Coronavirus in European hedgehogs (Erinaceus europaeus) from Denmark before and during the COVID-19 pandemic

The COVID-19 pandemic heightened public awareness and concern about the risks of zoonotic diseases potentially affecting the conservation of declining species such as the European hedgehog (Erinaceus europaeus). To investigate coronavirus prevalence, genetic diversity, and molecular characteristics relevant to the assessment of potential zoonotic risk in European hedgehogs, 430 hedgehog faecal samples were collected in Denmark and analysed using a pan-coronavirus RT-PCR assay followed by sequence analysis. Samples derived from two cohorts: 199 individuals sampled before the COVID-19 pandemic and 231 individuals sampled during the COVID-19 pandemic. Although the assay allowed detection of all coronavirus genera, only Betacoronavirus erinacei was found. The overall prevalence was 23% (98/430), with 16% (31/199) in 2016, and 29% (67/231) in 2021-22. In total 55 viral sequence types were identified, and their variability and geographical and temporal distribution were investigated. Moreover, key amino acids within the spike protein receptor-binding domain were characterised to evaluate potential receptor usage. The results indicate that European hedgehogs are unlikely to act as reservoirs for SARS-CoV-2. Furthermore, Betacoronavirus erinacei sequence types appear genetically stable across sampling years and regions. Viral prevalence was not associated with location, habitat type, age, sex, inbreeding, endoparasite infection, or the presence of methicillin-resistant Staphylococcus aureus (MRSA). However, exposure to pesticides, particularly herbicides, was associated with coronavirus infection (p = 0.049), warranting further investigation.