Sequencing SARS-CoV-2 in a Malaria Research Laboratory in Mali, West Africa: The Road to Sequencing the First SARS-CoV-2 Genome in Mali
, Bourema Kouriba 1,2, Amadou Daou 1, Abdoul Karim Sangare 1,2, Djibril Kassogue 3, Charles Dara 3 and Abdoulaye A. Djimde 1,*Round 1
Reviewer 1 Report
The manuscript describes the sequencing of the first SARS-CoV-2 genome in Mali; the authors implemented two variations during the process (compared to standard Illumina sequencing procedure), namely using the superscript IV reverse transcriptase instead of superscript II; in addition, the authors used agarose gel to visualize library size due to Bioanalyzer not being available.
As this is a manuscript on process adaptation/development/ capacity, one main suggestion is to additionaly demonstrate whether the facility can generate such sequences in a relatively high throughput, which is desirable during a pandemic such as SARS-CoV-2, for both research, tracing and possibly diagnostic purposes.
Author Response
Response to Reviewer #1 comments
Point 1: The manuscript describes the sequencing of the first SARS-CoV-2 genome in Mali; the authors implemented two variations during the process (compared to standard Illumina sequencing procedure), namely using the superscript IV reverse transcriptase instead of superscript II; in addition, the authors used agarose gel to visualize library size due to Bioanalyzer not being available.
As this is a manuscript on process adaptation/development/ capacity, one main suggestion is to additionaly demonstrate whether the facility can generate such sequences in a relatively high throughput, which is desirable during a pandemic such as SARS-CoV-2, for both research, tracing and possibly diagnostic purposes.
Response 1: We would like to thank the reviewer for taking the time to review the manuscript. The suggestion about the high throughput capacity of the approach has been taken into account by adding data from a second genome we generated using this approach. We also extended the discussion taking into account this point. Please read the paragraph 6 of the discussion, lines 270-280.
Reviewer 2 Report
Not suitable for publication as it is formatted as an academic thesis without a clear rationale. The scanty data analysis make this paper with few scientific significance.
Author Response
Not suitable for publication as it is formatted as an academic thesis without a clear rationale. The scanty data analysis make this paper with few scientific significance.
Response: Although we beg to differ with this reviewer, we have added a new creative solution of ours to the revised manuscript. Indeed, a device for enriching Plasmodium falciparum gametocytes was used to purify DNA libraries (figure 1). In addition, the text has been edited.
The approach of adapting a malaria lab to sequencing a virus is valuable for scientists like ourselves leaving in poor countries and working in under-funded laboratories. However, we reckon that the true value of this paper may not be seen by an Investigator used to working in an environment where reagents, supplies and opportunities are plenty.
Reviewer 3 Report
In this manuscript, the authors described their efforts of obtaining the first genome of SAR-CoV-2 in a resource-restricted environment in Mali. I recommend a minor revision to this article – please see my comments below.
- Please label the band in Fig. 1A with bp.
- Since the # of figures are low, I would recommend putting more data from the data analysis pipeline of sequencing. For example, the QC plots generated from the FastQC and the variant calling data from VCFTools. In a resource-limited setting, this will give the readers a more comprehensive understanding of the quality of sequencing and novel mutation revealed by this study. Some of the information are in the SI already – I personally feel they should be put in the main figure.
- I would recommend the authors to deposit their sequence to NCBI’s repository as well for better accessibility – I could not access their deposited information in GISAID for now.
Author Response
Response to Reviewer #3 comments
In this manuscript, the authors described their efforts of obtaining the first genome of SAR-CoV-2 in a resource-restricted environment in Mali. I recommend a minor revision to this article – please see my comments below.
Point 1: Please label the band in Fig. 1A with bp.
Response 1: The figure 1A reads now figure 2A and has been labelled as requested.
Point 2: Since the # of figures are low, I would recommend putting more data from the data analysis pipeline of sequencing. For example, the QC plots generated from the FastQC and the variant calling data from VCFTools. In a resource-limited setting, this will give the readers a more comprehensive understanding of the quality of sequencing and novel mutation revealed by this study. Some of the information are in the SI already – I personally feel they should be put in the main figure.
Response 2: Now two figures have been moved from the supplemental information and added to results’ section. The supplemental figure 2 and the table 1 are now figure 3 and table 1 respectively. In addition, we added a figure 1 that showed an “improvised bead-based purification devise”.
Point 3: I would recommend the authors to deposit their sequence to NCBI’s repository as well for better accessibility – I could not access their deposited information in GISAID for now.
Response 3: We thank the reviewer for this recommendation. The sequences have been deposited on NCBI’s repository under the GenBank accession numbers OL336607 and OL448870 in addition to the GISAID repository for better accessibility.
Round 2
Reviewer 2 Report
The manuscript was improved in all the sections. Methods and resultswere more clearly described and also in the discussion limitations of the study were added to more clearly depict the importance of the study in the African country
