Testing for Omicron: SA researchers say saliva swabs may be best

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  • Saliva swabs detect Omicron better than the widely-used nasal swabs, according to a new SA study.
  • The scientists compared saliva swabs and nasal swabs for PCR-based detection of Delta and Omicron.
  • They suggest that current diagnostic sampling methods should be reassessed for Omicron infections. 

As South Africa experiences its fourth wave of Covid-19 infections, Omicron is rapidly displacing Delta as the dominant variant in the country.

Findings from a recently published SA study suggest that a better method for testing the new variant may be saliva swabs. 

According to their paper, posted on the medRxiv preprint server, the scientists from the University of Cape Town found that saliva samples yielded more accurate results in PCR analyses for Omicron than those collected via mid-turbinate nasal swabs.

However, the nasal swabs were a more reliable indicator in people infected with the Delta variant, the authors say. 

The study was led by Dr Diana Hardie, a clinical virologist and head of the diagnostic virology laboratory at Groote Schuur Hospital, Cape Town.

Comparing the swabs

The researchers recruited 382 symptomatic, non-hospitalised patients who had a Covid test done between August and December 2021 at Groote Schuur Hospital.

Genome sequencing was performed on the isolates that tested positive – a total of 31 participants tested positive for the Delta variant while 36 were infected with Omicron.

Participants then had their saliva and nasal samples taken for PCR analysis. 

To compare saliva and nasal samples, the researchers used a composite standard for Covid infection. Infection was considered present if Covid viral RNA was detected in either of the swabs.

Following this, the team used the results from the test samples and composite standards and compared them in order to estimate the sensitivity and specificity of saliva and nasal swabs for detecting Omicron and Delta infections (referred to as the positive percent agreement).


For Delta, the positive percent agreement for each sampling method, compared with the composite standard, was 71% for the saliva and 100% for the nasal swabs. For Omicron, however, there was 100% agreement between saliva samples and the composite standard, but only 86% for nasal swabs.

While the nasal swabs were considered the gold standard for detecting and diagnosing SARS-CoV-2 infection since the start of the pandemic, this method may not be as valuable in an Omicron-dominated context, the authors said.

“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,” the researchers wrote.

'Suboptimal' diagnosis

The researchers added:

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.


In light of the findings, the authors pointed out that although saliva sampling may be easier to perform than nasal swabbing, it’s not a straightforward practice.

For example, the participants had to cough three to five times and have the inside of both cheeks, above and below the tongue, on the gums, and hard palate swabbed for at least 30 seconds. They also could not eat, drink, smoke, or chew anything for 30 minutes before the test.

If the research, which has not yet been peer-reviewed and should be interpreted with caution, is backed up by additional studies, it is not clear how soon saliva-based tests could become commercially available in SA. Currently, the nasal swab PCR test is predominantly used.

*For more Covid-19 research, science and news, click here. You can also sign up for our Daily Dose newsletter here.

READ | Covid-19: Powerful T cells likely to protect against severe illness from Omicron, SA and US studies find

READ | Withdrawal of new Covid-19 guidelines 'extremely disappointing', says Rural Doctors Association

READ | Omicron may not be the final variant, but it may be the final variant of concern

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