Metagenomic Discovery of a Novel Sarbecovirus in the United Kingdom at the Western Extreme of the Range of Rhinolophidae

Abstract

Purpose: The origin of the current COVID-19 pandemic is unknown but horseshoe bats, of the family Rhinolophidae, are natural hosts to a suite of sarbecoviruses. Global surveillance is key to monitoring potentially pathogenic viral strains and improving the capacity for surveillance across Europe will bolster our understanding of viral populations within zoonotic reservoirs. Methods & Materials: Faecal samples were collected from Lesser horseshoe bats (Rhinolophus hipposideros) in the UK during annual population monitoring surveys, stored in RNAlater and frozen prior to genomic analysis. For metagenomic analysis, the Sequence-independent Single-Primer Amplification (SISPA) method was employed and sequencing completed using Illumina Nextera and the Oxford Nanopore GridION platforms. Results: A De novo hybrid assembly utilising shorter Illumina reads with longer Nanopore reads acting as a scaffold, generated a 29kb contig named RhGB01. Mapping raw reads against RhGB01 demonstrated a combined depth of 50x across the genome. Sequence alignment exhibits genomic organisation comparable to other sarbecoviruses isolated from animal and human hosts. Within the receptor binding domain, but excluding the receptor binding motif, RhGB01 has 77% and 81% amino acid homology compared to SARS-CoV-2 and SARS respectively. Maximum likelihood phylogenies inferred from the nucleotide sequence of RNA dependent RNA polymerase, spike glycoprotein and entire coding sequence exhibit clustering with the only other fully sequenced zoonotic Sarbecovirus from Europe which was isolated from Rhinolophus blasii. The structure of the receptor binding domain of RhGB01 was predicted by homology modelling using a crystal structure of the receptor binding domain of SARS-CoV as a template. This model was selected with a Global Model Quality Estimate (GMQE) > 0.7 and Quaternary Structure Quality Estimate (QMEAN) of -2.18. Structural comparisons between the predicted receptor binding domain of RhGB01 and SARS-CoV-2 highlight structurally different regions which house hACE2 contact residues. Conclusion: Phylogenetic inference and structural modelling suggest an absence of pathogenic potential for RhGB01. However, the discovery of a novel Sarbecovirus at the western limit of Lesser horseshoe bats demonstrates their presence throughout the entire horseshoe bat distribution and indicates the need for viral surveillance systems in Western Europe.