Diagnostic performance of upper airway sampling sites for SARS-CoV-2 and influenza testing

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Abstract
Early diagnosis of upper respiratory infections is essential to control infectious disease transmission within the community and to initiate relevant antiviral treatments. Nonetheless, variable sensitivities of sampling sites are often overlooked. We conducted a clinical trial at a COVID-19 outpatient test center, where healthcare workers collected nasopharyngeal, throat, nasal swabs, and saliva specimens. Each specimen was tested by RT-PCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus A and B, and respiratory syncytial virus (RSV). Clinical information was collected at enrollment and again 13 months later using an online questionnaire. From 4 March to 31 March 2023, 253 individuals were enrolled. Data from 250 participants were included in the analysis. SARS-CoV-2 was the most frequent viral infection (48%), followed by influenza A or B (5%), and a combination of SARS-CoV-2 and influenza (9%). RSV was not detected in any specimen. Several participants carried two or three viruses simultaneously. Throat swabs were significantly more sensitive for detecting SARS- CoV-2 (79%) and influenza (64%) than samples from other sites. In contrast, saliva had the lowest sensitivity for SARS- CoV-2 (43 % ) and was unsuitable for detecting influenza. The sensitivity for SARS- CoV-2 (88 % ) and influenza (100 % ) improved when results from throat and nasal swabs were combined. Throat swabs were more sensitive than nasopharyngeal swabs and saliva for molecular detection of SARS-CoV-2 and influenza. A combined throat and nasal swab is highly recommended to increase test sensitivity in patients presenting with upper respiratory infection symptoms. IMPORTANCE: Upper respiratory infections are the most common condition in primary care. Therefore, their early diagnosis is essential to control infectious disease transmission within the community. Here, we show that throat swabs were more sensitive than nasopharyngeal swabs and saliva for detecting severe acute respiratory syndrome coronavirus 2. Furthermore, throat and nasal swabs were more effective in detecting influenza compared to nasopharyngeal swabs. CLINICAL TRIALS: Registered at ClinicalTrials.gov NCT05765838 .
Funding Information
  • Novo Nordisk Fonden (NNF21SA0069151)

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