Identification of Conserved Epitopes in SARS-CoV-2 Spike and Nucleocapsid Protein
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel virus that first occurred in Wuhan in December 2019. The spike glycoproteins and nucleocapsid proteins are the most common targets for the development of vaccines and antiviral drugs.
Objective:
We herein analyze the rate of evolution along with the sequences of spike and nucleocapsid proteins in relation to the spatial locations of their epitopes, previously suggested to contribute to the immune response caused by SARS-CoV-2 infections.
Methods:
We compare homologous proteins of seven human coronaviruses: HCoV-229E, HCoV- -OC43, SARS-CoV, HCoV-NL63, HCoV-HKU1, MERS-CoV, and SARS-CoV-2. We then focus on the local, structural order-disorder propensity of the protein regions where the SARS-CoV-2 epitopes are located.
Results:
We show that most of nucleocapsid protein epitopes overlap the RNA-binding and dimerization domains, and some of them are characterized by a low rate of evolutions. Similarly, spike protein epitopes are preferentially located in regions that are predicted to be ordered and wellconserved, in correspondence of the heptad repeats 1 and 2. Interestingly, both the receptor-binding motif to ACE2 and the fusion peptide of spike protein are characterized by a high rate of evolution.
Conclusion:
Our results provide evidence for conserved epitopes that might help develop broad- -spectrum SARS-CoV-2 vaccines.
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SciScore for 10.1101/2020.05.14.095133: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources We downloaded the coding sequences of these coronaviruses from the National Center for Biotechnological Information (NCBI) (available at https://www.ncbi.nlm.nih.gov/). https://www.ncbi.nlm.nih.gov/suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)2.2 Sequence alignment: To explore the evolutionary relationships among the proteins N and S in the seven human coronaviruses here considered, the selected protein sequences were aligned by using Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/ Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Results …
SciScore for 10.1101/2020.05.14.095133: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources We downloaded the coding sequences of these coronaviruses from the National Center for Biotechnological Information (NCBI) (available at https://www.ncbi.nlm.nih.gov/). https://www.ncbi.nlm.nih.gov/suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)2.2 Sequence alignment: To explore the evolutionary relationships among the proteins N and S in the seven human coronaviruses here considered, the selected protein sequences were aligned by using Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/ Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
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