Metagenomic identification of a new sarbecovirus from horseshoe bats in Europe

Jack M Crook,Miles Carroll,Diana Bell,Richard Vipond,Steven T Pullan,Daniel P Carter,Ivana Murphy,Andrew A Cunningham

doi:10.1038/s41598-021-94011-z

Abstract

The source of the COVID-19 pandemic is unknown, but the natural host of the progenitor sarbecovirus is thought to be Asian horseshoe (rhinolophid) bats. We identified and sequenced a novel sarbecovirus (RhGB01) from a British horseshoe bat, at the western extreme of the rhinolophid range. Our results extend both the geographic and species ranges of sarbecoviruses and suggest their presence throughout the horseshoe bat distribution. Within the spike protein receptor binding domain, but excluding the receptor binding motif, RhGB01 has a 77% (SARS-CoV-2) and 81% (SARS-CoV) amino acid homology. While apparently lacking hACE2 binding ability, and hence unlikely to be zoonotic without mutation, RhGB01 presents opportunity for SARS-CoV-2 and other sarbecovirus homologous recombination. Our findings highlight that the natural distribution of sarbecoviruses and opportunities for recombination through intermediate host co-infection are underestimated. Preventing transmission of SARS-CoV-2 to bats is critical with the current global mass vaccination campaign against this virus.

Highlights

The source of the COVID-19 pandemic is unknown, but the natural host of the progenitor sarbecovirus is thought to be Asian horseshoe bats
Metagenomic analysis revealed an unclassified betacoronavirus in a single sample with genome organisation consistent with Sarbecovirus
We discovered a novel sarbecovirus (RhGB01), the first to be described in the UK, after sampling just 53 lesser horseshoe bat faecal samples

Summary

Introduction

The source of the COVID-19 pandemic is unknown, but the natural host of the progenitor sarbecovirus is thought to be Asian horseshoe (rhinolophid) bats. We identified and sequenced a novel sarbecovirus (RhGB01) from a British horseshoe bat, at the western extreme of the rhinolophid range. Our results extend both the geographic and species ranges of sarbecoviruses and suggest their presence throughout the horseshoe bat distribution. The natural hosts of both SARS-CoV and SARS-CoV-2 (family Coronaviridae; subgenus Sarbecovirus)[2], the causative agents of SARS and COVID-19 respectively, are thought to be horseshoe bats (Rhinolophidae), with the zoonotic spillover process involving one or more intermediate hosts, during which time viral mutation, recombination and/or amplification could have o ccurred[3,4,5,6,7]. We expand the investigation of SARSr-CoVs to the lesser horseshoe bat (Rhinolophus hipposideros) in the UK, which is at the western extreme of the range of the Rhinolophidae

Methods

Results

Conclusion