With the Omicron variant now dominating, a local study showed that, if confirmed, testing for COVID could be more accurate with much easier saliva sampling.
University of Cape Town researchers reported in a paper uploaded to medRxiv [PDF] that in Omicron cases, saliva samples yielded more accurate results in PCR analyses compared to nasal swabs.
With the Delta variant, on the other hand, nasal swabs were more accurate, according to the group, led by Diana Hardie, MBChB, MMedPath, who also heads the diagnostic virology laboratory at Groote Schuur Hospital.
The findings came from an analysis of 382 patients tested at Groote Schuur from August through this month, with viral whole-genome sequencing performed on isolates from those with positive results.
All patients had both saliva and mid-turbinate nasal samples taken for RT-PCR analysis. The ‘gold standard’ for positivity in the study was detection of SARS-CoV-2 RNA with either swab.
For the Delta variant, the positive percent agreement for each sampling method, in comparison with this ‘gold standard’, was 71% for saliva and 100% for the nasal swabs. But Omicron reversed the trend, with 100% agreement between saliva samples and the gold standard, but only 86% for nasal swabs.
COVID testing has used nasal swabs as standard since the discovery of the virus, but that may no longer be appropriate in an Omicron-dominated pandemic landscape, the authors concluded.
“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,” Hardie and colleagues wrote.
They noted, as have others, that Omicron is distinguished by “more than 50 distinct mutations.” While these increased infectivity, they could also have other effects, including the tissues it may prefer to infect.
The researchers cited a recent unpublished lab study from Hong Kong indicating that Omicron preferentially infects the upper airway. Not only does it suggest Omicron is less lethal, but also that the many mutations confer “altered tissue tropism.”
However, saliva sampling is not as simple as it sounds. At Groote Schuur, patients were instructed to swab the inside of the mouth for a total of at least 30 seconds. They were also told not to eat, drink, smoke, or chew anything for at least 30 minutes beforehand.
While most of the COVID testing kits in the US and elsewhere rely on nasal swabs, any change to saliva sampling would take months – by which time Omicron may have been displaced by another variant.
Source: MedPage Today
