Accuracy of saliva for SARS-CoV-2 detection in outpatients and their household contacts during the circulation of the Omicron variant of concern

Abstract

Abstract Background While nasopharyngeal (NP) swabs are considered the gold standard for severe acute respiratory coronavirus 2 (SARS-CoV-2) real-time reverse transcriptase-polymerase chain reaction (RT-PCR) detection, several studies have shown that saliva is an alternative specimen for COVID-19 diagnosis and screening. Methods To analyze the utility of saliva for the diagnosis of COVID-19 during the circulation of the Omicron variant, participants were enrolled in an ongoing cohort designed to assess the natural history of SARS-CoV-2 infection in adults and children. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and Cohen’s kappa coefficient were calculated to assess diagnostic performance. Results Overall, 818 samples were collected from 365 outpatients from January 3 to February 2, 2022. The median age was 32.8 years (range: 3–94 years). RT-PCR for SARS-CoV-2 was confirmed in 97/121 symptomatic patients (80.2%) and 62/244 (25.4%) asymptomatic patients. Substantial agreement between saliva and combined nasopharyngeal/oropharyngeal samples was observed with a Cohen’s kappa value of 0.74 [95% confidence interval (CI): 0.67–0.81]. Sensitivity was 77% (95% CI: 70.9–82.2), specificity 95% (95% CI: 91.9–97), PPV 89.8% (95% CI: 83.1–94.4), NPV 87.9% (95% CI: 83.6–91.5), and accuracy 88.5% (95% CI: 85.0-91.4). Sensitivity was higher among samples collected from symptomatic children aged three years and older and adolescents [84% (95% CI: 70.5–92)] with a Cohen’s kappa value of 0.63 (95% CI: 0.35–0.91). Conclusions Saliva is a reliable fluid for detecting SARS-CoV-2, especially in symptomatic children and adolescents during the circulation of the Omicron variant.

Keywords

• COVID-19
• SARS-CoV-2
• Omicron
• Saliva
• Accuracy