Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh

Ishtiaque Ahammad; Mohammad Uzzal Hossain; Anisur Rahman; Zeshan Mahmud Chowdhury; Arittra Bhattacharjee; Keshob Chandra Das; Chaman Ara Keya; Md. Salimullah

doi:10.1371/journal.pone.0258019

Peer Review History

Original SubmissionJune 17, 2021
29 Jul 2021 Decision Letter - Narasimha Murthy Bhamidipati, Editor PONE-D-21-19985 Comparative Genomic Study for Revealing the Complete Scenario of COVID-19 Pandemic in Bangladesh PLOS ONE Dear Dr. Ahammad, 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 Sep 12 2021 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. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. [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: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No 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: Yes Reviewer #2: Yes ****** 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: The manuscript “Comparative Genomic Study for Revealing the Complete Scenario of COVID-19 Pandemic in Bangladesh” (PONE-D-21-19985) reports the SARS-CoV2 variants that have caused first and second wave in Bangladesh. The authors have compared the causative variants responsible for the two waves. The manuscript seems to be the first report detailing the molecular perspectives of the two consecutive waves of COVID19 infection in Bangladesh. The evolutionary perspectives of the viral genome has been studied. However, there are some queries which must be addressed by the authors to improve the manuscript. Abstract: OK. Introduction: Page 8; Line: 31-32: Please clearly state based on analyses of which molecular sequences you are stating that “it was discovered that the wave-2 samples had a significantly greater average rate of mutation/sample (30.79%) than the wave-1 samples (12.32%)” Materials and Methods: Page 16, Line 208: Please correct “Room Mean Square Fluctuation (RMSF)” to “Root Mean Square Fluctuation (RMSF)”. Results and Discussion: 1. Please specify the length of genomes that have been studied 2. What was the quality of sequencing (base calling)? 3. Compare the genomic constitution of the two waves or other specific variants. 4. The Spike protein is variable and have been reported to experience selection pressure (doi: 10.1016/j.heliyon.2020.e05001; DOI: 10.3390/pathogens9100829). Please report in the light of the samples of Bangladesh. 5. Please include elaborated analysis on selection pressure and the molecular phylogeny of the variants for the genes showing variation among the viral variants. English: The formation of sentences is not correct. There are several grammatical and syntactical errors. The English of the manuscript must be get thoroughly checked by a suitable English language professional. Some of the points have been indicated in the attached manuscript. Please don’t use the symbols like “>”, in running text, rather write “more than” or “greater than” Reviewer #2: The manuscript presented falls within the scope of the Journal and adds knowledge about the distribution of various clades of SARS-CoV-2 in Bangladesh. The manuscript is well written with enough data both in terms of extensiveness and representation. However there are certain minor corrections in the manuscript which can be found in pop-up notes of the attachment. I also suggest you to modify the title as indicated in the pop-up note of the title. ****** 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: CS Mukhopadhyay Reviewer #2: Yes:** KAMISETTY ASWANI KUMAR [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. Attachments Attachment Submitted filename: PONE-D-21-19985_reviewed.pdf Attachment Submitted filename: PONE-D-21-19985 (reviewed).pdf https://doi.org/10.1371/journal.pone.0258019.r001
Revision 1
1 Sep 2021 Author Response # Response to Queries from Reviewer 1 Reviewer’s Query: The manuscript “Comparative Genomic Study for Revealing the Complete Scenario of COVID-19 Pandemic in Bangladesh” (PONE-D-21-19985) reports the SARS-CoV2 variants that have caused first and second wave in Bangladesh. The authors have compared the causative variants responsible for the two waves. The manuscript seems to be the first report detailing the molecular perspectives of the two consecutive waves of COVID19 infection in Bangladesh. The evolutionary perspectives of the viral genome has been studied. However, there are some queries which must be addressed by the authors to improve the manuscript. Abstract: OK. Introduction: Page 8; Line: 31-32: Please clearly state based on analyses of which molecular sequences you are stating that “it was discovered that the wave-2 samples had a significantly greater average rate of mutation/sample (30.79%) than the wave-1 samples (12.32%)” Authors’ Response Abstract/Introduction 1. Information about the type of molecular sequences has been added into the abstract which can be found at page 2, line 30-33. Reviewer’s Query: Materials and Methods: Page 16, Line 208: Please correct “Room Mean Square Fluctuation (RMSF)” to “Root Mean Square Fluctuation (RMSF)”. Authors’ Response Materials and Methods “Room Mean Square Fluctuation (RMSF)” has been changed to “Root Mean Square Fluctuation (RMSF)” at page 10, line 222. Reviewer’s Query: Results and Discussion: 1. Please specify the length of genomes that have been studied 2. What was the quality of sequencing (base calling)? 3. Compare the genomic constitution of the two waves or other specific variants. 4. The Spike protein is variable and have been reported to experience selection pressure (doi: 10.1016/j.heliyon.2020.e05001; DOI: 10.3390/pathogens9100829). Please report in the light of the samples of Bangladesh. 5. Please include elaborated analysis on selection pressure and the molecular phylogeny of the variants for the genes showing variation among the viral variants. English: The formation of sentences is not correct. There are several grammatical and syntactical errors. The English of the manuscript must be get thoroughly checked by a suitable English language professional. Some of the points have been indicated in the attached manuscript. Please don’t use the symbols like “>”, in running text, rather write “more than” or “greater than” Authors’ Response Result and Discussion 1. Length of the genomes has been added at page 11, line 241-243. 2. The study was performed on assembled genomes from GISAID database. GISAID does not contain raw reads or quality score of the sequences. However, we only chose complete genomes for our study. 3. Comparison of genomic constitution between wave-1 and wave-2 has been provided in the following paragraphs; 3.2 Frequency of SARS-CoV-2 Mutations in Bangladesh 3.3 Type of SARS-CoV-2 Mutations in Bangladesh 3.4 Genomic Location of the SARS-CoV-2 Mutations 3.6 Distribution of SARS-CoV-2 Clades and Variants in Bangladesh 4 and 5. Analysis of selection pressure and changes in the variability in spike protein have been calculated and discussed along with molecular phylogeny of the variants. The newly added parts in this regard can be found in the following sections of the manuscript- Material methods section 2.4 Analysis on Selection Pressure and Molecular Phylogeny of The Variants in page 8-9, line 173-180. Result section 3.7 Selection Pressure and Phylogenetic Analysis in page 16-17, line 339-355. Discussion The findings regarding selection pressure and phylogeny analysis are discussed in page 23-24, line 468 to 483. Figure and Supplementary file Newly added Figures and Supplementary files- Fig 9 in page 47, line 815 Supplementary file 11 English: • “>” sign previously used to denote mutations has been replaced with “to” in running text. • Grammatical adjustments as highlighted in the honorable reviewer's attachment has been carried out. The whole of the manuscript was also checked for grammatical errors and corrected wherever needed. # Response to Queries from Reviewer 2 Reviewer’s Query: The manuscript presented falls within the scope of the Journal and adds knowledge about the distribution of various clades of SARS-CoV-2 in Bangladesh. The manuscript is well written with enough data both in terms of extensiveness and representation. However there are certain minor corrections in the manuscript which can be found in pop-up notes of the attachment. I also suggest you to modify the title as indicated in the pop-up note of the title. Authors’ Response We thank the honorable reviewer #2 for his suggestions for the title, considered it seriously and felt the need to modify the title slightly to better represent the contents of the study. The new title is as following- “Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh”. We did not include the word “clade-wise” in the title because the study was not just based on distribution of various clades of SARS-CoV-2 in Bangladesh but a complete scenario of the pandemic from a comparative genomics perspective. For example, we analyzed the distribution of mutations per sample, classes of mutations, most frequent mutational events, distribution of different clades, prevalence of different variants, selection pressure and phylogenetic analysis between wave-1 and wave-2 as well as the effect of mutations on the transmissibility of the virus. Honorable reviewer #2 also suggested to include the phrase “Genomic Surveillance” in the title. Even though our study encompassed genomic surveillance, it was more than that. Our main focus was on the comparison of genomic features of SARS-CoV-2 between the first and the second wave in Bangladesh. Therefore, we used “Wave-wise comparative genomic study” instead of “Genomic Surveillance” in the title to denote the nature of our work. Other minor corrections suggested by honorable reviewer #2 has also been executed in the revised manuscript. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0258019.r002
16 Sep 2021 Decision Letter - Narasimha Murthy Bhamidipati, Editor Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh PONE-D-21-19985R1 Dear Dr. Ahammad, 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, Narasimha Murthy Bhamidipati, Ph.D 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 #1: All comments have been addressed 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 #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 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 #1: Yes 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 #1: Yes 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 #1: The authors have made the required corrections/modifications. The manuscript may be accepted for publication. 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 #1: Yes: CHANDRA SEKHAR MUKHOPADHYAY Reviewer #2: Yes:** KAMISETTY ASWANI KUMAR https://doi.org/10.1371/journal.pone.0258019.r003
Formally Accepted
20 Sep 2021 Acceptance Letter - Narasimha Murthy Bhamidipati, Editor PONE-D-21-19985R1 Wave-wise comparative genomic study for revealing the complete scenario and dynamic nature of COVID-19 pandemic in Bangladesh Dear Dr. Ahammad: 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. Narasimha Murthy Bhamidipati Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0258019.r004

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