Detection and characterisation of alpha- and betacoronaviruses in rodents and bats from Germany, France, Belgium and Ireland
Abstract
Recent zoonotic coronavirus outbreaks have sparked an interest in understanding coronaviruses circulating in animal reservoirs. While bats are recognised as major reservoirs for these viruses, coronaviruses have also been detected in a wide range of terrestrial small mammals, particularly rodents. However, coronavirus diversity in these mammals, specifically in Europe, is still poorly characterised. In this study, we detected and characterised coronaviruses in terrestrial small mammals and bats from Belgium, France, Germany, and Ireland. We screened tissue samples from rodents and shrews and environmental bat guano using pan-coronavirus real-time and conventional PCRs, with positive results confirmed by sanger sequencing. Among 2667 bat and 1152 terrestrial mammal samples, we detected 59 positive samples, 36 from bats and 23 from rodents, from which we recovered 60 coronavirus sequences, spanning both Alphacoronavirus and Betacoronavirus lineages. Through next generation sequencing we identified one Pipistrellus pygmaeus bat guano sample carrying two distinct alphacoronaviruses, representing Nyctacovirus and Pedacovirus subgenera. Among rodents, most coronavirus-positive samples originated from a zoo in Belgium, where several CoV lineages co-circulated. The identified rodent coronaviruses clustered among previously described rodent-associated lineages, some of which also include human and other mammal-derived coronavirus sequences. Consistent with previous studies, we found sarbecoviruses in horseshoe bats (particularly Rhinolophus ferrumequinum and R. hipposideros ) and merbecoviruses in Plecotus auritus bats, and these viruses are distantly related to the human coronaviruses of the respective families. Similar to bat coronaviruses, some rodent coronaviruses strains seemed to be association with specific rodent species. In conclusion, our study enhances the understanding of coronaviruses in rodents and bats, revealing potential hotspots for these viruses and their implication for human and animal health. These findings underscore the necessity for continued surveillance of coronaviruses in wildlife reservoirs to mitigate future zoonotic spillover risks. Author Summary Following recent zoonotic outbreaks, there is growing interest in understanding wildlife reservoirs for coronaviruses. While bats are well-known carriers of these viruses, terrestrial small mammals, specifically rodents, have received less attention. As a result, our knowledge of the diversity of coronaviruses in rodent remains limited. Hence, we investigated the diversity of coronaviruses in bats from environmental guano and terrestrial small mammals from their tissues in Belgium, France, Germany and Ireland. We identified a diverse range of coronaviruses in both rodents and bats that related to other human and animal infecting coronaviruses, but this does not imply their immediate zoonotic potential. Additionally, we found that some bat and rodent coronaviruses seemed to be associated with particular host species. These finding broaden the current knowledge of the diversity of coronaviruses in European small mammals and highlight the role of including rodents alongside bats in wildlife surveillance to deepen our understanding of virus diversity and their associated potential zoonotic risks.
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BibTeX
@misc{sgarabotto2026detection,
title = {{Detection and characterisation of alpha- and betacoronaviruses in rodents and bats from Germany, France, Belgium and Ireland}},
author = {Elena Sgarabotto and Vinaya Venkat and Eda Altan and Daan Gyzels and Mert Erdin and Veronica Lehtinen and Thanakorn Niamsap and Sofia Greilich and Akseli Valta and Maxime Galan and Jasmin Firozpoor and Jana. Eccard and Jens Jacob and Christian Imholt and Vincent Sluydts and Valeria Colombo and Herwig Leirs and Andrew Mcmanus and Peter Stuart and Sophie Gryseels and Luc de Bruyn and Christian Voigt and Uwe Hoffmeister and Hussein Alburkat and Vincent Bourret and Teemu Smura and Guillaume Castel and Nathalie Charbonnel and Tarja Sironen and Lara Dutra},
howpublished = {HAL},
year = {2026},
month = sep,
doi = {10.64898/2026.09.23.753110},
url = {https://hal.inrae.fr/hal-05780282v1},
note = {CC BY 4.0},
}
RIS
TY - UNPB
TI - Detection and characterisation of alpha- and betacoronaviruses in rodents and bats from Germany, France, Belgium and Ireland
AU - Elena Sgarabotto
AU - Vinaya Venkat
AU - Eda Altan
AU - Daan Gyzels
AU - Mert Erdin
AU - Veronica Lehtinen
AU - Thanakorn Niamsap
AU - Sofia Greilich
AU - Akseli Valta
AU - Maxime Galan
AU - Jasmin Firozpoor
AU - Jana. Eccard
AU - Jens Jacob
AU - Christian Imholt
AU - Vincent Sluydts
AU - Valeria Colombo
AU - Herwig Leirs
AU - Andrew Mcmanus
AU - Peter Stuart
AU - Sophie Gryseels
AU - Luc de Bruyn
AU - Christian Voigt
AU - Uwe Hoffmeister
AU - Hussein Alburkat
AU - Vincent Bourret
AU - Teemu Smura
AU - Guillaume Castel
AU - Nathalie Charbonnel
AU - Tarja Sironen
AU - Lara Dutra
PY - 2026
DA - 2026/09/23
PB - HAL
DO - 10.64898/2026.09.23.753110
UR - https://hal.inrae.fr/hal-05780282v1
AB - Recent zoonotic coronavirus outbreaks have sparked an interest in understanding coronaviruses circulating in animal reservoirs. While bats are recognised as major reservoirs for these viruses, coronaviruses have also been detected in a wide range of terrestrial small mammals, particularly rodents. However, coronavirus diversity in these mammals, specifically in Europe, is still poorly characterised. In this study, we detected and characterised coronaviruses in terrestrial small mammals and bats from Belgium, France, Germany, and Ireland. We screened tissue samples from rodents and shrews and environmental bat guano using pan-coronavirus real-time and conventional PCRs, with positive results confirmed by sanger sequencing. Among 2667 bat and 1152 terrestrial mammal samples, we detected 59 positive samples, 36 from bats and 23 from rodents, from which we recovered 60 coronavirus sequences, spanning both Alphacoronavirus and Betacoronavirus lineages. Through next generation sequencing we identified one Pipistrellus pygmaeus bat guano sample carrying two distinct alphacoronaviruses, representing Nyctacovirus and Pedacovirus subgenera. Among rodents, most coronavirus-positive samples originated from a zoo in Belgium, where several CoV lineages co-circulated. The identified rodent coronaviruses clustered among previously described rodent-associated lineages, some of which also include human and other mammal-derived coronavirus sequences. Consistent with previous studies, we found sarbecoviruses in horseshoe bats (particularly Rhinolophus ferrumequinum and R. hipposideros ) and merbecoviruses in Plecotus auritus bats, and these viruses are distantly related to the human coronaviruses of the respective families. Similar to bat coronaviruses, some rodent coronaviruses strains seemed to be association with specific rodent species. In conclusion, our study enhances the understanding of coronaviruses in rodents and bats, revealing potential hotspots for these viruses and their implication for human and animal health. These findings underscore the necessity for continued surveillance of coronaviruses in wildlife reservoirs to mitigate future zoonotic spillover risks. Author Summary Following recent zoonotic outbreaks, there is growing interest in understanding wildlife reservoirs for coronaviruses. While bats are well-known carriers of these viruses, terrestrial small mammals, specifically rodents, have received less attention. As a result, our knowledge of the diversity of coronaviruses in rodent remains limited. Hence, we investigated the diversity of coronaviruses in bats from environmental guano and terrestrial small mammals from their tissues in Belgium, France, Germany and Ireland. We identified a diverse range of coronaviruses in both rodents and bats that related to other human and animal infecting coronaviruses, but this does not imply their immediate zoonotic potential. Additionally, we found that some bat and rodent coronaviruses seemed to be associated with particular host species. These finding broaden the current knowledge of the diversity of coronaviruses in European small mammals and highlight the role of including rodents alongside bats in wildlife surveillance to deepen our understanding of virus diversity and their associated potential zoonotic risks.
ER -