biological Records Centre (part of the Centre for Ecology & Hydrology), which receives support from both the Natural Environment Research Council and the Joint Nature Conservation Committee. The IOBC WPRS and Global Working Groups 'Benefits and Risks of Exotic Biological Control Agents' and the COST Action TD1209 'Alien Challenge' have facilitated discussions and collaborations on H. axyridis. This study was supported by the French Agropolis Fondation (Labex Agro-Montpellier, BIOFIS Project Number 1001-001) and by a grant from the ERA-Net BiodivERsA, with the national funders ANR (France), DFG (Germany) and BELSPO (Belgium), as part of the 2012-2013 BiodivERsA call for research proposals. Support has been also received from FONDECYT 1140662 (Chile). The study of M.J. Orlova-Bienkowskaja and I. A. Zakharov was supported by Russian Science Foundation, Project No. 16-16-00079. Gabriele Rondoni acknowledges financial support from Fondazione Cassa di Risparmio di Perugia. Riaan Stals acknowledges funding from the Department of Science and Technology, South Africa. The research of Peter Zach and colleagues was funded by the project VEGA 2/0035/13 and VEGA 2/0052/15. A. Honek and Z. Martinkova were supported by grants GACR 14-26561S and COST CZ LD14084. Research in Switzerland is funded by the Swiss Federal Office for the Environment. Hans Peter Ravn was supported by the Villum Foundation. Danny Haelewaters acknowledges funding from the David Rockefeller Center for Latin American Studies at Harvard University and from the Mycological Society of America., Sobell Department of Motor Neuroscience and Movement Disorders, Institute of Neurology, Research Institute for Nature and Forest, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Julius Kühn Institute (JKI), CABI Europe Switzerland, Universität der Bundeswehr München [Neubiberg], Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Grad Sch Agr, Lab Forest Ecol, Department of Biodiversity and Nature Conservation, NEMOD Biotherapeutics GmbH & Co. KG, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile (UC), RS: FSE MSP, and Maastricht Science Programme

Patrick Loulergue, Stéphane Bruzaud, Nicolas Hachet, Jean-Luc Audic, Yves-Marie Corre, Adélaïde Le Grand, Véronique Le Tilly, Anne Elain, Magali Le Fellic, Laboratoire d'Ingénierie des Matériaux de Bretagne (LIMATB), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO), Plateforme technologique ProDiaBio (PFT ProDiaBio), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), The authors acknowledge the regions of Bretagne and Pays de Loire for funding. We are grateful to Breizpack and Valorial pole for their help and to the industrial partners of PHApack consortium: Europlastiques, Séché Environnement, Triballat Noyal and Cap Ouest, for their contribution to this research program. We are also thankful to Mélanie Blanche Barbat and Laureen Van Steenberge for their contribution to this work. We thank Maja Bumke Scheer for taking time to help us improve the paper., Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Tim D. Smith, Maria Grazia Pennino, David M. Kaplan, Sophie Monsarrat, Ana S. L. Rodrigues, Randall R. Reeves, Christine N. Meynard, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UPVM), UMR 212 EME 'écosystèmes marins exploités' (EME), Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), World Whaling History, Okapi Wildlife Associates, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Virginia Institute of Marine Science (VIMS), College of William and Mary [Williamsburg] (WM), The MORSE project funded this project (Agence Nationale de la Recherche, CEP&S 2011 – Project ANR-11-CEPL-006). This paper benefited from discussions with members of the CESAB (Center for Synthesis and Analysis of Biodiversity) PELAGIC project, financed by the 'Fondation pour la diversité' (FRB) and the Fondation TOTAL., ANR-11-CEPL-0006,MORSE,Gestion de ressources marines sous des attendus changeants : amener la perspective historique dans la conservation de mammifères marins(2011), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud])

Marco Lucarelli, Andrea Fuso, Vincenzina Nicolia, Department of Surgery, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Department of Cellular Biotechnologies and Haematology, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome]-Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), European Center for Brain Research (CERC)/Santa Lucia Foundation I.R.C.C.S., This paper was supported by funding from the EC 7th Framework Program (FP7/2007–2013) grant no. 278486 'DEVELAGE' and from the Sapienza Università di Roma, Scientific Research Programs 2012 and 2013., European Project: 278486,EC:FP7:HEALTH,FP7-HEALTH-2011-two-stage,DEVELAGE(2012), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, and Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA)

Emilia Scharrig, María Florencia Ferrer, Agostina Carestia, Mathieu Picardeau, Maia Cédola, Ricardo Martín Gómez, Mirta Schattner, Gabriela Pretre, Ricardo Drut, CCT La Plata-CONICET-Facultad de Ciencias Veterinarias [La Plata, PBA, Argentine], Universidad Nacional de la Plata [Argentine] (UNLP), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Children Hospital 'Superiora Sor María Ludovica' LA PLATA, Biologie des Spirochètes / Biology of Spirochetes, Institut Pasteur [Paris], This work was supported by PICTs grant 12-0434 (RMG) and 11-733 (MS) from ANPCyT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., Conceived and designed the experiments: MP MS RMG. Performed the experiments: ES AC MFF GP. Analyzed the data: MC RD. Contributed reagents/materials/analysis tools: MP. Wrote the paper: MS RMG., and Institut Pasteur [Paris] (IP)

Amélie Desvars, Alain Michault, Florence Naze, Pascale Bourhy, Mathieu Picardeau, Laboratoire de Bactériologie-Parasitologie-Virologie-Hygiène, Groupe Hospitalier Sud Réunion (GHSR), Centre Collaborateur FAO/OMS pour l'épidémiologie de la leptospirose, Institut Pasteur [Paris] (IP), Centre National de Référence de la Leptospirose - National Reference Center Leptospirosis (CNR), Biologie des Spirochètes / Biology of Spirochetes, The authors have no support or funding to report., Conceived and designed the experiments: AM MP PB. Performed the experiments: FN AD. Analyzed the data: AD MP AM PB. Contributed reagents/materials/analysis tools: FN PB. Wrote the paper: FN AD MP PB AM., and Institut Pasteur [Paris]