GenomeBits insight into omicron and delta variants of coronavirus pathogen

Enrique Canessa; Livio Tenze

doi:10.1371/journal.pone.0271039

Peer Review History

Original SubmissionJanuary 20, 2022
27 Apr 2022 Decision Letter - Vladimir Makarenkov, Editor Transfer Alert This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present. PONE-D-22-01925GenomeBits insight into omicron and delta variants of coronavirus pathogenPLOS ONE Dear Dr. Canessa, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Jun 11 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. 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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Additional Editor Comments: It would be important to add a discussion (preferably to the Introduction section) about the origins and impact of the SARS-Cov-2 pandemic. Here you could cite the following works: Boni, Maciej F., et al. "Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic." Nature microbiology 5.11 (2020): 1408-1417. Makarenkov, V., Mazoure, B., Rabusseau, G. et al. Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin. BMC Ecol Evo 21, 5 (2021). Domingo JL. What we know and what we need to know about the origin of SARS-CoV-2. Environ Res. 2021;200:111785. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Partly Reviewer #2: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: No Reviewer #2: No ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: 1. The write-up of the manuscript seems to be premature and very difficult to understand. There are several sweeping statements without any references. For instance, the statement “The first known confirmed delta variant was detected in India in late 2020 and the B.1.1.529 infection appeared from a specimen collected in South Africa a year later, early November 2021” should have a citation. Several sentences are incomplete or do not have a meaning. For example “Although omicron seems to cause less severe COVID-19 than delta.” 2. Authors should clearly explain the computation of binary scores for a given genomic sequence. Illustration or outline graphic may be required. 3. It is trivial that a mononucleotide composition can reveal similar information. How Genomebit information is different from mononucleotide computation with a sliding window?. 4. There is no discussion on their results. The authors should compare their analysis with their previous work and also with similar research by others. Reviewer #2: The manuscript on the topic GenomeBits insight into omicron and delta variants of coronavirus pathogen is an interesting research article. The manuscript is with the interest to the reader and fully in the scope of journal. I will suggest the manuscript to be accepted for publication after revision. 1. Abstract section looks incomplete. I will suggest the author to focus on following important points on writing the abstract. An abstract summarizes, usually in one paragraph of 300 words or less, the major aspects of the entire paper in a prescribed sequence that includes: 1) the overall purpose of the study and the research problem(s) you investigated; 2) the basic design of the study; 3) major findings or trends found as a result of your analysis; and, 4) a brief summary of your interpretations and conclusions. 2. English of the script is very poorly written. Please write your text in good English (American or British usage is accepted, but not a mixture of these). English language manuscript may require editing to eliminate possible grammatical or spelling errors and to conform to correct scientific English. 3. There are several sentences in the script which are really hard to understand. I will suggest the authors should carefully read the script and amend the English language correction throughout the script. 4. Introduction section need to be more elaborated. 5. Provide a general interpretation of the results in the context of other evidence, and implications for future research. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: Yes: Dr Kishore Sesham Reviewer #2: Yes:** SADANAND PANDEY [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0271039.r001
Revision 1
13 May 2022 Author Response See also attached file "Response_to_Reviewers.pdf" for our reply to each specific reviewer and editor comments. Response to Reviewers of PONE-D-22-01925 “GenomeBits insight into omicron and delta variants of coronavirus pathogen”, by E. Canessa, L. Tenze We are indebted to the academic editor and the two reviewers for providing insightful comments on the manuscript. Our responds to each point raised are as follows: � Reply to Additional Editor Comments: The Introduction section was revised and completely rewritten. In particular, we added a discussion in the Introduction section about the origins of the SARSCov- 2 pandemic as sugested by the Editor, and cited the three works suggested: (i) Boni, Maciej F., et al. (ii) Makarenkov, V., Mazoure, B., Rabusseau, G. et al., and (iii) Domingo JL. We also briefly mentioned the impact of the SARS-Cov-2 pandemic and added 11 new references to support our findings throughout the text. The abstract and conclusions have also been improved based on the data presented. All sequence data analysed here are publicly available at GSIAD and all custom code used in the manuscript is fully available at https://github.com/canessae/GenomeBits/ We have made an effort to present our manuscript in an intelligible fashion with an standard English. At revision, we corrected few typographical and grammatical errors. � Reply to Reviewer #1: 1. We have made an effort to rewrite our manuscript and present it in an intelligible fashion with an standard English. Our statements now carry out associated new references and few sentences have been completed with a clear meaning. 2. We have added a new Table to aIllustrate the computation of binary scores for a given genomic sequence. This Table helps us to explain that in our case, the mapping into four binary projections of genome sequences carries alternating plus and minus signs, where + and - signs are chosen sequentially starting with +1 at k = 1 as default. The Table shows a particular mapping 1 example for converting the brief fragment AGATCTGTTCTC of 12 nucleotides into the alternating binary array. As a principal difference with previous binary representations (see, e.g., new Refs [19, 20]), our mapping (whose terms change sign –i.e., if a term X_k is positive then X_k+1 is negative and vice versa) displays their occurrence as +1 or -1 as well as their non existence as 0 at a given base pair k. 3. The inclusion of different smoothing sliding window sizes of up to about 500 bp (moving along the target genome sequences and repeating the GenomeBits procedure as described, lead to a data noise reduction in the curves and preserve the average behavior of the sums displayed in Figures 1 and 2. 4. Our results have been further elaborated. We emphasize that the regions of main discrepancies as found in the Similarity identities curves of Fig 1, e.g., around N=10000 are also reflected by the red lines of Fig 2 via GenomeBits. The main difference between both comparative genomics approaches is that changes via Eq (1) can be analyzed and characterized at each single A,C,G,T nucleotide level separately. Beside such comparision of Similarity studies and our previous analysis on Fast Fourier Transforms for coronavirus genome of other variants as reported in Ref[6], our present findings are new and have not similars to those reported by others. We report a kind of 'ordered' (constant) to 'disordered' (peaked) phase transition phenomena around the NSP5 polymerase within the open reading frames ORF1a region, up to the nucleotide region of the S-Protein. As seen in Fig 2, the black arrows indicate an analogous phase transition point appearing close to the coding region of the Sspike genes. � Reply to Reviewer #2: We particularly thanks this referee for finding our research article interesting and fully in the scope of PLOS One journal. 1. As suggested, the new Abstract now reads: “We apply the new GenomeBits method to uncover underlying genomic features of omicron and delta 2 coronavirus variants. This is a statistical algorithm whose salient feature is to map the nucleotide bases into a finite alternating (+-) sum series of distributed terms of binary (0,1) indicators. We show how by this method, distinctive signals can be uncovered out of the intrinsic data organization of amino acid progressions along their base positions. Results show a sort of 'ordered' (or constant) to 'disordered' (or peaked) transition around the coronavirus S-spike protein region. Together with our previous results for past variants of coronavirus: Alpha, Beta, Gamma, Epsilon and Eta, we conclude that the mapping into GenomeBits strands of omicron and delta variants can help to characterize mutant pathogens.” 2. We have made an effort to present our manuscript in an intelligible fashion with an standard English. At revision, we corrected few typographical and grammatical errors. 3. (idem as 2) 4. As also replied to the Academic Editor, the Introduction section was revised and completely rewritten. In particular, we added a discussion in the Introduction section about the origins of the SARS-Cov-2 pandemic and cited several new references. The abstract and conclusions have also been improved based on the data presented 5. In the Conclusion section we now provide a general reinterpretation of the results in the context of the present study and other evidence published, and also briefly discussed implications for future research. -oOo- Attachments Attachment Submitted filename: Response_to_Reviewers.pdf https://doi.org/10.1371/journal.pone.0271039.r002
23 Jun 2022 Decision Letter - Vladimir Makarenkov, Editor GenomeBits insight into omicron and delta variants of coronavirus pathogen PONE-D-22-01925R1 Dear Dr. Canessa, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Vladimir Makarenkov Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: N/A ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #2: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #2: (No Response) ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #2: Yes: SADANAND PANDEY ******** https://doi.org/10.1371/journal.pone.0271039.r003
Formally Accepted
1 Jul 2022 Acceptance Letter - Vladimir Makarenkov, Editor PONE-D-22-01925R1 GenomeBits insight into omicron and delta variants of coronavirus pathogen Dear Dr. Canessa: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Vladimir Makarenkov Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0271039.r004

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