Abstract
The Omicron variants boast the highest infectivity rates among all SARS-CoV-2 variants. Despite their lower disease severity, they can reinfect COVID-19 patients and infect vaccinated individuals as well. The high number of mutations in these variants render them resistant to antibodies that otherwise neutralize the spike protein of the original SARS-CoV-2 spike protein. Recent research has shown that despite its strong immune evasion, Omicron still induces strong T Cell responses similar to the original variant. This work investigates the molecular basis for this observation using the neural network tools NetMHCpan-4.1 and NetMHCiipan-4.0. The antigens presented through the MHC Class I and Class II pathways from all the notable SARS-CoV-2 variants were compared across numerous high frequency HLAs. All variants were observed to have equivalent T cell antigenicity. A novel positive control system was engineered in the form of spike variants that did evade T Cell responses, unlike Omicron. These evasive spike proteins were used to statistically confirm that the Omicron variants did not exhibit lower antigenicity in the MHC pathways.
Original language | English (US) |
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Pages (from-to) | 1-11 |
Number of pages | 11 |
Journal | IEEE/ACM Transactions on Computational Biology and Bioinformatics |
DOIs | |
State | Accepted/In press - 2024 |
Keywords
- Amino acids
- Antigens
- COVID-19
- COVID-19
- Histocompatibility Antigens Class I
- Histocompatibility Antigens Class II
- Immunogenicity
- Peptides
- Proteins
- Receptor (biochemistry)
- Spike Glycoprotein
- Vaccines
ASJC Scopus subject areas
- Biotechnology
- Genetics
- Applied Mathematics