1. Differential epitope prediction across diverse circulating variants of SARS-COV-2 in Brazil.
- Author
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Cavalcanti-Dantas VM, Fernandes B, Dantas PHLF, Uchoa GR, Mendes AF, Araújo Júnior WO, Castellano LRC, Fernandes AIV, Goulart LR, Oliveira RADS, Assis PAC, Souza JR, and Morais CNL
- Subjects
- Humans, Brazil, Epitopes, B-Lymphocyte immunology, Epitopes, B-Lymphocyte chemistry, Epitopes immunology, Epitopes chemistry, Interferon-gamma immunology, Histocompatibility Antigens Class II immunology, Histocompatibility Antigens Class II genetics, SARS-CoV-2 immunology, SARS-CoV-2 genetics, Spike Glycoprotein, Coronavirus immunology, Spike Glycoprotein, Coronavirus genetics, Spike Glycoprotein, Coronavirus chemistry, COVID-19 immunology, COVID-19 virology, COVID-19 prevention & control
- Abstract
COVID-19, caused by the SARS-COV-2 virus, induces numerous immunological reactions linked to the severity of the clinical condition of those infected. The surface Spike protein (S protein) present in Sars-CoV-2 is responsible for the infection of host cells. This protein presents a high rate of mutations, which can increase virus transmissibility, infectivity, and immune evasion. Therefore, we propose to evaluate, using immunoinformatic techniques, the predicted epitopes for the S protein of seven variants of Sars-CoV-2. MHC class I and II epitopes were predicted and further assessed for their immunogenicity, interferon-gamma (IFN-γ) inducing capacity, and antigenicity. For B cells, linear and structural epitopes were predicted. For class I MHC epitopes, 40 epitopes were found for the clades of Wuhan, Clade 2, Clade 3, and 20AEU.1, Gamma, and Delta, in addition to 38 epitopes for Alpha and 44 for Omicron. For MHC II, there were differentially predicted epitopes for all variants and eight equally predicted epitopes. These were evaluated for differences in the MHC II alleles to which they would bind. Regarding B cell epitopes, 16 were found in the Wuhan variant, 14 in 22AEU.1 and in Clade 3, 15 in Clade 2, 11 in Alpha and Delta, 13 in Gamma, and 9 in Omicron. When compared, there was a reduction in the number of predicted epitopes concerning the Spike protein, mainly in the Delta and Omicron variants. These findings corroborate the need for updates seen today in bivalent mRNA vaccines against COVID-19 to promote a targeted immune response to the main circulating variant, Omicron, leading to more robust protection against this virus and avoiding cases of reinfection. When analyzing the specific epitopes for the RBD region of the spike protein, the Omicron variant did not present a B lymphocyte epitope from position 390, whereas the epitope at position 493 for MHC was predicted only for the Alpha, Gamma, and Omicron variants., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)
- Published
- 2024
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