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Published on: November 28, 2016
Improved oral detection is a characteristic of Omicron infection and has implications for clinical sampling and
Gert Marais1, Nei-Yuan Hsiao2, Arash Iranzadeh3
1Department of Medical Microbiology, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa.
Background:
The Omicron variant of concern is characterised by more than 50 distinct mutations, most in the spike protein. The implications of these for disease transmission, tissue tropism and diagnostic testing needs study.
Objectives:
We evaluated the performance of RT-PCR on saliva (SA) swabs and antigen testing on mid-turbinate MT samples relative to RT-PCR on MT swabs. Patients (n = 453) presenting for outpatient testing at the Groote Schuur Hospital COVID-19 testing centre in Cape Town South Africa were recruited. Participants were recruited during the Delta (n = 304) and Omicron (n = 149) waves.
Results:
In 30 confirmed Delta infections, positive percent agreement (PPA) of RT-PCR on saliva was only 73% compared to a composite standard of either MT or SA RT-PCR positivity, with rapid decay by day 3 after symptom onset. In contrast, in the 70 Omicron infections, SA performed as well as, or better than, MT samples up to day 5, with an overall PPA of SA swabs of 96% and MT of 93%. A change in antigen test performance was noted, with PPA of 93% in Delta, but only 68% for Omicron.
Conclusions:
Altered shedding kinetics appear to be present in Omicron-infected patients with more viral RNA detectable in saliva. Saliva swabs are a promising alternative to nasal samples, especially early in infection when sampling of both sites could improve detection. Lower sensitivity of antigen tests in Omicron is a concern and requires further study.
Insights
Saliva RT-PCR testing shows high accuracy for Omicron variant detection, outperforming nasal swabs. Antigen tests are less sensitive for Omicron, necessitating further research.
Area of Science:
- Virology
- Infectious Diseases
- Diagnostic Testing
Background:
- The Omicron variant possesses over 50 mutations, primarily in the spike protein.
- The impact of these mutations on transmission, tropism, and diagnostics requires investigation.
Purpose of the Study:
- To evaluate the performance of saliva RT-PCR and antigen testing compared to nasal RT-PCR.
- To assess diagnostic accuracy during the Delta and Omicron waves in South Africa.
Main Methods:
- Compared RT-PCR on saliva (SA) and mid-turbinate (MT) swabs with a composite standard.
- Evaluated antigen test performance on MT samples.
- Recruited 453 outpatients during Delta (n=304) and Omicron (n=149) waves.
Main Results:
- For Omicron, saliva RT-PCR showed high positive percent agreement (PPA) of 96% compared to MT RT-PCR (93%), outperforming nasal swabs up to day 5.
- Saliva RT-PCR PPA for Delta was 73%, with rapid decay after symptom onset.
- Antigen test PPA decreased from 93% for Delta to 68% for Omicron.
Conclusions:
- Omicron infections exhibit altered shedding kinetics with increased viral RNA in saliva.
- Saliva swabs are a viable alternative to nasal samples, especially early in infection.
- Reduced sensitivity of antigen tests for Omicron requires further study.
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