ABSTRACTBackgroundComparison of clinical value of RT-qPCR-based SARS-CoV-2 tests performed on saliva samples (SSs) and nasopharyngeal swab samples (NPSs) for prediction of the COVID-19 disease severity.MethodsThree paired SSs and NPSs collected every 3 days from 100 hospitalised COVID-19 patients during 2020 Jul-2021 Jan were tested by RT-qPCR for the original SARS-CoV-2 virus and compared to 150 healthy controls. Cases were divided into mild+moderate (Cohort I,N= 47) and severe disease (Cohort II,N= 53) cohorts and compared.ResultsSARS-CoV-2 was detected in 65% (91/140) vs. 53% (82/156) of NPSs and 49% (68/139) vs. 48% (75/157) of SSs collected from Cohort I and II, respectively, resulting in the total respective detection rates of 58% (173/296) vs. 48% (143/296) (P= 0.017). Ct values of SSs were lower than those of NPSs (mean Ct = 28.01 vs. 30.07,P= 0.002). Although Ct values of the first SSs were significantly lower in Cohort I than in Cohort II (P= 0.04), it became negative earlier (mean 11.7 vs. 14.8 days,P= 0.005). Multivariate Cox proportional hazards regression analysis showed that Ct value ≤30 from SSs was the independent predictor for severe COVID-19 (HR = 10.06, 95% CI: 1.84–55.14,P= 0.008).ConclusionSalivary RT-qPCR testing is suitable for SARS-CoV-2 infection control, while simple measurement of Ct values can assist in prediction of COVID-19 severity.