Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus.
Human respiratory syncytial virus (RSV) is a major cause of lower respiratory infection. Despite more than 60 years of research, there is no licensed vaccine. While B cell response is a major focus for vaccine design, the T cell epitope profile of RSV is also important for vaccine development. Here,...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2023-01-01
|
| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1010360 |
| _version_ | 1797736808034861056 |
|---|---|
| author | Jiani Chen Swan Tan Vasanthi Avadhanula Leonard Moise Pedro A Piedra Anne S De Groot Justin Bahl |
| author_facet | Jiani Chen Swan Tan Vasanthi Avadhanula Leonard Moise Pedro A Piedra Anne S De Groot Justin Bahl |
| author_sort | Jiani Chen |
| collection | DOAJ |
| description | Human respiratory syncytial virus (RSV) is a major cause of lower respiratory infection. Despite more than 60 years of research, there is no licensed vaccine. While B cell response is a major focus for vaccine design, the T cell epitope profile of RSV is also important for vaccine development. Here, we computationally predicted putative T cell epitopes in the Fusion protein (F) and Glycoprotein (G) of RSV wild circulating strains by predicting Major Histocompatibility Complex (MHC) class I and class II binding affinity. We limited our inferences to conserved epitopes in both F and G proteins that have been experimentally validated. We applied multidimensional scaling (MDS) to construct T cell epitope landscapes to investigate the diversity and evolution of T cell profiles across different RSV strains. We find the RSV strains are clustered into three RSV-A groups and two RSV-B groups on this T epitope landscape. These clusters represent divergent RSV strains with potentially different immunogenic profiles. In addition, our results show a greater proportion of F protein T cell epitope content conservation among recent epidemic strains, whereas the G protein T cell epitope content was decreased. Importantly, our results suggest that RSV-A and RSV-B have different patterns of epitope drift and replacement and that RSV-B vaccines may need more frequent updates. Our study provides a novel framework to study RSV T cell epitope evolution. Understanding the patterns of T cell epitope conservation and change may be valuable for vaccine design and assessment. |
| first_indexed | 2024-03-12T13:19:17Z |
| format | Article |
| id | doaj.art-425eb1f32a3c495e9b17ae9d594b72c4 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-03-12T13:19:17Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-425eb1f32a3c495e9b17ae9d594b72c42023-08-26T05:31:14ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582023-01-01191e101036010.1371/journal.pcbi.1010360Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus.Jiani ChenSwan TanVasanthi AvadhanulaLeonard MoisePedro A PiedraAnne S De GrootJustin BahlHuman respiratory syncytial virus (RSV) is a major cause of lower respiratory infection. Despite more than 60 years of research, there is no licensed vaccine. While B cell response is a major focus for vaccine design, the T cell epitope profile of RSV is also important for vaccine development. Here, we computationally predicted putative T cell epitopes in the Fusion protein (F) and Glycoprotein (G) of RSV wild circulating strains by predicting Major Histocompatibility Complex (MHC) class I and class II binding affinity. We limited our inferences to conserved epitopes in both F and G proteins that have been experimentally validated. We applied multidimensional scaling (MDS) to construct T cell epitope landscapes to investigate the diversity and evolution of T cell profiles across different RSV strains. We find the RSV strains are clustered into three RSV-A groups and two RSV-B groups on this T epitope landscape. These clusters represent divergent RSV strains with potentially different immunogenic profiles. In addition, our results show a greater proportion of F protein T cell epitope content conservation among recent epidemic strains, whereas the G protein T cell epitope content was decreased. Importantly, our results suggest that RSV-A and RSV-B have different patterns of epitope drift and replacement and that RSV-B vaccines may need more frequent updates. Our study provides a novel framework to study RSV T cell epitope evolution. Understanding the patterns of T cell epitope conservation and change may be valuable for vaccine design and assessment.https://doi.org/10.1371/journal.pcbi.1010360 |
| spellingShingle | Jiani Chen Swan Tan Vasanthi Avadhanula Leonard Moise Pedro A Piedra Anne S De Groot Justin Bahl Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus. PLoS Computational Biology |
| title | Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus. |
| title_full | Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus. |
| title_fullStr | Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus. |
| title_full_unstemmed | Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus. |
| title_short | Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus. |
| title_sort | diversity and evolution of computationally predicted t cell epitopes against human respiratory syncytial virus |
| url | https://doi.org/10.1371/journal.pcbi.1010360 |
| work_keys_str_mv | AT jianichen diversityandevolutionofcomputationallypredictedtcellepitopesagainsthumanrespiratorysyncytialvirus AT swantan diversityandevolutionofcomputationallypredictedtcellepitopesagainsthumanrespiratorysyncytialvirus AT vasanthiavadhanula diversityandevolutionofcomputationallypredictedtcellepitopesagainsthumanrespiratorysyncytialvirus AT leonardmoise diversityandevolutionofcomputationallypredictedtcellepitopesagainsthumanrespiratorysyncytialvirus AT pedroapiedra diversityandevolutionofcomputationallypredictedtcellepitopesagainsthumanrespiratorysyncytialvirus AT annesdegroot diversityandevolutionofcomputationallypredictedtcellepitopesagainsthumanrespiratorysyncytialvirus AT justinbahl diversityandevolutionofcomputationallypredictedtcellepitopesagainsthumanrespiratorysyncytialvirus |