{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T11:45:16Z","timestamp":1782992716008,"version":"3.54.5"},"reference-count":35,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T00:00:00Z","timestamp":1782950400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005230","name":"Natural Science Foundation of Chongqing","doi-asserted-by":"publisher","award":["CSTB2025NSCQ-GPX1047"],"award-info":[{"award-number":["CSTB2025NSCQ-GPX1047"]}],"id":[{"id":"10.13039\/501100005230","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Chongqing Municipal Financial Grant Project","award":["25524C"],"award-info":[{"award-number":["25524C"]}]},{"name":"National Center of Technology Innovation for Pigs","award":["NCTIP-XD\/B19"],"award-info":[{"award-number":["NCTIP-XD\/B19"]}]},{"name":"Observation and Research on Basic and Long-term Agricultural Scientific and Technological Work","award":["MARA-ORS261-AH024"],"award-info":[{"award-number":["MARA-ORS261-AH024"]}]},{"name":"Chongqing Special Postdoctoral Science Foundation","award":["25B3N01"],"award-info":[{"award-number":["25B3N01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Porcine epidemic diarrhea virus (PEDV) continues to undergo genetic evolution and remains a major etiological agent of enteric disease in swine, causing significant economic losses worldwide. This study investigated the molecular epidemiology and genetic characteristics of PEDV circulating in Chongqing, China, between 2022 and 2024. A total of 296 diarrheic piglet samples collected from nine regions were screened using RT-qPCR, of which 48.31% (143\/296) tested positive for PEDV. A subset of positive samples was subjected to S gene amplification and sequencing, yielding 15 complete sequences. Phylogenetic analysis revealed that all sequenced strains clustered within the G2c lineage and showed high nucleotide similarity (93.37\u201394.09%) to the classical CV777 strain. Recombination analysis indicated potential recombination events among field strains involving S-INDEL and G2b-like parental lineages, although these findings are based on a limited number of sequences. Sequence analysis identified multiple amino acid substitutions within the COE antigenic region, while other neutralizing epitopes (SS2, SS6, and 2C10) remained largely conserved. In addition, variation in predicted N-glycosylation sites was observed among some strains. Structural modelling suggested that these changes may influence spike protein conformation and antigenic properties; however, these interpretations are based on in silico analysis and require experimental validation. Overall, the findings indicate ongoing genetic evolution of PEDV in Chongqing and suggest circulation of G2c-associated variants in diarrheic piglets. However, given the limited and non-random nature of sequencing, these results may not fully represent the broader viral population. Continued large-scale molecular surveillance and functional studies are needed to better understand PEDV evolution and to support the development of improved control strategies and vaccines.<\/jats:p>","DOI":"10.3390\/ani16132033","type":"journal-article","created":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T10:04:44Z","timestamp":1782986684000},"page":"2033","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genetic Diversity and Molecular Evolution of Porcine Epidemic Diarrhea Virus in Chongqing, China (2022\u20132024)"],"prefix":"10.3390","volume":"16","author":[{"given":"Qianlin","family":"Chen","sequence":"first","affiliation":[{"name":"College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaomei","family":"Li","sequence":"additional","affiliation":[{"name":"Chongqing Academy of Animal Science, Chongqing 402460, China"},{"name":"National Center of Technology Innovation for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"},{"name":"Chongqing Engineering Technology Research Center for Veterinary Biological Products, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjie","family":"Ma","sequence":"additional","affiliation":[{"name":"National Center of Technology Innovation for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"},{"name":"Chongqing Engineering Technology Research Center for Veterinary Biological Products, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4167-4998","authenticated-orcid":false,"given":"Yassein M.","family":"Ibrahim","sequence":"additional","affiliation":[{"name":"National Center of Technology Innovation for Pigs, Chongqing 402460, China"},{"name":"Faculty of Veterinary Science, University of Nyala, Nyala 155, Sudan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Luo","sequence":"additional","affiliation":[{"name":"Chongqing Academy of Animal Science, Chongqing 402460, China"},{"name":"National Center of Technology Innovation for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"},{"name":"Chongqing Engineering Technology Research Center for Veterinary Biological Products, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuandi","family":"Yu","sequence":"additional","affiliation":[{"name":"Chongqing Academy of Animal Science, Chongqing 402460, China"},{"name":"National Center of Technology Innovation for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"},{"name":"Chongqing Engineering Technology Research Center for Veterinary Biological Products, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3329-8152","authenticated-orcid":false,"given":"Lizhi","family":"Fu","sequence":"additional","affiliation":[{"name":"Chongqing Academy of Animal Science, Chongqing 402460, China"},{"name":"National Center of Technology Innovation for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"},{"name":"Chongqing Engineering Technology Research Center for Veterinary Biological Products, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingyong","family":"Guo","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"198045","DOI":"10.1016\/j.virusres.2020.198045","article-title":"Porcine epidemic diarrhea virus (PEDV): An update on etiology, transmission, pathogenesis, and prevention and control","volume":"286","author":"Jung","year":"2020","journal-title":"Virus Res."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.coviro.2018.12.001","article-title":"Emerging and re-emerging coronaviruses in pigs","volume":"34","author":"Wang","year":"2019","journal-title":"Curr. 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