Can Omicron variant, Stealth Variant, evade RT-PCR testing?

March 3, 2022
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Ba.2 Variant

Can Omicron’s sub-variant, ‘BA.2’, also known as the ‘Stealth Variant’ evade RT-PCR testing?


A new coronavirus variant has been discovered, sparking concern amongst the scientific community. Omicron’s sub-variant BA.2 was first detected in Europe in late January and has since spread across the world, becoming the dominant strain of all new COVID-19 infections in at least 18 countries and counting – and it has also been found in every U.S. state.

Despite the fact that variant BA.2 is spreading at such a rapid rate, with one study in Japan stating that this strain spreads up to 30% more easily than the original Omicron variant, it has been dubbed ‘Stealth Omicron’.

It is titled as such due to the fact that it doesn’t show up on PCR-tests as an S-gene target failure, in the same way that Omicron does. Essentially, it lacks the omission of the spike gene, which is the contagious protein that is responsible for mutation.

In this way, PCR tests are not designed to detect this variant, although this is not to say that PCR tests do not show positive readings for coronavirus from Stealth Omicron.

Laboratory testing will still show a result for COVID-19, it is just that further genetic sequencing will need to be done to the sample, to determine whether or not this is the Stealth variant. So, although RT-PCR tests are considered the gold standard for detecting COVID-19 (with research showing that in laboratory settings the tested RT-PCRs achieved 100% sensitivity on positive samples, and more than 96% specificity on negative tests), when it comes to the ‘Stealth Variant’, this becomes much more difficult to name the variant, as it is not made up of the same protein spike deficiencies that a PCR test is capable of detecting.

Dr Wesley Long, a pathologist at Houston Methodist in Texas explains this best to the Associated Press, stating that, “It’s not that the test doesn’t detect it; it’s just that it doesn’t look like Omicron”.

However, it is important to note that although RT-PCR tests detect stealth Omicron as a subvariant strain of coronavirus, it is somewhat difficult to detect BA.2 through throat or nasal swabbing. This is because, unlike the coronavirus strains that we know, BA.2 infects the gut, and not the lungs, hence traces of coronavirus are not likely to be found in the mouth or nose for testing. That is why it is essential to look out for the signs and symptoms and to get tested and self-isolate, even if you come back with a negative result, to avoid putting others at risk.

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What are the symptoms to look out for?

This is still being researched, but for the time being Omicron BA.2 is associated with the following 6 gut-related illnesses: bloating, abdominal pain, nausea, vomiting, heartburn and the final one being diarrhea, although this is less common. Two additional symptoms have been announced this week following reports and added to the potential cues to watch out for – dizziness and fatigue.

To reiterate, if you have any of these symptoms, you might not necessarily test positive for coronavirus, even if you do have it, so it is advised that you stay home until you have fully recovered regardless.

Who is more likely to catch the BA.2 variant?

At the time of publishing this article, Denmark was one of the countries that has had the highest recorded rate of Omicron stealth variant, with this being the dominant lineage of coronavirus across the country, so a lot of the following BA.2 related research hails from there. According to one of their studies, reinfections are almost four times more likely for those that have recovered from the Delta variant, versus those that had fallen ill with Omicron. This is largely due to BA.2 being a subvariant of Omicron, so people whose immune systems have already had to deal with one variant, will be more capable of combating another.

So, although stealth Omicron is said to be much more contagious than any other previously known strain of coronavirus, there is good news here. It appears that those who have already had Omicron and have been fully vaccinated seem to have enough protection against the BA.2 variant for the time being, although research in this field continues.

This says a lot, considering the fact that, in the last week of February, the Centers for Disease Control and Prevention estimated that the stealth variant was causing 8% of all new COVID-19 infections, at a rate that doubled (and looks like it is set to do so, going forward) every week.

What you can do to protect yourself against stealth Omicron:

Hospitalisations and deaths remain low but it is essential to continue to be careful with a lot still unknown about the stealth variant. In order to remain as safe as possible, wearing a face covering is recommended when in crowded places, ensuring you have both doses of vaccines, and if you do have any symptoms, make sure to take a test.

Ongoing Research:

Despite the clear differences between the other variants and BA.2, WHO’s Technical Advisory Group on SARS-CoV-2 Virus Evolution states that this must be regarded as a distinct sublineage of Omicron by public health authorities and may be a variant of concern so must continue to be monitored.

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