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.

ASTRE Montpellier University CIRAD INRA Montpellier France

Centre International de Recherches Médicales de Franceville Franceville Gabon

Charité Universitätsmedizin Berlin corporate member of Freie Universität Berlin Humbolt Universität zu Berlin and Berlin Institute of Health Institute of Virology Berlin Germany

CIRAD UMR ASTRE Harare Zimbabwe

Forestry Board Directorate of Strandja Natural Park Malko Tarnovo Bulgaria

German Centre for Infection Research associated partner Charité Universitätsmedizin Berlin Berlin Germany

Institut de Recherche pour le Développement UMR 224 IRD CNRS Montpellier University Montpellier France

Institute of Vertebrate Biology Academy of Sciences of the Czech Republic v v i Brno Czech Republic

Institute of Virology University of Bonn Medical Centre Bonn Germany

KU Leuven University of Leuven Department of Microbiology Immunology and Transplantation Rega Institute for Medical Research Leuven Belgium

Kumasi Centre for Collaborative Research in Tropical Medicine Kumasi Ghana

Kwame Nkrumah University of Science and Technology Kumasi Ghana

Noctalis Centre for Bat Protection and Information Bad Segeberg Germany

Sechenov University Moscow Russia

Université des Sciences et Technique de Masuku Institut National d'Agronomie et de Biotechnologies Franceville Gabon

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