Abstract
Background: The present study was set up to evaluate the efficacy of virological surveillance using posterior oropharyngeal saliva samples to monitor the COVID-19 pandemic in general practice. Methods: Posterior oropharyngeal saliva samples were collected without restriction on timing or alimentation by general practitioners from patients with acute respiratory infection (ARI) seen in consultation. Saliva samples were tested by real-time reverse transcription polymerase chain reaction for SARS-CoV-2 and 21 other respiratory pathogens. Results for SARS-CoV-2 in saliva samples were compared to results obtained using a nasopharyngeal swab (NPS) collected in a certified medical laboratory before or after the ARI consultation. Results: Overall, 143 ARI patients were enrolled between 6 June 2020, and 19 January 2021. SARS-CoV-2 RNA was detected in 37.0% (n = 53) of saliva samples and in 39.0% (n = 56) of NPS. Both saliva and NPS were positive in 51 patients. Positive and negative results were concordant between saliva samples and NPS in 51 (96.2%) and in 85 (94.4%) patients, respectively, with a Cohen’s Kappa coefficient of 0.89 (95% CI 0.82–0.97, p < 0.001). Other respiratory viruses were detected in 28.0% (n = 40) of the 143 saliva samples. Conclusions: Findings suggest that saliva samples could represent an attractive alternative to NPS for surveillance of SARS-CoV-2 in patients consulting for an ARI in primary care.
Highlights
Reverse transcription–quantitative polymerase chain reaction (RT–qPCR) of nasopharyngeal samples is widely used to detect SARS-CoV-2 and other respiratory viruses [1,2]
Of the 143 patients, SARS-CoV-2 RNA was detected in 39.0% (n = 56) of nasopharyngeal swab (NPS) and in 37.0% (n = 53) of saliva samples (Table 2)
Both saliva and NPS were positive in 51 patients (2 patients were positive only in saliva samples and 5 only in NPS)
Summary
Reverse transcription–quantitative polymerase chain reaction (RT–qPCR) of nasopharyngeal samples is widely used to detect SARS-CoV-2 and other respiratory viruses [1,2]. Collecting nasopharyngeal samples (NPS) causes patient discomfort, which may discourage patients with mild symptoms from seeking diagnostic tests This could compromise the detection of cases and epidemiological surveillance. The French Sentinelles network monitors acute respiratory infection (ARI) in primary health care in France from epidemiological and virological data collected by general practitioners (GPs) and pediatricians. This allows to detect and characterize the circulating respiratory viruses, as SARS-CoV-2, influenza and RSV [3]. Methods: Posterior oropharyngeal saliva samples were collected without restriction on timing or alimentation by general practitioners from patients with acute respiratory infection (ARI) seen in consultation. Conclusions: Findings suggest that saliva samples could represent an attractive alternative to NPS for surveillance of SARS-CoV-2 in patients consulting for an ARI in primary care
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