PONE-D-21-22703

Sampling site for SARS-CoV-2 RT-PCR - an intrapatient four-site comparison from Tampere, Finland

PLOS ONE

Dear Dr. Kerimov,

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Academic Editor

PLOS ONE

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“This work was supported by funding from Tampere Tuberculosis Foundation; Research Foundation of the Pulmonary Diseases; Competitive State Research Financing of the Expert Responsibility area of Tampere University Hospital; Tampere University Hospital Support Foundation. Funders did not have any role in any part of the study.”

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: I Don't Know

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: No

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The manuscript is a short report on a very important study of the importance of the sampling site for diagnosis of SARS- CoV 2. Studies like this should have been done in the beginning of the pandemic and the actual study adds important information. For the standard diagnostics with nasopharyngeal samples trained health care workers are needed and because of discomfort several patients, especially children, don’t accepted repeated examinations.

The actual study is well done and presented. That anterior nasal swabs perform as good as nasopharynx swabs is an important finding.

The material is small with only 43 diagnosed positive patients and small differences could have been missed. I recommend to add a sentence about this limitation. At all places I recommend to instead of “no difference” write “ no statistically significant difference” .

I recommend to remove row 129-131 “No significant correlation was found between patient age or duration of symptoms and Ct values of any sampling site. No statistically significant difference was found in chronic disease, allergies, smoking, body temperature or symptoms between sexes”. It is not likely there was enough statistical power to detect significant differences in these subgroup-analyses in such a small patient group.

Reviewer #2: The manuscript by Kerimov et al describes results from SARSCoV2 PCR in samples from different sampling sites. The main finding is that samples from anterior nasal cavity are as good as nasopharyngeal samples for detection of SARSCoV2. This is in line with previous reports.

The manuscript is concise and well written.

Major comments;

My major concern is the small sample size and the fact that all patients were symptomatic, presumably with a short duration of symptoms before sampling. This must be discussed in the discussion section, ie adding a paragraph on limitations of the study. Futhermore no patients with low or no virsl load was included in the study.

The conclusion must be corrected accordingly, anterior nasal cavity samples yields comparable results to nasopharyngeal samples in symptomatic patients with rather high viral load.

Minor comments;

Line 125 is this correct? Should it read higher ct values instead?

Reviewer #3: I welcome to review this paper on appropriate sampling sites for RT-PCR Sars-Cov-2. A highly interesting topic during the present pandemic. The authors show that sampling in the upper airways could be done at different sampling sites (anterior nose, oropharynx and saliva) with satisfactory result compared to the established sampling site nasopharyx. This could be more convenient and enhance sampling frequency in some patient groups. But, the major drawback of the present study is the number of the studied patient cohort, only 43 patients. Due to this small number the conclusion will undeniable be vague. Other sampling sites than nasopharynx in the upper airways could be used, but the sensitivity is reduced and this reduced sensitivity, the magnitude, could not be assessed in this study, due to the low number of observations. Minor concerns are: the authors don't specify which symptoms qualify for inclusion in the study. For the sampling of oropharynx and anterior nose two different testing kits are in use, with no information on comparing prestanda. The target genes for RT-PCR is only presented in a footnote in a table, a more vigorous description is required, and also the reason for pooling the  resulting means of three different genes for each sampling site, and than comparing the medians of this operation. A description and discussion of the problem with the sampling volume is lacking.

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Reviewer #1: Yes: Rune Andersson

Reviewer #2: No

Reviewer #3: Yes: Gunnar Jacobsson

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Sampling site for SARS-CoV-2 RT-PCR - an intrapatient four-site comparison from Tampere, Finland

PONE-D-21-22703R1

Dear Dr. Kerimov,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Robert Jeenchen Chen, MD, MPH

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: No

Reviewer #2: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: (No Response)

Reviewer #2: All comments have been adressed.

Minor :

Under limitations: the authors should consider rephrasing the sentence stating that samples from asymptomatic patients were not included. Behave is probably not the right word to use.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: Yes: Rune Andersson

Reviewer #2: No