Sequencing of Betacoronavirus erinacei from faeces of pet hedgehogs demonstrates a continuity of MERS-CoV like viruses in European and Eurasian hedgehog species.

Hedgehogs have been recently identified as carriers of Betacoronavirus erinacei (also known as Erinaceus coronavirus, EriCoV) a virus closely related to B. cameli responsible for human Middle East Respiratory Syndrome (MERS), raising questions about the risk of hedgehog-to-human transmission and suggesting the need for coronavirus (CoV) surveillance in hedgehogs. This study investigated the presence of CoVs in fecal samples of hedgehogs kept as pets in Italy in 2021-2022. A pan-CoV nested RT-PCR targeting the RdRp gene was used for screening and positive samples were sequenced and phylogenetically analyzed. Two (6.2%) out of 30 hedgehogs analyzed were positive for B. erinacei represented by 2/3 (66.7%) long eared hedgehog (Hemiechinus auritus) while all the 27 tested African pygmy hedgehog (Atelerix albiventris) were negative. Whole genome sequence obtained from one B. erinacei-positive sample showed closest homology (85.7%) with B. erinacei previously detected in Erinaceus sp. from Eastern Russia. Phylogeny showed that the virus of this study formed a separate clade in the cluster with other B. erinacei identified in Europe and European Russia and did not cluster with other B. erinacei identified in China in Amur hedgehog (E. amurensis). No recombination events were observed. Analysis of the Spike protein revealed the presence of six out of the 11 key receptor binding residues, including two out of the three critical residues recently identified for the binding of Erinaceus europaeus receptor APN and B. erinacei. Results of this study suggest the presence of a long-eared hedgehog-specific strain of B. erinacei. Overall results support the circulation of coronaviruses along a phylogenetic continuum among different species of hedgehogs and geographic locations, suggesting the need for further CoV surveillance in both domestic and wild animals. There is also a need for studies on the affinity of EriCoV with the H. auritus APN specific receptor to confirm its involvement in the viral entry process.