Coronavirus surveillance in passerines reveals novel deltacoronaviruses in Eurasian tree sparrows with implications for One Health and livestock biosecurity.

Coronaviruses (CoVs) are widespread RNA viruses infecting a broad range of avian and mammalian hosts. Although gammacoronaviruses and deltacoronaviruses (DCoVs) are common in wild birds, their presence in Eurasian passerines remains poorly understood. We screened 243 birds (35 species) at migratory stopover sites in Slovenia (2020-2021) using pan-coronavirus RT-PCR. Coronavirus RNA was detected only in four Eurasian Tree Sparrows (Passer montanus). Whole-genome sequencing yielded genomes of 26,017-26,018 bp with high internal conservation (99.95-99.98% identity). Phylogenetic analysis revealed notable evolutionary incongruence: isolates were highly related to porcine DCoVs in the ORF1ab region (95.6-96.1% amino acid identity) but clustered with divergent avian DCoVs in the spike gene (75.7-76.8% identity). RDP5 analysis provided strong evidence for a large-scale recombination event (p = 1.17 × 10-43), consistent with a mosaic genomic architecture combining an ORF1ab region closely related to porcine DCoVs with an avian-associated spike gene. This genomic pattern highlights evolutionary connectivity among DCoVs associated with different host groups and the potential role of recombination in changes in host association. The synanthropic behaviour and mobility of P. montanus facilitate contact with diverse hosts, making this species relevant for investigating DCoV ecology at wildlife-livestock interfaces. These findings represent the first genomic characterisation of DCoVs in P. montanus in Europe and support the inclusion of passerines in broader coronavirus surveillance. Genomic surveillance of underrepresented wild-bird hosts can improve our understanding of DCoV diversity, recombination, and evolution across wildlife-livestock interfaces.