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. 2022 Aug;2(3):100090.
doi: 10.1016/j.jcvp.2022.100090. Epub 2022 Jun 7.

From Delta to Omicron SARS-CoV-2 variant: Switch to saliva sampling for higher detection rate

Margot Cornette  1 , Bieke Decaesteker  1 , Geert Antoine Martens  2 , Patricia Vandecandelaere  1 , Stijn Jonckheere  1
Affiliations

From Delta to Omicron SARS-CoV-2 variant: Switch to saliva sampling for higher detection rate

Margot Cornette et al. J Clin Virol Plus. 2022 Aug.

Abstract

Background: Real-time polymerase chain reaction (RT-PCR) testing on a nasopharyngeal swab is the current standard for SARS-CoV-2 virus detection. Since collection of this sample type is experienced uncomfortable by patients, saliva- and oropharyngeal swab collections should be considered as alternative specimens.

Objectives: Evaluation of the relative performance of oropharyngeal swab, nasopharyngeal swab and saliva for the RT-PCR based SARS-CoV-2 Delta (B.1.617.2) and Omicron (B.1.1.529) variant detection.

Study design: Nasopharyngeal swab, oropharyngeal swab and saliva were collected from 246 adult patients who presented for SARS-CoV-2 testing at the screening centre in Ypres (Belgium). RT-PCR SARS-CoV-2 detection was performed on all three sample types separately. Variant type was determined for each positive patient using whole genome sequencing or Allplex SARS-CoV-2 variants I and II Assay.

Results and conclusions: Saliva is superior compared to nasopharyngeal swab for the detection of the Omicron variant. For the detection of the Delta variant, nasopharyngeal swab and saliva can be considered equivalent specimens. Oropharyngeal swab is the least sensitive sample type and shows little added value when collected in addition to a single nasopharyngeal swab.

Keywords: Delta; Nasopharyngeal swab; Omicron; Oropharyngeal swab; SARS-CoV-2; Saliva.

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Conflict of interest statement

The authors declare no conflicts of interest

Figures

Image, graphical abstract
Graphical abstract
Fig 1
Fig. 1
A. Ct values for each gene (E, RdRP/S and N-gene) for the three sample types (nasopharyngeal swab, oropharyngeal swab, saliva) (n = 114). Thirty-nine samples were omitted due to lack of Ct values for all genes detected in all sample types. Statistically significant difference in Ct value was found for oropharyngeal swab as compared to nasopharyngeal swab and saliva for all genes (ANOVA, p<0.001). Statistically significant difference in Ct value was found for nasopharyngeal swab as compared to saliva for the RdRP/S gene (ANOVA, p<0.001; post-hoc Tukey test, p = 0.004) and N gene (ANOVA, p<0.001; post-hoc Tukey test, p = 0.014). B. Ct values for each gene in nasopharyngeal swab versus saliva for SARS-CoV-2 Delta (n = 62) and Omicron (n = 91) variants. Ct value for nasopharyngeal swab is statistically significant lower as compared to saliva for RdRP/S and N gene in both variants, as well as for the E gene in Delta variant (paired t-test).
See this image and copyright information in PMC

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