Study suggests that saliva samples may be more suitable for omicron detection

A team of researchers from South Africa has recently demonstrated that saliva inoculations are more effective than mid-turbinate polymers for polymerase chain reaction (PCR) -based detection of omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

The study is currently available at medRxiv* preprint server.

Study: Saliva inoculations are the preferred sample for Omicron detection.  Image credit: UvGroup / ShutterstockStudy: Saliva inoculations are the preferred sample for Omicron detection. Image credit: UvGroup / Shutterstock


The emerging omicron variant of SARS-CoV-2 has caused a sharp increase in new cases of coronavirus disease 2019 (COVID-19) worldwide. The variant has been shown to increase the risk of re-infection as well as vaccine breakthrough infections. With about 40 mutations in the spike protein, the variant exhibits significantly increased transmissibility compared to other identified variants of concern (VOCs), including the alpha, beta, gamma, and delta variants.

Currently, the omicron variant differs from other SARS-CoV-2 variants by the S-gene target failure approach. Due to the presence of a deletion mutation in the spike gene of the omicron variant, PCR cannot detect this particular gene. This phenomenon is called S-gene target failure and is used as a marker to detect omicron infections. However, the pattern of viral secretion during omicron infection and its impact on diagnostic sampling methods is still largely unknown.

In the current study, the researchers compared the performance of saliva inoculations and mid-turbinate inoculations for PCR-based detection of delta and omicron variants.

Study design

The researchers collected saliva and inoculations in the middle of the turbinates from 382 symptomatic, non-hospitalized patients who appeared for SARS-CoV-2 testing at a hospital in Cape Town between August and December 2021. They subsequently tested the samples using reverse transcription PCR (RT-PCR).

The categorization of delta and omicron was performed based on whole genome sequencing data, PCR-derived S gene target error data, and sampling date. To compare saliva and mid-turbinate samples, a composite standard for SARS-CoV-2 infection was used. The detection of viral RNA in one of the matched samples was considered a positive infection.

The results obtained from test samples and composite standards were compared to estimate the sensitivity and specificity of saliva and mid-turbinate inoculations for the detection of omicron and delta infections (positive percentage agreement).

Important observations

The positive percentage agreement between saliva and mid-turbinate inoculations to the composite standard was estimated to be 71% and 100% for the delect infection, respectively. In contrast, saliva and mid-turbinate inoculations showed 100% and 86% positive percent, respectively, for detection of omicron infection.

Considering the nucleocapsid gene as a target reference, the mean differences in RT-PCR cycle threshold (Ct value) between salivary and mid-turbinate inoculations were estimated to be 5.2 and 1.5 for delta and omicron, respectively. infections.

The mean duration between onset of symptoms and the positive test result was 3 days and 2 days for the delta and omicron infections, respectively.

The significance of the study

The study results reveal that saliva samples are more useful than mid-turbinate samples for accurate detection of omicron infection. As observed in the study, saliva samples contain more viral RNA than nasal samples. This may be due to altered viral excretion patterns during omicron infection.

There is evidence to suggest that the replication rate of the omicron variant is significantly higher in the upper airways than in the delta variant. In the lower respiratory tract, however, the omicron replicates significantly more slowly than the wild-type SARS-CoV-2 (Wuhan strain). These observations indicate that certain host tissues preferentially support the growth of the omicron variant (tissue tropism). The altered tissue tropism during omicron infection may be the cause of the altered virus secretion pattern.

In view of the study results, the researchers suggest that currently used diagnostic sampling methods should be re-evaluated for omicron infections, as analysis of nasal or nasopharyngeal samples may lead to a suboptimal diagnosis.

*Important message

medRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore should not be considered as crucial, guide clinical practice / health-related behavior or be treated as established information.


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