Genomic characterization and cross-species transmission potential of hedgehog coronavirus

In the 21st century, three betacoronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have emerged in humans worldwide as a result of animal spillover, causing severe respiratory infections and resulting in more than seven million deaths. In 2013, a novel <i>Betacoronavirus</i> closely related to MERS-CoV (<i>Betacoronavirus cameli)</i> was discovered in European hedgehogs (<i>Erinaceus europaeus</i>), raising questions on the possibility of hedgehog-to-human transmission. Hence, the present study aimed to investigate and characterize the presence and genetic diversity of coronaviruses in hedgehogs from Portugal, as well as their potential for cross-species transmission. To achieve this, fecal samples from 110 hedgehogs at two recovery centers and one environmental non-governmental organization were tested for coronaviruses using a broad-spectrum nested RT-PCR assay targeting the <i>RdRp</i> gene. Of these samples, 24.5 % tested positive, most belonging to the <i>Betacoronavirus</i> genus. However, the present study also reports, for the first time, <i>Alphacoronaviruses</i> in hedgehogs, showing 100 % identity with a Bat coronavirus (a variant of <i>Alphacoronavirus miniopteri)</i>. The genome sequencing of one betacoronavirus-positive sample yielded 65 % of a full-length genome, with the closest homology (93.5 %) to <i>Betacoronavirus erinacei</i> from the United Kingdom. Computational protein-protein docking studies predicted the binding affinity between the spike protein of hedgehog coronavirus and cell receptors of mammal species that interact with hedgehogs. The results obtained raise the question of whether hedgehog CoV uses the same receptor as MERS-CoV or a different receptor to enter host cells. Thus, this study enhances our understanding of the epidemiology of coronaviruses, emphasizing the need for further investigation into cross-species transmission risks.