Coronavirus surveillance in Eurasian passerines reveals deltacoronaviruses in Eurasian Tree Sparrows

Coronaviruses (CoVs) are enveloped, single-stranded RNA viruses that infect various avian and mammalian hosts. Although gammacoronaviruses and deltacoronaviruses (DCoVs) are frequently reported in wild birds, information on their occurrence in Eurasian passerines is limited.

We investigated the occurrence of CoVs in passerines sampled during autumn migration 2020–2021. Faecal samples from 243 individuals representing 35 species were analysed using two pan-coronavirus RT-PCR assays. Viral RNA was detected in four pooled samples, all from Eurasian tree sparrows (Passer montanus). Subsequent testing of individual samples confirmed positivity in these individual samples, which were then subjected to Illumina whole-genome sequencing. The assembled genomes (26,017–26,018 bp) showed a nucleotide identity of 99.95–99.98%. Comparative analyses revealed a strong similarity of ORF1ab with porcine DCoV (95.64–96.12% amino acid identity) and with a previously described DCoV strain from sparrow (97.5%). In contrast, the spike (S) gene had lower amino acid identity (75.71–76.81%) and belonged to a separate group of avian DCoVs, suggesting recombination or a divergent evolutionary pathway.

The synanthropic behaviour and wide distribution of P. montanus may favour frequent contact with both wild and domestic hosts, increasing the potential for interspecies transmission of the virus. The genetic relatedness of these sparrow-derived DCoVs to porcine strains emphasises their potential importance for animal health and possible cross-species spread. This study provides the first genomic characterisation of DCoVs in P. montanus from Europe. The results emphasise the importance of including passerine birds in coronavirus surveillance and support the implementation of integrated One Health surveillance strategies linking wildlife, livestock and environmental data. Such approaches are crucial for the early detection of novel CoVs and for mitigating the risks of cross-border spread and transmission across different species.