Etiology of Four Waves of the COVID-19 Pandemic in Ukraine according to the SARS-CoV-2 Virus Genome Sequencing Data: A Pilot Study

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Dear Authors,

Your article entitled "Etiology of four waves of the COVID-19 pandemic in Ukraine according to the SARS-CoV-2 virus genome sequencing data" has been reviewed,

This work deserves attention since it highlights an important topic related to the identification of different SARS-CoV-2 dominant variants during four different epidemiological waves based on genome sequencing data, using different molecular tools.

The article is well written in English, with a good design, the topic is important, but several points are weak in this study and must be improved, kindly find below the list of my minor and major comments.

Minor Comments:

01- In the List of affiliations, Authors are invited to explain what do they mean by "SI" and "JSC".

02- In the list of affiliations, Authors are invited to remove the email addresses from the affiliations. 

03- In the Materials and Methods section, lines 55-56, this sentence "Samples were... described" can be removed since it is duplicated.

04- In the Results section, Line 134, Authors are invited to remove the reference, since their is no need for it.

05- In the Results section, Figure 5, In the Figure's legend, Authors are invited to replace (upper figure) by (Figure 5A) and (lower figure) by (Figure 5B).

06- The Discussion lacks a lot of references, Authors are invited to use and to add several references for ideas in the Discussion. They can use the following articles as references, concerning the importance of lockdown and social distancing, risk and protective factors of COVID-19. 

Reference 01: COVID-19 pandemic: A review of the global lockdown and its far-reaching effects

Reference 02: Risk Markers of COVID-19, a Study from South-Lebanon

Reference 03: Impact of Social Distancing Measures on Coronavirus Disease Healthcare Demand, Central Texas, USA

Reference 04: Risk and Protective Factors for COVID-19 Morbidity, Severity, and Mortality

 

Major Comments:

01- The Introduction section contains just "2 References", this number of references is very small, you need to use more references in the introduction.

02- The Introduction section is very short and weak, Authors are invited to talk in the introduction about SARS-CoV-2 variants, discovery, origin, transmission and virulence, since the main point of this work tackles the identification of dominant variant during four different waves of COVID-19 in Ukraine. Authors can use the following articles as reference for this point:

Reference 05: Emerging Variants of SARS-CoV-2 and Novel Therapeutics Against Coronavirus (COVID-19)

Reference 06: SARS-CoV-2 variant biology: immune escape, transmission and fitness

Reference 07: The Emergence of SARS-CoV-2 Variant(s) and Its Impact on the Prevalence of COVID-19 Cases in the Nabatieh Region, Lebanon

Reference 08: A comparison of transmissibility of SARS-CoV-2 variants of concern

03- In the Materials and Methods section, Authors used high number of references, authors are invited to remove some if these references.

04- In the Materials and Methods section, Concerning the number of samples used in this study, I see that "167" sample from a large country such as Ukraine is not representative for the population. I think that the sample size should be higher (bigger).

05- In the Results section, in the Table 1, as for the previous comment (Major 04) I see that the number of samples collected from different cities in Ukraine is very weak, for example in the first wave, 25 total samples were collected from 7 cities!!! I see that this number is very weak. Same comment for the second wave, 37 samples from 6 cities, it is also very weak and nor representative for the population.

06- In the Results section, in the Table one, It seems very wired that all samples in each one of the four waves belong to the same lineage, several studies from different countries showed the presence of different lineages with dominance of one lineage. So for me it is wired to see that all samples in each wave belong to the same lineage.

07- The present article lacks a separate Conclusion, Authors are invited to add a Conclusion for this paper.

Best Regards,

Author Response

Thank you very much for taking the time to review this manuscript. Please find the responses below. In our updated and resubmitted manuscript, we highlighted all changes with yellow color. We believe that this manuscript has been significantly improved due to your effort. Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

Its amazing that the author(s) analyzed samples from 2020 - 2022 , this is valuable data and was presented well. Would recommend the author(s) to continue sampling until present if possible (2024)

Author Response

Thank you very much for taking the time to review this manuscript. We are glad that your comments about our article were positive. We improved our manuscript. Main changes are highlighted in updated version. 

Regarding your recommendation to continue sampling until present - unfortunately we don't have possibility to perform it now.

Reviewer 3 Report

Comments and Suggestions for Authors

The manuscript by Mironenko analyzed SARS-CoV-2 genome sequencing data to identify viral variants circulating during different four waves of COVID-19 pandemic in Ukraine. The authors employed epidemiological information to establish associations between variants and disease spread. Moreover, the authors also claimed that the shared nucleotide mutations among SARS-CoV-2 sequences from Poland and Ukraine can be further used to identify the directions of spreading. The overall logic, data presentations, and results are fine for this reviewer. This reviewer has some minor concerns for authors’ to improve their manuscript.

The introduction section doesn’t provide enough information for readers to grasp the importance and background of this study, which needs to be significantly improved.

2) The font size in some figures (e.g., Fig. 4) is too small to be clearly seen. Please improve.

3) How about the comparison of the local pandemic in Ukraine and the global trends? Also compare with other countries? Any unique findings?

4) Clearly state the limitations of this study.

Comments on the Quality of English Language

Needs improvement.

Author Response

Thank you very much for taking the time to review this manuscript. Please find the responses below. In our updated and resubmitted manuscript, we highlighted all changes with yellow color. We believe that this manuscript has been significantly improved due to your effort. Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Dear Authors,

Thank you for the modifications you made,

The Article is more suitable for publication in its present form, under one condition "If you add A pilot study in the title".

BR,

Author Response

Thank you very much for taking the time to review this manuscript. We've already corrected the title of our manuscript, as you recommended. In our updated and resubmitted manuscript, we highlighted all changes with yellow color. We believe that this manuscript has been significantly improved due to your effort.