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I agree with the reviewers that the authors addressed all the raised questions and the current version of the manuscript is acceptable for publication in PeerJ.
[# PeerJ Staff Note - this decision was reviewed and approved by Jun Chen, a PeerJ Section Editor covering this Section #]
No comments
No comments
No comments
All the critiques are adequately addressed and the manuscript is revised accordingly. I am please to see that terminology was fixed and definitions of all the network-related terms were added. I am satisfied with revision and do not have new suggestions.
The article provides sufficient background information. The theory that was used was clearly stated.
The experimental design was well defined. The authors have improved a lot in describing the experimental design.
The findings and conclusions are well stated.
Authors have made a full effort to revise the manuscript. I suggest accepting this manuscript.
I agree with the comments and suggestions provided by the reviewers. In particular, more appropriate terms or at least describing most network-related terms should be considered. Also, a brief description of the synthetic network construction should be provided.
[# PeerJ Staff Note: Please ensure that all review and editorial comments are addressed in a response letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. It is a common mistake to address reviewer questions in the response letter but not in the revised manuscript. If a reviewer raised a question then your readers will probably have the same question so you should ensure that the manuscript can stand alone without the response letter. Directions on how to prepare a response letter can be found at: https://peerj.com/benefits/academic-rebuttal-letters/ #]
The manuscript is well written and easy to read. Background material is presented in a clear and concise way. Figures and tables are of high quality.
The research question is well defined. Methods are described in full detail.
The findings are valid, and can be easily replicated. However, see the general comments below.
The authors focus their study on the SARS-CoV protein-protein interaction network because of the high genetic similarity of SARS-CoV and SARS-CoV-2, but the protein-protein interaction network of SARS-CoV-2 has also been studied (10.1038/s41586-020-2286-9). The manuscript will be much more meaningful by performing the same analysis on the SARS-CoV-2 protein-protein interaction network as well. This would allow to draw further conclusions about the pattern of disease propagation from virus to human.
This is an interesting and important study that adds significantly to the field and will have a noticeable impact.
Although the manuscript is written in a professional English, in my view an excessive usage of "transmission of infection", "transmit the infection", "infected proteins", "susceptible proteins which are not yet infected but are at risk of getting infected", "proteins that have recovered and again become susceptible: and other alike terms is misleading. Protein cannot be infected. A node in PPIN cannot transmit infection. Therefore, statement on lines 282-284 "the infection will penetrate further in human PPIN resulting in a significant fall in human immunity level followed by the severe acute respiratory syndrome" is misleading and confusing. Although it is clear what the authors want to say here, the used terminology is wrong, as in reality they are considering transmission of information, and not infection. Therefore, all related parts of the manuscript should be rewritten to make ideas less ambiguous.
Also, it is highly advisable to provide definitions of all the network-related terms (e.g., centrality, degree, node weight, neighborhood density, etc.) in a layman language. In fact, readers not familiar with graph theory would be completely lost.
Experimental design is appropriate.
Findings are interesting and important, but their description uses wrong terminology and therefore is very confusing.
The idea of introduction of the spreadability index for the analysis of the transmission of information within SARS-CoV and human PPINs and from SARS-CoV PPIN to human PPIN is very interesting and promising. Data generated as the result of the implementing of this measure are useful. However, the terminology used for the description of the work is misleading and confusing.
The article provides sufficient background information. The theory that was used was clearly stated. But there are several points in the article that need attention.
- Several outdated references, e.g. in line 81-88. The authors might need to add the updated references.
- Line 108-111: redundant information with line 91- 102.
- Line 176: typo error, “hole”.
The authors need to improve in the methods section.
- The author should add the data collection part. Even though it is noted in the results section, it is necessary to clarify how the data for this study was gathered.
- How did the synthetic network was constructed? What are the data (protein and interaction) that have been used to construct the synthetic network?
- Line 248-250: this sentence is confusing. The author might either use PPIN or network, instead of using both PPIN and network. Term of network or PPIN should be consistently used throughout the manuscript.
- The results section need to be improved and organized, can organize the results into subsections.
- Several terms should be adequately defined, such as level-1, level-2, unique proteins.
- All figure captions should clearly describe the figures. For example, the authors should add the explanation on the spreader node in Figure 1. The figure caption for figure 1 and figure 4 sound alike.
- Figure 3 should be rearranged. Figure A and B should be placed on top of Figure C. The caption is confusing. The meaning of the node colors is unclear. Typo error on the caption and the label of the figure.
- Figure 4 is the SARS-CoV network or SARS-CoV-human network? The difference between SARS-CoV and SARS-CoV-human PPIN should be described in the manuscript.
- Line 285: redundant terms. PPIN of the SARS-CoV network. It might be either SARS-CoV PPIN or SARS-CoV network.
- Line 308-309: the complete network has been generated online. Specific tool and parameters used to construct the network should be mentioned in the methods section.
- Discussion part should be elaborated more. For example, how do the most spreader nodes (at least top 3 or top 5 spreader nodes) relate to COVID19. How do the network in Figure 4, 5 and 6 relate to COVID19.
- Can you highlight the significance of the network, proteins and edges identified in this study with COVID19?
- How does the developed network attribute, spreadability index, and the generated SIS model perform better than existing approaches? How do you know SIS model performs better than other approaches? @as any testing carried out? Please explain.
- Discussion and conclusion parts can be separated.
The background is well structured and written. However, the authors need to improve on other sections, as followed:
- Please improve on figures and all figure captions.
- There are grammatical mistakes and typo errors throughout the manuscript.
- Several points, such as data collection and the network construction (tools, parameters in constructing the network), need to be addressed in the methods.
- The organization of results need to be improved.
- The results need to be critically discussed and concluded.
- Please be consistent with the term of PPIN and network. Several terms need to be clearly defined.
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