Saliva swabs detected Omicron variant more accurately compared to the nasal swabs, according to a study from South Africa, published as a preprint on medRxiv.¹

In this study, researchers from the University of Cape Town enrolled 382 acutely symptomatic, non-hospitalized patients who came for Covid-19 test. The data was collected between August and December 2021. Nasal (mid-turbinate) and saliva swabs were collected for RT PCR testing. Based on gene target failures (probable) on RT PCR and whole genome sequencing (confirmed), the positive samples were grouped as either Delta or Omicron. The local dominant circulating variant at the time of sample collection was also used to segregate the samples (possible).

Thirty-one samples tested positive for delta variant; 74% as probable due to RdRp gene target failure, 23% as possible due to the dominant circulating variant at the  time of sample collection and 3% as confirmed by whole genome sequencing. Similarly, 36 samples were positive for Omicron; 75% as probable due to S gene target failure, 17% as possible due to the dominant circulating variant at the time of sample collection and 8% as confirmed by whole genome sequencing. “For the delta variant, no samples tested saliva swab positive only, while for the Omicron variant, no samples tested nasal midturbinate swab positive only”.

Data analysis showed that nasal swabs were more accurate than saliva samples in detecting delta variants with 100% positive percent agreement compared to 71% for saliva swabs. However, for Omicron, a reversal in these numbers was observed. Saliva samples had 100% positive percent agreement for Omicron, while this number was 86% for nasal swabs.

The nucleocapsid (N) gene was taken as the reference as both the Delta and Omicron variants are not associated with N gene target failure. The differences (mean) in the N gene Ct value between the nasal and saliva samples were 5.2 and 1.5 for delta and omicron respectively.  The median time from symptom onset to positive test for delta was 3 days (range 1-10) and in Omicron cases, this duration was 2 days (range 0-7).

However, the authors also caution that the saliva sample is not collected simply by spitting into a cup. Instead, to obtain the saliva sample, patients were asked to swab the inside of the mouth (covering both cheeks, gums, hard palate and above and below the tongue) for a minimum duration of 30 seconds. They were also instructed to avoid eating, drinking or smoking anything for at least half an hour prior to collecting the sample.

This study has compared the efficacy of saliva and the standard nasal swabs in detecting the Delta and Omicron variants. It has demonstrated that saliva swabs and not nasal swabs were more accurate in detecting Omicron. This has been attributed to possible altered tissue tropism of Omicron consequent to the large number (more than 50) of mutations. Recently, a laboratory study from Hong Kong has shown that the new Omicron SARS-CoV-2 variant can infect the airways “faster and better” than the lungs. Viral replication was 70 times higher in the human bronchus compared to that in the lungs, where the replication was more than 10 times lower.

The authors concluded 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”. In view of these findings, will the nasal RT PCR continue to be the appropriate diagnostic test if the Omicron becomes the globally dominant strain? It is certainly showing all signs of becoming so, given the increasing numbers of Omicron cases across countries.

Reference

1. Marais G, et al. Saliva swabs are the preferred sample for Omicron detection. medRxiv Posted December 24, 2021; DOI: 10.1101/2021.12.22.21268246.