SARS-CoV-2: Saliva swabs may be more effective for Omicron detection than nasal swabs

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Researchers from the University of Cape Town-South Africa in a new study have found that saliva swabs are more effective than nasal mid-turbinate swabs for the polymerase chain reaction (PCR)-based detection of omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

The new emerged Omicron variant is characterized by more than 50 distinct mutations, the majority of which are located in the spike protein. The implications of these mutations for disease transmission, tissue tropism and diagnostic testing are still to be determined.

The study team evaluated the relative performance of saliva and mid-turbinate swabs as RT-PCR samples for the Delta and Omicron variants.

It was found that the positive percent agreement (PPA) of saliva swabs and mid-turbinate swabs to a composite standard was 71% (95% CI: 53-84%) and 100% (95% CI: 89-100%), respectively, for the Delta variant. However, for the Omicron variant saliva and mid-turbinate swabs had a 100% (95% CI: 90-100%) and 86% (95% CI: 71-94%) PPA, respectively.

The study findings support ex-vivo data of altered tissue tropism from other labs for the Omicron variant. Reassessment of the diagnostic testing standard-of-care may be required as the Omicron variant becomes the dominant variant worldwide.

The study findings were published on a preprint server and are currently being peer reviewed. https://www.medrxiv.org/content/10.1101/2021.12.22.21268246v1

Conclusion

These findings suggest that the pattern of viral shedding during the course of infection is altered for Omicron with higher viral shedding in saliva relative to nasal samples resulting in improved diagnostic performance of saliva swabs. This supports the ex-vivo finding of improved viral replication in upper respiratory tract tissue and possibly altered tissue tropism.5 This is an important finding as the current standard of care for diagnosis using swabs of the nasal or nasopharyngeal mucosa may be
suboptimal for the Omicron variant.

Figure 1. The cycle threshold (Ct) or cycle number (CN) values for paired midturbinate (MT) and saliva (SA) swabs are shown for Delta and Omicron variant
positive samples. Paired samples were tested on the same diagnostic platform on the same day and samples where only the MT or SA swab was positive were
excluded from the analysis. The nucleocapsid (N) gene Ct value was used for analysis if the sample was tested with the Allplex™ 2019-nCoV assay (Seegene,
South Korea). This was because the Delta and Omicron variants are not associated with N gene target failure and other assays used also target the N gene. Statistical analysis consisted of paired t-tests performed using GraphPad Prism version 9.3.0 for macOS, GraphPad Software, San Diego, California USA, www.graphpad.com.
The bar represents the mean Ct value with error bars showing 1 standard deviation. ns: not significant. ****: P value < 0.0001.

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