Impact of swab removal in the detection of SARS-CoV-2 weakly-positive specimens
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Early removal of swabs can accelerate laboratory work and enhance quality by decreasing contamination and errors in downstream procedures. This article aims to compare the traditional testing workflow in a diagnostic laboratory (red), with manual swab removal and aliquoting vs a swab-out laboratory workflow (blue).
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I am pleased to tell you that your article has now been accepted for publication in Access Microbiology.
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Comments to Author
This is a well written paper describing a small study looking at the impact of removing a swab from sample transport medium/buffer prior to extraction for SARS-CoV-2 detection using two PCR platforms. The data is reproducible across both platforms and shows that the detection of low level positive samples with ct values >32 is compromised. This data adds to the body of evidence regarding the implementation of laboratory processes that are designed to support workflow, but that might impact on the sensitivity of the downstream assay. The authors describe the limitations of the study and also what further work needs to happen to support the findings. The only point that needs to be reviewed is around the conclusions which suggest that the study will add to the body of evidence regarding clinical …
Comments to Author
This is a well written paper describing a small study looking at the impact of removing a swab from sample transport medium/buffer prior to extraction for SARS-CoV-2 detection using two PCR platforms. The data is reproducible across both platforms and shows that the detection of low level positive samples with ct values >32 is compromised. This data adds to the body of evidence regarding the implementation of laboratory processes that are designed to support workflow, but that might impact on the sensitivity of the downstream assay. The authors describe the limitations of the study and also what further work needs to happen to support the findings. The only point that needs to be reviewed is around the conclusions which suggest that the study will add to the body of evidence regarding clinical interpretation of low level positives. I cannot see anything in the results or discussion that might support this statement. Indeed the study was performed with contrived material and not clinical samples where the outcome of missing a late positive might be determined. Without that data and follow-up, it would be difficult to make that conclusion. If work has been performed following the submission of this manuscript, it would be worth considering a revision to include it to substantiate what this might mean clinically.
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?
Partially 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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Two reviewers were positive and enthusiastic about your manuscript. They have recommended revisions, which I agree with. Please address all points. Specifically, please address the point from reviewer 2 which asks you to support your conclusions with evidence from your results and discussion. If you need additional time to complete these revisions, please don't hesitate to let us know.
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Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data Excellent and neatly presented study which is much required to enhance laboratory workflow. 2. Presentation of results No major issues. Very neat. 3. How the style and organization of the paper communicates and represents key findings Minor issues detailed here: Line 63 Nasopharyngeal specimen as a terminology is used in USA and Middle East for adult swabbing for SARS-CoV-2 RNA testing. In UK, nasopharyngeal specimens are exclusively used in UK for Bordatella pertussis diagnosis in paediatric setting and is not used in UK for adults for SARS-CoV-2 RNA testing. To clarify further, combined throat and nose swabs are used in UK for many decades and this has been emphasised even for self-swabbing guidelines [How to …
Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data Excellent and neatly presented study which is much required to enhance laboratory workflow. 2. Presentation of results No major issues. Very neat. 3. How the style and organization of the paper communicates and represents key findings Minor issues detailed here: Line 63 Nasopharyngeal specimen as a terminology is used in USA and Middle East for adult swabbing for SARS-CoV-2 RNA testing. In UK, nasopharyngeal specimens are exclusively used in UK for Bordatella pertussis diagnosis in paediatric setting and is not used in UK for adults for SARS-CoV-2 RNA testing. To clarify further, combined throat and nose swabs are used in UK for many decades and this has been emphasised even for self-swabbing guidelines [How to take a combined throat and nose swab - Postal version (publishing.service.gov.uk) https://assets.publishing.service.gov.uk/media/5ea1c5a3e90e070494e34c6c/Combined_throat_nose_swab_instruction_sheet_postal.pdf ]. I suggest the authors to not to confuse nasopharyngeal specimens with combined throat and nose swabs and correct the manuscript to combined throat and nose swabs. Lines 106, 107 The three terminologies "weakly positive, strongly positive and moderately positive" need to be defined. In clinical practice, these terms are not exported to patient charts but can be used within the laboratory setup for internal discussions. Lines 111 and 112 - there is a new term "Working at the end of the detection limit of the Real-Time PCR platforms". Again this 'end of the detection limit" needs to be defined. 4. Literature analysis or discussion Line 64 VPSS is not defined anywhere in the manuscript. There must be a reference for this to ensure international readers can understand the importance of widespread use of VPSS. 5. Any other relevant comments The authors must discuss a pathway for laboratories who have long standing protocols for reject empty containers and process containers which has a retained swab. The authors should clarify whether there was a decrease in number of "inhibitory" samples when swabs were taken out.
Please rate the manuscript for methodological rigour
Very good
Please rate the quality of the presentation and structure of the manuscript
Very 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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