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1. At least seven distinct rotavirus genotype constellations in bats with evidence of reassortment and zoonotic transmissions

Author

Ceren Simsek, Alexander N. Lukashev, Ward Deboutte, Yaw Adu Sarkodie, Daan Jansen, Hermann Ulrich Everling, Kwe Claude Yinda, Tabea Binger, Florian Gloza-Rausch, Eric M. Leroy, Mathieu Bourgarel, Leen Beller, Victor M. Corman, Augustina Sylverken, Stoian Yordanov, Marc Van Ranst, Jan Felix Drexler, Samuel Oppong, Gael Darren Maganga, Jelle Matthijnssens, Peter Vallo, Christian Drosten, Antje Seebens-Hoyer, Andrea Rasche, Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], German Center for Infection Research, Partnersite Munich (DZIF), University of Bonn, Sechenov First Moscow State Medical University, Université des Sciences et Techniques de Masuku [Franceville, Gabon] (USTM), Centre International de Recherches Médicales de Franceville (CIRMF), Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Noctalis, Centre for Bat Protection and Information, Forestry Board Directorate of Strandja Natural Park, Strandja Natural Park, Kwame Nkrumah University of Science and Technology [GHANA] (KNUST), Institute of Vertebrate Biology of the Czech Academy of Sciences (IVB / CAS), Czech Academy of Sciences [Prague] (CAS), 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]), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), This project has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie agreement no. 721367 granted to J.F.D., J.M., and M.V.R. EU Horizon 2020 projects EVAg (grant agreement number 653316) and COMPARE (agreement number 643476) granted to C.D., and the Russian Science Foundation grant 19-15-00055 to A.N.L. also provided funding to the current study. H.U.E. had a personal scholarship from the BONFOR intramural program at the University of Bonn. German Federal Ministry of Education and Research (BMBF) (project code 01KIO16D), Deutsche Forschungsgemeinschaft (DFG DR 772-3/1), Deutsche Forschungsgemeinschaft within the Africa Infectious Diseases program gave grants to C.D. and Y.A.S. (DR 772/3-1) and to S.O. (KA1241/18-1) that were also among the funding contributions. A personal scholarship granted to A.R. from the German Academic Exchange Service (DAAD) supported field work in Costa Rica. D. J. was supported by the Fonds Wetenschappelijk Onderzoek (Research foundation Flanders) (1S78019N). L.B. was supported by the Fonds Wetenschappelijk Onderzoek (1S61618N). K.C.Y. was funded by the Interfaculty Council for Development Cooperation (IRO) from the KU Leuven. The computing power in this work was provided by the VSC (Flemish Supercomputer Centre), financed by the FWO and the Flemish government, department EWI., European Project: 777657,H2020-EU.1.3.3. - Stimulating innovation by means of cross-fertilisation of knowledge,777657,MSCA-RISE(2018), European Project: 653316,H2020,H2020-INFRAIA-2014-2015,EVAg(2015), European Project: 643476,H2020,H2020-PHC-2014-single-stage,COMPARE(2014), Universität Bonn = University of Bonn, Université des Sciences et Techniques de Masuku (USTM), and Kwame Nkrumah University of Science and Technology (KNUST)

Subjects
Rotavirus, Viral metagenomics, [SDV]Life Sciences [q-bio], viruses, Reassortment, medicine.disease_cause, L73 - Maladies des animaux, Genome, Zoonoses, Chiroptera, Genotype, Phylogeny, 0303 health sciences, Phylogenetic tree, Strain (biology), [SDV.BA]Life Sciences [q-bio]/Animal biology, Zoonosis, virus diseases, QR1-502, 3. Good health, S50 - Santé humaine, Middle East Respiratory Syndrome Coronavirus, Research Article, Diarrhea, zoonose, Middle East respiratory syndrome coronavirus, relation homme-faune, Genome, Viral, Ecological and Evolutionary Science, Biology, Microbiology, Rotavirus Infections, rotavirus genetic diversity, SA11, 03 medical and health sciences, Coronavirus 2 du syndrome respiratoire aigu sévère, Virology, medicine, Animals, Humans, Horses, Transmission des maladies, 030304 developmental biology, Genetic diversity, 030306 microbiology, SARS-CoV-2, COVID-19, Genetic Variation, zoonosis, medicine.disease, respiratory tract diseases, Evolutionary biology, bat rotavirus, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Metagenomics, Virus pathogène
Abstract

The increased research on bat coronaviruses after severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) allowed the very rapid identification of SARS-CoV-2. This is an excellent example of the importance of knowing viruses harbored by wildlife in general, and bats in particular, for global preparedness against emerging viral pathogens., Bats host many viruses pathogenic to humans, and increasing evidence suggests that rotavirus A (RVA) also belongs to this list. Rotaviruses cause diarrheal disease in many mammals and birds, and their segmented genomes allow them to reassort and increase their genetic diversity. Eighteen out of 2,142 bat fecal samples (0.8%) collected from Europe, Central America, and Africa were PCR-positive for RVA, and 11 of those were fully characterized using viral metagenomics. Upon contrasting their genomes with publicly available data, at least 7 distinct bat RVA genotype constellations (GCs) were identified, which included evidence of reassortments and 6 novel genotypes. Some of these constellations are spread across the world, whereas others appear to be geographically restricted. Our analyses also suggest that several unusual human and equine RVA strains might be of bat RVA origin, based on their phylogenetic clustering, despite various levels of nucleotide sequence identities between them. Although SA11 is one of the most widely used reference strains for RVA research and forms the backbone of a reverse genetics system, its origin remained enigmatic. Remarkably, the majority of the genotypes of SA11-like strains were shared with Gabonese bat RVAs, suggesting a potential common origin. Overall, our findings suggest an underexplored genetic diversity of RVAs in bats, which is likely only the tip of the iceberg. Increasing contact between humans and bat wildlife will further increase the zoonosis risk, which warrants closer attention to these viruses.

Published
2021

2. Bats host major mammalian paramyxoviruses

Author

Jan Felix Drexler, Victor Max Corman, Marcel Alexander Müller, Gael Darren Maganga, Peter Vallo, Tabea Binger, Florian Gloza-Rausch, Veronika M. Cottontail, Andrea Rasche, Stoian Yordanov, Antje Seebens, Mirjam Knörnschild, Samuel Oppong, Yaw Adu Sarkodie, Célestin Pongombo, Alexander N. Lukashev, Jonas Schmidt-Chanasit, Andreas Stöcker, Aroldo José Borges Carneiro, Stephanie Erbar, Andrea Maisner, Florian Fronhoffs, Reinhard Buettner, Elisabeth K. V. Kalko, Thomas Kruppa, Carlos Roberto Franke, René Kallies, Emmanuel R.N. Yandoko, Georg Herrler, Chantal Reusken, Alexandre Hassanin, Detlev H. Krüger, Sonja Matthee, Rainer G. Ulrich, Eric M. Leroy, Christian Drosten, Institute of Virology, University of Bonn Medical Centre, Centre International de Recherches Médicales de Franceville (CIRMF), Institute of Vertebrate Biology, Czech Academy of Sciences [Prague] (CAS), Noctalis, Centre for Bat Protection and Information, Institute of Virology [Hannover], Hannover Medical School [Hannover] (MHH), Forestry Board Directorate of Strandja Natural Park, Strandja Natural Park, Kwame Nkrumah University of Science and Technology [GHANA] (KNUST), University of Lubumbashi, Chumakov Institute of Poliomyelitis and Viral Encephalitides, Department of Virology, Bernhard Nocht Institute for Tropical Medicine - Bernhard-Nocht-Institut für Tropenmedizin [Hamburg, Germany] (BNITM), Infectious Diseases Research Laboratory, Universidade Federal da Bahia (UFBA)-University Hospital Professor Edgard Santos, School of Veterinary Medicine, Universidade Federal da Bahia (UFBA), Institut für Virologie, Philipps University, Institute of Pathology, University of Cologne Medical Centre, Smithsonian Tropical Research Institute, Institute of Experimental Ecology, Universität Ulm - Ulm University [Ulm, Allemagne], Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Institut Pasteur de Bangui, Réseau International des Instituts Pasteur (RIIP), Netherlands Center for Infectious Disease Control, Muséum national d'Histoire naturelle (MNHN), Institute of Medical Virology (Helmut Ruska Haus), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Department of Conservation Ecology and Entomology, Stellenbosch University, Institute of Novel and Emerging Infectious Diseases (INNT), Friedrich-Loeffler-Institut (FLI), Institut de Recherche pour le Développement (IRD [France-Sud]), This study was funded by the European Union FP7 projects EMPERIE (Grant agreement number 223498) and EVA (Grant agreement number 228292), the German Federal Ministry of Education and Research (BMBF, project code 01KIO701), the German Research Foundation (DFG, Grant agreement number DR 772/3-1) to CD, the German Federal Ministry of Education and Research (BMBF) through the National Research Platform for Zoonoses (project code 01KI1018), the Umweltbundesamt (FKZ 370941401) and the Robert Koch-Institut (FKZ 1362/1-924) to RGU, through the Government of Gabon, Total-Fina-Elf Gabon and the Ministère des Affaires Etrangères, France., European Project: 223498,EC:FP7:HEALTH,FP7-HEALTH-2007-B,EMPERIE(2009), Kwame Nkrumah University of Science and Technology (KNUST), and Université de Lubumbashi (UNILU)

Subjects
animal structures, Paramyxoviridae, viruses, Molecular Sequence Data, General Physics and Astronomy, Mumps virus, medicine.disease_cause, Article, General Biochemistry, Genetics and Molecular Biology, Mice, 03 medical and health sciences, Pneumovirinae, Dogs, Chiroptera, Veterinary virology, medicine, Animals, Humans, Phylogeny, Disease Reservoirs, 030304 developmental biology, Mammals, 0303 health sciences, Paramyxoviridae Infections, Multidisciplinary, Ebola virus, biology, 030306 microbiology, Canine distemper, General Chemistry, biology.organism_classification, medicine.disease, Virology, Sendai virus, 3. Good health, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Henipavirus
Abstract

The large virus family Paramyxoviridae includes some of the most significant human and livestock viruses, such as measles-, distemper-, mumps-, parainfluenza-, Newcastle disease-, respiratory syncytial virus and metapneumoviruses. Here we identify an estimated 66 new paramyxoviruses in a worldwide sample of 119 bat and rodent species (9,278 individuals). Major discoveries include evidence of an origin of Hendra- and Nipah virus in Africa, identification of a bat virus conspecific with the human mumps virus, detection of close relatives of respiratory syncytial virus, mouse pneumonia- and canine distemper virus in bats, as well as direct evidence of Sendai virus in rodents. Phylogenetic reconstruction of host associations suggests a predominance of host switches from bats to other mammals and birds. Hypothesis tests in a maximum likelihood framework permit the phylogenetic placement of bats as tentative hosts at ancestral nodes to both the major Paramyxoviridae subfamilies (Paramyxovirinae and Pneumovirinae). Future attempts to predict the emergence of novel paramyxoviruses in humans and livestock will have to rely fundamentally on these data., The large virus family, Paramyxoviridae, includes several human and livestock viruses. This study, testing 119 bat and rodent species distributed globally, identifies novel putative paramyxovirus species, providing data with potential uses in predictions of the emergence of novel paramyxoviruses in humans and livestock.

Published
2012

3. At Least Seven Distinct Rotavirus Genotype Constellations in Bats with Evidence of Reassortment and Zoonotic Transmissions.

Author

Simsek C, Corman VM, Everling HU, Lukashev AN, Rasche A, Maganga GD, Binger T, Jansen D, Beller L, Deboutte W, Gloza-Rausch F, Seebens-Hoyer A, Yordanov S, Sylverken A, Oppong S, Sarkodie YA, Vallo P, Leroy EM, Bourgarel M, Yinda KC, Van Ranst M, Drosten C, Drexler JF, and Matthijnssens J

Subjects
Animals, COVID-19 transmission, COVID-19 virology, Diarrhea virology, Genetic Variation, Genome, Viral, Genotype, Horses, Humans, Metagenomics, Middle East Respiratory Syndrome Coronavirus isolation & purification, Phylogeny, SARS-CoV-2 isolation & purification, Chiroptera virology, Rotavirus genetics, Rotavirus Infections transmission, Rotavirus Infections virology, Zoonoses transmission, Zoonoses virology
Abstract

Bats host many viruses pathogenic to humans, and increasing evidence suggests that rotavirus A (RVA) also belongs to this list. Rotaviruses cause diarrheal disease in many mammals and birds, and their segmented genomes allow them to reassort and increase their genetic diversity. Eighteen out of 2,142 bat fecal samples (0.8%) collected from Europe, Central America, and Africa were PCR-positive for RVA, and 11 of those were fully characterized using viral metagenomics. Upon contrasting their genomes with publicly available data, at least 7 distinct bat RVA genotype constellations (GCs) were identified, which included evidence of reassortments and 6 novel genotypes. Some of these constellations are spread across the world, whereas others appear to be geographically restricted. Our analyses also suggest that several unusual human and equine RVA strains might be of bat RVA origin, based on their phylogenetic clustering, despite various levels of nucleotide sequence identities between them. Although SA11 is one of the most widely used reference strains for RVA research and forms the backbone of a reverse genetics system, its origin remained enigmatic. Remarkably, the majority of the genotypes of SA11-like strains were shared with Gabonese bat RVAs, suggesting a potential common origin. Overall, our findings suggest an underexplored genetic diversity of RVAs in bats, which is likely only the tip of the iceberg. Increasing contact between humans and bat wildlife will further increase the zoonosis risk, which warrants closer attention to these viruses. IMPORTANCE The increased research on bat coronaviruses after severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) allowed the very rapid identification of SARS-CoV-2. This is an excellent example of the importance of knowing viruses harbored by wildlife in general, and bats in particular, for global preparedness against emerging viral pathogens. The current effort to characterize bat rotavirus strains from 3 continents sheds light on the vast genetic diversity of rotaviruses and also hints at a bat origin for several atypical rotaviruses in humans and animals, implying that zoonoses of bat rotaviruses might occur more frequently than currently realized., (Copyright © 2021 Simsek et al.)

Published
2021
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