PMID- 35432316
OWN - NLM
STAT- MEDLINE
DCOM- 20220419
LR  - 20220703
IS  - 1664-3224 (Electronic)
IS  - 1664-3224 (Linking)
VI  - 13
DP  - 2022
TI  - Computer-Based Immunoinformatic Analysis to Predict Candidate T-Cell Epitopes for 
      SARS-CoV-2 Vaccine Design.
PG  - 847617
LID - 10.3389/fimmu.2022.847617 [doi]
LID - 847617
AB  - Since the first outbreak of coronavirus disease 2019 (COVID-19), caused by severe 
      acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, its high 
      infectivity led to its prevalence around the world in an exceptionally short 
      time. Efforts have been made to control the ongoing outbreak, and among them, 
      vaccine developments are going on high priority. New clinical trials add to 
      growing evidence that vaccines from many countries were highly effective at 
      preventing SARS-CoV-2 virus infection. One of them is B cell-based vaccines, 
      which were common during a pandemic. However, neutralizing antibody therapy 
      becomes less effective when viruses mutate. In order to tackle the problem, we 
      focused on T-cell immune mechanism. In this study, the mutated strains of the 
      virus were selected globally from India (B.1.617.1 and B.1.617.2), United Kingdom 
      (B.1.1.7), South Africa (B.1.351), and Brazil (P.1), and the overlapping peptides 
      were collected based on mutation sites of S-protein. After that, residue scanning 
      was used to predict the affinity between overlapping peptide and HLA-A*11:01, the 
      most frequent human leukocyte antigen (HLA) allele among the Chinese population. 
      Then, the binding free energy was evaluated with molecular docking to further 
      verify the affinity changes after the mutations happen in the virus genomes. The 
      affinity test results of three epitopes on spike protein from experimental 
      validation were consistent with our predicted results, thereby supporting the 
      inclusion of the epitope (374)FSTFKCYGL(382) in future vaccine design and 
      providing a useful reference route to improve vaccine development.
CI  - Copyright (c) 2022 Mei, Gu, Shen, Lin and Li.
FAU - Mei, Xueyin
AU  - Mei X
AD  - Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, 
      School of Life Science and Technology, Southeast University, Nanjing, China.
FAU - Gu, Pan
AU  - Gu P
AD  - Department of Math and Computer Sciences, College of Letters and Science, 
      University of Wisconsin-Madison, Madison, WI, United States.
FAU - Shen, Chuanlai
AU  - Shen C
AD  - Department of Microbiology and Immunology, Medical School of Southeast 
      University, Nanjing, China.
FAU - Lin, Xue
AU  - Lin X
AD  - Department of Bioinformatics, School of Biomedical Engineering and Informatics, 
      Nanjing Medical University, Nanjing, China.
FAU - Li, Jian
AU  - Li J
AD  - Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, 
      School of Life Science and Technology, Southeast University, Nanjing, China.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20220330
PL  - Switzerland
TA  - Front Immunol
JT  - Frontiers in immunology
JID - 101560960
RN  - 0 (COVID-19 Vaccines)
RN  - 0 (Epitopes, T-Lymphocyte)
RN  - 0 (Spike Glycoprotein, Coronavirus)
RN  - 0 (Vaccines)
RN  - 0 (spike protein, SARS-CoV-2)
RN  - SARS-CoV-2 variants
SB  - IM
MH  - *COVID-19/prevention & control
MH  - COVID-19 Vaccines
MH  - Computers
MH  - Epitopes, T-Lymphocyte
MH  - Humans
MH  - Molecular Docking Simulation
MH  - SARS-CoV-2
MH  - Spike Glycoprotein, Coronavirus
MH  - *Vaccines
PMC - PMC9006954
OTO - NOTNLM
OT  - S protein
OT  - SARS-CoV-2
OT  - T-cell epitopes
OT  - molecular docking
OT  - vaccine
COIS- The authors declare that the research was conducted in the absence of any 
      commercial or financial relationships that could be construed as a potential 
      conflict of interest.
EDAT- 2022/04/19 06:00
MHDA- 2022/04/20 06:00
PMCR- 2022/03/30
CRDT- 2022/04/18 06:34
PHST- 2022/01/03 00:00 [received]
PHST- 2022/02/28 00:00 [accepted]
PHST- 2022/04/18 06:34 [entrez]
PHST- 2022/04/19 06:00 [pubmed]
PHST- 2022/04/20 06:00 [medline]
PHST- 2022/03/30 00:00 [pmc-release]
AID - 10.3389/fimmu.2022.847617 [doi]
PST - epublish
SO  - Front Immunol. 2022 Mar 30;13:847617. doi: 10.3389/fimmu.2022.847617. eCollection 
      2022.