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Shi K, Li B, Shi Y, Feng S, Yin Y, Long F, Pan Y, Wei Y. Phylogenetic and Evolutionary Analysis of Porcine Epidemic Diarrhea Virus in Guangxi Province, China, during 2020 and 2024. Viruses 2024; 16:1126. [PMID: 39066288 PMCID: PMC11281377 DOI: 10.3390/v16071126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/28/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
The variant porcine epidemic diarrhea virus (PEDV) has caused considerable economic losses to the global pig industry since 2010. In this study, a total of 5859 diarrhea samples were collected from different pig farms in China's Guangxi province during January 2020 and March 2024 and tested for PEDV using RT-qPCR. The positivity rate of PEDV was 11.90% (697/5859). Ninety-two PEDV-positive samples were selected based on sampling time, and the sampling region for amplification, sequencing, and analysis of the S1, M, and N genes. Phylogenetic analysis of the S1 gene revealed that all strains from Guangxi province were distributed in three subgroups, i.e., 81.5% (75/92) in the G2a subgroup, 4.3% (4/92) in the G2b subgroup, and 14.1% (13/92) in the G2c subgroup. The sequence analysis revealed that the S1 gene sequences from Guangxi province had higher homology with the variant strains than with the classical strains, showing as high as 99.2% with the variant strain AJ1102 and only 94.3% with the classical strain CV777. Recombination analysis revealed that the GX-BS08-2023 strain (G2c) from Guangxi province originated from inter-lineage recombination between the GX-BS09-2023 (G2a) and CH-JN547228-2011 (G1a) strains. In addition, the S1 gene of the G2a and G2b subgroup strains shared many mutations and insertions. There were common mutations of N143D and P235L in the G2a subgroup. Evolutionary analysis revealed that all Guangxi strains belonged to the G2 genotype. These strains have spread rapidly since the PEDV variant strains that emerged in 2010, weakened until 2021, and then remained stable. In conclusion, the results revealed the latest genetic evolution of circulating PEDV strains in Guangxi province in recent years, providing important information for preventing and controlling PEDV infection. Currently, the G2a subgroup strains are the predominant strains circulating in pig herds in Guangxi province, southern China.
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Affiliation(s)
- Kaichuang Shi
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise 533000, China
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
- Guangxi Center for Animal Disease Control and Prevention, Nanning 530001, China
| | - Biao Li
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Yuwen Shi
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
| | - Shuping Feng
- Guangxi Center for Animal Disease Control and Prevention, Nanning 530001, China
| | - Yanwen Yin
- Guangxi Center for Animal Disease Control and Prevention, Nanning 530001, China
| | - Feng Long
- Guangxi Center for Animal Disease Control and Prevention, Nanning 530001, China
| | - Yi Pan
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise 533000, China
| | - Yingyi Wei
- College of Animal Science and Technology, Guangxi University, Nanning 530005, China
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Sira EMJS, Banico EC, Odchimar NMO, Fajardo LE, Fremista FF, Refuerzo HAB, Dictado APA, Orosco FL. Immunoinformatics approach for designing a multiepitope subunit vaccine against porcine epidemic diarrhea virus genotype IIA spike protein. Open Vet J 2024; 14:1224-1242. [PMID: 38938443 PMCID: PMC11199741 DOI: 10.5455/ovj.2024.v14.i5.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/26/2024] [Indexed: 06/29/2024] Open
Abstract
Background Porcine epidemic diarrhea (PED), caused by the porcine epidemic diarrhea virus (PEDV), is associated with high mortality and morbidity rates, especially in neonatal pigs. This has resulted in significant economic losses for the pig industry. PEDV genotype II-based vaccines were found to confer better immunity against both heterologous and homologous challenges; specifically, spike (S) proteins, which are known to play a significant role during infection, are ideal for vaccine development. Aim This study aims to design a multi-epitope subunit vaccine targeting the S protein of the PEDV GIIa strain using an immunoinformatics approach. Methods Various bioinformatics tools were used to predict HTL, CTL, and B-cell epitopes. The epitopes were connected using appropriate linkers and conjugated with the CTB adjuvant and M-ligand. The final multiepitope vaccine construct (fMEVc) was then docked to toll-like receptor 4 (TLR4). The stability of the fMEVc-TLR4 complex was then simulated using GROMACS. C-immsim was then used to predict the in vitro immune response of the fMEVc. Results Six epitopes were predicted to induce antibody production, ten epitopes were predicted to induce CTL responses, and four epitopes were predicted to induce HTL responses. The assembled epitopes conjugated with the CTB adjuvant and M-ligand, fMEVc, is antigenic, non-allergenic, stable, and soluble. The construct showed a favorable binding affinity for TLR4, and the protein complex was shown to be stable through molecular dynamics simulations. A robust immune response was induced after immunization, as demonstrated through immune stimulation. Conclusion In conclusion, the multi-epitope subunit vaccine construct for PEDV designed in this study exhibits promising antigenicity, stability, and immunogenicity, eliciting robust immune responses and suggesting its potential as a candidate for further vaccine development.
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Affiliation(s)
- Ella Mae Joy S. Sira
- Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig City, Philippines
| | - Edward C. Banico
- Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig City, Philippines
| | - Nyzar Mabeth O. Odchimar
- Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig City, Philippines
| | - Lauren Emily Fajardo
- Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig City, Philippines
| | - Ferdinand F. Fremista
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Philippines
| | | | - Ana Patrisha A. Dictado
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Philippines
| | - Fredmoore L. Orosco
- Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Department of Science and Technology, Taguig City, Philippines
- Department of Biology, College of Arts and Sciences, University of the Philippines Manila, Philippines
- S&T Fellows Program, Department of Science and Technology, Taguig City, Philippines
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Le BT, Gallage HC, Kim MH, Park JE. Molecular Characterization of Porcine Epidemic Diarrhea Virus from Field Samples in South Korea. Viruses 2023; 15:2428. [PMID: 38140669 PMCID: PMC10748127 DOI: 10.3390/v15122428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly contagious enteric pathogen of swine. PEDV has been a major problem in the pig industry since its first identification in 1992. The aim of this study was to investigate the diversity, molecular characteristics, and phylogenetic relationships of PEDVs in field samples from Korea. Six PEDVs were identified from the field samples, and the full spike (S) glycoprotein gene sequences were analyzed. A phylogenetic analysis of the S gene sequences from the six isolates revealed that they were clustered into the G2b subgroup with genetic distance. The genetic identity of the nucleotide sequences and deduced amino acid sequences of the S genes of those isolates was 97.9-100% and 97.4-100%, respectively. A BLAST search for new PEDVs revealed an identity greater than 99.5% compared to the highest similarity of two different Korean strains. The CO-26K equivalent (COE) epitope had a 521H→Y/Q amino acid substitution compared to the subgroup G2b reference strain (KNU-1305). The CNU-22S11 had 28 amino acid substitutions compared to the KNU-1305 strain, which included two newly identified amino acid substitutions: 562S→F and 763P→L in the COE and SS6 epitopes, respectively. Furthermore, the addition and loss of N-linked glycosylation were observed in the CNU-22S11. The results suggest that various strains of PEDV are prevalent and undergoing evolution at swine farms in South Korea and can affect receptor specificity, virus pathogenicity, and host immune system evasion. Overall, this study provides an increased understanding of the prevalence and control of PEDV in South Korea.
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Affiliation(s)
| | | | | | - Jung-Eun Park
- College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea; (B.T.L.); (H.C.G.); (M.-H.K.)
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Zang Y, Feng B, Huang Z, Zhao D, Qi W, Qiu Y, Qiu M, Li C, Lin H, Zheng W, Zhu J, Chen N. Epidemiologic and Genomic Characterizations of Porcine Kobuviruses in Diarrheic and Healthy Pigs. Animals (Basel) 2023; 13:3129. [PMID: 37835735 PMCID: PMC10571770 DOI: 10.3390/ani13193129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/30/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
Porcine kobuvirus (PKV) is an enteric virus commonly detected in both diarrheic and healthy pigs. Little is known about the role of PKV in enteric diseases. In this study, an epidemiological investigation based on 324 intestinal samples collected from six provinces of China during the period of 2018 to 2022 was performed, and showed that PKV has an overall 65.43% (212/324) positive rate. Noticeably, 89.47% (17/19) of PKV and porcine epidemic diarrhea virus (PEDV) double-positive pigs were clinically diseased, while 91.71% (177/193) of PKV-positive but PEDV-negative pigs were clinically healthy, suggesting that PKV infection in itself is unlikely to cause enteric diseases. In addition, three PKV genomes were obtained from both diseased and healthy pigs. Phylogenetic analysis showed that Chinese PKV strains could be divided into three groups (SH-W-CHN-like, S-1-HUN-like and JXAT2015-like strains). All three obtained PKV genomes belong to SH-W-CHN-like strains and JSYZ1806-158 was detected as a recombinant virus. Furthermore, multiple comparisons showed that nucleotide similarities are clearly lower than amino acid similarities for PKV polyproteins. Selective pressure analysis indicated that Chinese PKV polyproteins are predominantly under negative selection. Overall, this study provided new insights into the prevalence and evolution of PKV in both diarrheic and healthy pigs in China.
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Affiliation(s)
- Yu Zang
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Binghui Feng
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Zitao Huang
- Animal Health Supervision Institute of Fengxi District, Chaozhou 521031, China;
| | - Dashi Zhao
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Wenhao Qi
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Yuejia Qiu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Ming Qiu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Chen Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Hong Lin
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Wanglong Zheng
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
| | - Jianzhong Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Nanhua Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (B.F.); (D.Z.); (W.Q.); (Y.Q.); (M.Q.); (C.L.); (H.L.); (W.Z.); (J.Z.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou 225009, China
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou 225009, China
- Comparative Medicine Research Institute, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, Fuzhou 350002, China
- Fujian Provincial Key Laboratory for Prevention and Control of Animal Infectious Diseases and Biotechnology, Longyan University, Longyan 364012, China
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Ge Y, Jiang F, Wang S, Wu H, Liu Y, Wang B, Hou W, Yu X, Wang H. Natural Evolution of Porcine Epidemic Diarrhea Viruses Isolated from Maternally Immunized Piglets. Animals (Basel) 2023; 13:1766. [PMID: 37889642 PMCID: PMC10252125 DOI: 10.3390/ani13111766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/18/2023] [Accepted: 05/24/2023] [Indexed: 10/29/2023] Open
Abstract
The porcine epidemic diarrhea virus (PEDV) can cause severe piglet diarrhea or death in some herds. Genetic recombination and mutation facilitate the continuous evolution of the virus (PEDV), posing a great challenge for the prevention and control of porcine epidemic diarrhea (PED). Disease materials of piglets with PEDV vaccination failure in some areas of Shanxi, Henan and Hebei provinces of China were collected and examined to understand the prevalence and evolutionary characteristics of PEDV in these areas. Forty-seven suspicious disease materials from different litters on different farms were tested by multiplex PCR and screened by hematoxylin-eosin staining and immunohistochemistry. PEDV showed a positivity rate of 42.6%, infecting the small and large intestine and mesenteric lymph node tissues. The isolated strains infected Vero, PK-15 and Marc-145 multihost cells and exhibited low viral titers in all three cell types, as indicated by their growth kinetic curves. Possible putative recombination events in the isolates were identified by RDP4.0 software. Sequencing and phylogenetic analysis showed that compared with the classical vaccine strain, PEDV SX6 contains new insertion and mutations in the S region and belongs to genotype GIIa. Meanwhile, ORF3 has the complete amino acid sequence with aa80 mutated wild strains, compared to vaccine strains CV777, AJ1102, AJ1102-R and LW/L. These results will contribute to the development of new PEDV vaccines based on prevalent wild strains for the prevention and control of PED in China.
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Affiliation(s)
- Yufang Ge
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Feiyang Jiang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Sibei Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Heqiong Wu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Yuan Liu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Bin Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
- Single Molecule Nanometry Laboratory (Sinmolab), Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Hou
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Xiuju Yu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Haidong Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
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