A Novel Inactivated Vaccine Based on an Emerging PEDV GIIc Variant Provides Cross-Protection Against Heterologous GII Strains

2764 vaccines Vaccines Vaccines (Basel) Multidisciplinary Digital Publishing Institute (MDPI) PMC12945236 12945236 12945236 41746072 10.3390/vaccines14020151 A Novel Inactivated Vaccine Based on an Emerging PEDV GIIc Variant Provides Cross-Protection Against Heterologous GII Strains Xu Jingjing Conceptualization, Investigation, Methodology, Writing – original draft, Writing – review & editing 1 † Fu Ningning Conceptualization, Investigation, Writing – original draft 1 † Liu Zimin Formal analysis, Software, Writing – review & editing 1 Chen Mengli Investigation, Writing – review & editing 1 Ma Guijun Investigation, Supervision 1 Li Hehai Conceptualization, Methodology 1 Wang Jianghui Investigation, Supervision 1 2 Yin Bo Supervision, Funding acquisition, Formal analysis, Methodology, Writing – review & editing 1 3 4 Zhang Zhen Funding acquisition, Supervision, Writing – review & editing, Formal analysis, Methodology 1 * Diao Feifei Data curation, Formal analysis, Methodology, Software, Writing – original draft, Project administration 1 * Meurens François Academic Editor Niu Qingli Academic Editor 1 Shanghai ShenLian Biomedical Corporation, Shanghai 200241, China 2 Key Laboratory of Animal Disease Diagnostics and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China 3 Shanghai ShenRay United Biomedical Co., Ltd., #48, East Jiangchuan Road, Minhang District, Shanghai 200241, China 4 National University of Singapore (Suzhou) Research Institute, #377 Linquan Street, Suzhou Industrial Park, Suzhou 215123, China * Correspondence: zzhang@slbio.com.cn (Z.Z.); ffdiao@slbio.com.cn (F.D.); Tel.: +86-135-6435-3416 (Z.Z.); +86-137-7031-1226 (F.D.) † These authors contributed equally to this work. 3 2 2026 14 2 151 151 27 2 2026 © 2026 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license . Abstract Background/Objectives: Porcine epidemic diarrhea virus (PEDV), particularly the emerging GII genotype, poses a severe threat to the swine industry in affected regions, primarily in Asia. Current vaccines based on classical strains often provide limited cross-protection against these heterogeneous variants, though it should be noted that these vaccines are primarily designed to induce maternal immunity in sows. The objective of this study was to develop a novel inactivated vaccine using an emerging PEDV GIIc variant and evaluate its immunogenicity and cross-protective efficacy against heterologous strains. Methods: A novel PEDV strain, designated PEDV-HeN2024, was isolated from clinical samples and identified through cell culture, immunofluorescence assay (IFA), genetic sequencing, and phylogenetic analysis. An inactivated vaccine was prepared by emulsifying the purified virus with ISA 201 VG adjuvant (1:1, v / v ). Immunogenicity was assessed in piglets by measuring virus-neutralizing antibody titers and PEDV-specific IgG levels. Cross-protective efficacy was evaluated through in vitro neutralization assays and in vivo challenge studies with homologous GIIc and heterologous GIIa and GIIb strains. Results: The isolated PEDV-HeN2024 strain demonstrated pathogenicity, causing severe diarrhea and 100% mortality in PEDV-naïve neonatal piglets. Sera from vaccinated animals showed potent cross-neutralizing activity against homologous GIIc, as well as heterologous GIIa and GIIb strains. In challenge studies, vaccinated piglets were significantly protected against clinical disease, showing no diarrhea or viral shedding, and maintained normal intestinal architecture. Conclusions: The inactivated vaccine developed from the emerging PEDV GIIc variant elicits robust humoral immunity and provides cross-protection against prevalent heterologous GII strains. These findings highlight its potential as a promising spectrum vaccine candidate for controlling PEDV outbreaks. This study underscores the importance of using recently circulating strains for vaccine development to overcome the limitations of current vaccines. Keywords: porcine epidemic diarrhea virus, GIIc strain, pathogenicity, inactivated vaccine, cross-protection against heterologous GII strains status released display-pdf yes is-olf no is-manuscript no is-preprint no is-journal-matter no is-scanned no is-retracted no Received 2025 Dec 16; Revised 2026 Jan 31; Accepted 2026 Feb 2; Collection date 2026 Feb. 1. Introduction Porcine epidemic diarrhea virus (PEDV), a member of the Coronaviridae family, can cause disease in susceptible pigs of various ages, although it is most severe in neonatal piglets, leading to substantial economic losses in the global swine industry [ 1 ]. Since its initial identification in the 1970s, PEDV has evolved into multiple genotypes, with the emerging GI (classical) and GII (variant) strains becoming dominant in recent outbreaks [ 2 ]. Among these, the GII genotype, particularly the GIIa, GIIb, and GIIc subgroups, has shown increased virulence and antigenic variability, posing significant challenges to existing vaccine strategies [ 3 , 4 ]. Current commercial vaccines, primarily based on classical GI strains (such as CV777), have demonstrated limited efficacy against emerging GII variants due to antigenic drift and poor cross-neutralization [ 5 , 6 ]. Although several inactivated and attenuated vaccines derived from GIIa strains have been developed, their protective scope remains narrow, often failing to elicit broad immune responses against heterologous GIIb and GIIc variants [ 7 ]. This immunological gap underscores the urgent need for novel vaccine candidates that can address the ongoing genetic divergence of PEDV. The PEDV genome is approximately 28 kb in length and consists of a 5′ cap structure, a 3′ poly(A) tail, and at least seven open reading frames (ORFs), namely ORF1a, ORF1b, S, ORF3, E, M, and N genes [ 8 ]. These ORFs encode four structural proteins (spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins), sixteen nonstructural proteins (NSPs), and one accessory protein, ORF3 [ 9 ]. The S protein, located on the surface of the virion, is the largest structural protein and can induce the production of neutralizing antibodies [ 10 ]. The PEDV S gene can be classified into three genotypes: GI, GII, and S-Indel. Variations such as nucleotide substitutions, deletions, or insertions in the S gene occur among different PEDV strains [ 11 ]. Consequently, the S gene is frequently used as a target for molecular epidemiological and phylogenetic analyses of PEDV. Recent studies have highlighted the critical role of the spike (S) protein in mediating viral entry and neutralizing antibody responses [ 12 , 13 ]. Phylogenetic analyses of circulating strains in China (2020–2022) indicate that GIIc variants have become increasingly prevalent, with distinct mutations in the S gene receptor-binding domain potentially contributing to immune evasion [ 14 ]. However, few studies have focused on the development of GIIc-based vaccines, and their cross-protective potential against other prevalent genotypes remains unexplored. In this study, we isolated and characterized a novel PEDV strain, designated PEDV-HeN2024, belonging to the GIIc subgroup. This strain demonstrated pathogenicity in neonatal piglets (3–5 days old and PEDV-naive herds), causing severe enteric pathology and high viral shedding. We further developed an inactivated vaccine using this strain adjuvanted with ISA 201 VG and evaluated its immunogenicity and cross-protective efficacy. 2. Materials and Methods 2.1. Cells and Viruses Vero cells (ATCC CCL-81) were purchased from BeNa Culture Collection (Xinyang, China). The cells were cultured in Gibco™ DMEM (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% Gibco™ fetal calf serum (Thermo Fisher Scientific, Waltham, MA, USA) and Gibco™ penicillin/streptomycin antibiotics (100 U/mL penicillin, 100 mg/mL streptomycin; Thermo Fisher Scientific, Waltham, MA, USA). The cells were maintained at 37 °C, 5% CO 2 , and 90% relative humidity. The PEDV-GIIa and PEDV-GIIb strains were isolated and preserved by our laboratory. 2.2. Virus Isolation and Propagation The intestinal contents or fecal samples from piglets with severe watery diarrhea were collected from a swine farm in China. The samples were homogenized, centrifuged, and filtered through a 0.22 μm filter. The filtrate was inoculated onto confluent monolayers of Vero cells (ATCC CCL-81) maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10 μg/mL trypsin (TPCK-treated) and 5% fetal bovine serum (FBS) at 37 °C in a 5% CO 2 incubator. After 1 h of adsorption, the inoculum was removed, and fresh maintenance medium was added. The cells were monitored daily for cytopathic effects (CPEs). Blind passages were performed until stable CPEs (syncytium formation and cell detachment) were observed [ 2 , 7 ]. Plaque Purification: When the cell density in the 6-well plate reached approximately 90%, a plaque assay was performed. The virus was diluted in DMEM, inverted, and vortexed twice. The pipette tip was changed, and the nutrient solution in the 6-well plate was aspirated and discarded in two steps. Subsequently, 1 mL of virus-containing DMEM was added to the wells at dilutions ranging from 10 −7 to 10 −2 . The plate was incubated for 2 h and gently shaken every 20 min. Agar was melted in a water bath 1 h in advance, and both the melted agar and 2× DMEM (supplemented with 2% serum, pH = 7.6) were placed in a 37 °C water bath 0.5 h prior to use. A mixture of 2% low-melting-point agarose and 2× DMEM was prepared at a 1:1 ratio, with 14 mL of each combined in a 50 mL centrifuge tube. After aspirating the virus-containing DMEM from the wells (10 −7 to 10 −2 ), 2 mL of the mixed agarose was added to each well and allowed to solidify at room temperature for 0.5 h. Once solidified, the plate was transferred to a 5% CO 2 incubator at 37 °C for 72–96 h. When distinct plaques became visible, the plate was removed, stained with crystal violet solution for 12 h at room temperature, rinsed under running water to remove the agarose, and plaque morphology was observed. 50% Tissue Culture Infective Dose (TCID 50 ) Assay: On the appearance of significant cytopathic effects (CPEs), the collected viral supernatant was titrated. Vero cells were seeded into a 96-well cell culture plate one day prior to the assay. On the day of the assay, the viral solution was serially diluted two-fold in DMEM containing 10 μg/mL trypsin, ranging from 10 −1 to 10 −8 . The supernatant of confluent Vero cell monolayers in the 96-well plate was discarded, and the cells were washed twice with PBS. The diluted viral solution was then inoculated into the cell culture plate, with eight parallel replicates per dilution, and 100 μL of viral solution was added per well. Normal cells were used as a blank control, with 100 μL of DMEM containing 10 μg/mL trypsin added per well. After 5–7 days of incubation, CPE was observed, and the data were analyzed using the Reed–Muench method [ 15 ]. 2.3. Virus Identification and Characterization Immunofluorescence Assay (IFA): Vero cells infected with the isolated virus were fixed with 80% acetone. The cells were then incubated with a porcine anti-PEDV-specific antibody (MEDIAN Diagnostics, Chuncheon-si, Gangwon-do, Republic of Korea) for 1 h at 37 °C, followed by incubation with a FITC-conjugated goat anti-pig IgG antibody (1:200 dilution; Sigma-Aldrich, St. Louis, MO, USA). The nuclei were stained with DAPI. The cells were visualized under a fluorescence microscope (Nikon Eclipse Ti2, Nikon Instruments Inc., Tokyo, Japan). Genetic Sequencing and Phylogenetic Analysis: Viral RNA was extracted from the cell culture supernatant using TRIzol LS Reagent (Invitrogen, Carlsbad, CA, USA). The full-length spike (S) gene was amplified by RT-PCR using specific primers (S1-Forward: 5′-AGATTGCTCTACCTTATACCTG-3′, S1-Reverse: 5′-GAAAGAACTAAACCCATTGATA-3′; S2-Forward: 5′-AGCCAACTCAAGTGTTCTCAGG-3′, S2-Reverse: 5′-AGCCACAGTGTTCAAACCCTT-3′; S3-Forward: 5′-TTAATAAAGTGGTTACTAATGGC-3′, S3-Reverse: 5′-ATAATAAAGAGCGCATTTTTATA-3′). The amplified products were purified and sequenced (Sangon Biotech, Shanghai, China). A phylogenetic tree was constructed using the complete nucleotide sequence of the spike (S) gene. Phylogenetic analysis was performed based on the complete nucleotide sequence of the spike (S) gene, which is the standard genomic region used for PEDV genotyping. Reference sequences of different genotypes (GI, S-Indel, GII) were downloaded from GenBank. 2.4. Animal Challenge Studies All animal experiments were approved by the Animal Welfare and Ethics Committee (AWEC) of ShenLian Bio-medicine (Shanghai) Co., Ltd., Shanghai, China. (Approval No: 2025003-1 and 2025009-1) and were conducted in accordance with relevant guidelines and regulations. All piglets were sourced from specific pathogen-free (SPF) herds with confirmed PEDV-naive status. Specific pathogen-free (SPF) piglets from two age groups (3–5 days old, n = 3; 28–30 days old, n = 3) were orally inoculated with 10 mL of the fifth-passage virus stock (10 5 TCID 50 ). A control group ( n = 3 for each age group) was inoculated with an equal volume of sterile PBS. Clinical signs (diarrhea, vomiting, lethargy) were recorded daily. Fecal swabs were collected daily for viral RNA detection by RT-PCR targeting the PEDV N gene. At 5 days post inoculation (dpi), all piglets were euthanized for necropsy. Intestinal tissues were collected for histopathological examination and viral load quantification. For cross-protection evaluation, piglets were challenged with 10 5 TCID 50 of GIIa (strain HuN2016), GIIb (strain MSCH2020) and GIIc (strain HeN2024) strains via oral inoculation. Clinical signs and viral shedding were monitored daily for 7 days post-challenge. 2.5. Vaccine Preparation and Immunization The isolated PEDV-GIIc virus was propagated, inactivated with 0.1% binary ethylenimine (BEI) at 37 °C for 24 h, and confirmed to be completely inactivated by three blind passages in Vero cells. The inactivated antigen was emulsified with ISA 201 VG adjuvant (Seppic) at a ratio of 1:1 ( v / v ) to form a Water-in-Oil-in-Water (W/O/W) emulsion. Twenty-one 3–5-day-old SPF piglets were randomly divided into three groups ( n = 3 per group): Group 1 (Our vaccine): immunized intramuscularly with 2 mL of the inactivated vaccine. Group 2 (Commercial Vaccine): immunized intramuscularly with 2 mL of the inactivated vaccine. The commercial vaccine’s instruction manual indicated that the antigen component was the complete inactivated strain of PEDV GIIa. Additionally, the commercial vaccine employed in this study is indicated for use in piglets. The product insert explicitly states that it is suitable for vaccinating piglets, with a recommended regimen of one dose per animal followed by a booster vaccination after a 14-day interval, due to commercial confidentiality agreements, the precise product name, antigen dose, and adjuvant formulation cannot be disclosed; Group 3 (Placebo Control): inoculated with 2 mL of PBS emulsified with ISA 201 VG adjuvant (1:1); and Group 4 (Blank Control): inoculated with 2 mL of PBS ( Table 1 ). A booster immunization was administered with the same formulation 14 days later. Table 1 Animal Grouping for HeN2024 Inactivated Vaccine Immunization Study. Group Immunization Challenge Strain Number of Animals Experimental Purpose Group 1 HeN2024 Inactivated Vaccine 1A HeN2024 3 piglets Evaluation of homologous (GIIc) strain challenge efficacy 1B HuN2016 3 piglets Evaluation of GIIa strain challenge efficacy 1C MSCH2020 3 piglets Evaluation of GIIb strain challenge efficacy 1D No challenge 3 piglets Serological evaluation for GII subtype strains Group 2 Commercial Vaccine No challenge 3 piglets Serological evaluation for GII subtype strains Group 3 ISA 201 VG HeN2024 3 piglets Adjuvant control for immunization Group 4 PBS No challenge 3 piglets Blank control 2.6. Serological Assay Sera were collected at 0, 14, 21, 28, and 35 days post immunization (dpi). Virus Neutralization (VN) Assay: Serum samples were serially diluted two-fold and mixed with an equal volume of 200 TCID 50 of PEDV strains (GIIa, GIIb, and GIIc). The mixture was incubated and then added to Vero cell monolayers. The neutralizing antibody titer was calculated as the highest serum dilution that completely inhibited CPE [ 16 ]. Enzyme-Linked Immunosorbent Assay (ELISA): PEDV-specific total antibodies (IgG) in serum were detected using a commercial PEDV Antibody Test Kit (Lanzhou Shou yan Biotechnology Co., Ltd., Lanzhou, China) according to the manufacturer’s instructions. 2.7. Statistical Analysis All data were expressed as mean ± standard deviation (SD). Statistical significance was determined by one-way analysis of variance (ANOVA) followed by Tukey’s post hoc test using GraphPad Prism 9.0. A p -value < 0.05 was considered statistically significant. 3. Results 3.1. Virus Isolation and Genetic Characterization A novel PEDV strain was successfully isolated from the clinical samples using Vero cells. The two processed intestinal homogenates (Intestine-1 and Intestine-2) were identified by RT-PCR ( Figure S1A ). The results showed that, compared with the positive control, both samples produced a specific band of approximately 830 bp. The culture supernatant harvested after five serial blind passages in Vero cells was also analyzed by RT-PCR. As shown in Figure S1B , with properly functioning negative and positive controls, the amplified products exhibited bands of the expected size. This indicates that the PEDV isolate obtained from the processed intestinal homogenate was stably passaged from passages 1 to 5 (P1–P5). After four blind passages, typical cytopathic effects (CPEs), characterized by syncytium formation and cell detachment, were consistently observed ( Figure 1 A). Subsequent plaque purification was performed on the F5 viral harvest originating from intestinal sample 2. After three rounds of purification, a single clone exhibiting the fastest growth was selected as the seed virus ( Figure S1C ). To further verify the viral identity, an immunofluorescence assay (IFA) was performed. The assay utilized a monoclonal antibody that specifically targets the spike (S) protein of PEDV, which yielded positive results, thereby confirming the virus’s identity. Robust fluorescence signals were observed in the cytoplasm of virus-infected Vero cells, whereas no signal was detected in mock-infected cells ( Figure 1 B). The isolated virus was designated as PEDV-HeN2024. Figure 1 Isolation and identification of the porcine epidemic diarrhea virus (PEDV) strain. ( A ) Cytopathic effects observed in Vero cells infected with PEDV. The scale represents 0.01. ( B ) Specific identification of PEDV infection by indirect immunofluorescence assay. The scale represents 0.01. ( C ) A maximum-likelihood (ML) phylogenetic tree of PEDV was constructed from S gene sequences, incorporating 893 complete PEDV genome sequences retrieved from the NCBI database and the strain isolated in this study. ( D ) An ML phylogenetic tree of PEDV was constructed from S gene sequences, incorporating 56 selected PEDV genome sequences retrieved from the NCBI database and the PEDV strain isolated in this study. The ★ symbol denotes the PEDV/HeN2024 strain identified in this study. Genetic characterization based on the complete spike (S) gene sequence (GenBank accession no. PX470115 ) was performed. Sequence alignment revealed that our isolate harbored the signature insertions and deletions in the S gene characteristic of variant strains, distinguishing it from classical CV777-like strains Further analysis of the S gene sequence revealed characteristic amino acid substitutions and deletions within the receptor-binding domain compared to the classical CV777 strain and other prevalent GII strains, which may influence antigenicity. Phylogenetic analysis demonstrated that PEDV/HeN2024 clustered within the GIIc genogroup, which has been increasingly reported in China since 2020. Notably, it formed a distinct branch with other recently emerged GIIc strains, indicating its status as a new and evolving variant within this genogroup ( Figure 1 C,D). While the primary genetic characterization focused on the S gene, preliminary analysis of the complete genome sequence did not reveal evidence of recombination events with other common porcine coronaviruses under the parameters examined. Future work will include a more comprehensive recombination analysis across other genomic regions. 3.2. Pathogenicity of PEDV/HeN2024/GIIc in Piglets The pathogenicity of the PEDV/HeN2024/GIIc isolate was evaluated in both neonatal (3–5 days old) and weaned (28–30 days old) specific-pathogen-free (SPF) piglets. All inoculated piglets in both age groups developed severe clinical signs, including watery diarrhea and vomiting, within 24–48 h post inoculation (hpi) ( Table 2 ). The clinical disease was notably more acute in neonatal piglets. Consistent with field observations of variant PEDV strains, 100% mortality ( n = 3/3) was observed in the neonatal group by 96 hpi ( Figure 2 A). In contrast, weaned piglets showed significant morbidity (e.g., severe diarrhea, lethargy, anorexia) but no mortality, highlighting the age-dependent susceptibility to PEDV ( Table 2 ). And the attenuated pathogenicity observed in the weaned piglets (~31 days old) may compromise the rigorous assessment of protective efficacy, particularly against heterologous challenges. Consequently, we have emphasized that the protection claims in this age group should be interpreted with caution. No clinical signs were observed in the PBS-inoculated control groups throughout this study. High levels of viral shedding were detected via RT-qPCR in fecal swabs collected from all challenged piglets, starting from 1 day post inoculation (dpi) and persisting until the endpoint of the experiment (for weaned piglets) or death (for neonates) ( Figure 2 B,C). Viral RNA copies in feces peaked at around 2–4 dpi. Table 2 Clinical symptoms among piglet pathogenesis experiments of PEDV-HeN2024. No., the number of animals. C, control. ID, inoculated doses (TCID50). MTA, mean time loss of appetite (hours). MTD, mean time to show watery diarrhea (days). MTH, mean time to death after showing clinical signs (hours). M/M, morbidity/mortality (%). RI, recovery rate after MEV-SD1 infection (%). /, not found. Groups Neonatal Piglets Weaned Piglets No. 3 3 3 3 ID 10 4.0 C 10 6.0 C MTA 18 ± 3 / 25 ± 4 / MTD 1.0 ± 0.3 / 1.5 ± 0.4 / MTH 36 ± 24 / / / M/M 100/100 / 100/0 / RI 0 / 100 / Figure 2 Animal challenge study with the PEDV/HeN2024 strain. ( A ) Survival distribution and time to death in neonatal piglets following viral challenge. ( B ) Viral shedding dynamics monitored by RT-qPCR in fecal samples from challenged neonatal piglets. ( C ) Viral shedding kinetics detected via RT-qPCR in fecal samples from weaned piglets post-challenge. Postmortem examination of dead piglets revealed lesions characteristic of severe PEDV infection. The small intestines, particularly the duodenum and jejunum, were thin-walled, transparent, and distended with yellow, watery fluid ( Figure S2 ). Histopathological analysis (H&E staining) of the duodenum and jejunum from infected piglets revealed villus atrophy and degeneration of intestinal epithelial cells compared to the control groups ( Figure 3 ). These findings confirm the enteropathogenicity of the PEDV/HeN2024/GIIc isolate. Figure 3 Histopathological examination of the small intestine in neonatal piglets. ( A ) Histopathological analysis of the duodenum from neonatal piglets. ( B ) Histopathological analysis of the ileum from neonatal piglets. Epithelial cell edema (indicated by yellow arrow), numerous epithelial cells missing (indicated by orange arrow), a few necrotic cell fragments can be seen in the lamina propria (indicated by blue arrow), multiple focal capillary dilation and congestion (indicated by cyan arrow). Scale bars: 500 μm for H&E staining at 2.0× magnification; 50 μm for H&E staining at 20.0× magnification. 3.3. Immunogenicity of the Inactivated Vaccine The inactivated vaccine formulated with ISA 201 VG adjuvant (1:1 ratio) induced robust humoral immune responses in immunized piglets. Virus-neutralizing (VN) antibody titers and PEDV-specific IgG antibody levels were measured weekly ( Figure 4 A). From 21 days post immunization (dpi) onwards, the geometric mean titers (GMTs) of virus-neutralizing (VN) antibodies and the concentrations of IgG antibodies in the vaccinated group were significantly higher than those in the placebo (adjuvant-only) group, the blank control group ( p < 0.01), and the commercial vaccine group. The VN antibody titers in the vaccinated group continued to rise until the challenge study at 28 dpi, indicating a strong and sustained immune response elicited by the vaccine ( Figure 4 B,C). Figure 4 Evaluation of the immunogenicity of the PEDV/HeN2024 inactivated vaccine. ( A ) Immunization schedule for neonatal piglets. ( B ) Levels of virus-neutralizing antibodies induced in neonatal piglets following immunization with the PEDV/HeN2024 inactivated vaccine and commercial vaccine. The dashed line indicates the protective threshold of neutralizing antibodies. The dashed line (threshold of 1:32) was set based on previously published studies indicating that a virus neutralization titer of 1:32 or higher is generally considered indicative of a potential protective immune response against PEDV in piglets [ 17 , 18 ]. ( C ) Levels of PEDV-specific IgG antibodies produced in neonatal piglets after immunization with the PEDV/HeN2024 inactivated vaccine and commercial vaccine. Statistical differences in mean antibody were analyzed by two-way ANOVA followed by Dunnett’s multiple comparisons test (*** p < 0.001, **** p < 0.0001). All data are presented as mean ± SEM (Standard Error of the Mean). 3.4. Cross-Protective Efficacy Against Heterologous Challenges The key finding of this study was the cross-neutralizing activity elicited by the GIIc-based inactivated vaccine. At 28 days post immunization, serum samples were tested for neutralization activity in vitro. The sera demonstrated potent neutralizing activity against both the homologous GIIc strain (PEDV/HeN2024/GIIc) and heterologous GIIa and GIIb strains. Notably, the neutralizing antibody titers against all tested strains were significantly higher than those elicited by the commercial vaccine. The sera effectively neutralized all three tested strains, with the highest GMT observed against the homologous virus ( Figure 5 A). This result demonstrated the induction of cross-reactive neutralizing antibodies. But the comparison with the commercial vaccine was conducted in vitro at the serological level, serving as a preliminary assessment of immune response magnitude rather than aiming to mimic complex mucosal or maternal immunity. Figure 5 Cross-protective efficacy of the PEDV/HeN2024 inactivated vaccine against heterologous strains. ( A ) Neutralizing antibody titers induced in neonatal piglets immunized with the PEDV/HeN2024 inactivated vaccine against different PEDV subtypes (GIIa, GIIb, and GIIc). The dashed line indicates the protective threshold for neutralizing antibodies. ( B ) Fecal viral shedding monitored by RT-qPCR in piglets challenged with GIIa, GIIb, and GIIc strains at 4 weeks post immunization. All three challenged groups exhibited only low-level and transient viral shedding. ( C ) Histopathological examination of the jejunum at 7 days post-challenge. Loss of epithelial cells (indicated by the orange arrow), numerous necrotic cell fragments (indicated by the blue arrow) can be seen within the lamina propria, and there are frequent dilated and congested capillaries (indicated by the cyan arrow). Scale bar: 50 μm for H&E staining at 20.0× magnification. Statistical differences in mean antibody were analyzed by two-way ANOVA followed by Dunnett’s multiple comparisons test (*** p < 0.001), ns, not significant. All data are presented as mean ± SEM (Standard Error of the Mean). The PEDV-HeN2024 vaccine conferred significant protection against clinical disease upon challenge with all three genotypes (GIIa, GIIb, and GIIc); the absence of diarrhea and fecal viral shedding served as the primary endpoints for efficacy evaluation. Following heterologous viral challenges (with GIIa and GIIb strains), piglets in the vaccinated group exhibited significant protection: they showed no clinical signs, and significantly reduced viral shedding in feces was detected via RT-qPCR ( Figure 5 B). Histopathological examination of the jejunum post-challenge revealed well-preserved intestinal villus structures in the vaccinated group, in marked contrast to the villus atrophy observed in the control groups ( Figure 5 C). 4. Discussion The continuous emergence of PEDV variants, particularly within the GII genogroup, poses a significant and ongoing challenge to the global swine industry [ 2 , 19 , 20 ]. Vaccination remains the most effective strategy for controlling PED; however, the efficacy of existing commercial vaccines, often based on classical or earlier variant strains, is frequently compromised against these emerging variants due to antigenic differences [ 21 , 22 ]. In this study, we successfully isolated a novel PEDV strain, identified it as a GIIc variant through comprehensive genetic and phylogenetic analyses, and developed an inactivated vaccine that demonstrated immunogenicity and cross-protective efficacy against homologous and heterologous (GIIa, GIIb) challenges. Our phylogenetic analysis confirmed that the isolated strain, PEDV-HeN2024, clusters with recently emerging GIIc strains but occupies a distinct branch, suggesting ongoing viral evolution [ 23 ]. This genetic divergence is a primary driver of the suboptimal protection offered by existing vaccines, as mutations, especially in the S protein, the major target of neutralizing antibodies, can lead to antigenic drift and immune evasion [ 24 , 25 ]. The pathogenicity of our isolate was unequivocally demonstrated in both neonatal and weaned piglets. The 100% mortality in neonatal piglets and significant morbidity in weaned piglets align with the severe clinical manifestations reported in outbreaks caused by contemporary variants, underscoring the urgent need for effective countermeasures [ 5 , 26 , 27 ]. It is important to note that a key limitation of this study is the small group size ( n = 3) used in the animal experiments, which affects the statistical power and generalizability of the findings. The study is therefore more appropriately considered a proof-of-concept investigation rather than a definitive efficacy trial. The sample size was selected based on the exploratory nature of this initial investigation and constraints related to the availability of specific-pathogen-free (SPF) piglets meeting the stringent age requirements. The cornerstone of our findings is the remarkable cross-protective ability induced by the GIIc-based inactivated vaccine. Sera from vaccinated animals potently neutralized not only the homologous GIIc virus but also heterologous GIIa and GIIb strains in vitro. This was further corroborated by in vivo challenge studies: vaccinated piglets challenged with all three genotypes (GIIa, GIIb, GIIc) exhibited significant protection, with no clinical symptoms and substantially reduced viral shedding, and maintained normal intestinal architecture. This spectrum protection is likely attributable to the presentation of conserved antigenic epitopes shared among the contemporary GII variants by our vaccine strain [ 7 ]. By utilizing a recently circulating GIIc variant as the vaccine seed, we may have elicited a broader and more relevant immune response compared to vaccines based on older strains. This finding is critically important, as it suggests that updating vaccine strains to match currently prevalent variants can overcome the limitations of cross-protection [ 28 , 29 ]. But the cross-protection observed is against the specific genotypes tested and that efficacy against a wider range of circulating strains requires further investigation. We have also acknowledged that the use of naive piglets does not fully represent the complex immune status of herds in endemic areas. We now state that future studies should evaluate the vaccine’s efficacy in sows to assess its impact on maternal-derived immunity (MDA) and protection in piglets, which is the primary goal of PEDV vaccination in the field. Our results are consistent with and extend the findings of other research groups focusing on PEDV variants. For instance, Li et al. highlighted the role of nonstructural proteins, such as nsp1, in the immune evasion mechanisms of variant strains, which may explain the virulence of our isolate, and while a protective vaccine is the ultimate goal, selecting a vaccine strain that is antigenically well-matched to circulating field strains is one strategy to potentially enhance the breadth [ 30 , 31 ] and potency of the immune response, especially given the genetic diversity of PEDV [ 20 , 32 , 33 , 34 ]. In addition, antigen concentration and adjuvants are equally critical factors. While our inactivated vaccine candidate shows great promise, several aspects warrant further investigation. First, the duration of immunity conferred by this vaccine needs to be evaluated in a long-term study, especially in sows, to assess the level and persistence of maternal antibodies transferred to piglets [ 6 , 13 ]. Second, exploring the vaccine’s efficacy in a prime-boost regimen, potentially combining it with a live-attenuated vaccine, could further enhance the strength and breadth of the immune response [ 35 , 36 , 37 ]. Furthermore, the challenge strain of porcine epidemic diarrhea virus (PEDV) exhibited attenuated pathogenicity in older piglets [ 38 ]. Our results indicated that 31-day-old piglets challenged with the virus exhibited only mild, transient clinical diarrhea, which complicated the assessment of protective efficacy. Finally, investigating the specific conserved epitopes responsible for cross-neutralization could guide the development of even more effective next-generation vaccines, such as subunit or epitope-based vaccines [ 39 ]. In conclusion, we have developed a novel inactivated vaccine based on an emerging PEDV GIIc variant. This vaccine elicits neutralizing antibodies and provides cross-protection against the predominant heterologous GII (GIIa, GIIb, GIIc) strains currently in circulation, and its efficacy against more distantly related strains requires further investigation. Our study underscores the importance of continuous viral surveillance and the timely development of vaccines based on prevalent strains as a viable strategy to control the devastating losses caused by PEDV variants in the swine industry. This study has certain limitations that should be considered when interpreting the results. The primary limitation is the relatively small group size ( n = 3 per group), which was constrained by the availability of specific-pathogen-free (SPF) piglets meeting the stringent age requirements and the exploratory nature of this initial investigation. This affects the statistical power and generalizability of the findings. Furthermore, while control groups (Placebo Control: ISA 201 VG; Blank Control: PBS) were included for the immunization and homologous challenge study, the heterologous challenge experiments focused on evaluating the vaccine group against internal baselines rather than including separate control groups for each heterologous challenge due to animal use constraints. Consequently, the scientific relevance of this work is limited by these experimental design constraints, and the validity and relevance of the findings should be interpreted with caution. To build upon these promising preliminary findings, we are currently conducting additional animal experiments with larger sample sizes and more comprehensive control group designs. Once these results are available, we plan to report them in subsequent, more comprehensive manuscripts that are well-prepared from the outset. Acknowledgments We thank Wentao Fan at the Institute of MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, for his valuable guidance and insightful opinions throughout this research. We thank the Key Laboratory of Novel Animal Biologics Creation, Ministry of Agriculture and Rural Affairs, for providing the research platform and technical support for this study. Supplementary Materials The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/vaccines14020151/s1 . Supplementary Figure S1: Isolation, identification, and plaque purification of PEDV. Figure S2: Clinical manifestations and post-mortem findings in piglets challenged with the PEDV/HeN2024 strain. Author Contributions Conceptualization, J.X., N.F. and H.L.; methodology, J.X., M.C., H.L., B.Y., Z.Z. and F.D.; software, Z.L. and F.D.; formal analysis, Z.L., B.Y., Z.Z. and F.D.; investigation, J.X., N.F., M.C., G.M. and J.W.; data curation, F.D.; writing—original draft, J.X., N.F. and F.D.; writing—review and editing, J.X., Z.L., M.C., B.Y., Z.Z. and F.D.; supervision, G.M., J.W., B.Y., Z.Z. and F.D.; project administration, F.D.; funding acquisition, B.Y. and Z.Z. All authors have read and agreed to the published version of the manuscript. Institutional Review Board Statement All animal experiments were approved by the Animal Welfare and Ethics Committee (AWEC) of ShenLian Bio-medicine (Shanghai) Co., Ltd. (Approval No: 2025003-1, 1 March 2025 and 2025009-1, 1 September 2025) and were conducted in accordance with relevant guidelines and regulations. Informed Consent Statement Not applicable. Data Availability Statement Data and materials supporting the findings of this study are available through the NCBI Nucleotide. The dataset has been deposited under the GenBank accession no. PX470115 . The raw data of virus-neutralization titers, individual animal data, and complete RT-qPCR datasets generated during this study are available from the corresponding author upon reasonable request. Conflicts of Interest All authors were employed by the company Shanghai ShenLian Biomedical Corporation.Author Bo Yin was employed by the company Shanghai ShenRay United Biomedical Co., Ltd. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Funding Statement This research was funded by the Shanghai Agricultural Science and Technology Innovation Project (grant numbers K2024002). 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The raw data of virus-neutralization titers, individual animal data, and complete RT-qPCR datasets generated during this study are available from the corresponding author upon reasonable request.