key: cord-0861147-0i1e2634
authors: Cornette, M.; Decaesteker, B.; Martens, G. A.; Vandecandelaere, P.; Jonckheere, S.
title: From Delta to Omicron SARS-CoV-2 variant: switch to saliva sampling for higher detection rate
date: 2022-03-18
journal: nan
DOI: 10.1101/2022.03.17.22272538
sha: a3fdbf007c2b067c631ba7a323b3bc47116e22ce
doc_id: 861147
cord_uid: 0i1e2634

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.

• Oropharyngeal swab is the least preferred sample type for SARS-CoV-2 detection

The current standard for SARS-CoV-2 virus detection includes real-time polymerase chain reaction (RT-PCR) testing on a nasopharyngeal swab (NPS), yet the collection of this sample type is experienced uncomfortable by patients. Saliva-and oropharyngeal swab (OPS) collections are considered less invasive. In addition, saliva can be collected by the patients themselves and does not require trained healthcare providers equipped with protective material. OPS is less sensitive as compared to NPS [1], but combining NPS and OPS collection results in a small sensitivity increase compared to the use of a single NPS [1] . Existing literature suggests that saliva can be used as an equivalent alternative specimen for the PCR-based detection of the SARS-CoV-2 virus [2] [3] [4] . In fact, preliminary data suggest that saliva may show higher sensitivity compared to NPS regarding the Omicron variant [5] . In this study, we evaluated the relative performance of OPS, NPS and saliva for the Delta (B.1.617.2) and

Omicron (B.1.1.529) SARS-CoV-2 variants.

Adult patients who presented at the screening centre in Ypres (Belgium) for a SARS-CoV-2 RT-PCR test between the 3th of December 2021 and 15th of February 2022 were asked to voluntarily participate in the study. Informed consent and questionnaire (assessing eating, drinking, chewing or smoking 30 minutes before test and test indication) were completed under the guidance of the researcher. OPS and NPS were separately collected by the nurse. Based on the Belgian Sciensano guidelines for saliva collection [6] , the participant collected the saliva sample in a CE-labeled sterile buffer-free recipient by spitting. No saliva swabbing device was . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity.

is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint , p=0.021) . Furthermore, 13 participants tested negative on NPS but positive on saliva (two Delta and ten Omicron). From these 13 participants, a follow-up sample was taken two to four days later, and 11 patients tested positive on follow-up of which 10 were positive on NPS in addition to saliva. Logistic regression showed no impact of eating, drinking, chewing or smoking 30 minutes before the test on SARS-CoV-2 positivity rate for the three sample types.

In this study, we show that saliva is superior compared to NPS for the detection of the Omicron variant, consistent with the preliminary data shown by Marais et al. [5] . Ten of 91 Omicron positive patients tested positive on saliva and negative on NPS, but presented two to four days later with a positive test on both specimen. This suggests that RT-PCR on saliva sample is more sensitive in an early phase of Omicron infection, which might be explained by altered is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted March 18, 2022. ; https://doi.org/10.1101/2022.03.17.22272538 doi: medRxiv preprint entry pathways and viral shedding of this variant [8] [9] [10] [11] . In addition, we show that OPS is the least sensitive sample type for the PCR-based detection of SARS-CoV-2 virus and that combining OPS with NPS has little added value, as was already described by Wang et al. [1] .

In summary, our data show that NPS and saliva can be considered equivalent specimen for the detection of the Delta variant, but saliva is the preferred sample type for detection of the Omicron variant.

The Study Protocol was approved by the Ethics committee of AZ Delta (B1172022000004).

The authors declare no conflicts of interest.

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted March 18, 2022. ; https://doi.org/10.1101/2022.03.17.22272538 doi: medRxiv preprint Figure 1 . A. Ct value 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 values were found for oropharyngeal swabs as compared to nasopharyngeal swabs and saliva for all genes (ANOVA, p<0.001). Statistically significant difference in Ct values were found for nasopharyngeal swabs 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 value 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 significantly lower as compared to saliva sample for RdRP/S and N gene in both variants, as well as for the E gene in Delta variant (paired t-test). is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted March 18, 2022. ; https://doi.org/10.1101/2022.03.17.22272538 doi: medRxiv preprint

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