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. 2023 Aug:165:105496.
doi: 10.1016/j.jcv.2023.105496. Epub 2023 May 24.

Direct comparison of clinical diagnostic sensitivity of saliva from buccal swabs versus combined oro-/nasopharyngeal swabs in the detection of SARS-CoV-2 B.1.1.529 Omicron

Andreas Puyskens  1 , Janine Michel  1 , Anna Stoliaroff-Pepin  2 , Fatimanur Bayram  1 , Akin Sesver  1 , Ole Wichmann  2 , Thomas Harder  2 , Lars Schaade  1 , Andreas Nitsche  1 , Caroline Peine  3
Affiliations

Direct comparison of clinical diagnostic sensitivity of saliva from buccal swabs versus combined oro-/nasopharyngeal swabs in the detection of SARS-CoV-2 B.1.1.529 Omicron

Andreas Puyskens et al. J Clin Virol. 2023 Aug.

Abstract

Background/purpose: While current guidelines recommend the use of respiratory tract specimens for the direct detection of SARS-CoV-2 infection, saliva has recently been suggested as preferred sample type for the sensitive detection of SARS-CoV-2 B.1.1.529 (Omicron). By comparing saliva collected using buccal swabs and oro-/nasopharyngeal swabs from patients hospitalized due to COVID-19, we aimed at identifying potential differences in virus detection sensitivity between these sample types.

Methods: We compare the clinical diagnostic sensitivity of paired buccal swabs and combined oro-/nasopharyngeal swabs from hospitalized, symptomatic COVID-19 patients collected at median six days after symptom onset by real-time polymerase chain reaction (PCR) and antigen test.

Results: Of the tested SARS-CoV-2 positive sample pairs, 55.8% were identified as SARS-CoV-2 Omicron BA.1 and 44.2% as Omicron BA.2. Real-time PCR from buccal swabs generated significantly higher quantification cycle (Cq) values compared to those from matched combined oro-/nasopharyngeal swabs and resulted in an increased number of false-negative PCR results. Reduced diagnostic sensitivity of buccal swabs by real-time PCR was observed already at day one after symptom onset. Similarly, antigen test detection rates were reduced in buccal swabs compared to combined oro-/nasopharyngeal swabs.

Conclusion: Our results suggest reduced clinical diagnostic sensitivity of saliva collected using buccal swabs when compared to combined oro-/nasopharyngeal swabs in the detection of SARS-CoV-2 Omicron in symptomatic individuals.

Keywords: B.1.1.529 (Omicron); Buccal swab sampling; Clinical diagnostic sensitivity; SARS-CoV-2; Saliva.

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Conflict of interest statement

Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Image, graphical abstract
Graphical abstract
Fig 1
Fig. 1
Comparison of SARS-CoV-2 B1.1.529 Omicron detection performance of matched buccal and combined oro-/nasopharyngeal swabs by real-time PCR. A Comparison of cycle threshold (Cq) values for two distinct genomic regions of SARS-CoV-2 (E-gene and Orf1ab) of matched buccal and combined oro-/nasopharyngeal swabs (ONS) by quantitative real-time PCR (RKI/ZBS1 SARS-CoV-2 protocol, Michel et al. Virol J (2021) 18:110); n = 107. B Estimation plot of SARS-CoV-2 positive sample pairs with Cq values ≤45; n = 77. Line at mean with 95% Confidence Interval; Paired t-test, p **** <0,0001.
Fig 2
Fig. 2
Comparison of real-time PCR results from buccal and combined oro-/nasopharyngeal swabs at different time periods after symptom onset. Comparison of cycle threshold (Cq) values for two distinct genomic regions of SARS-CoV-2 (E-gene and Orf1ab) of matched buccal and combined oro-/nasopharyngeal swabs (ONS) by quantitative real-time PCR (RKI/ZBS1 SARS-CoV-2 protocol, Michel et al. Virol J (2021) 18:110) at different days post (d.p.) symptom onset. Data displayed as Tukey box plot.
Fig 3
Fig. 3
Comparison of SARS-CoV-2 B.1.1.529 Omicron detection performance of matched buccal and combined oro-/nasopharyngeal swabs by antigen test. PCR positive buccal and combined oro-/nasopharyngeal (ONS) sample pairs (n = 77) were tested using the Panbio™ COVID-19 Ag Rapid Test Device. Shown are the number of positive and negative antigen test results. All tests showed a visible control line.
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