Mutation Trajectory of Omicron SARS-CoV-2 Virus, Measured by Principal Component Analysis

Round 1

Reviewer 1 Report

Dear Authors

Your article is relevant to understand the recent evolution of the Omicron lineage. However, the presentation of your results lacks clarity. I had to go back-and-forth between Figures and Supplementary Figures all the time, and in many instances the Supplementary Figures were more important than the Figures themselves. The Figure legends also lacked clarity. 

Moreover, you overstated your Conclusions and did not explain to the reader the limitations of your approach, especially concerning the contribution of these mutations (variants) to evasion of neutralizing antibodies from natural infection and vaccines.

Line 110: greater magnitude of mutation; does it mean greater incidence of mutations among samples or greater effect of mutations?

Fig 1B: PC1 and time does not seem to be the best way to represent evolution across time.

Lines 123-124: however, due to mutations occurring in unsequenced regions, intermediate stages were unrecorded. Please clarify what you meant by unsequenced regions and their relevance to your results and conclusions.

Lines 132-133: Many of the sequence features exhibited by BA.1 and shared among Omicrons have been lost from JN.1. You need more data and evidence from other sources, especially experimental data, to make these affirmations.

Line 138 This trend is also consistent across the other axes (Figure S3). But the figure only shows PC1, where are other PCs?

Lines 138-142: Additionally, in SARS-CoV-2, the contribution of the primary PC axis is minimal (Figure S2), suggesting that the individual mutations occur independently and lack coherence. In contrast, for the hemagglutinin of the influenza virus, PC1 shows a continuous increase (Figure S1), with a concentration of high contribution rates to higher PC observed (Figure S2). You do not present enough evidence for this affirmative; rewrite it having in mind the limitations of your data.

Line 149: It seems you are using the mutability criteria not very precisely.

Line 154: You should present a Figure without synonymous mutations.

Lines 163-164: where is this shown?

Lines 167-170: meaning very obscure.

Lines 182-183: higher PCs; Figure S1 does not show this.

Lines 209-210: This should be illustrated with a Figure

Lines 213-214: lack references to recent publications

Lines 215-216: lack references to recent publications

Lines 228-229: the article does not present enough evidence for this affirmative.

Line 241: repeated vaccinations. Present further evidence and references or exclude this.

Lines 246-247: it is an authors' opinion not based on evidence.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

This manuscript analysed big data from the GISAID scope on the Omicron variant. The information and quality provide insight information into the Omicron variant. They contribute to an area lacking existing literature and are likely to interest readers.

1. This finding used genomic data. However, viral genes may or may not be expressed depending on various factors.
I think the outcomes could be discussed with another finding in a wet lab, such as microarray or transcriptome analysis to prove the hypotheses of this manuscript.

1. Figures: You can use different symbols to make them more distinguishable.

For example, in Figure 1B, circle for Omicon, squared for Alpha, triangle for Delta...

2. This journal is an online platform. The visualisation should be in colour to make it easy to read. (optional)
However, if you use a colourised figure, ensure the colour is friendly for colourblindness.
http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/#a-colorblind-friendly-palette

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

I congratulate the authors for their efforts to make their manuscript clearer and their Discussion more pertinent to their findings including the limitations of these findings.

However, they introduced important stylistic problems in their manuscript.

The focus of the manuscript should (must) be the potential readers and not the reviewers. Sometimes, it seemed that the authors were replying to the reviewers (in an angry mode) and not focusing on readers, the readability of their manuscript, their contribution to Science and Public Health.

It seems that the authors have considered the reviewers comments from a very personal point of view, as if they were an aggression to their knowledge and not part of a normal peer-review process. It even seemed that the authors considered the reviewers as ignorant or stupid.

This is very unscientific. This is not how Science evolves. We are not in a political battlefield.

Reviewers and authors are not adversaries. 

Mutation trajectory of Omicron SARS-CoV-2 virus, measured by PCA. (2)

Do not use acronyms in the title. The only acronym permitted is SARS-CoV-2; spell out PCA.

Materials and Methods

2.1 PCA

The text became unnecessarily too lengthy, as if the authors were given a lecture to a lay audience. This is completely unnecessary and does not match the usual English scientific language.

A sentence like: First, let us explain the principle of PCA. (84) is not adequate for the usual style of manuscripts submitted to MDPI journals. Moreover, the explanation lacked conciseness and did not achieve its goal - being comprehensible although brief. This is not a textbook on PCA, it is the Materials and Methods of a manuscript that will become an article of a high-impact factor journal.

4. Discussion 303

Here we are exclusively observing variation in the sequence of the strain. Note that what is discussed here is the inferences that can be drawn from it. 304-305

You should not begin a Discussion Section with a Disclaimer to the readers. You should convince the readers throughout your Discussion that your conclusions are supported by your results and that you are considering previous publications within the existing literature and are aware of the limitations of your data and results.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf