Classification Evolution and Epitope Prediction of the Porcine Epidemic Diarrhea Virus (PEDV) Spike Protein in Thailand (2008–2024): Updated Insights for Preventive Strategies
The findings reveal the emergence of unique insertion/deletion strains and establish that primitive Thai strains likely represent the original structural template of PEDV in the region prior to subsequent divergence into G1 and G2b-related lineages.
Abstract
Simple Summary Porcine epidemic diarrhea virus (PEDV) continues to cause severe watery diarrhea and devastating piglet production losses worldwide. To map the long-term evolutionary trends of the virus in Thailand, this study evaluated clinical samples collected over a 16-year period (2008–2024) using a comprehensive molecular and bioinformatic pipeline. By analyzing the predicted full-length spike (S) protein structures modeled from nucleotide sequences, we tracked critical mutational shifts and predicted antigenic variation within major neutralizing domains (including COE, SS2, SS6, and 2C10) that may influence antibody recognition. The findings reveal the emergence of unique insertion/deletion (InDel) strains and establish that primitive Thai strains (Cluster 1) likely represent the original structural template of PEDV in the region prior to subsequent divergence into G1 and G2b-related lineages. Ultimately, this framework bridges genomic evolution with structural biology, providing essential data to guide vaccine selection, optimize planned exposure protocols, and update swine biosecurity strategies.
Introduction Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric pathogen that causes severe diarrhea and high mortality in neonatal piglets, leading to substantial economic losses in the swine industry. The nucleocapsid (N) protein is highly conserved and abundantly expressed during infection, making it a suitable target for serological detection. Methods In this study, twomonoclonal antibodies (mAbs), C9 and G11, directed against the PEDV N protein were used to define minimal linear epitopes. A stepwise truncation approach based on overlapping recombinant fragments was applied to localize the antigenic regions. Results The results showed that mAb C9 and mAb G11 recognized the minimal epitopes 58RWRM61 and 15PLSL18, respectively. Sequence analysis indicated that both epitopes are highly conserved among representative PEDV strains from different genotypes. In addition, structural modeling suggested that these regions are exposed on the surface of the N protein, consistent with their accessibility to antibody binding. Discussion These findings provide a more precise characterization of antigenic sites within the PEDVNprotein andmay be useful for the development of specific and reliable serological assays.
Youhao Bu, Ruiqin Zhu, Ao Jiang et al.· Frontiers in Microbiology· 0 citations
Porcine epidemic diarrhea virus (PEDV) is an important pathogen in swine, causing severe economic losses to the global swine industry. As a coronavirus, PEDV is prone to mutations and recombination. Therefore, characterizing circulating strains is essential for disease control. In this study, a PEDV strain (GD1) was isolated from diarrheic piglets in Guangdong Province, China, and identified by RT-PCR and immunofluorescence. Pathogenicity was evaluated in piglet challenge experiment. The results showed that GD1 strain could be stably passaged in Vero cells, forming syncytia. Phylogenetic analysis based on the complete genome and spike (S) gene both placed GD1 strain within the GIIc genotype. Amino acid sequence alignment of the S protein revealed multiple amino acid mutations in the neutralizing epitopes COE, SE16, and SS6 of GD1 strain compared with the classical vaccine strain CV777. Recombination analysis suggested that GD1 may be a novel recombination strain originating from strains SD2021 and GDS28, with the recombination breakpoint located in the ORF1a region. Pathogenicity assessment demonstrated that GD1 is highly virulent, inducing severe watery diarrhea and vomiting in newborn piglets within 24 h post-inoculation, and causing histopathological lesions characterized by intestinal villous atrophy and shedding. Immunohistochemistry confirmed that PEDV antigen was predominantly distributed in the villous epithelial cells of the small intestine. The successful isolation and characterization of the GD1 strain provide important viral resources for further research on the genetic evolution of PEDV and the development of matched vaccines.
Shuxia Shi, Qiuxia Wang, Xufan Cheng et al.· Frontiers in Veterinary Scie...· 0 citations
Porcine epidemic diarrhoea virus (PEDV) is a highly contagious enteric coronavirus causing acute watery diarrhoea and high mortality in neonatal piglets, threatening the global swine industry. In recent years, GIIc subtype PEDV has spread rapidly across China via natural recombination and antigenic drift, undermining conventional vaccine efficacy. Here, we isolated and characterized a novel GIIc PEDV strain CHjx2025 from diarrheic piglets in Ji'an City, Jiangxi Province, China. Full-length genome sequencing and recombination analysis identified CHjx2025 as a natural intra-lineage recombinant of two GIIc strains (CH-JXJA-2017 as major parent and CH-SWM-RN-2025 as minor parent), with a recombination breakpoint at nucleotide 11,201 of ORF1a. Comparative analysis revealed 49 unique amino acid substitutions in the spike (S) protein core region relative to the classic vaccine strain CV777, including 10 in the core receptor-binding domain (COE) and 1 in the 2C10 neutralizing epitope. Structural modeling confirmed CHjx2025 retains a canonical homotrimeric type I fusion protein structure but exhibits distinct NTD and D0 domains versus CV777. In vitro, CHjx2025 showed strong replicative capacity, forming larger plaques and reaching 106.5TCID50/mL in Vero cells at 24 hpi. Notably, in vivo challenge induced vomiting and anorexia in neonatal piglets as early as 12 hpi, with 100% mortality within 60 h, severe intestinal villous atrophy, and unprecedented multinucleated syncytia in intestinal epithelial cells. These findings highlight the evolving diversity and enhanced pathogenicity of GIIc PEDV via intra-subtype recombination and epitope mutations, underscoring the need for continuous surveillance and GIIc-specific vaccine development to control PED outbreaks.
Jinpeng Fan, Yan-ling Liu, Wenqian Fu et al.· BMC Veterinary Research· 1 citation· ⚡1
This research presents a comprehensive analysis of the genetic landscape of prevalent NDV strains in Bangladesh between 2010 and 2024 using full‐length coding sequences of the fusion (F) gene and unraveled considerable genetic divergence.
Farah Zereen, Md. Abdur Rahman, M. Hossain et al.· Veterinary Medicine Internat...· 0 citations
ABSTRACT The high genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV) poses a significant challenge to effective vaccination and infection prevention. Recently, NADC30-like PRRSV has become dominant in China. In this study, we characterized a PRRSV isolate XJ2020 from a vaccinated pig. The isolate exhibited moderate pathogenicity in piglets and clustered within the same sub-lineage as NADC30. Sequence analysis identified a unique deletion of the serine residue at position 32 (S32) in the GP5 protein. This deletion was introduced into a highly pathogenic PRRSV (HP-PRRSV) strain, JX2015, to generate the mutant JX2015-ΔS32 using a reverse genetic approach. We found that JX2015-△S32 showed reduced propagation in Marc-145 cells and decreased sensitivity to neutralization by MLV-derived anti-PRRSV positive serum, but exhibited enhance replication in primary porcine alveolar macrophages (PAMs) compared to its parental strain JX2015. Interestingly, the viral load in lung and ileum samples from JX2015-△S32-infected piglets was higher, but the lung injury was milder than in JX2015-infected piglets. Overall, this study highlights the S32 site in the PRRSV GP5 protein as an important factor influencing virus propagation, neutralization, cell tropism and pathogenicity in piglets, and suggests that targeting this residue could lead to the development of more effective PRRSV vaccines.
Xingdong Zhou, Xiao-Hui Zhang, E. Kan et al.· Virulence· 0 citations
ABSTRACT Bovine coronavirus (BCoV) is an important pathogen associated with enteric disease in calves, contributing to significant economic losses worldwide. To provide an updated overview of BCoV epidemiology, we conducted a systematic review and meta-analysis of studies published up to October 2025. Seventy-two eligible studies comprising 29,045 samples from nine countries were included, yielding a pooled global prevalence of 20.39% (95% CI: 15.07–26.99). Substantial heterogeneity was observed, reflecting variations in geographic regions, detection methods, and study populations. To complement the epidemiological analysis, 298 fecal samples from diarrheic calves in northeastern China were screened by RT-PCR, identifying 36 BCoV-positive samples (12.08%). Co-infection analysis revealed that most positive samples contained additional enteric viruses, indicating complex viral interactions in calf diarrhea. A novel BCoV strain was isolated in MDBK cells and designated DDFX98. Viral identity was confirmed by PCR, transmission electron microscopy, and immunofluorescence assay. Complete genome sequencing demonstrated that DDFX98 belongs to the GIIb subtype and shares high nucleotide identity with contemporary circulating strains. Comparative analysis of the spike (S) protein revealed multiple amino acid substitutions predominantly located within the S1 subunit. Structural modeling suggested localized conformational variations, particularly in surface-exposed and flexible regions, while preserving the overall spike architecture. In silico predictions further indicated minor alterations in glycosylation potential and epitope-associated regions. Collectively, this study integrates global epidemiological evidence with molecular and structural characterization of a contemporary BCoV isolate, providing insights into S protein variability and its potential structural – functional implications.
