Predicting Immunogenic Epitopes Variation of Envelope 2 Gene Among Chikungunya Virus Clonal Lineages by an In Silico Approach
Chikungunya virus (CHIKV), responsible for a mosquito-borne viral illness, has rapidly spread worldwide, posing a significant global health threat. In this study, we explored the immunogenic variability of CHIKV envelope 2 (E2), a pivotal component in the anti-CHIKV immune response, using an in sili...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2024-10-01
|
| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/16/11/1689 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850146933430026240 |
|---|---|
| author | Sung-Yeon Cho Dong-Gun Lee Jung Yeon Park Won-Bok Kim Raeseok Lee Dukhee Nho Eun-Jee Oh Hyeyoung Lee Chulmin Park |
| author_facet | Sung-Yeon Cho Dong-Gun Lee Jung Yeon Park Won-Bok Kim Raeseok Lee Dukhee Nho Eun-Jee Oh Hyeyoung Lee Chulmin Park |
| author_sort | Sung-Yeon Cho |
| collection | DOAJ |
| description | Chikungunya virus (CHIKV), responsible for a mosquito-borne viral illness, has rapidly spread worldwide, posing a significant global health threat. In this study, we explored the immunogenic variability of CHIKV envelope 2 (E2), a pivotal component in the anti-CHIKV immune response, using an in silico approach. After extracting the representative sequence types of the CHIKV E2 antigen, we predicted the structure-based B-cell epitopes and MHC I and II binding T-cell epitopes. Variations in key T-cell epitopes were further analyzed using molecular docking simulations. We extracted 258 E2 gene sequences from a pool of 1660 blast hits, displaying homology levels ranging from 93.6% to 100%. This revealed 44 sequence types, each representing a unique genetic variant. Phylogenetic analysis revealed distinct geographically distributed clonal lineages (clades I-IV). The B-cell linear and discontinuous epitopes demonstrated a similar distribution across the E2 protein of different strains, spanning domains A, B, and C, with some slight variations. Moreover, T-cell epitope prediction revealed eight conserved MHC class I hot spots and three MHC II hot spots, displaying variations among lineages. Among clade II strains, there were significant variations (N5H, S118G, G194S, L248F/S, and I255V/T) observed in epitopes, distinct from strains belonging to other lineages. Additionally, molecular docking showed that variations in MHC I epitopes across clonal lineages induced changes in the structure of the peptide–MHC complexes, potentially resulting in immunogenic disparities. We expect that this in silico approach will serve as a complementary tool to experimental platforms for exploring immunogenic variation or developing biomarkers for vaccine design and other related studies. |
| format | Article |
| id | doaj-art-737c63c7653e4ce697527100f07d1a65 |
| institution | OA Journals |
| issn | 1999-4915 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj-art-737c63c7653e4ce697527100f07d1a652025-08-20T02:27:42ZengMDPI AGViruses1999-49152024-10-011611168910.3390/v16111689Predicting Immunogenic Epitopes Variation of Envelope 2 Gene Among Chikungunya Virus Clonal Lineages by an In Silico ApproachSung-Yeon Cho0Dong-Gun Lee1Jung Yeon Park2Won-Bok Kim3Raeseok Lee4Dukhee Nho5Eun-Jee Oh6Hyeyoung Lee7Chulmin Park8Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Republic of KoreaVaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Republic of KoreaVaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Republic of KoreaVaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Republic of KoreaVaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Republic of KoreaVaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Republic of KoreaDepartment of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of KoreaDepartment of Laboratory Medicine, International St. Mary’s Hospital, College of Medicine, Catholic Kwandong University, Incheon 22711, Republic of KoreaVaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Republic of KoreaChikungunya virus (CHIKV), responsible for a mosquito-borne viral illness, has rapidly spread worldwide, posing a significant global health threat. In this study, we explored the immunogenic variability of CHIKV envelope 2 (E2), a pivotal component in the anti-CHIKV immune response, using an in silico approach. After extracting the representative sequence types of the CHIKV E2 antigen, we predicted the structure-based B-cell epitopes and MHC I and II binding T-cell epitopes. Variations in key T-cell epitopes were further analyzed using molecular docking simulations. We extracted 258 E2 gene sequences from a pool of 1660 blast hits, displaying homology levels ranging from 93.6% to 100%. This revealed 44 sequence types, each representing a unique genetic variant. Phylogenetic analysis revealed distinct geographically distributed clonal lineages (clades I-IV). The B-cell linear and discontinuous epitopes demonstrated a similar distribution across the E2 protein of different strains, spanning domains A, B, and C, with some slight variations. Moreover, T-cell epitope prediction revealed eight conserved MHC class I hot spots and three MHC II hot spots, displaying variations among lineages. Among clade II strains, there were significant variations (N5H, S118G, G194S, L248F/S, and I255V/T) observed in epitopes, distinct from strains belonging to other lineages. Additionally, molecular docking showed that variations in MHC I epitopes across clonal lineages induced changes in the structure of the peptide–MHC complexes, potentially resulting in immunogenic disparities. We expect that this in silico approach will serve as a complementary tool to experimental platforms for exploring immunogenic variation or developing biomarkers for vaccine design and other related studies.https://www.mdpi.com/1999-4915/16/11/1689chikungunya feverChikungunya virusAlphavirusenvelope 2in silico approachMHC binding epitopes |
| spellingShingle | Sung-Yeon Cho Dong-Gun Lee Jung Yeon Park Won-Bok Kim Raeseok Lee Dukhee Nho Eun-Jee Oh Hyeyoung Lee Chulmin Park Predicting Immunogenic Epitopes Variation of Envelope 2 Gene Among Chikungunya Virus Clonal Lineages by an In Silico Approach Viruses chikungunya fever Chikungunya virus Alphavirus envelope 2 in silico approach MHC binding epitopes |
| title | Predicting Immunogenic Epitopes Variation of Envelope 2 Gene Among Chikungunya Virus Clonal Lineages by an In Silico Approach |
| title_full | Predicting Immunogenic Epitopes Variation of Envelope 2 Gene Among Chikungunya Virus Clonal Lineages by an In Silico Approach |
| title_fullStr | Predicting Immunogenic Epitopes Variation of Envelope 2 Gene Among Chikungunya Virus Clonal Lineages by an In Silico Approach |
| title_full_unstemmed | Predicting Immunogenic Epitopes Variation of Envelope 2 Gene Among Chikungunya Virus Clonal Lineages by an In Silico Approach |
| title_short | Predicting Immunogenic Epitopes Variation of Envelope 2 Gene Among Chikungunya Virus Clonal Lineages by an In Silico Approach |
| title_sort | predicting immunogenic epitopes variation of envelope 2 gene among chikungunya virus clonal lineages by an in silico approach |
| topic | chikungunya fever Chikungunya virus Alphavirus envelope 2 in silico approach MHC binding epitopes |
| url | https://www.mdpi.com/1999-4915/16/11/1689 |
| work_keys_str_mv | AT sungyeoncho predictingimmunogenicepitopesvariationofenvelope2geneamongchikungunyavirusclonallineagesbyaninsilicoapproach AT donggunlee predictingimmunogenicepitopesvariationofenvelope2geneamongchikungunyavirusclonallineagesbyaninsilicoapproach AT jungyeonpark predictingimmunogenicepitopesvariationofenvelope2geneamongchikungunyavirusclonallineagesbyaninsilicoapproach AT wonbokkim predictingimmunogenicepitopesvariationofenvelope2geneamongchikungunyavirusclonallineagesbyaninsilicoapproach AT raeseoklee predictingimmunogenicepitopesvariationofenvelope2geneamongchikungunyavirusclonallineagesbyaninsilicoapproach AT dukheenho predictingimmunogenicepitopesvariationofenvelope2geneamongchikungunyavirusclonallineagesbyaninsilicoapproach AT eunjeeoh predictingimmunogenicepitopesvariationofenvelope2geneamongchikungunyavirusclonallineagesbyaninsilicoapproach AT hyeyounglee predictingimmunogenicepitopesvariationofenvelope2geneamongchikungunyavirusclonallineagesbyaninsilicoapproach AT chulminpark predictingimmunogenicepitopesvariationofenvelope2geneamongchikungunyavirusclonallineagesbyaninsilicoapproach |