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

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.

Automated summary

This study evaluated the performance of oropharyngeal swab, nasopharyngeal swab, and saliva in detecting SARS-CoV-2 Delta and Omicron variants using RT-PCR. The results showed that saliva was superior to nasopharyngeal swab in detecting the Omicron variant. For the Delta variant, nasopharyngeal swab and saliva were considered equivalent specimens. Oropharyngeal swab was the least sensitive sample type and provided little additional value when collected in addition to a single nasopharyngeal swab.