Outbreak of porcine deltacoronavirus in pigs in central China, 2024

Abstract

Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus responsible for acute diarrhea, vomiting, and dehydration in piglets, thereby posing a substantial threat to the global swine industry. In December 2024, a severe diarrheal disease outbreak occurred on an intensive pig farm in Hubei Province, located in central China. Here, we describe the isolation and genomic characterization of a novel PDCoV strain, designated SP2403-2, obtained from the intestinal contents of an affected piglet. The virus was successfully propagated in cell culture and confirmed by immunofluorescence staining and transmission electron microscopy. The near-complete genome of SP2403-2, comprising 25,244 nucleotides, was sequenced. Comparative genomic analyses showed that SP2403-2 shares 97.0–99.2% nucleotide identity with reference PDCoV strains, with the highest similarity (99.2%) to the recently reported Chinese strain JSTZ2025. Phylogenetic analyses based on complete genome, ORF1ab, and S gene sequences demonstrated that SP2403-2 belongs to the Chinese lineage. Notably, alignment of the spike (S) protein of SP2403-2 with that of the vaccine strain CHN-HN-2014 revealed 25 amino acid substitutions. Structural mapping indicated that these mutations are predominantly located on the surface-exposed regions of critical domains within the S protein, potentially influencing antigenic epitopes and receptor-binding properties. Our findings demonstrate that SP2403-2 represents a contemporary Chinese-lineage PDCoV strain carrying substantial S protein variation relative to the vaccine strain, underscoring the imperative for ongoing surveillance of emerging PDCoV variants and re-evaluation of current vaccine efficacy.