A novel genotyping system based on site polymorphism on spike gene reveals the evolutionary pathway of porcine epidemic diarrhea virus
Abstract Porcine epidemic diarrhea virus (PEDV) is a lethal coronavirus in neonatal piglets characterized by rapid evolution in both genotype and phenotype. However, the underlying genetic mechanism has not been completely elucidated. In this study, we investigated and characterized PEDV field strai...
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| Format: | Article |
| Language: | English |
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Wiley
2025-06-01
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| Series: | iMetaOmics |
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| Online Access: | https://doi.org/10.1002/imo2.70013 |
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| author | Mingkai Lei Huimin Li Xiaoyu Chen Xiaozhen Li Xuexiang Yu Shengnan Ruan Hao Wu Ahmed H. Ghonaim Ziyang Yan Wentao Li Qigai He |
| author_facet | Mingkai Lei Huimin Li Xiaoyu Chen Xiaozhen Li Xuexiang Yu Shengnan Ruan Hao Wu Ahmed H. Ghonaim Ziyang Yan Wentao Li Qigai He |
| author_sort | Mingkai Lei |
| collection | DOAJ |
| description | Abstract Porcine epidemic diarrhea virus (PEDV) is a lethal coronavirus in neonatal piglets characterized by rapid evolution in both genotype and phenotype. However, the underlying genetic mechanism has not been completely elucidated. In this study, we investigated and characterized PEDV field strains circulating in China between 2021 and 2022, which revealed significant genetic divergence. To improve the classification of PEDV, we developed a site‐polymorphism‐based genotyping system utilizing global PEDV genetic sequences from public databases. While there are currently multiple genotypic classification‐based systems for PEDV, our proposed approach could offer more stable classification by considering both genetic characteristics and evolutionary dynamics. Our analysis indicates that the most prevalent PEDV lineages originated from South Korea and China, with G2c: L4 predominating in China and G2c: L10 in the United States. Importantly, discrete phylogenetic analysis revealed potential evolutionary pathways of PEDV, showing that the termini of the S gene are prone to recombination, while adaptive selection is evident in the middle region. Overall, our findings provide a complementary and practical methodology for PEDV classification and offer novel insights into the evolutionary pathway of coronaviruses. |
| format | Article |
| id | doaj-art-625d5cdc90fe408f8e5643e84ce2ee0b |
| institution | Kabale University |
| issn | 2996-9506 2996-9514 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Wiley |
| record_format | Article |
| series | iMetaOmics |
| spelling | doaj-art-625d5cdc90fe408f8e5643e84ce2ee0b2025-08-20T03:25:59ZengWileyiMetaOmics2996-95062996-95142025-06-0122n/an/a10.1002/imo2.70013A novel genotyping system based on site polymorphism on spike gene reveals the evolutionary pathway of porcine epidemic diarrhea virusMingkai Lei0Huimin Li1Xiaoyu Chen2Xiaozhen Li3Xuexiang Yu4Shengnan Ruan5Hao Wu6Ahmed H. Ghonaim7Ziyang Yan8Wentao Li9Qigai He10National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine Huazhong Agricultural University Wuhan ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine Huazhong Agricultural University Wuhan ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine Huazhong Agricultural University Wuhan ChinaYunnan Southwest Agricultural and Animal Husbandry Group Co, Ltd Kunming ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine Huazhong Agricultural University Wuhan ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine Huazhong Agricultural University Wuhan ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine Huazhong Agricultural University Wuhan ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine Huazhong Agricultural University Wuhan ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine Huazhong Agricultural University Wuhan ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine Huazhong Agricultural University Wuhan ChinaNational Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine Huazhong Agricultural University Wuhan ChinaAbstract Porcine epidemic diarrhea virus (PEDV) is a lethal coronavirus in neonatal piglets characterized by rapid evolution in both genotype and phenotype. However, the underlying genetic mechanism has not been completely elucidated. In this study, we investigated and characterized PEDV field strains circulating in China between 2021 and 2022, which revealed significant genetic divergence. To improve the classification of PEDV, we developed a site‐polymorphism‐based genotyping system utilizing global PEDV genetic sequences from public databases. While there are currently multiple genotypic classification‐based systems for PEDV, our proposed approach could offer more stable classification by considering both genetic characteristics and evolutionary dynamics. Our analysis indicates that the most prevalent PEDV lineages originated from South Korea and China, with G2c: L4 predominating in China and G2c: L10 in the United States. Importantly, discrete phylogenetic analysis revealed potential evolutionary pathways of PEDV, showing that the termini of the S gene are prone to recombination, while adaptive selection is evident in the middle region. Overall, our findings provide a complementary and practical methodology for PEDV classification and offer novel insights into the evolutionary pathway of coronaviruses.https://doi.org/10.1002/imo2.70013adaptive selectionevolutionary pathwaygenetic polymorphismgenotypingintraspecific recombinationporcine epidemic diarrhea virus |
| spellingShingle | Mingkai Lei Huimin Li Xiaoyu Chen Xiaozhen Li Xuexiang Yu Shengnan Ruan Hao Wu Ahmed H. Ghonaim Ziyang Yan Wentao Li Qigai He A novel genotyping system based on site polymorphism on spike gene reveals the evolutionary pathway of porcine epidemic diarrhea virus iMetaOmics adaptive selection evolutionary pathway genetic polymorphism genotyping intraspecific recombination porcine epidemic diarrhea virus |
| title | A novel genotyping system based on site polymorphism on spike gene reveals the evolutionary pathway of porcine epidemic diarrhea virus |
| title_full | A novel genotyping system based on site polymorphism on spike gene reveals the evolutionary pathway of porcine epidemic diarrhea virus |
| title_fullStr | A novel genotyping system based on site polymorphism on spike gene reveals the evolutionary pathway of porcine epidemic diarrhea virus |
| title_full_unstemmed | A novel genotyping system based on site polymorphism on spike gene reveals the evolutionary pathway of porcine epidemic diarrhea virus |
| title_short | A novel genotyping system based on site polymorphism on spike gene reveals the evolutionary pathway of porcine epidemic diarrhea virus |
| title_sort | novel genotyping system based on site polymorphism on spike gene reveals the evolutionary pathway of porcine epidemic diarrhea virus |
| topic | adaptive selection evolutionary pathway genetic polymorphism genotyping intraspecific recombination porcine epidemic diarrhea virus |
| url | https://doi.org/10.1002/imo2.70013 |
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