According to an outpatient surveillance study in Hong Kong, minimally invasive nose-only swabs achieved high agreement with joint nose and throat swabs (NTS) for reverse transcription polymerase chain reaction (RT-qPCR) detection of influenza and SARS-CoV-2, thus presenting a viable alternative specimen type for supervised respiratory virus testing.
RT-qPCR testing is the gold standard for detecting influenza and SARS-CoV-2, but its accuracy depends on the quality of the specimen, which in turn is influenced by the anatomical site where active viral replication is sampled. In Hong Kong, diagnostic testing is typically carried out using nasopharyngeal swabs or joint 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 swabs compared with joint NTS, as it is easier to perform and less uncomfortable. [BMC Glob Public Health 2025;3:5]
The aim of the present study was to estimate the concordance between nose-only swabs and joint NTS for detecting influenza and SARS-CoV-2 via RT-qPCR among symptomatic outpatients in Hong Kong. The data were collected between May 2023 and April 2024 from participants of an ongoing outpatient surveillance study, who sought medical care for a febrile acute respiratory illness. All were first sampled using rapid antigen tests (RAT) followed by a joint NTS (Copan’s SLASSIQSwabs), and were then invited to provide a nose-only swab (RhinoMed’s Rhinoswab) sample, which they could opt out of. Nose-only swabs were subsequently supervised by trained staff. [PLoS One 2026;21:e0355869]
Influenza A was detected in 136 of 488 participants who provided paired samples (mean age, 25 years; female, 55.5 percent) acquired through joint NTS and nose-only swabs, with a concordance of 98.0 percent and Cohen’s kappa of 0.95. There were 42 influenza B and 32 SARS-CoV-2 positive test results by both swab tests. The concordance for detecting influenza B and SARS-CoV-2 was 99.0 percent for both viruses, with respective Cohen’s kappa values of 0.94 and 0.92. “Concordance was similar among different age groups, time since onset and vaccination status,” highlighted the researchers.
Of note, nose-only swabs maintained high concordance with joint NTS, despite being carried out after sampling for RAT and joint NTS, which may have reduced the amount of viral material available and therefore underestimated the degree of agreement between the two tests.
Since samples were collected ≤3 days from symptom onset, when viral loads are typically at their highest, the high concordance observed may be overestimated relative to patients with lower viral loads or asymptomatic infections. Indeed, discordance was primarily detected in samples with cycle threshold values of ≥30 (collected ≤24 hours from symptom onset). According to the researchers, this finding is similar to those previously reported for non-nasopharyngeal samples at low viral loads and should not affect case detection at peak transmissibility (ie, at higher viral loads). [Infect Dis (Lond) 2021;53:581-589]
“To conclude, supervised nose-only swab testing demonstrated high concordance with joint NTS for the detection of influenza and SARS-CoV-2 in symptomatic outpatients. Given their minimal invasiveness, nose-only swabs are viable alternative specimens for supervised respiratory virus testing,” wrote the researchers.