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

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 <i>Merbecovirus</i> 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 <i>Erinaceus</i> hedgehog coronavirus HKU31 (<i>Ea</i>-HedCoV HKU31) with genome-wide nucleotide identities of 93.24-96.42%, and evidence of recombination with <i>Tylonycteris</i> 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.