Omicron & throat swabs: What type of testing is best?

Early research suggests that the diagnostic tests most commonly used in the U.S. may not be the most effective at detecting the omicron coronavirus variant.  

Amid surging demand for rapid antigen tests, a small real-world study suggests they may not be a reliable tool to curb COVID-19 transmission. Preliminary results published Jan. 5 in MedRxiv indicated people with the omicron variant were contagious for several days before rapid antigen tests detected a positive result. On Dec. 28, the FDA said rapid antigen tests may have reduced sensitivity detecting the variant.  

Some preliminary findings suggest that omicron virus particles may appear in the throat before the nasal passages, according to USA Today. In a study published Dec. 24 in MedRxiv, researchers examined the performance of saliva tests for the delta and omicron variants. The study, which has yet to be peer reviewed, found saliva swabs may be better at detecting omicron than nasal swabs. The percent agreement of saliva swabs and mid-turbinate swabs was 71 percent and 100 percent for the delta variant. In comparison, omicron variant saliva and mid-turbinate swabs had 100 percent and 86 percent agreement.  

Some Americans are using at-home tests to swab both the back of their throat and their nose. However, experts are urging tests be used as directed and to not throat swab for now.  

Becker's spoke with Michael Blaivas, MD, emergency department physician and chief medical officer at Anavasi Diagnostics, a Seattle-based medical device company, about the potential changes in testing. A main challenge right now, according to Dr. Blaivas, is that many tests are formulated for samples from the throat or nose, but not both. Abundant literature and clinical experience indicate that getting a good throat sample is also more challenging than a lower nasal sample, increasing sampling error rates and thus false negative results, Dr. Blaivas said.

Data indicates throat swabs are less accurate at detecting COVID-19 than nasal swabs, Dr. Blaivas said. However, omicron has nearly 50 mutations and expresses itself differently than past variants. Dr. Blaivas cited early data that suggests higher viral loads in the mouth/throat and saliva than previous variants when compared to the nose. However, he said there isn't good data available yet, as almost everything has not been peer reviewed or properly published in a medical journal. Thus, it may turn out that there is no difference in viral loads, the CMO said.

There is existing data, prior to omicron, that combining throat and nose sampling gives better accuracy than either alone. If it's proven that omicron leads to greater viral loads in the mouth than the nose, testing may have to be adjusted. Companies will need to evaluate and verify test performance with throat sampling of their nasal swabs and then apply for FDA authorization, a process that can take many months, Dr. Blaivas said.

If omicron does result in higher viral loads in the mouth than nose, it will decrease the ability to detect cases early on, when less virus is being shed. This is compounded by the fact that rapid tests are less accurate than molecular tests. Broadly speaking, since vaccination doesn't necessarily prevent infection and infection spread, the earliest possible detection of COVID-19 is the best weapon for fighting the spread of omicron, Dr. Blaivas said.  

However, the next dominant variant may not be like omicron and may express low levels of virus in the throat and saliva, Dr. Blaivas said. If companies are in the middle of switching production and supply to mouth swabs, will they be able to switch back rapidly enough? Future tests should be designed to deal equally well with mouth and nasal sampling, Dr. Blaivas concluded.


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