Quality control of loop-mediated isothermal amplification (LAMP) using external control: Detection of SARS-CoV-2 using nasopharyngeal specimens
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We evaluated an external control for loop-mediated isothermal amplification (LAMP) for the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using 100 nasopharyngeal specimens (20 positives and 80 negatives). We performed LAMP for the specimens and distilled water. We collected threshold time (Tt) and calculated the difference in Tt values between specimens and distilled water. All specimens showed amplification of the external control. Regarding the Tt values (median, min), no difference was found between the positive specimens (15.9) and the negative specimens (15.8) (p = 0.75). For the difference in Tt values, no difference was found between the positive specimens (1.4) and the negative specimens (1.3) (p = 0.78). No specimens were found with noticeable inhibitory reactions. These results indicate that the external control has the potential to monitor the inhibitory reactions in specimens. Future work will include the evaluation of specimens with inhibitory reactions.
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Comments to Author
Thank you for your manuscript. LAMP technology is of growing importance and identifying new techniques to improve it are very important. Unfortunately, I am not able to recommend your submission for publication at this time. The key reason is that your manuscript is essentially a description of a new method but it lacks the key to a good methods paper which is complete and extensive detail. Your manuscript introduces the use of a novel external control to a LAMP protocol, but there is no information about what the external control is. Fundamentally, this must be present in my opinion and is key to allowing others to reproduce the results presented. Beyond that, some other improvements that should be made are: More background information about LAMP and its use as a diagnostic would be nice to see in …
Comments to Author
Thank you for your manuscript. LAMP technology is of growing importance and identifying new techniques to improve it are very important. Unfortunately, I am not able to recommend your submission for publication at this time. The key reason is that your manuscript is essentially a description of a new method but it lacks the key to a good methods paper which is complete and extensive detail. Your manuscript introduces the use of a novel external control to a LAMP protocol, but there is no information about what the external control is. Fundamentally, this must be present in my opinion and is key to allowing others to reproduce the results presented. Beyond that, some other improvements that should be made are: More background information about LAMP and its use as a diagnostic would be nice to see in the introduction. The English needs to be improved across the manuscript The introduction or discussion does not explain why an external control is needed nor why the extra information it would provide beyond the controls that are already in place is needed. This should be included, with examples provided from other assays if available please. Please provide the primers used in all reactions as well as reaction conditions for the PCR used. I wish you luck if you choose to resubmit, Thank you
Please rate the manuscript for methodological rigour
Poor
Please rate the quality of the presentation and structure of the manuscript
Poor
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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Firstly, thank you very much for your patience throughout this long peer review process. I acknowledge that it has been considerably longer than any of us would have liked. I have now received 3 peer reports on your manuscript, which give very mixed reviews of the work presented. Taken together with my own assessment, I have recommended major revisions as a substantial re-write will be required to convey the scientific importance of the work, to improve legibility, and to make it useful as a methodology paper. If you wish to proceed with this submission, please can you address the comments of the reviewers, paying particular attention to questions about the requirements for an external control and what additional information they provide beyond stand controls, as well as including fundamental details on the methodology to allow it to …
Firstly, thank you very much for your patience throughout this long peer review process. I acknowledge that it has been considerably longer than any of us would have liked. I have now received 3 peer reports on your manuscript, which give very mixed reviews of the work presented. Taken together with my own assessment, I have recommended major revisions as a substantial re-write will be required to convey the scientific importance of the work, to improve legibility, and to make it useful as a methodology paper. If you wish to proceed with this submission, please can you address the comments of the reviewers, paying particular attention to questions about the requirements for an external control and what additional information they provide beyond stand controls, as well as including fundamental details on the methodology to allow it to be replicated. Reviewer 1 has suggested some papers that they think should be cited. If these suggestions are indeed formative papers in the LAMP diagnostics field please include them. If they are not formative works, it is at your discretion to include them or not.
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Comments to Author
This an good report and I approve of its publication. It is comprehensive and the key findings were analysed critically. The literature review, result representation and conclusion demonstrated that the assay and controls should be further investigated with different types of specimens.
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
Comments to Author
This an good report and I approve of its publication. It is comprehensive and the key findings were analysed critically. The literature review, result representation and conclusion demonstrated that the assay and controls should be further investigated with different types of specimens.
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
-
Comments to Author
First of all, this study is an informative and novel idea during this COVID-19 pandemic era. Please improve the grammatically mistake in whole manuscript, especially in abstract. I have corrected some lines in abstract and introduction parts and add 1-2 latest references in these lines. For example, Replace your abstract with this effective line as followed: We evaluated loop-mediated isothermal amplification (LAMP) assay as external control for diagnosis of novel severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) within 100 nasopharyngeal specimens. Our LAMP assay were exhibited a positive results as an external control for samples of SARS-CoV-2 patients, while distilled water (DW) were taken as a control subjects. We were found to be threshold time (Tt) vales difference between specimens of …
Comments to Author
First of all, this study is an informative and novel idea during this COVID-19 pandemic era. Please improve the grammatically mistake in whole manuscript, especially in abstract. I have corrected some lines in abstract and introduction parts and add 1-2 latest references in these lines. For example, Replace your abstract with this effective line as followed: We evaluated loop-mediated isothermal amplification (LAMP) assay as external control for diagnosis of novel severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) within 100 nasopharyngeal specimens. Our LAMP assay were exhibited a positive results as an external control for samples of SARS-CoV-2 patients, while distilled water (DW) were taken as a control subjects. We were found to be threshold time (Tt) vales difference between specimens of SARC-CoV-2 and DW. On the basis of Tt values (Median/Min), no significant (p
Please rate the manuscript for methodological rigour
Satisfactory
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