Vaccine Development – Project Overview

In a project to identify epitopes for vaccine development, Immunitrack applies the NeoScreen immunogenicity prediction platform to assess the binding of candidate epitopes to MHC I and MHC II molecules.

The general workflow for an epitope prediction project is shown in the figure above. Typically, a client or partner approaches Immunitrack with either the identity or genome sequence of the target pathogen, or particular target proteins or protein regions of interest. An initial teleconference will clarify the scope of the project to be undertaken by Immunitrack, including decisions about:

• Which assays to run and whether to include in silico-predicted epitope binders. We always advise to run stability assays first and then affinity assays as this order is most cost-effective.
• How many MHC I & II alleles should be included in the screening and which populations they should represent.
• Whether Immunitrack should screen the entire proteome of a virus or bacteria (or other pathogen), or whether it is relevant to screen select proteins or protein regions of interest.

Immunitrack will then compile a list of the epitopes to be tested, and these epitopes will be tested in vitro on the NeoScreen platform. Once testing is complete, Immunitrack will generate a project report containing the raw assay data as well as a ranked list of the epitopes most likely to bind the analysed MHC molecules. These epitopes can be then advanced by clients and partners for vaccine development as well as immune monitoring of infected patients.

COVID-19

In March 2020, Immunitrack and collaborators released a list of novel candidate CD4 and CD8-stimulating epitopes from COVID-19 and that data was made available as a free download. The resulting data report represents the typical output from an epitope prediction project. View the report and associated details here ▸.

Vaccine Links

• Vaccine development: Introduction ▸
• Vaccine development: Project overview ▸
• Vaccine development: Case studies ▸
• Vaccine development: COVID-19 ▸
• Spike CD4⁺ and CD8⁺ T Cell Epitope Kits▸
• COVID-19 CD8⁺ T Cell Tetramer Panel ▸

References

1. Barnes, E. et al. (2012). Novel Adenovirus-Based Vaccines Induce Broad and Sustained T Cell Responses to HCV in Man. Science translational medicine 4, 115ra111.
2. Panagioti, E., Klenerman, P., Lee, L.N., van der Burg, S.H., and Arens, R. (2018). Features of Effective T Cell-Inducing Vaccines against Chronic Viral Infections. Frontiers in Immunology 9, 276.
3. Sridhar, S., Begom, S., Bermingham, A., Hoschler, K., Adamson, W., Carman, W., Bean, T., Barclay, W., Deeks, J.J., and Lalvani, A. (2013). Cellular immune correlates of protection against symptomatic pandemic influenza. Nature Medicine 19, 1305-1312.
4. Valkenburg, S.A., Li, O.T.W., Li, A., Bull, M., Waldmann, T.A., Perera, L.P., Peiris, M., and Poon, L.L.M. (2018). Protection by universal influenza vaccine is mediated by memory CD4 T cells. Vaccine 36, 4198-4206.
5. Harndahl, M. et al. Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity. Eur J Immunol. 2012, 42(6):1405-16.