Investigating host-virus interaction mechanism and phylogenetic analysis of viral proteins involved in the pathogenesis

Ahmad Abu Turab Naqvi; Farah Anjum; Alaa Shafie; Sufian Badar; Abdelbaset Mohamed Elasbali; Dharmendra Kumar Yadav; Md. Imtaiyaz Hassan

doi:10.1371/journal.pone.0261497

Peer Review History

Original SubmissionOctober 15, 2021
8 Nov 2021 Decision Letter - Timir Tripathi, Editor PONE-D-21-33085Investigating Host-Virus Interaction Mechanism and Phylogenetic Analysis of Viral Proteins Involved in the PathogenesisPLOS ONE Dear Dr. Hassan, 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. The manuscript has been reviewed by two independent reviewers. They find merit in this manuscript but have highlighted several areas in which improvement and corrections are necessary. These areas include the organization of the text as well as technical details and must be addressed for the manuscript to be considered for publication. Few language issues also need to be resolved by the authors. Please submit your revised manuscript by Dec 23 2021 11:59PM. 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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: This paper attempts to bring and correlation between viral pathogenies with that of viral genome organization. Specifically deciphering the role of viral attachment proteins. This topic is very broad. The first half of the paper contains a very general description of the virus biology of several human pathogens. In the latter half, the authors produce phylogenetic evidence of major viral attachment protein and look for some common ground to relate it the pathogenesis. 1. In my view the paper could have a more organized approach. This manuscript contains lots of facts, general things. 2. The authors need to make it more appealing by detailing the phylogenetic information with that of virus biology cum viral pathogenesis. In a simple way, please answer how the phylogenetic information is important to predict viral pathogenesis. 3. How does the structural/viral attachment protein genetic make-up predictably results in viral entry, attachment, receptor binding, and providing an opportunity for drug discovery? 4. Working with too many viruses at a time is clearly going out of the focus. I recommend that the authors should pick a family of viruses such as flaviviruses, rhabdovirus, coronaviridae, etc goes to the species level, look at the minute details in viral attachment proteins and establish the link between the host receptor and pathogenies. More importantly, the introduction and abstract section should highlight specific new findings, insights, or perspectives. 5. Grammar and English sentences need thorough checking, 6. Please focus on a specific group of viruses, and look at the species variation, link it to virus biology. Coronavirus shoudl be highlighted. 7. Quality of figures may be improved. 8. Please avoid passive grammars in sentence structure. References should be thoroughly checked. Reviewer #2: In this review article, authors discuss the host-virus interaction mechanisms and the molecular machinery involved in the pathogenesis of the influenza virus, hepatitis virus, human immunodeficiency virus, and coronaviruses. They discuss the genomic organization of these viruses, including the viral proteins that play crucial roles in viral attachment, membrane fusion, cell entry, replication and subsequent release of the mature virion particles in the host environment where they infect. To gain insights into the viral origin's evolutionary perspectives, they have claimed to envisage the phylogeny of viral proteins to understand the changes in the sequence organization of these proteins during evolution for various strains of the viruses. 1. The phylogenetic analysis, which is the main highlight of the review according to the authors, seems weak. 2. Why authors have relied on summarizing viral pathogenesis in almost half of the manuscript. 3. Out of phylogenetic analysis presented, it is difficult to fetch what conclusion authors want to draw. 4. Till, they will discuss the take home messages of each of the trees and MSA representations, it is difficult to understand what evolutionary significance they provide. 6. The manuscript needs to express in the introduction/ background section comments on the current body of literature, after that, what are the gaps in our understanding of viral molecular evolution. 7. Language editing is required to improve the quality of manuscript. ****** 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: Yes:** RAJESH SINHA [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.0261497.r001
Revision 1
10 Nov 2021 Author Response Reviewers’ Comments Reviewer #1: This paper attempts to bring and correlation between viral pathogenies with that of viral genome organization. Specifically deciphering the role of viral attachment proteins. This topic is very broad. The first half of the paper contains a very general description of the virus biology of several human pathogens. In the latter half, the authors produce phylogenetic evidence of major viral attachment protein and look for some common ground to relate it the pathogenesis. 1. In my view the paper could have a more organized approach. This manuscript contains lots of facts, general things. Response 1: As per the suggestion of the review the authors have revised and updated the structure and language of the manuscript to make it more readable. 2. The authors need to make it more appealing by detailing the phylogenetic information with that of virus biology cum viral pathogenesis. In a simple way, please answer how the phylogenetic information is important to predict viral pathogenesis. Response 2: As suggested, changes have been made in the manuscript to elaborate the role of phylogenetic analysis and pathogenesis. 3. How does the structural/viral attachment protein genetic make-up predictably results in viral entry, attachment, receptor binding, and providing an opportunity for drug discovery? Response 3: This is evident from the literature available and ongoing vaccine development projects worldwide, understanding of host-virus interaction mechanism play a crucial role for the development of effective vaccines and therapeutic interventions. Therefore, we aim to shed light on these processes that help the virus to enter host cell and replicate. 4. Working with too many viruses at a time is clearly going out of the focus. I recommend that the authors should pick a family of viruses such as flaviviruses, rhabdovirus, coronaviridae, etc., goes to the species level, look at the minute details in viral attachment proteins and establish the link between the host receptor and pathogenies. More importantly, the introduction and abstract section should highlight specific new findings, insights, or perspectives. Response 4: The authors have selected the various based on the prevalence of disease they cause across the globe. Mainly those viruses that have been and are associated with epidemic and pandemic like situations are discussed. As suggested, the manuscript has been revised to eliminate possible grammatical errors. 5. Grammar and English sentences need thorough checking, Response 5: As suggested by the reviewer, the manuscript has been revised and checked for grammatical and spelling mistakes. 6. Please focus on a specific group of viruses, and look at the species variation, link it to virus biology. Coronavirus should be highlighted. Response 6: The authors have selected the various based on the prevalence of disease they cause across the globe. Mainly those viruses that have been and are associated with epidemic and pandemic like situations are discussed. 7. Quality of figures may be improved. Response 7: Figures have been improved to match the required quality measures. 8. Please avoid passive grammars in sentence structure. References should be thoroughly checked. Response 8: As per the suggestion of the reviewer, the manuscript has been revised to remove grammatical errors and passive sentence structure as much as possible. Reviewer #2 In this review article, authors discuss the host-virus interaction mechanisms and the molecular machinery involved in the pathogenesis of the influenza virus, hepatitis virus, human immunodeficiency virus, and coronaviruses. They discuss the genomic organization of these viruses, including the viral proteins that play crucial roles in viral attachment, membrane fusion, cell entry, replication and subsequent release of the mature virion particles in the host environment where they infect. To gain insights into the viral origin's evolutionary perspectives, they have claimed to envisage the phylogeny of viral proteins to understand the changes in the sequence organization of these proteins during evolution for various strains of the viruses. 1. The phylogenetic analysis, which is main highlight of the review according to the authors, seems weak. Response 1: As per the suggestion of the reviewer, the section discussing phylogenetic analysis has been updated to make it more elaborate. 2. Why authors have rely on summarizing the viral pathogenesis almost half of the manuscript. Response 2: The rationale behind discussing the pathogenesis and viral proteins involved in pathogenesis was to lay the foundation for highlighting the role of these proteins and to link their significant in the phylogenetic analysis. However, the pathogenesis section has been trimmed to reduce the redundancy. 3. Out of phylogenetic analysis presented, it is difficult to fetch, what conclusion authors wants to draw. Response 3: Phylogenetic analysis has been updated to make it more comprehensible. Our aim was to elaborate the evolutionary changes in the viral proteins over the span of time that play significant role in hurdles in vaccine development since most vaccine and antiviral drugs target proteins involved in cell attachment and fusion. 4. Till, they will discuss the take home messages of each of the trees and MSA representations, it is difficult to understand what evolutionary significance they provide. Response 4: Phylogenetic analysis has been modified for clarity and comprehension. 5. The manuscript need to express in the introduction/ background section comments on current body of literature, after that, what are the gaps in our understanding of viral molecular evolution. The title of the manuscript is totally a mismatch from the contents. Response 5: As per the suggestion of the reviewer, introduction section of the manuscript has been updated. 6. Language editing is required to improve the quality of manuscript. Response 6: In the light of reviewer’s comment, the manuscript has been revised thoroughly to improve the quality of language and eliminate grammatical and spelling mistakes. Attachments Attachment Submitted filename: Rebuttle Letter.docx https://doi.org/10.1371/journal.pone.0261497.r002
3 Dec 2021 Decision Letter - Timir Tripathi, Editor Investigating Host-Virus Interaction Mechanism and Phylogenetic Analysis of Viral Proteins Involved in the Pathogenesis PONE-D-21-33085R1 Dear Dr. Hassan, 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, Timir Tripathi, 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: (No Response) ****** 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: Authors have revised the manuscript according to reviewers suggestions and comments. The manuscript in the present form 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: No Reviewer #2: Yes:** RAJESH SINHA https://doi.org/10.1371/journal.pone.0261497.r003
Formally Accepted
7 Dec 2021 Acceptance Letter - Timir Tripathi, Editor PONE-D-21-33085R1 Investigating Host-Virus Interaction Mechanism and Phylogenetic Analysis of Viral Proteins Involved in the Pathogenesis Dear Dr. Hassan: 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. Timir Tripathi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0261497.r004

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