Spread of endemic SARS-CoV-2 lineages in Russia before April 2021

Galya V. Klink; Ksenia R. Safina; Sofya K. Garushyants; Mikhail Moldovan; Elena Nabieva; Andrey B. Komissarov; Dmitry Lioznov; Georgii A. Bazykin; The CoRGI (Coronavirus Russian Genetic Initiative) Consortium

doi:10.1371/journal.pone.0270717

Peer Review History

Original SubmissionJanuary 6, 2022
30 Mar 2022 Decision Letter - Luis M Schang, Editor PONE-D-22-00516Spread of endemic SARS-CoV-2 lineages in Russia before April 2021PLOS ONE Dear Dr. Klink, 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 refer to the additional editor comments. Looking forward to receiving a revised manuscript. Please submit your revised manuscript by May 14 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. 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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Additional Editor Comments (if provided): Thank you for submitting your manuscript PLOS ONE. As you can see from the reviewers' comments, they both had a major concern regarding the discussion of growth advantages for alleles and variants in the absence of experimental evidence. Please, edit the manuscript thoroughly to limit the descriptions to the actual evidence. You may follow the suggestion of reviewer No.2 to add a paragraph to the discussion discussing this POTENTIAL mechanism for the spread of these particular alleles. [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: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes 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 “Spread of endemic SARS-CoV-2 lineages in Russia before April 2021" by Klink et al. focuses on the spread of two SARS-CoV-2 lineages B.1.1.317 and B.1.1.397+ which were highly prevalent in Russia but rarely detected in sample outside of Russia. The authors speculate that specific nucleotide changes within the spike gene (including E484k), and not epidemiology, lead to the increase in the frequency of these lineages in Russia. Overall the data is well presented and the manuscript is interesting. One issue is the authors’ suggestion that these variants have a transmission advantage or disadvantage, this is eluded to many time throughout the manuscript and is purely speculation. As there is no experimental data included which demonstrates that these variants have different biological properties that make them more or less transmissible, it is advisable that they remove or reword some of the speculation on transmissibility. Minor points to clarify: 1. For the alignment to the original Wuhan sequence what was the length fraction and similarity fraction? How were nonspecific or repeats match handled? 2. The authors mention the global frequency of B.1.1.317 and B.1.1.397+ was low, and B.1.1.397+ isolates have been found in Kazakhstan. What other countries have B.1.1.317 and B.1.1.397+ isolates been identified? 3. Unclear what the authors mean by “suspicious” in the sentence (page 24, line 391-394): “The combinations of mutations seen in the three variants that emerged in 2021, AT.1, B.1.1.524 and B.1.1.525 (Fig. 8C-E), look more suspicious, because their estimated rate of frequency increase was higher and because they include mutations with known effects and occurring in other variants of interest or concern.” 4. The authors use the acronym VOC without defining it when it is used for the first time (page 8, line 83). Reviewer #2: The submitted manuscript presents an analysis of the evolution of SARS-CoV-2 variants and lineage in Russia between February 25, 2020 and March 28, 2021, described according to the Pango lineage nomenclature. In brief, the B.1.1 lineage was preponderant, with the B.1..7, B1.1.317, and B.1.1.397 constituting the main sub lineages.Both geographical and temporal frequency distribution of several specific alleles are analyzed and logistic growth models are presented. The analyses are generally well and clearly presented, but some conclusions are overstated. Major points. In several instances, the authors discuss predicted fitness advantages of the alleles observed. Although this may well be correct, no actual experimental evidence is presented to substantiate these conclusions, which should therefore be removed. Wording of the entire manuscript should be carefully edited to avoid any claim of fitness advantages for alleles that have not been supported by experimental evidence. The discussion section may include a paragraph discussing this possibility, but founder and similar effects should not be dismissed without evidence. ****** 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: No Reviewer #2: No [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.0270717.r001
Revision 1
14 Jun 2022 Author Response Additional Editor Comments (if provided): Thank you for submitting your manuscript PLOS ONE. As you can see from the reviewers' comments, they both had a major concern regarding the discussion of growth advantages for alleles and variants in the absence of experimental evidence. Please, edit the manuscript thoroughly to limit the descriptions to the actual evidence. You may follow the suggestion of reviewer No.2 to add a paragraph to the discussion discussing this POTENTIAL mechanism for the spread of these particular alleles. Thank you, we now softened all statements about potential transmission advantage of considered lineages. Reviewer #1: The manuscript “Spread of endemic SARS-CoV-2 lineages in Russia before April 2021" by Klink et al. focuses on the spread of two SARS-CoV-2 lineages B.1.1.317 and B.1.1.397+ which were highly prevalent in Russia but rarely detected in sample outside of Russia. The authors speculate that specific nucleotide changes within the spike gene (including E484k), and not epidemiology, lead to the increase in the frequency of these lineages in Russia. Overall the data is well presented and the manuscript is interesting. We thank the Reviewer for the interest in our study. One issue is the authors’ suggestion that these variants have a transmission advantage or disadvantage, this is eluded to many time throughout the manuscript and is purely speculation. As there is no experimental data included which demonstrates that these variants have different biological properties that make them more or less transmissible, it is advisable that they remove or reword some of the speculation on transmissibility. We now carefully removed from the text all suggestions about the role of mutations in the transmissions of lineages, and left them only in the Discussion section. In Discussion, we make sure it is explicit that this is no more than a hypothesis. Minor points to clarify: 1. For the alignment to the original Wuhan sequence what was the length fraction and similarity fraction? How were nonspecific or repeats match handled? The average length of sequences was 29687.29 bp, and the average Hamming distance from the reference was 0.000799 (figures below). Therefore, the sequences had good coverage, and were reliable in that they did not have unexpectedly high divergence. Genomes were aligned with MAFFT using its default parameters for handling nonspecific matches. This is now stated in Methods. 2. The authors mention the global frequency of B.1.1.317 and B.1.1.397+ was low, and B.1.1.397+ isolates have been found in Kazakhstan. What other countries have B.1.1.317 and B.1.1.397+ isolates been identified? Both B.1.1.317 and B.1.1.397+ have been found in many countries, but in most of them their frequencies remained low. We now added Tables S1 and S2 to show the prevalence of B.1.1.317 and and B.1.1.397+ in different countries in the month when this prevalence was the highest. 3. Unclear what the authors mean by “suspicious” in the sentence (page 24, line 391-394): “The combinations of mutations seen in the three variants that emerged in 2021, AT.1, B.1.1.524 and B.1.1.525 (Fig. 8C-E), look more suspicious, because their estimated rate of frequency increase was higher and because they include mutations with known effects and occurring in other variants of interest or concern.” We mean that these lineages were to be considered as candidates for changed transmissibility, due to their mutational composition and a fast frequency increase. We now reformulated the phrase to “may be of more interest”. 4. The authors use the acronym VOC without defining it when it is used for the first time (page 8, line 83). Now we define VOC at first use, and give a link to the WHO website with this definition. Reviewer #2: The submitted manuscript presents an analysis of the evolution of SARS-CoV-2 variants and lineage in Russia between February 25, 2020 and March 28, 2021, described according to the Pango lineage nomenclature. In brief, the B.1.1 lineage was preponderant, with the B.1..7, B1.1.317, and B.1.1.397 constituting the main sub lineages.Both geographical and temporal frequency distribution of several specific alleles are analyzed and logistic growth models are presented. The analyses are generally well and clearly presented, but some conclusions are overstated. Major points. In several instances, the authors discuss predicted fitness advantages of the alleles observed. Although this may well be correct, no actual experimental evidence is presented to substantiate these conclusions, which should therefore be removed. Wording of the entire manuscript should be carefully edited to avoid any claim of fitness advantages for alleles that have not been supported by experimental evidence. The discussion section may include a paragraph discussing this possibility, but founder and similar effects should not be dismissed without evidence. We agree with the Reviewer and tone down all claims about any possible fitness advantage of considered lineages. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0270717.r002
16 Jun 2022 Decision Letter - Luis M Schang, Editor Spread of endemic SARS-CoV-2 lineages in Russia before April 2021 PONE-D-22-00516R1 Dear Dr. Klink, 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, Luis M Schang, MV. Ph.D. Section Editor PLOS ONE Additional Editor Comments (optional): Thank you very much for submitting a revised manuscript addressing all critiques to the original version 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 ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: (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: No ******** https://doi.org/10.1371/journal.pone.0270717.r003
Formally Accepted
24 Jun 2022 Acceptance Letter - Luis M Schang, Editor PONE-D-22-00516R1 Spread of endemic SARS-CoV-2 lineages in Russia before April 2021 Dear Dr. Klink: 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. Luis M Schang Section Editor PLOS ONE https://doi.org/10.1371/journal.pone.0270717.r004

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