COVID-19 coronavirus vaccine T cell epitope prediction analysis based on distributions of HLA class I loci (HLA-A, -B, -C) across global populations. Issue 4 (3rd April 2021)

• Record Type: Journal Article
• Authors: Cun, Yina; Li, Chuanyin; Shi, Lei; Sun, Ming; Dai, Shuying; Sun, Le; Shi, Li; Yao, Yufeng
• Is Part Of: Human vaccines & immunotherapeutics. Volume 17:Issue 4(2021)
• Page Start: 1097
• Page End: 1108
• Publication Date: 2021-04-03
• Subjects: SARS-CoV-2 -- Human Leukocyte Antigen (HLA) -- T cell epitopes -- population coverage -- vaccine; Vaccines -- Periodicals; 615.372
• DOI: 10.1080/21645515.2020.1823777
• Languages: English
• ISSNs: 2164-5515

Abstract

ABSTRACT: T cell immunity, such as CD4 and/or CD8 T cell responses, plays a vital role in controlling the virus infection and pathological damage. Several studies have reported SARS-CoV-2 proteins could serve as ideal vaccine candidates against SARS-CoV-2 infection by activating the T cell responses. In the current study, based on the SARS-CoV-2 sequence and distribution of host human leukocyte antigen (HLA), we predicted the possible epitopes for the vaccine against SARS-CoV-2 infections. Firstly, the current study retrieved the SARS-CoV-2 S and N protein sequences from the NCBI Database. Then, using the Immune Epitope Database Analysis Resource, we predicted the CTL epitopes of the SARS-CoV-2 S and N proteins according to worldwide frequency distributions of HLA-A, -B, and -C alleles (>1%). Our results predicted 90 and 106 epitopes of N and S proteins, respectively. Epitope cluster analysis showed 16 and 34 respective clusters of SARS-CoV-2 N and S proteins, which covered 95.91% and 96.14% of the global population, respectively. After epitope conservancy analysis, 8 N protein epitopes and 6 S protein epitopes showed conservancy within two SARS-CoV-2 types. Of these 14 epitopes, 13 could cover SARS coronavirus and Bat SARS-like coronavirus. The remaining epitope (KWPWYIWLGF1211-1220 ) could cover MERS coronavirus. Finally, the 14-epitope combination could vaccinate 89.60% of all individuals worldwide. Our results propose single or combined CTL epitopes predicted in the current study as candidates for vaccines to effectively control SARS-CoV-2 infection and development.