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There May Be A Better Way Of Detecting Omicron


Dr. Katie Spalding

Katie has a PhD in maths, specializing in the intersection of dynamical systems and number theory.

Freelance Writer


Nasal swabs are the standard way to test for COVID-19 - but Omicron may have changed the game. Image: Andrey_Popov/Shutterstock

To paraphrase Mrs Gump: COVID-19 is like a box of chocolates. You never know what you're gonna get. For some people, it can be a debilitating disease that lasts for months on end – while others never even know they had it. For those lucky individuals, the nastiest bit of the disease was the swab up their nose to diagnose them, which, let’s face it, definitely sucks, but is probably better than an ICU stay with a potentially fatal virus.

Well, bad news folks (or good news if you’re a nasty lil freak, which we know you are): it looks like the Omicron variant may double the number of swabs we have to endure. A new study (yet to be peer-reviewed) on the preprint server MedRxiv suggests that a nasal swab may not be enough to confirm a case of the new strain: while a swizzle up the schnoz was enough for a positive result in around six out of every seven cases of Omicron, saliva samples beat them hands-down with a 100 percent accuracy rate.


“These findings suggest that the pattern of viral shedding during the course of infection is altered for Omicron … resulting in improved diagnostic performance of saliva swabs,” explain the study authors. “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.”


Now, a saliva test may sound nicer than a nasal swab, but the researchers point out that collecting a sample is no simple task – and it takes more than half an hour to do properly.

“Participants should not have had any food, drink, tobacco or gum in the 30 minutes preceding saliva swab collection,” the study notes, and once ready for testing, the first step is to “cough 3-5 times.” Swabs were then taken from “the inside of both cheeks, above and below the tongue, on the gums and hard palate. A minimum swabbing duration of 30 seconds was required.”

The study, while only a preprint, has caused something of a stir already – and for good reason. People have already noticed a difference in their test results depending on whether they swab just their nose or their throat as well, with the latter often producing a positive result that the former missed.


Why the difference in methodology? According to immunologist and epidemiologist Michael Mina, who was not involved in the study, it likely has something to do with Omicron’s increased transmissibility and slightly different pathology.

“Symptoms are starting [very] early [with] Omicron,” he tweeted earlier this week as awareness of the effectiveness of throat swabs started to increase across social media. “This means that there is a chance the virus isn’t yet growing in the nose when you first test.”

“[The] virus may start further down,” he explained. “Throat swab + nasal may improve [the] chances a swab picks up [the] virus.”

So what does this mean for the future of testing? The study participants were tested with PCR tests – the most sensitive option, which test for the presence of virus RNA. For somebody currently infected with COVID-19, they are the most accurate diagnostic tool available, but, in the US at least, they are heavily weighted towards nasal swab tests.


For Mina – and many others – the answer is simple: stick the swab down your throat as well. It’s “not FDA authorized to do throat + nasal swabs,” he pointed out, and it “may increase rates of false positives slightly. But it's most likely to be most sensitive.”

It’s also standard in some other countries – like the UK, where a throat swab is advised by the NHS for PCR tests along with a nasal swab. So with the caveat that this is not medical advice – here’s a video showing you how to do it.

“Strictly speaking, [US PCR tests] weren’t tested this way,” tweeted healthcare entrepreneur and immunology PhD Paul Bleicher. “But given the prominence of Omicron in the upper airway, I am going to do a throat swab followed by 15 sec per nares from now on.”

“Makes sense to me,” he added. “Not advice for you.”


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