Abstract
BackgroundTo contain the pandemics caused by SARS-CoV-2, early detection approaches with high accuracy and accessibility are critical. Generating an antigen-capture based detection system would be an ideal strategy complementing the current methods based on nucleic acids and antibody detection. The spike protein is found on the outside of virus particles and appropriate for antigen detection.MethodsIn this study, we utilized bioinformatics approaches to explore the immunodominant fragments on spike protein of SARS-CoV-2.ResultsThe S1 subunit of spike protein was identified with higher sequence specificity. Three immunodominant fragments, Spike56-94, Spike199-264, and Spike577-612, located at the S1 subunit were finally selected via bioinformatics analysis. The glycosylation sites and high-frequency mutation sites on spike protein were circumvented in the antigen design. All the identified fragments present qualified antigenicity, hydrophilicity, and surface accessibility. A recombinant antigen with a length of 194 amino acids (aa) consisting of the selected immunodominant fragments as well as a universal Th epitope was finally constructed.ConclusionThe recombinant peptide encoded by the construct contains multiple immunodominant epitopes, which is expected to stimulate a strong immune response in mice and generate qualified antibodies for SARS-CoV-2 detection.
Highlights
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious and has caused more than one hundred million infection cases and over 2.4 million deaths, posing a huge economic and social burden internationally (Lan et al, 2020; Shang et al, 2020)
Sequence alignment of spike protein in different coronaviruses We performed sequence alignment to determine the evolutionary relationships between SARS-CoV-2 and other beta-coronaviruses that could infect humans
To better understand the divergence of spike protein sequences between SARS-CoV-2 and SARS-CoV, we further analyzed the sequences of main domains
Summary
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious and has caused more than one hundred million infection cases and over 2.4 million deaths (https://www.who.int/, as of February 15, 2021), posing a huge economic and social burden internationally (Lan et al, 2020; Shang et al, 2020). Early detection and isolation of infected people are still indispensable means to control the spread of the epidemic, which requires accurate, early, economical, and easy-to-operate diagnostic methods (Yan, Chang & Wang, 2020). To contain the pandemics caused by SARS-CoV-2, early detection approaches with high accuracy and accessibility are critical. Methods: In this study, we utilized bioinformatics approaches to explore the immunodominant fragments on spike protein of SARS-CoV-2. All the identified fragments present qualified antigenicity, hydrophilicity, and surface accessibility. A recombinant antigen with a length of 194 amino acids (aa) consisting of the selected immunodominant fragments as well as a universal Th epitope was constructed. Conclusion: The recombinant peptide encoded by the construct contains multiple immunodominant epitopes, which is expected to stimulate a strong immune response in mice and generate qualified antibodies for SARS-CoV-2 detection
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