Genomic screening of UK bats reveals novel coronaviruses with zoonotic potential

Deep sequencing study of samples from 16 native bats in the UK uncovers presence of new coronavirus species with zoonotic capacity, and highlights potential viral hotspots in distinct regions of the country

GBIF-mediated data resources used : 42,953 species occurrences
Plecotus auritus
Brown long-eared bat [Plecotus auritus (Linnaeus, 1758)] observed in Lockington, Derby, UK by FPCR (CC BY 4.0)

Zoonotic diseases—arising from animal-to-human pathogen transmission—represent the majority of emerging infectious diseases worldwide. SARS-CoV-2, the agent responsible for the COVID-19 pandemic, is just one of seven major coronaviruses known to infect humans, but many more may exist.

In a study published today in Nature Communications, researchers from the UK and Switzerland collaborated with conservationist networks to screen native bat species in the UK for the presence of coronaviruses using deep RNA sequencing of faecal samples.

The analysis detected viral RNA from at least 30 families while nine complete coronavirus genomes were recovered from six bat species. Phylogenetic analyses of these revealed two new virus species present in samples—one from a lesser horseshoe bat (Rhinolophus hipposideros) and the other from a brown long-eared bat (Plecotus auritus).

By synthetic construction of the so-called spike proteins from the recovered viral genomes, the authors tested the in vitro ability of viruses to bind and enter cell lines expressing angiotensin-converting enzyme 2 (ACE2) receptors (known to facilitate SARS-CoV-2 infection in human cells). They found that at least one of the viruses identified was able to bind and use the receptor for cellular entry, albeit suboptimally.

Four of the genomes represented a single viral species recovered from two distinct bat species (Rhinolophus ferrumequinum and R. hipposideros) indicating an ability to infect a broader range of hosts. Using bat occurrences from the National Biodiversity Network (NBN) Atlas and GBIF, the authors modelled the species distributions, finding a high overlap between the two species.

Expanding the distribution analysis to all UK breeding bat species, the authors identified the highest bat diversity in three regions near Bristol, Birmingham and Brighton, representing potential viral sharing hotspots important for future coronavirus surveillance.

Tan CCS, Trew J, Peacock TP, Mok KY, Hart C, Lau K, Ni D, Orme CDL, Ransome E, Pearse WD, Coleman CM, Bailey D, Thakur N, Quantrill JL, Sukhova K, Richard D, Kahane L, Woodward G, Bell T, Worledge L, Nunez-Mino J, Barclay W, Dorp Lv, Balloux F, Savolainen V (2023) Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential. Nature Communications. Springer Science and Business Media LLC. Available at: