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. 2026 Aug 11;21(8):e0355869. doi: 10.1371/journal.pone.0355869

Diagnostic agreement between Rhinoswabs and joint nose and throat swabs for the detection of influenza and SARS-CoV-2 among symptomatic ambulatory patients in Hong Kong

Caitriona Murphy 1, Samuel M S Cheng 1, Loretta Mak 1, Hau Chi So 1, Dennis K M Ip 1, Malik Peiris 1,2, Benjamin J Cowling 1,*
Editor: Hin Fung Tsang3
PMCID: PMC13460600  PMID: 42579694

Abstract

Background

Accurate detection of respiratory viruses relies on appropriate sample collection, but whether joint nose and throat sampling is necessary for high diagnostic performance or whether nose sampling alone can provide comparable results remains uncertain.

Objectives

We evaluated the diagnostic agreement between joint nose and throat swabs (NTS) and Rhinoswab (RhinoMed, Cremorne, Australia), a novel anterior nasal swab for RT-qPCR detection of respiratory viruses among symptomatic outpatients.

Study design

Outpatients with febrile acute respiratory illness were enrolled at a clinic in Hong Kong and paired joint NTS and Rhinoswab samples were tested by reverse transcription polymerase chain reaction (RT-qPCR) for influenza A, influenza B, SARS-CoV-2 and human ribonuclease P (RNase P) as an internal control. Diagnostic agreement and RT-qPCR Ct values were compared between the paired samples.

Results

Between May 2023 and April 2024, 488 participants provided paired samples. Overall concordance between Rhinoswab and NTS was 98.0% (95% CI: 96.3% to 99.0%) for influenza A, 99.0% (95% CI: 97.6% to 99.7%) for influenza B, and 99.0% (95% CI: 97.6% to 99.7%) for SARS-CoV-2. Cohen’s kappa also indicated high agreement for all viruses: 0.95 (95% CI: 0.92 to 0.98) for influenza A, 0.94 (95% CI: 0.88 to 0.99) for influenza B, and 0.92 (95% CI: 0.85 to 0.99) for SARS-CoV-2. Ct values from Rhinoswab were moderately correlated with NTS for all three viruses and RNase P. The majority of discordant samples had Ct values of 30 and above (16/18, 88.9%).

Conclusions

Rhinoswabs achieved high agreement with joint NTS for RT-qPCR detection of influenza and SARS-CoV-2. Given their minimal invasiveness Rhinoswabs are a viable alternative specimen type for supervised respiratory virus testing.

Background

Accurate and timely detection of influenza and SARS-CoV-2 is important for surveillance and clinical management. Molecular testing by polymerase chain reaction (PCR) is the gold standard but its accuracy is contingent on the quality of the specimen collected which is influenced by the anatomical site of active viral replication sampled. In Hong Kong, diagnostic testing is typically carried out using nasopharyngeal swabs or joint nose and throat swabs (NTS). In contrast to nasopharyngeal swabbing, which requires deep insertion into the nasal cavity by a trained professional, joint NTS is less invasive and suitable for self-collection. However, an evaluation of the UK COVID-19 National Testing Programme observed a preference for nose-only swabbing compared to joint NTS, reporting it was easier to perform and less uncomfortable [1]. The Rhinoswab™ was developed by RhinoMed (Cremorne, Australia) in 2020 [2,3] aiming to be minimally invasive by collecting nasal discharge from the anterior nares.

Objectives

We aimed to estimate the concordance between Rhinoswabs and joint NTS for detecting influenza and SARS-CoV-2 via RT-PCR among symptomatic outpatients in Hong Kong.

Study design

Study participants

We utilised data from an ongoing outpatient surveillance study in Hong Kong, between 03/05/2023 and 29/04/2024. Eligible patients were aged ≥6 months and were seeking medical care for a febrile acute respiratory illness, defined as the presence of ≥2 respiratory symptoms within 3 days of symptom onset. A questionnaire was administered to collect vaccination history and demographics. The study protocol was approved by the Institutional Review Board of the University of Hong Kong. Written informed consent was obtained from all participants or their legal guardians for minors. The individual pictured in this manuscript has given written informed consent to publish the image.

Specimen collection and laboratory testing

All participants were first sampled using rapid antigen tests (unrelated to this study), followed by a joint NTS (CLASSIQSwabs™, Copan) and then by the Rhinoswab as participants could opt out of being sampled using a Rhinoswab. A demonstration video was shown and a junior version of the Rhinoswab was available for children (S1 Fig). For participants that agreed to provide a Rhinoswab sample, collection was performed by study staff according to manufacturers’ instructions. Swabs were inserted into the anterior nares and left for 15 seconds while the participant breathed normally and then moved back and forth in the nostril for an additional 15 seconds. After removal, each loop of the swab was snapped off into the collection tube at predefined break points. All swabs were transported to the laboratory in viral transport media and tested for influenza A, influenza B, and SARS-CoV-2 using a ViiA7 RT-qPCR system (ThermoFisher). RNA extraction and RT-qPCR targets and conditions have been described previously [4]. A cycle threshold (Ct) value of <40 was considered positive.

Statistical analysis

Participants were included if they had paired joint NTS and Rhinoswab samples. Agreement was assessed by estimating concordance, defined as the percentage of paired swabs with identical results (positive or negative) and Cohen’s kappa with 95% confidence intervals (CI). Concordance was also evaluated by age, time since the onset of symptoms and vaccination status (received influenza or COVID-19 vaccination within a year before seeking medical care). Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) with 95% confidence intervals are also reported to evaluate the diagnostic performance of the Rhinoswab compared to joint NTS.

In addition, the correlation between the Ct values for both swabs was assessed using Pearson’s correlation coefficients. We plotted the difference in Ct values (Rhinoswab minus NTS) against NTS Ct values to assess variability across a range of viral loads. Analyses were performed using R version 4.0.2 (R Foundation for Statistical Computing, Vienna, Austria).

Results

During the study period, 531 participants were enrolled and invited to provide paired samples, of whom 488 (91.9%) provided paired samples, while 43 (8.1%) opted out. Of those that opted out, 16/43 (37.2%) were unwilling after viewing the demonstration video. Of the 488 Rhinoswabs collected, 246 (50.4%) were Rhinoswab junior. The mean age was 25 years and the majority of participants were female (55.5%) (Table 1).

Table 1. Study participant characteristics by virus detected by both Rhinoswab and joint nose-throat swab.

Characteristic Influenza A

(n = 136)		 Influenza B

(n = 42)		 SARS-CoV-2

(n = 32)		 Negative

(n = 260)		 Discordant

(n = 18)		 Overall

(n = 488)
Age, Mean (SD) 25.6 (20.3) 25.1 (15.9) 41.7 (22.1) 22.4 (20.3) 29.2 (18.5) 25.1 (20.5)
Male 62 (45.6%) 23 (54.8%) 10 (31.3%) 117 (45.0%) 5 (27.8%) 217 (44.5%)
Chronic condition 12 (8.8%) 2 (4.8%) 5 (15.6%) 28 (10.8%) 3 (16.7%) 50 (10.2%)
Vaccinated within a year
 Influenza vaccine 41 (30.1%) 5 (11.9%) 9 (28.1%) 111 (42.7%) 5 (27.8%) 171 (35.0%)
 COVID-19 vaccine 6 (4.4%) 0 (0%) 1 (3.1%) 4 (1.5%) 1 (5.6%) 12 (2.5%)
Symptom onset
  ≤ 24 hours 71 (52.2%) 12 (28.6%) 26 (81.3%) 132 (50.8%) 12 (66.7%) 253 (51.8%)
  > 24–47 hours 27 (19.9%) 8 (19.0%) 3 (9.4%) 38 (14.6%) 3 (16.7%) 79 (16.2%)
  > 48–72 hours 38 (27.9%) 22 (52.4%) 3 (9.4%) 90 (34.6%) 3 (16.7%) 156 (32.0%)
Open in a new tab

Influenza A was detected in 136 participants by both joint NTS and Rhinoswab, with a concordance of 98.0% (95% CI: 96.3% to 99.0%) and Cohen’s kappa of 0.95 (95% CI: 0.92 to 0.98). There were 42 influenza B and 32 SARS-CoV-2 positives by both swabs respectively (Table 1). The concordance for detecting influenza B and SARS-CoV-2 was 99.0% (95% CI: 97.6% to 99.7%) for both viruses, with corresponding Cohen’s kappa values of 0.94 (95% CI: 0.88 to 0.99) and 0.92 (95% CI: 0.85 to 0.99), respectively. Concordance was similar among different age groups, time since onset and vaccination status (S2 Fig).

The Ct values from Rhinoswabs were significantly positively correlated with those from joint NTS for all three viruses and the internal control, human RNase P (Fig 1 panels A-D). Correlations coefficients were 0.76 for influenza A, 0.818 for influenza B, and 0.729 for SARS-CoV-2, while human RNase P showed a moderate correlation (r = 0.616). When the difference between Ct values (Rhinoswab minus NTS) was plotted against the NTS Ct value there was no evidence of substantially different Rhinoswab agreement for higher or lower Ct values (Fig 1 panels E-H). The majority of discordant samples (16/18, 88.9%) had Ct values of ≥30 (S1 Table) and occurred within 24 hours of symptom onset (Table 1).

Fig 1. Correlation of cycle threshold (Ct) values between joint NTS and Rhinoswab for influenza A, influenza B, SARS-CoV-2 test positives and the internal control, human ribonuclease P (panels A–D).

Fig 1

Open in a new tab

The bottom row (panels E–H) shows the difference in Ct-values (Rhinoswab Ct minus NTS Ct) plotted against the NTS Ct-values. Solid lines represent a perfect agreement, and dotted lines indicate the fitted linear regression. Pearson correlation coefficients (r) are displayed in each panel.

When comparing the Rhinoswab to joint NTS as the reference test, sensitivity was 95.8% (95% CI: 91.0% to 98.4%) for influenza A, 91.3% (95% CI: 79.2% to 97.6%) for influenza B, and 91.4% (95% CI: 76.9% to 98.2%) for SARS-CoV-2. Specificity was 98.8% (95% CI: 97.1% to 99.7%) for influenza A, 99.8% (95% CI: 98.7% to 100.0%) for influenza B, and 99.6% (95% CI: 98.4% to 99.9%) for SARS-CoV-2. PPV ranged from 94.1% to 97.7%, while NPV were all above 98.3% (S2 Table).

Discussion

Rhinoswabs had a high concordance with joint NTS for detecting influenza A (98.0%), influenza B (99.0%), and SARS-CoV-2 (99.0%). This is higher than the 95.2% concordance reported for SARS-CoV-2 estimated among symptomatic patients in Australia [2]. Two other studies have evaluated Rhinoswabs, observing a positive percent agreement of 96.2% for detecting six viruses in a hospital setting [3] and sensitivity of 95% in patients with high viral loads (Ct < 20) compared to combined oro-nasopharyngeal swabs in an emergency department population [5].

This is similar to the sensitivity for detecting influenza A and a bit higher than that for influenza B and SARS_CoV-2. The observed high concordance could be driven by a high proportion of concordant negative samples. Influenza B and SARS-CoV-2 had a lower prevalence resulting in a higher concordance (99.0%) due to a greater number of true negatives while influenza A had the highest prevalence in this study with a slightly lower concordance (98.0%). However, despite prevalence-driven differences, Cohen’s kappa remained consistently high across all viruses (0.92–0.95), indicating strong agreement between the two sampling methods beyond what would be expected by chance alone. Discordance was among samples with Ct values of ≥30, similar to previous literature for non-nasopharyngeal samples at low viral loads [6]. This may not affect case detection when transmissibility is greatest (higher viral loads) [7].

We observed a lower (compared to influenza and SARS-CoV-2) correlation for RNase P between Rhinoswab and joint NTS Ct values, which could reflect variability in the amount of cellular material collected by the two swab types. However, differences in host-cell yield do not necessarily translate into poorer viral RNA detection. For example, a comparison of oropharyngeal, nasopharyngeal and combined swabs observed varied RNase P and total human RNA levels but these differences did not correlate with viral load measured by RT-qPCR [8]. Similar patterns were reported for nasal and saliva specimens, suggesting more variable host-cell recovery while still maintaining comparable SARS-CoV-2 detection to nasopharyngeal swabs [9].

Rhinoswabs in this study were the third sequential sampling of the anterior nares, which may have reduced the amount of viral material available and lead to an underestimate of Rhinoswab agreement. Despite this conservative sampling sequence, Rhinoswabs maintained comparable concordance to joint NTS. This finding is similar to studies that carried out sequential sampling to compare self-collected samples followed by a healthcare worker collecting swabs, finding that self-collected nasal and mid-turbinate swabs yielded viral loads equivalent to or even higher than healthcare-worker-collected nasopharyngeal swabs [10,11]. Nevertheless, the fixed sampling order precludes assessment of whether agreement would be equivalent (or potentially superior) if the Rhinoswab had been collected first.

Limitations include sample collection early in the course of infection, when viral loads are typically highest. Consequently, the high concordance observed may be overestimated relative to patients with lower viral loads or asymptomatic infections. Rhinoswab collection was supervised by trained staff, and we did not evaluate self-collection. However, several studies have shown that self-collected nasal swabs yield viral loads and diagnostic performance similar to healthcare worker collected swabs [10,11]. Given the user-friendly design of Rhinoswabs the agreement could be similar between collection methods, but dedicated studies utilizing self-collected swabs and among asymptomatic are needed.

To conclude, supervised testing using Rhinoswabs demonstrated a high concordance with joint NTS for the detection of influenza and SARS-CoV-2 in symptomatic outpatients. Given Rhinoswabs only sample the nose and are child friendly, they could be a practical alternative for supervised respiratory virus testing in outpatient settings.

Supporting information

S1 Fig. Sample collection from outpatients using Rhinoswabs.

Research staff collected samples using flocked nylon Rhinoswabs (available in adult and junior sizes). The swab design includes snap points to detach into a standard collection tube (Panel A). The sampling technique involves inserting the swab into both nostrils (Panel B). Collected samples were suspended in viral transport media and subsequently tested for influenza and SARS-CoV-2 via PCR.

(PDF)

pone.0355869.s001.pdf (536.2KB, pdf)
S2 Fig. Agreement of pooled NT swabs and Rhinoswabs by age, time since the onset of symptoms and vaccination status (vaccinated within a year).

(PDF)

pone.0355869.s002.pdf (6.4KB, pdf)
S1 Table. Number of concordant and discordant results between Rhinoswab and joint NTS, with mean cycle threshold values for each category.

(DOCX)

pone.0355869.s003.docx (15.6KB, docx)
S2 Table. Diagnostic performance of Rhinoswab compared to joint NTS by virus.

(DOCX)

pone.0355869.s004.docx (15.1KB, docx)

Acknowledgments

The authors thank colleagues at St Teresa’s Hospital for facilitating participant enrolment. The authors thank Julie Au for technical support.

Data Availability

All data and code supporting the findings of this study are fully available without restriction from a public GitHub repository: https://github.com/caitmurphy/rhinoswab_concordance.

Funding Statement

This research was financially supported by a grant received by BJC from the Health and Medical Research Fund, Health Bureau, the Government of the Hong Kong Special Administrative Region (grant number INF-HKU-3) and the Theme-based Research Scheme (grant number T11-712/19-N) of the Research Grants Council of the Hong Kong SAR Government. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Reviewers' comments:

Comments to the Author

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

Reviewer #5: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: No

Reviewer #5: Yes

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

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

Reviewer #5: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

Reviewer #5: Yes

**********

Reviewer #1:  The manuscript addresses an important and clinically relevant topic regarding minimally invasive respiratory virus sampling methods.

The paired-sample design and use of RT-PCR strengthen the technical quality of the study.

The results demonstrate high concordance between Rhinoswabs and joint nose and throat swabs, supporting the potential utility of Rhinoswabs in outpatient settings.

The manuscript is generally well written and logically organized.

Statistical analysis is appropriate; however, inclusion of Cohen’s kappa statistics, sensitivity, specificity, and predictive values would provide a more comprehensive assessment of diagnostic agreement.

Additional discussion regarding applicability in asymptomatic individuals and unsupervised self-collection settings would strengthen the manuscript.

Reviewer #2:  The manuscript by Murphy et al addresses a practical question for clinical diagnostics. The authors provide a clear evaluation of a less invasive Rhinoswab swabbing method compared with standard practices. The manuscript is methodologically sound. The results are useful in clinical practice. I have several comments to improve the clarity and robustness before acceptance.

There were 18 discordant samples stated in Table 1. Please specify which swab yielded the positive result in these cases. It will be useful to know whether the Rhinoswab failed to detect viruses found by the NTS, or if the NTS missed viruses detected by the Rhinoswab. This also helps to address the next comment.

Negative cases are the majority here, which could skew the concordant value. For example, there are 32 positive SARS-CoV-2 cases, which means 456 negative cases. Let’s assume that Rhioswab couldn’t get any SARS-CoV-2 virus at all, thus it would only generate negative cases. In this scenario, the concordant value could still be as high as 456/488 = 93.4%. Please comment on this in the Discussion session.

1. Please consider using RT-qPCR since Ct values are obtained from qPCR.

2. “Written informed consent..” is stated twice at lines 64 and 67.

3. How is the Ct value determined? Baseline-Threshold or regression method?

4. Have any abnormal amplification curves been observed? If yes, how were the abnormal curves handled? This information should be included in the manuscript.

5. It will also be useful to detail the discordant cases (see above). Such as, how many have tested positive by Rhinoswab, but negative by joint NTS?

6. Figure 1 legend: Please use NTS for consistency. Please indicate that the r is Pearson’s correlation (I assume).

7. Figure 1: There are two linear regression lines, a solid and a dashed one, in the figure. What are they?

8. Figure 1: I assume in the figure only positive cases are plotted. Please make this clear in the legend.

9. Figure 1: Please consider indicating the discordant samples, maybe with a different color, to support the conclusion at line 114.

10. I found it interesting that the authors note that 43 participants opted out of providing paired samples, and 16 of those were unwilling after viewing the demonstration video. The Rhinoswab is marketed as a less invasive, patient-friendly alternative, but the video deterred some patients. No response for this comment is needed from the authors.

Reviewer #3:  Reviewer

It is a pleasure to review the manuscript entitled "Agreement of Rhinoswabs and joint nose and throat swabs for detecting influenza and SARS-CoV-2 among symptomatic ambulatory patients in Hong Kong” (PONE-D-26-15719). I have carefully reviewed this manuscript. I found that it is straightforward, the sample size is reasonable (488 paired samples), the statistics are appropriate for the objective, and the conclusions are generally supported by the data. This manuscript appears scientifically sound, clinically relevant, and appropriate for publication in PLOS ONE. In particular, the manuscript is concise and well written. Nevertheless, a few minor issues should be addressed to strengthen the manuscript. After this revision, I support accepting this manuscript in PLOS ONE.

Manor’s suggestion for revision

1. The study mainly reports “concordance” but does not provide sensitivity, specificity, positive predictive agreement, negative predictive agreement, and Cohen’s kappa. Because NTS is effectively treated as a reference standard, reporting these metrics would strengthen diagnostic interpretation. Thus, the study would be strengthened by providing additional reporting of the sensitivity, specificity, positive/negative agreement, and Cohen’s kappa statistics to provide a more comprehensive assessment of diagnostic performance.

2. The Rhinoswab was always collected AFTER rapid antigen testing and joint NTS sampling. This could reduce the amount of viral material remaining in the nose. The authors briefly mention this in the discussion. I think this deserves stronger acknowledgment. Because Rhinoswab collection was performed after other respiratory sampling procedures, the order of sampling may have influenced viral recovery. Please discuss this potential sampling-order bias in greater detail and clarify whether randomization of sampling order was considered.

3. I found a very important issue. The manuscript promotes Rhinoswab as suitable for easy or minimally invasive collection, yet all samples were collected by trained staff. Thus, the conclusions about usability and self-testing are somewhat overstated. Because all Rhinoswab specimens were collected under supervision by trained staff, the manuscript should avoid overgeneralizing the findings to unsupervised self-collection settings.

4. The authors used Ct ≤ 40 as the positivity cutoff. However, a Ct of 40 is relatively permissive. Please justify the use of a Ct of 40 as the positivity threshold and indicate whether equivocal results were observed near the cutoff.

5. The manuscript reports concordance percentages but only briefly presents confidence intervals. Please ensure that all concordance estimates include 95% confidence intervals in the main text and/or tables.

6. Please correct minor typographical and formatting errors throughout the manuscript.

Reviewer #4:  The manuscript addresses a practical question: whether a minimally invasive anterior nasal Rhinoswab can provide comparable RT-PCR detection of influenza A/B and SARS-CoV-2 to joint nose-and throat swabs in symptomatic outpatients. Overall, the study is clearly written, the sample size is reasonable, and the paired-sample design is appropriate for assessing diagnostic agreement. The reported concordance is high for all three viruses, and the analysis of Ct-value correlation and discordant samples supports the main conclusion that Rhinoswab may be a practical alternative in ambulatory settings.

However, the manuscript would benefit from a more careful framing of "agreement" versus diagnostic performance. Because neither specimen type is treated as an independent gold standard, term such as sensitivity or diagnostic accuracy should be avoided unless a composite reference standard is defined. The authors appropriately report concordance, but the Discussion occasionally implies broader diagnostic equivalence. This should be softened.

The statistical analysis is somewhat limited. Percent agreement alone maybe inflated by the large number of negative samples. The authors should consider adding positive percent agreement, negative percent agreement, and Cohen's kappa for each virus. Given the paired design, a McNemar test or equivalent comparison of discordant pairs would also strengthen the analysis. Confidence intervals should be provided consistently for all agreement metrics.

The sequential sampling order is another important limitation. Rhinoswab was collected after rapid antigen testing and joint NTS, which may affect available nasal material. The authors interpret the preserved performance as reassuring, but fixed order still prevents assessments of whether Rhinoswab performance would be similar if collected first. This should be stated more explicitly.

The manuscript also needs cleaner reporting of discordant results. A small table indicating which swab was positive, virus detected, Ct values, and symptom timing would help readers understand whether discordance reflects low viral load, sampling variability, or possible false positives.

Finally, the conclusion should be slightly narrower. The data support use in supervised collection among symptomatic outpatients early after symptom onset, but do not yet establish performance for self-collection, asymptomatic screening, later illness. or inpatient populations.

Overall, this is a concise and useful study with practical implications. i would support publication after minor revision, mainly to improve statistical reporting, clarify limitations, and avoid overinterpreting concordance as full diagnostic equivalence.

Reviewer #5:  Firstly, I truly appreciate for giving me this opportunity and selecting me to be apart of this work.

After carefully reviewing- Minor to moderate changes are required.

Clinically relevant study, highly suitable for publication.

Real time outpatient settings and patient population

Pairing of samples

Inclusion of three different respiratory viruses and large sample size study before conducting rhinoswab studies.

The topic is very interesting. Based on scientific reasoning- the conclusion is that ANS captures enough or sufficient viral RNA for reliable RT PCR in symptomatic patients is because respiratory viruses both SARS COV2 virus, RSV and influenza viruses-viral replication is more in the nasal cavity and helps in premature detection during infection and therefore, nasal swabs diagnostically works well during initial stages and thats why rhinoswabs are enough for molecular diagnostic detection of viruses.

Even MERS virus, other human coronovirus, human bocavirus, Adenoviruses, Human Parainfluenza Viruses, Human Metapneumovirus common rhinovirus can be detected-even though there is low viral load but still can be captured.

There fore, ANS is a friendly, easier to use and delivers the same results.

A great tool for detection leading to diagnosis of the viruses.

It has the same quality and accuracy that helps in faster outcomes and optimizes health outcomes.

Cost efficient

Flexible

Validation of care

Concise and well executed diagnostic concordance study.

The concept and comparison is excellent.

The findings from the study is a feasible and alternative specimen specially in outpatient settings particularly given the high concordance observed.

Prior to publication-several methodological and reporting issues should be clarified.

The reporting is more general and overall agreement of percentages.

Additional reporting includes- Negative and positive percent agreement and cohen Kappa statistics. These metrics will help in method comparison.

The exact distribution in terms of samples is unclear- Only 18 paired samples were discordant- Positive by NTS only vs Rhinoswab only must be provided.

Virus specific Discordance counts

Provision of CT values for both specimen types

To strengthen the interpretation summarizing all the discordant specimens.

Clarification of sampling order was fixed with participants, nostril sampling was repeatedly sampling.

Randomization order was considered

Since it is a self collection, the collection is lacking, self collection feasibility and evidence supporting diagnostic performance under supervised collection. The whole advantage of the rhinoswab is self collection and was collected by study staff.

There is a room for improvement on statistical reporting- Correlation alone does not assess concordance with agreements.

For the improvement use of Bland Altmann Analysis or report mean ct differences considering limitations.

Helps in systematic bias on specimens.

The title can be streamlined. Diagnostic concordance or agreement between Rhinoswab ans and jns for detection of influenza virus and SARS COV2.

Redundancy - Informed consent statement appears twice in the methods sections.

CT value <40 (Clarification of positivity threshold format)

Typographical issues

formatting issues

spacing

figure labelling

After interpretation - the overall study does not exactly show or talk about anterior nasal sampling captures higher viral loads that NTS.

It shows that ANS captures enough or sufficient viral RNA for reliable RT PCR in symptomatic patients and in outpatient settings.

**********

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Reviewer #1: Yes:  DR LAKSHMI JYOTHI T

Reviewer #2: No

Reviewer #3: No

Reviewer #4: No

Reviewer #5: Yes:  MONISHA KANDALA

**********

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PLoS One. 2026 Aug 11;21(8):e0355869. doi: 10.1371/journal.pone.0355869.r002

Author response to Decision Letter 1

23 Jul 2026

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This research was financially supported by a grant from the Health and Medical Research Fund, Health Bureau, the Government of the Hong Kong Special Administrative Region (grant number INF-HKU-3) and the Theme-based Research Scheme (grant number T11-712/19-N) of the Research Grants Council of the Hong Kong SAR Government.

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We have updated the statement to include that there was no additional funding received for this study.

This research was financially supported by a grant received by BJC from the Health and Medical Research Fund, Health Bureau, the Government of the Hong Kong Special Administrative Region (grant number INF-HKU-3) and the Theme-based Research Scheme (grant number T11-712/19-N) of the Research Grants Council of the Hong Kong SAR Government. There was no additional external funding received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Thank you. The picture is of the manuscripts first author, not a study participant. We have consent and as such have updated the ethics statement of the manuscript.

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Thank you. The references have been edited to ensure all of them contain their doi as requested. We have not referenced any retracted papers or preprints.

Reviewer #1:

The manuscript addresses an important and clinically relevant topic regarding minimally invasive respiratory virus sampling methods.

The paired-sample design and use of RT-PCR strengthen the technical quality of the study.

The results demonstrate high concordance between Rhinoswabs and joint nose and throat swabs, supporting the potential utility of Rhinoswabs in outpatient settings.

The manuscript is generally well written and logically organized.

Thank you.

1.1 Statistical analysis is appropriate; however, inclusion of Cohen’s kappa statistics, sensitivity, specificity, and predictive values would provide a more comprehensive assessment of diagnostic agreement.

Thank you. We have added Cohen’s kappa statistics to the main text and a supplementary table containing the other diagnostic performance metrics.

1.2 Additional discussion regarding applicability in asymptomatic individuals and unsupervised self-collection settings would strengthen the manuscript.

Thank you. We have now mentioned that the concordance observed in our study may not generalize to those with lower viral loads or asymptomatic individuals and included further discussion on collection methods in the limitations paragraph of the discussion.

Reviewer #2: The manuscript by Murphy et al addresses a practical question for clinical diagnostics. The authors provide a clear evaluation of a less invasive Rhinoswab swabbing method compared with standard practices. The manuscript is methodologically sound. The results are useful in clinical practice. I have several comments to improve the clarity and robustness before acceptance.

Thank you.

There were 18 discordant samples stated in Table 1. Please specify which swab yielded the positive result in these cases. It will be useful to know whether the Rhinoswab failed to detect viruses found by the NTS, or if the NTS missed viruses detected by the Rhinoswab. This also helps to address the next comment.

Negative cases are the majority here, which could skew the concordant value. For example, there are 32 positive SARS-CoV-2 cases, which means 456 negative cases. Let’s assume that Rhioswab couldn’t get any SARS-CoV-2 virus at all, thus it would only generate negative cases. In this scenario,

Attachment

Submitted filename: Response to Reviewers.docx

pone.0355869.s008.docx (40.4KB, docx)

Decision Letter 1

Hin Fung Tsang

27 Jul 2026

Diagnostic agreement between Rhinoswabs and joint nose and throat swabs for the detection of influenza and SARS-CoV-2 among symptomatic ambulatory patients in Hong Kong

PONE-D-26-15719R1

Dear Prof. Cowling,

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.

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Kind regards,

Hin Fung Tsang

Academic Editor

PLOS One

Additional Editor Comments (optional):

Reviewers' comments:

Acceptance letter

Hin Fung Tsang

PONE-D-26-15719R1

PLOS One

Dear Dr. Cowling,

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Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Fig. Sample collection from outpatients using Rhinoswabs.

    Research staff collected samples using flocked nylon Rhinoswabs (available in adult and junior sizes). The swab design includes snap points to detach into a standard collection tube (Panel A). The sampling technique involves inserting the swab into both nostrils (Panel B). Collected samples were suspended in viral transport media and subsequently tested for influenza and SARS-CoV-2 via PCR.

    (PDF)

    pone.0355869.s001.pdf (536.2KB, pdf)
    S2 Fig. Agreement of pooled NT swabs and Rhinoswabs by age, time since the onset of symptoms and vaccination status (vaccinated within a year).

    (PDF)

    pone.0355869.s002.pdf (6.4KB, pdf)
    S1 Table. Number of concordant and discordant results between Rhinoswab and joint NTS, with mean cycle threshold values for each category.

    (DOCX)

    pone.0355869.s003.docx (15.6KB, docx)
    S2 Table. Diagnostic performance of Rhinoswab compared to joint NTS by virus.

    (DOCX)

    pone.0355869.s004.docx (15.1KB, docx)
    Attachment

    Submitted filename: PONE-D-26-15719-2.pdf

    pone.0355869.s005.pdf (869.6KB, pdf)
    Attachment

    Submitted filename: Reviewer 1 recommendation.pdf

    pone.0355869.s006.pdf (20.5KB, pdf)
    Attachment

    Submitted filename: Response to Reviewers.docx

    pone.0355869.s008.docx (40.4KB, docx)

    Data Availability Statement

    All data and code supporting the findings of this study are fully available without restriction from a public GitHub repository: https://github.com/caitmurphy/rhinoswab_concordance.

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