Designing of cytotoxic and helper T cell epitope map provides insights into the highly contagious nature of the pandemic novel coronavirus SARS-CoV-2

Novel coronavirus, SARS-CoV-2, has emerged as one of the deadliest pathogens of this century, creating an unprecedented pandemic. Belonging to the betacoronavirus family, it primarily spreads through human contact via symptomatic and asymptomatic transmission. Despite several attempts since it emerged, there is no known treatment in the form of drugs or vaccines. Hence, work on developing a potential multi-subunit vaccine is the need of the hour. In this study, attempts have been made to find globally conserved epitopes from the entire set of SARS-CoV-2 proteins as there is as yet, no clear information on the immunogenicity of these proteins. Using diverse computational tools, a ranked list of probable immunogenic, promiscuous epitopes generated through all the three main stages of antigen processing and presentation pathways has been prioritized. Moreover, several useful insights were gleaned during these analyses. One of the most important insights is that all of the proteins in this pathogen present unique epitopes, so that the targeting of a few specific viral proteins is not likely to result in an effective immune response in humans. Due to the presence of these unique epitopes in all of the SARS-CoV-2 proteins, stronger immune responses generated by T cell hyperactivation may lead to cytokine storm and immunopathology and consequently, remote chances of human survival. These epitopes, after due validation in vitro, may thus need to be presented to the human body in that form of multi-subunit epitope-based vaccine that avoids such immunopathologies.

overlapping epitopes in multi-subunit vaccines." It is not clear what is meant by "immune system backfiring". 16.
On page 20, line 37, the sentence "Even as this study is important in pointing out the possible mechanisms in contagious nature of SARSCoV-2 , more evidence is required in the form of experiments." It's not clear how the analysis performed in this work point to possible mechanisms of contagious nature of SARS-COV2. This sentence should be revised.
Decision letter (RSOS-201141.R0) We hope you are keeping well at this difficult and unusual time. We continue to value your support of the journal in these challenging circumstances. If Royal Society Open Science can assist you at all, please don't hesitate to let us know at the email address below.
Dear Dr Mishra, The editors assigned to your paper ("Designing of cytotoxic and helper T cell epitope map provides insights into the highly contagious nature of the pandemic novel coronavirus SARS-CoV-2") have now received comments from reviewers.
The referee and Associate Editor have responded favourably to publication. However, the reviewer raises a number of substantive points regarding both over-interpretation and the need for additional verification of the statistics applied. It will be important to carefully consider and respond to these points. We would like you to revise your paper in accordance with the referee and Associate Editor suggestions which can be found below (not including confidential reports to the Editor). Please note this decision does not guarantee eventual acceptance.
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Comments to Author:
Reviewers' Comments to Author: Reviewer: 1 Comments to the Author(s) In this work, Mishra explore the immunogenicity of thee produced proteins in the SARS-CoV2 RNA genome. Using 2 different computational approaches that takes into account the stages of antigen processing and presentation, MHC I and MHCII binding, and immunogenicity, the authors proposes a list of peptides in almost all of the predicted SARS-CoV2 proteins that may be tested for possible vaccine candidates. The work is very comprehensive, timely and will be of interest to the field. However, in some places, the data is overinterpreted, and there are a number of awkward statements, and some concerns about the presentation of the work as detailed below: 1. The manuscript would be enhanced with a figure depicting the viral proteins being evaluated. 2. On page 1, line 44, the author suggests that this work would be used to determine virulence of the proteins. The word virulence should be replaced with immunogenicity. 3. The statement on page 1, line 54 in the sentence "…if one protein is attacked by the immune system, weakening the virus, other proteins can continue to assist in its survival." This statement should be revised to reflect the fact that immune targeting of specific proteins is not likely to result in such a response. 4. On page 2, line 2, the author suggests that the presence of unique epitopes in SARS-Cov2 may result in a "…a stronger immune response generated may lead to cytokine storm and immunopathology". While SARS-CoV2 has been shown to induce cytokine storm, it is not likely that this is due to the number of unique epitopes. 5. On page 3, line 6, the author states "..vaccination is indispensable in order to cure an entire population." Vaccines generally do not cure infections, but prevent infection or symptoms. This statement should be corrected. 6. On page 3, line 48, the author states "As opposed to common perception that membrane and spike proteins confer better immunogenic ability, an interesting perception is found from this study that it may be the opposite case in context of SARS-CoV-2 when studied across populations with different HLA-I supertypes." This statement should be qualified to indicate that antibody responses may preferentially target membrane and spike proteins given their locations on the virus, and that this current analysis is geared towards T cell epitopes. 7. The author refers "promiscuous" (e.g. page 5 line 48). The parameters used to determine promiscuous should be stated. 8. On page 6, line 25, in the sentence "…lending support to the theory that these selected epitopes may mount a high immune response in vitro.", the reference to "in vitro" should be "in vivo". 9. On page 13, line 9, the sentence " Another immunogenicity prediction tool, Tcell, was used to predict immunogenic epitopes across two alleles DRB1*01:01 and DRB1*15:01 as it uses PDB files for TCR and there was no structure for other alleles in PDB." What does the author mean by "..PDB files for TCR and there was no structure for other alleles in PDB". 10. The headings and text in the tables, particularly Table 2, need to better described as it's a bit confusing. Particularly, the heading, "clustering with HLA-II epitopes" and "conservation in MSA". 11. The title of Table 2 is "Immunogenic CTL epitopes…" It is not clear if this represents peptides identified as HLA II binders that also bind to HLA I. 12. The author refers to yellow highlights in Table 3, but there is no such yellow highlighting. 13. There is a section on "B cell epitopes", however, this work does not analyze for B cell epitopes. This section should be removed. 14. On page 19, line 51, the author states that "Including B cell epitopes in the vaccination strategy with T cell epitopes may not be a good strategy, and may even be counter-productive." This statement should be revised to reflect that fact that both B and T cell epitopes are important since antibody responses are also critical to generate virus neutralizing antibodies. 15. On page 20, line 9, the author states "This is so done in order to minimize the possible immune system backfiring (22, 23) due to the presence of too many overlapping as well as nonoverlapping epitopes in multi-subunit vaccines." It is not clear what is meant by "immune system backfiring". 16. On page 20, line 37, the sentence "Even as this study is important in pointing out the possible mechanisms in contagious nature of SARSCoV-2 , more evidence is required in the form of experiments." It's not clear how the analysis performed in this work point to possible mechanisms of contagious nature of SARS-COV2. This sentence should be revised.

Author's Response to Decision Letter for (RSOS-201141.R0)
See Appendix A.

Decision letter (RSOS-201141.R1)
We hope you are keeping well at this difficult and unusual time. We continue to value your support of the journal in these challenging circumstances. If Royal Society Open Science can assist you at all, please don't hesitate to let us know at the email address below.
Dear Dr Mishra, It is a pleasure to accept your manuscript entitled "Designing of cytotoxic and helper T cell epitope map provides insights into the highly contagious nature of the pandemic novel coronavirus SARS-CoV-2" in its current form for publication in Royal Society Open Science.
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