Dynamics of Variants of Concern (VOC) of SARS-CoV-2 during the Different Waves of COVID-19 in Senegal

Round 1

Reviewer 1 Report

This is a very interesting study presenting new data for an African country, but a lot of work should be done to improve the presentation of data. For this reason, I indicated "reconsider after major revision" because a lot of points are unclear, but for me, this paper deserves a high level of priority for publication. A very careful revision is needed.

Detail comments:

1. Title: please add "of SARS-CoV-2"
2. Abstract: revise after revising the text of the paper. In particular, sentence of lines 22 to 24 should be clarified.
3. Introduction: 
   • lines 61-63: how many waves of the epidemic did affect Senegal. Here, you use the word "phase", but is it a distinct concept from "wave"? Figure 3 suggests 4 waves.
   • line 68: is I don't abuse, WHO asked not to qualify the VOCs by name of country where they were first recognized, but by Greek letters. Here "Alpha" and not "British".
   • lines 60 - 63: you speak only about first and third "phases". This is unclear and disturbing for the reader. This passage should be improved. It could be interesting to make a figure describing the temporal evolution of the number of cases.
   • There is no mention of severity of cases or even mortality in Senegal. This should be added.
   • in general, the introduction should be rewritten for more clarity.
4. Materials and methods
   • Lines 110 - 111  and following: from the abstract, I understood that the samples were positive for a detection PCR assay and afterwards tested with a PCR assays looking for variants. But here, you mention only one, and the denomination does not point to variants. I do not understand! 
   • Line 124: figure 3 does not treat of Ct values etc.. Don't you mean figure 2?
   • Figure 2: to what part of the text does it refer? What does mean "recherche" and "XXX" (in red)?Maybe, you should add numbers at the different steps, to make it more understandable.
   • Figure 3: I do not see another mention of figure 3 in the text. This should be added, with some clarification. This figure 3 is very interesting. Could you add numbers of sequences involved in each of the waves?
   • Two figures are figure 5 !
   • Figure 5, first one: what does mean the stars at Delta and Omicron? 
   • Line 175: figure shows the geographic provenance of the samples. Nothing to do with clades, lineages  and waves.
   • Lines 203 to 208: it refers to both table 1 and the first figure 5. This is not clear.
   • Line 207: you mention "non-worrying variants". But, there no mention at all of severity of disease or even mortality in all the paper. How can you speak of "worrying variants"? From some references outside Senegal?
   • Lines 216-2019: do you think that young people were not affected? Could this difference rather mean that they were only mildly affected and did not ask for testing?
   • Table 2: it should be interesting to have a first column with the Wuhan strain, to compare with the VOCs. Should ETA variant not be mentioned too? Or "others"?
   • Table 3: could you add "Eta" in the column with WHO?
   • Figure 5, second one: there is nowhere an explanation or discussion. Is this figure useful? It is very small and unreadable.
5. Discussion
   • line 222: how much waves? three or four?
   • Line 236: what VOC? what wave? You did not introduce it in the text and you did not speak about a fourth wave.
   • Line 239: contamination rate over 75% of what? I think you mean that 75% of new cases are caused by Omicron, but on line 201, you tell 100% What is it?. 
   • line 244-43: it is not clear from you text that there is a delay; You should compare with data from other countries to establish that.
6. Conclusion: again, the unclear number of waves in Senegal.

 

Author Response

Dear Editor,

 

Thank you so much for your suggestions.

Please find in attached file the responses for your comments.

 

Best regards

Author Response File: Author Response.docx

Reviewer 2 Report

Padane and colleagues described the variants distribution of SARS-CoV-2 in Senegal over a nearly two-year period from April 2020 to January 2022. Virus genotyping was performed by Nanopore NGS followed by phylogenetic analysis. They found that the four waves of COVID-19 in Senegal were contributed by different variants of concern (VOCs) which is in line with the epidemiology outside Africa. The genomic data itself would be very helpful to understand the introduction, spread and evolution of SARS-CoV-2 in Africa. The manuscript, however, is not very clearly written and could be improved by attention to the following points -

1. Abstract: It is mentioned that 817 positive samples were sequenced but it is unclear how many samples were positive for SARS2 RN Such information should be provided.
2. In the abstract, the authors concluded that “In Senegal, the SARS-39 CoV-2 pandemic has disrupted the organization of the health system.”. While there are no doubts that COVID-19 has crippled many healthcare systems around the world, I do not think the molecular and virus sequence data provided in this work can support the authors to make this “clinical” conclusion. They should be more prudent in the presentation.    
3. Attention is needed on the capitalisation of scientific terms. (a) SARS-CoV-2, not Sars-Cov-2; (b) variant of concerns, not Variant Of Concerns.
4. Introduction: “In Senegal, only the British variant was reported during the first two waves of the 68 epidemic [12].”. Avoid using the non-specific term “British variant”. Use WHO’s designation (e.g., alpha, omicron variant) or PANGO nomenclature instead to avoid confusion.
5. Figure 1: (a) Replace “recherche” with a more commonly used word; (b) meaning of the two boxes labelled as “Negative 10%”, “Negative” and “Positive” is not clear. Suggest elaborate in the figure legend. (c) Librairly is misspelled. (d) Protocole should have read as Protocol; (e) clarify the meaning of XXX
6. Line 124: Figure 3 should have read as Figure 2.
7. Method, Data Analysis: Why they included data (Figures 4 and 5)? Instead, it would be helpful to include more technical details about the selection criteria for NGS.
8. Results: Have all virus genomes generated in this work been deposited on GISAID or GenBank? If so, please add accession numbers into the current supplementary table. If no, why?
9. Figure 5: (a) This figure is not very helpful in the current format. If the authors want to illustrate age difference among the SARS2 variants, one can show the proportion of each age group in stacked bar charts. (b) Legend: replace “strain” with “variant”. (c) Specify the meaning of asterisks. Are they P-values? If so, then need to add a section on statistical analysis in Method.
10. Method: Clarify which nomenclature system (WHO, PANGO, NextStrain) was used in this work (Table 3?).
11. Figure 4 can be improved by using a stacked bar charts to make it easier to highlight the predominant variant over time. E.g. https://www.mdpi.com/viruses/viruses-13-02097/article_deploy/html/images/viruses-13-02097-g002-550.jpg.
12. Result: Suggest describing the number of samples tested positive for SARS2 and the number and proportion of samples sequenced by NGS at the beginning of this section.
13. Table 1 is not referred in the main text.
14. Tables 1 and 2: Why not show the mean (with SD) age instead? This way you can also consolidate both tables into one for easy reference. What does “NF” mean? Avoid all capital letter terms. Indicate the unit of age.
15. Some sentences are a bit difficult to read. E.g., (1) “From the screened samples, 817 positives were sequenced and 10% of the negatives screened samples for detection of new variants not yet described.”. (2) “…previous waves. Form samples collect in June. We observed a high prevalence…”. This manuscript would greatly benefit from professional English editing.

 

Author Response

Dear Editor,

 

Thank you so much for your suggestions and comments to improve the document.

 

Best regards

 

Abdou

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

As underlined in my first review, this paper deserves a high level of priority for publication. I asked a very careful revision, but I see that the authors did only consider the points I mentioned, but did not reconsider the whole manuscript for revision. I have again to recommend again major revision.

I fear I received a working file and not the final revision of the paper !!!! However, I started the review, but I think that all the last changes are still due. So, I do not consider my review to be complete.

In a further revision, the authors should highlight the changes rather than delivering a version with track changes, very difficult to dear and review!

Detail comments:

Page 1, lines 29 and 30: the “negative samples” is still unclear. See, comments about methods and then revise it in the abstract too.

Page 2 line 20 : I think that “justified” is not the right word. Replace by “can be explained”.

Page 5, genomic sequencing and data analysis: I think I understand now what you are telling with 10% negative samples were selected: as I look at figure 2, I think you consider here that all samples with CT > 35 are negative. This is in contradiction with page 5, lines 26 – 27, where you mention that samples with CT > 25 and <= 38 are indeterminate. I wonder if you had any sample with CT > 38 with a successful library preparation and sequencing. Please explain this better. You should also mention in this section how the samples were selected (at random?).

Figure 3: please add a legend. In particular, mention what you mean by “failed”.

Page 10, Before, “characteristics of the patients”, please mention how many samples were selected for an attempt of sequencing in each group (positives, indeterminates and negatives) and mention the percentage of successful sequencing for each group.

 

Rebuttal: this seems not to be finished:

• You mention that a new figure was added describing the temporal evolution of the number of cases. Where is it?
• About severity of cases and mortality, you write “It’s done at line …”. Where is it?
• Figure 5: if the stars have no signification, they should be removed.

Author Response

1. Page 1, lines 29 and 30: "negative samples" are still not clear. See, comments on methods, then revise it in the abstract too.

            For this aspect two steps have to be considered

• The cut-off Ct value for positive samples was set at ≤35. When, the Ct value is Ct >38, the sample is considered COVID-19 negative. Finally if the Ct value is between >35 and ≤38, the sample is considered undetermined.
• In order for a positive sample to be included in the sequencing, it must have a Ct 35.

 

2. Page 2 line 20: I think "justified" is the wrong word. Replace with "can be explained".

Thank you. On page 2 line 20 we are not found the word “justified”. It’s possible because we are forgotten to send the last revised version.

 

3. Page 5, Genomic Sequencing and Data Analysis: I think I understand now what you are saying with 10% negative samples that have been selected: looking at figure 2, I think you are considering here that all samples with TC > 35 are negative. This is in contradiction with page 5, lines 26-27, where you mention that samples with TC > 25 and < = 38 are indeterminate. I wonder if you had a sample with TC > 38 with successful library preparation and sequencing. Please explain this better. You should also mention in this section how the samples were selected (randomly?).

Thank you for your observation. As mentioned above, we have established threshold values to determine the positivity to COVID-19 of a sample by RT-PCR. In addition, a novel RT-PCR method (Seegene) was used to screen for new variants before sequencing of positive samples. Recall that the Ct values used to include these positive samples in the sequencing batch were 35.

4. Figure 3: Please add a legend. In particular, mention what you mean by "failed".

            Thank you for your suggestion. Figure 3 has been modified with a more detailed description.

5. Page 10, before, "Patient characteristics", please mention how many samples were selected for sequencing attempt in each group (positive, indeterminate and negative) and mention the percentage of successful sequencing for each group. In general, the introduction should be rewritten for more clarity.

Thank you for this suggestion. We have in the detailed methodology the number of samples tested, the number of RT-PCR positive samples and the number of samples sequenced (Page 6, line 9-13).

6. You mention that a new figure has been added describing the temporal evolution of the number of cases. Where is this?

We apologize for this misunderstanding. We have presented in figure 5 of the evolution of the variants during the 4 waves of the   epidemic.

7. Figure 5: If the stars have no meaning, they should be removed

Thank you for your observation. It’s done.

Reviewer 2 Report

The authors have attempted to address all my comments and suggestions. Overall, this revised version has improved greatly from the previous version. I have no further comments. Last but not the least, it was brought to my attention that my comments shown in the authors' reply are not exactly the version I submitted to the journal office,  they appear to have been modified either before relaying to the authors or by the authors themselves.

Author Response

Thank you for the comments.