Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology

Horseshoe bats are the natural hosts of theSarbecovirussubgenus that includes SARS-CoV-1 and 2. Despite the devastating impacts of the COVID-19 pandemic, there is still little known about the underlying epidemiology and virology of sarbecoviruses in their natural hosts, leaving large gaps in our pandemic preparedness. Here we describe the results of PCR testing for sarbecoviruses in the two horseshoe bat species (Rhinolophus hipposiderosandR. ferrumequinum) present in Great Britain, collected in 2021-22 during the peak of COVID-19 pandemic. One hundred and ninety sevenR. hipposiderossamples from 33 roost sites and 277R. ferremequinumsamples from 20 roost sites were tested. No coronaviruses were detected in any samples fromR. ferrumequinumwhereas 44% and 56% of individual and pooled (respectively) faecal samples fromR. hipposiderosacross multiple roost sites tested positive in a sarbecovirus-specific qPCR. Full genome sequences were generated from three of the positive samples (and partial genomes from two more) using Illumina RNAseq on unenriched samples. Phylogenetic analyses showed that the obtained sequences belong to the same monophyletic clade, with >95% similarity, as previously reported European isolates fromR. hipposideros. The sequences differed in the presence or absence of accessory genes ORF 7b, 9b and 10. All lacked the furin cleavage site of SARS-CoV-2 spike gene and are therefore unlikely to be infective for humans. These results demonstrate a lack, or at least low incidence, of SARS-CoV-2 spill over from humans to susceptible GB bats, and confirm that sarbecovirus infection is widespread inR. hipposideros. Despite frequently sharing roost sites withR. ferrumequinum, no evidence of cross-species transmission was found.