Bat-associated coronavirus found in pigs in the Iberian Peninsula: insights into potential cross-species transmission

Abstract

Coronaviruses (CoVs) are a diverse group of RNA viruses that affect both human and animal health. Swine populations are particularly relevant in the ecology of CoVs, acting as potential intermediate hosts for zoonotic transmission. This study aimed to assess the occurrence of CoVs in farmed pigs in Portugal and Spain. A total of 400 fecal samples were collected from pigs in northern Portugal and northern Spain and screened using a broad-spectrum pan-CoV nested RT-PCR assay. Of these, 18 samples (4.5%) tested positive for CoV, and phylogenetic analyses confirmed their classification within the Alphacoronavirus genus. The detected sequences shared high nucleotide identity with bat-associated Alphacoronaviruses from Portugal, Spain, Italy, and the United Kingdom, emphasizing the importance of continued research on the role of bats in the transmission cycle and the zoonotic potential of Alphacoronaviruses. These findings highlight the importance of ongoing surveillance in swine populations to monitor emerging CoV strains and assess potential zoonotic risks.

Keywords: Coronavirus; Epidemiology; One health; Swine; Zoonosis.

Fig. 1

Geographic origin of swine farms included in the study, located in northern Portugal and Spain, near Porto region and Santiago de Compostela. Shaded areas and pig icons represent the approximate locations of the regions where sampled farms are situated

Fig. 2

Phylogenetic tree of the RdRp sequences of CoV detected in this study. The tree was inferred using MEGA X software with the General Time Reversible substitution model and visualized using the Interactive Tree of Life (iTOL). The tree includes 15 sequences obtained in the present study (highlighted in bold) and 46 reference CoV nucleotide sequences retrieved from GenBank, displayed with their isolate source, location, date and accession number (without bold or shading). Only bootstrap values ≥ 50% are shown. The alignment size of the sequences was 405 base pairs

Fig. 3

Phylogenetic tree of the RdRp sequences of CoV detected in this study for further subgenus characterization of Alphacoronavirus sequences detected. The tree was inferred using MEGA X software with the General Time Reversible substitution model and visualized using the Interactive Tree of Life (iTOL). The tree includes 15 sequences obtained in the present study (highlighted in bold) and 42 reference CoV nucleotide sequences retrieved from GenBank, displayed with their isolate source, location, date and accession number (without bold or shading). Only bootstrap values ≥ 50% are shown. The alignment size of the sequences was 366 base pairs