Phylogenetic Characteristics and High Prevalence of a Merbecovirus in Hedgehogs from Greenspace of a Metropolis, China

TL;DR

A new coronavirus with high prevalence in hedgehogs in Beijing is found to be closely related to known coronaviruses, raising concerns about potential human transmission.

Contribution

Discovery of a Merbecovirus in hedgehogs with high prevalence and evidence of recombination with a bat coronavirus.

Findings

30% prevalence of Merbecovirus in 317 hedgehogs in Beijing's greenspaces.

Viral genomes show close relation to Ea-HedCoV HKU31 with 93.24–96.42% nucleotide identity.

Evidence of recombination with Tylonycteris bat coronavirus HKU4 identified.

Abstract

SARS-CoV, MERS-CoV, and SARS-CoV-2 have posed tremendous threats to human health, highlighting the necessity of monitoring cross-species transmission of animal coronaviruses to humans. Hedgehogs infected with coronaviruses have been reported in several countries across Europe and Asia, raising concerns about the potential transmission of coronaviruses from hedgehogs to humans. In this study, we investigated coronavirus infections in hedgehogs inhabiting greenspaces in metropolitan Beijing and identified a Merbecovirus subgenus coronavirus with a prevalence rate of 30% (95% CI: 25–35%) among 317 hedgehogs. Phylogenetic analysis of 23 complete viral genome sequences revealed a monophyletic origin, showing close relatedness to Erinaceus hedgehog coronavirus HKU31 (Ea-HedCoV HKU31) with genome-wide nucleotide identities of 93.24–96.42%, and evidence of recombination with Tylonycteris bat coronavirus HKU4. These findings suggest that the increase in wildlife populations associated with urban greenspace development may pose a potential threat to human health that should not be overlooked.

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