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. 2023 May 17;15(1):2213106.
doi: 10.1080/20002297.2023.2213106. eCollection 2023.

SARS-CoV-2 RT-qPCR Ct values in saliva and nasopharyngeal swab samples for disease severity prediction

Kristina Snipaitiene  1   2 , Birute Zablockiene  3   4 , Rasa Sabaliauskaite  2 , Kristina Zukauskaite  1   2 , Elzbieta Matulyte  3   4 , Tautvile Smalinskaite  5 , Mindaugas Paulauskas  3   4 , Rolandas Zablockis  6   7 , Mantvydas Lopeta  8 , Julius Gagilas  8 , Alina Puriene  9 , Ligita Jancoriene  3   4 , Sonata Jarmalaite  1   2
Affiliations

SARS-CoV-2 RT-qPCR Ct values in saliva and nasopharyngeal swab samples for disease severity prediction

Kristina Snipaitiene et al. J Oral Microbiol. .

Abstract

Background: Comparison 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.

Methods: Three 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.

Results: SARS-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).

Conclusion: Salivary 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.

Keywords: COVID-19; Ct values; RT-qPCR; SARS-CoV-2; saliva; severity; viral dynamics.

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Conflict of interest statement

Mantvydas Lopeta and Julius Gagilas are employees at JSC Diagnolita. JSC Diagnolita has developed the kits used in this research. The authors declare no other conflicts of interest.

Figures

Figure 1.
Figure 1.
Detection rates of SARS-CoV-2 in saliva and nasopharyngeal samples collected from COVID-19 patients and controls (a) and in patients dichotomised into mild/moderate (Cohort I, b) and severe cases (Cohort II, c).
Figure 2.
Figure 2.
Comparison of Cycle threshold (Ct) values from positive saliva specimens and nasopharyngeal swabs between all samples altogether (a), all samples dichotomised into Cohort I vs. Cohort II, (b) and the first test only (c).
Figure 3.
Figure 3.
Correlation analysis of cycle threshold (Ct) values from positive saliva specimens and nasopharyngeal swabs: corresponding first (a), second (b), and third (c) sample tests, altogether (d) and according to cohorts (e and f).
Figure 4.
Figure 4.
Analysis of serial saliva and nasopharyngeal samples: comparison of cycle threshold (Ct) values (a–c) and correlation of Ct values from saliva, nasopharyngeal and days since onset of symptoms (d–f). r, Pearson correlation.
Figure 5.
Figure 5.
Kaplan–Meier analysis of positivity for SARS-CoV-2 prediction from saliva samples and nasopharyngeal swabs when the entire cohort (a) and mild to moderate illness (Cohort I) vs. severe disease (Cohort II) cases are analysed in saliva samples (b) and nasopharyngeal swab samples (c) separately.
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