Molecular characterization and evolutionary dynamics of a recombinant PDCoV strain in a swine diarrhea epidemic with SADS-CoV co-infection

Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus that poses a significant threat to the swine industry. In this study, a novel PDCoV strain, designated PDCoV-ZJHZ2024, was identified from fecal samples of diarrheic pigs in China. Metagenomic analysis revealed co-detection of PDCoV and swine acute diarrhea syndrome coronavirus (SADS-CoV), with the microbial community predominantly composed of bacteria and characterized by abnormal enrichment of <i>Bacillus cereus</i> and pronounced gut microbiota dysbiosis. Genomic analyses demonstrated that PDCoV-ZJHZ2024 has undergone independent recombination events involving the ORF1b region and the spike (S) gene, accompanied by cross-regional genetic exchange, highlighting the critical role of recombination in PDCoV evolution and diversification. Codon usage analysis further indicated that codon preferences in this strain are primarily shaped by natural selection, potentially conferring enhanced translational efficiency in the host. Collectively, these findings underscore the evolutionary adaptability and transmission potential of PDCoV-ZJHZ2024 and provide new insights into PDCoV evolutionary dynamics, thereby informing future surveillance efforts and prevention strategies in swine populations.