Monitoring and Tracking the Spread of SARS-CoV-2 in Asturias, Spain
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Mutational analysis of SARS-CoV-2 can quantify their relative importance over time, enable the dominant mutations to be identified and facilitate near real-time detection, comparison, and tracking of evolving variants. Collected samples in Asturias an autonomous community of Spain with a large aged population, and high levels of migration and tourism was monitored and tracked from its beginning in February 2020 until its decline and stabilization in August 2021, were characterized using whole genomic sequence and single nucleotide polymorphism. Data held in the GISAID database was analyzed to establish patterns in the appearance and persistence of SARS-CoV-2 strains. Only 138 non-synonymous mutations occurring in more than 1% of the population of SARS-CoV-2 were found, identifying 10 major variants worldwide (7 arose before January 2021), 19 regional and 1 local. In Asturias only 17 different variants were found. After vaccination, no further regional majority variants were found. Only half of the defined variants circulated and no new variants were generated, indicating that infection control measures (fast diagnosis, prevention measures and vaccination) were efficient.
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I am pleased to tell you that your article has now been accepted for publication in Access Microbiology. The work presented is clear and the arguments well formed. The manuscript is well written and contributes to the literature. Thank you for addressing all comments satisfactorily and in a timely manner.
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Thank you for submitting your revised manuscript for publication in Access Microbiology. After reviewing the manuscript, I'm happy that all reviewer's comments have been addressed. However, some minor changes are needed to include: - Please update lines 38 and 49/50 based on reviewer 1’s comment: Careful with the infection control points as we don't exactly know what works best for keeping COVID infections low so I would not be as explcit here and merely list examples of things that coud be involved (e.g. isolation, vaccination etc). - Line 62 : link is not working. Please update with the correct link and include this as a reference rather than having the link in the article. - Line 79 – 83, 161, 279-280, 313, 408: Rather than including the link in the main text, please cite these websites in the text and include in the bibliography - …
Thank you for submitting your revised manuscript for publication in Access Microbiology. After reviewing the manuscript, I'm happy that all reviewer's comments have been addressed. However, some minor changes are needed to include: - Please update lines 38 and 49/50 based on reviewer 1’s comment: Careful with the infection control points as we don't exactly know what works best for keeping COVID infections low so I would not be as explcit here and merely list examples of things that coud be involved (e.g. isolation, vaccination etc). - Line 62 : link is not working. Please update with the correct link and include this as a reference rather than having the link in the article. - Line 79 – 83, 161, 279-280, 313, 408: Rather than including the link in the main text, please cite these websites in the text and include in the bibliography - Line 100: Referencing style is not consistent – first couple of references are in Vancouver style and then reference 3 is Harvard style – please pick one and reference consistently throughout the manuscript. (Alessandrini et al., 2020) reference is not in the bibliography, please include this. - Line 232: Update this sentence to: In South Africa, fewer major variants (16) were found than in Asturias (Table 4). - Line 242, 250, 252, 259, 262, 263, 272, 376 : add the year after the month in text - Line 542 – remove 7. from reference - Line 562 – 564 – this is one reference not two? Please update and fix in text citations - Please check remaining references are correct and match in text citations - Figure 1: Can you please include the year in the date on the x axis. Can you please label the y axis. - Figure 2: Can you please include the year in the date - Figure S1: Can you please include the year in the date on the x axis - Figure S2: Spelling mistake – Souh America update to South America. Can you please include the year in the date on the x axis - Table S3, 4, 5: Please add the year in the date in the column titles in the table
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Thank you for submitting your manuscript for publication in Access Microbiology. It has been examined by expert reviewers who have concluded that the work is of interest to the readership of Access Microbiology. Based on the comments received, a major amendment of this manuscript will be required. I will be pleased to consider a revised manuscript along with a document including a point by point response to each of the reviewers comments. Your revised manuscript may be returned to one or more of the original reviewers, along with your itemised response to the reviewers’ comments. I look forward to receiving the revised manuscript.
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Comments to Author
This paper studies the Monitoring and Tracking the Spread of SARS-CoV-2 in Asturias, Spain. It is a interesting topic. The study is well-written and presented. Data are well-showed. The authors have used a mutational approach to analyse sequences. However, this not traditional method allowed us to obtain interesting results about the monitoring and tracking the spread of SARS-CoV2 in the region described. However, some aspects must be taken into account before their publication. My minor suggestions are as follows: In “Methods” section, the authors must insert a paragraph “SARS-CoV-2 PCR method” and to explain it. Table 1 and 3 are not clear. Please edit this part as well I suggest to include a “Conclusions” section in order to emphasize the purpose of the study I suggest to improve clarity …
Comments to Author
This paper studies the Monitoring and Tracking the Spread of SARS-CoV-2 in Asturias, Spain. It is a interesting topic. The study is well-written and presented. Data are well-showed. The authors have used a mutational approach to analyse sequences. However, this not traditional method allowed us to obtain interesting results about the monitoring and tracking the spread of SARS-CoV2 in the region described. However, some aspects must be taken into account before their publication. My minor suggestions are as follows: In “Methods” section, the authors must insert a paragraph “SARS-CoV-2 PCR method” and to explain it. Table 1 and 3 are not clear. Please edit this part as well I suggest to include a “Conclusions” section in order to emphasize the purpose of the study I suggest to improve clarity and flow of the text. English could be improved with better sentence formulation.
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Satisfactory
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Comments to Author
Gonzalez-Alba et al., SARS2 variant analysis in a region in Spain over a period of 1.5 years early in the pandemic (pre-omicron). They detail their experiences tracking SARS2 through whole-genome sequencing and RT-qPCR SNP based assays. They do not use traditional phylogenetics to analyse sequences (which would be challenging at best for SNP assays), they use a mutational approach. Through this, the team define variants (co-occurring SNPs/genome sequences), and linking them to later established variant names (e.g. alpha, delta, etc). This is a nice study to read and is well-written and presented. The mutational approach is somewhat unique but is likely to be widely used as many low-resource labs may use SNP-based PCR assays. The results are not ground-breaking but they are important to publish for …
Comments to Author
Gonzalez-Alba et al., SARS2 variant analysis in a region in Spain over a period of 1.5 years early in the pandemic (pre-omicron). They detail their experiences tracking SARS2 through whole-genome sequencing and RT-qPCR SNP based assays. They do not use traditional phylogenetics to analyse sequences (which would be challenging at best for SNP assays), they use a mutational approach. Through this, the team define variants (co-occurring SNPs/genome sequences), and linking them to later established variant names (e.g. alpha, delta, etc). This is a nice study to read and is well-written and presented. The mutational approach is somewhat unique but is likely to be widely used as many low-resource labs may use SNP-based PCR assays. The results are not ground-breaking but they are important to publish for several reasons, including that the evolution of the pandemic has not been described for this region, and that every little helps us understand this virus and protect ourselves during the next pandemic, especially at a local level as is described here. However, there are a few improvements that could be made but the majority are minor: Major: A section in the discussion highlighting comparison to phylogenetic-based methods and limitations of SNP approaches should be added It would be of interest to compare the SNP and WGS approaches - is this possible? Is one "better" than the other? Fig2. Add in established names (alpha etc) so it is clearer how this hypothesis reflects accepted SARS2 evolution. Fig3: Integrate this better with your variant analysis. Mark on where each variant was first/last observed. Careful with the infection control points as we don't exactly know what works best for keeping COVID infections low so I would not be as explcit here and merely list examples of things that coud be involved (e.g. isolation, vaccination etc). The paper uses data from GISAID. Have the authors checked they have cited GISAID and the data original producers adequately? Minor: Line 176: 3x106-what does this mean? Be explicit when using GISAID data The first SARS2 sequences were not uploaded to GISAID but posted on Virological.org There is a typo somewhere: D614D Line 344 - 4 new variants (delta) - does this refer to 4 distinct lineages of delta?
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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