ORIGINAL RESEARCH article
Front. Vet. Sci.
Sec. Veterinary Infectious Diseases
Molecular Characterization and Evolutionary Dynamics of a Recombinant PDCoV Strain in a Swine Diarrhea Epidemic with SADS-CoV Co-infection
Provisionally accepted
Hong-Tao Cao1,2Ren-Jie Sun3
Qian-Yu Qian4Dong Yang1Yang-Yang Sun1Ling-Yan Zhao3Gao-Yu Zhang4Meng-Di Zhang1,2Han Gu1Hong-Wei Cao5
Bin Wang2
Yao-Wei Huang2*
Yong-Le Yang1*- 1Xianghu Laboratory, Hangzhou, China
- 2South China Agricultural University, Guangzhou, China
- 3Zhejiang Provincial Center for Animal Disease Control and Prevention, Hangzhou, China
- 4Zhejiang Chinese Medical University, Hangzhou, China
- 5Yancheng Teachers University, Yancheng, China
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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 Bacillus cereus 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.
Keywords: Gut microbiota dysbiosis, PDCoV, phylogenetic analysis, SADS-CoV, Viral co-infection, Viral recombination
Received: 24 Nov 2025; Accepted: 04 Feb 2026.
Copyright: © 2026 Cao, Sun, Qian, Yang, Sun, Zhao, Zhang, Zhang, Gu, Cao, Wang, Huang and Yang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Yao-Wei Huang
Yong-Le Yang
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