Insights into Cross-species Evolution of Novel Human Coronavirus SARS-CoV-2 and Defining Immune Determinants for Vaccine Development
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak in the city of Wuhan, China during December 2019, has now spread to various countries across the globe triggering a heightened containment effort. This human pathogen is a member of betacoronavirus genus carrying 30 kilobase of single positive-sense RNA genome. Understanding the evolution, zoonotic transmission, and source of this novel virus would help accelerating containment and prevention efforts. The present study reported detailed analysis of SARS-CoV-2 genome evolution and potential candidate peptides for vaccine development. This new coronavirus genotype might have been evolved from a bat-coronavirus by accumulating non-synonymous mutations, indels, and recombination events. Structural proteins Spike (S), and Membrane (M) had extensive mutational changes, whereas Envelope (E) and Nucleocapsid (N) proteins were very conserved suggesting differential selection pressures exerted on SARS-CoV-2 during evolution. Interestingly, SARS-CoV-2 Spike protein contains a 39 nucleotide sequence insertion relative to SARS-like bat-SL-CoVZC45/2017. Furthermore, we identified eight high binding affinity (HBA) CD4 T-cell epitopes in the S, E, M and N proteins, which can be commonly recognized by HLA-DR alleles of Asia and Asia-Pacific Region population. These immunodominant epitopes can be incorporated in universal subunit SARS-CoV-2 vaccine. Diverse HLA types and variations in the epitope binding affinity may contribute to the wide range of immunopathological outcomes of circulating virus in humans. Our findings emphasize the requirement for continuous surveillance of SARS-CoV-2 strains in live animal markets to better understand the viral adaptation to human host and to develop practical solutions to prevent the emergence of novel pathogenic SARS-CoV-2 strains.
Article activity feed
-
-
SciScore for 10.1101/2020.01.29.925867: (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 The genome sequences of 2019-nCoV were obtained on 29 January 2020 along with genetically related 10 SARS-CoV/SARS-CoV-like virus genome sequences that we identified through the BLASTN search in NCBI database. BLASTNsuggested: (BLASTN, RRID:SCR_001598)NCBIsuggested: (NCBI, RRID:SCR_006472)Structural genes/proteins were aligned with closely related sequences using Clustal Omega Program11. 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 Na…
SciScore for 10.1101/2020.01.29.925867: (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 The genome sequences of 2019-nCoV were obtained on 29 January 2020 along with genetically related 10 SARS-CoV/SARS-CoV-like virus genome sequences that we identified through the BLASTN search in NCBI database. BLASTNsuggested: (BLASTN, RRID:SCR_001598)NCBIsuggested: (NCBI, RRID:SCR_006472)Structural genes/proteins were aligned with closely related sequences using Clustal Omega Program11. 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.
-
-