Can Omicron evade detection from PCR and lateral flow tests for Covid-19?

Every day, scientists learn more about how Omicron may be evading traditional screening

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Concerns are being raised over whether lateral flow and polymerase chain reaction tests are less effective at detecting Omicron than they are at picking up other coronavirus variants.

Lateral flow tests, also called rapid antigen tests, have never been the gold standard when it comes to coronavirus testing.

But because they are cheap and give results in about 30 minutes, they are widely used, especially in the home.

Polymerase chain reaction tests are carried out in laboratories and, although more expensive, are typically more sensitive. This means they are less likely to produce a false negative result.

What are the concerns regarding LFTs and Omicron?

There have been instances of people repeatedly testing negative on LFTs despite having Covid-19 symptoms, only to test positive later after taking a PCR test.

Lateral flow tests use antibodies to detect viral proteins, or antigens, in the nasal passages. Their sensitivity is between about 40 per cent and 60 per cent.

In PCR testing, laboratories look for the virus’s genetic material of the virus. They heat and cool this material several times to encourage it to replicate.

Because of this difference in sensitivity, a series of negative LFTs followed by a positive PCR test is not, in itself, evidence that LFTs struggle to detect Omicron, as opposed to other coronavirus variants.

“They are less sensitive. It’s quite expected someone that will do a number of lateral flows that will be negative, and then have a positive PCR,” said Paul Hunter, a professor in medicine and infectious disease at the University of East Anglia in England.

What do officials say about LFTs and Omicron?

In a briefing document released on December 17, the UK Health Security Agency said “initial data” indicated that the LFTs used by the UK Test and Trace service were able to detect Omicron.

These tests use two or more antibodies that recognise distinct parts of the nucleocapsid, the protein shell that surrounds the pathogen’s genetic material.

According to the UKHSA document, the nucleocapsid in Omicron has “a single mutational difference from other Sars-CoV-2 variants”.

“As such, the general risk to LFD [lateral flow device] performance being impacted by Omicron was considered low,” the organisation said. Further laboratory analysis was under way, it said.

A paper published by South African researchers last week indicated that, with Omicron, mouth swabs are better than nasal swabs at picking up the coronavirus. With Delta, it is the other way around.

As a result, the researchers said, as Omicron becomes dominant, testing methods may have to be reviewed. Their paper has yet to be peer reviewed.

The US Food and Drug Administration said last week that rapid tests may be less able to detect Omicron.

“Early data suggest that antigen tests do detect the Omicron variant, but may have reduced sensitivity,” the FDA said.

Why might Omicron be showing up less often on LFTs?

Dr Michael Mina is a former associate professor at Harvard University and is now chief science officer of eMed, which supplies at-home test kits.

In mid-December, he shared his theory that the immune systems of vaccinated people and those who previously had the virus react quickly to a new infection.

This causes symptoms to develop earlier, before the amount of viral matter is sufficient to be detected through lateral flow testing.

Another theory, also unconfirmed, is that Omicron can cause symptoms even when levels of the virus in the nasal passages are below those typically detected by LFTs.

If this is the case, it would be even more crucial that anyone displaying Covid-19 symptoms isolates, because they could be infectious even if their LFT is negative.

How much should we rely on lateral flow tests?

Dr Al Edwards, an associate professor in the school of pharmacy at the University of Reading, England, said LFTs have always missed some positive cases.

“There may be some differences with the ability of lateral flow tests to pick up the variants, but they never have been able to pick up every case,” he said.

They are, he said, “very, very reliable” as a red flag – meaning that if you test positive, you have the virus and could infect others – but have never been reliable as a green flag, because they cannot confirm that you do not have the virus and are not infectious.

“There’s been advice you should use them before meeting people,” he said. “You should use them, but they can never prove you’re safe.”

If a person plans to meet a friend who is not likely to be vulnerable to Covid-19, he indicated that it may be sensible to take an LFT beforehand and to go ahead with the meeting if the result is negative.

On the other hand, if a person is thinking of seeing a person who is more medically vulnerable, such as an elderly relative, they may not want to rely on an LFT in the same way.

Prof Hunter said people with a negative LFT result were “probably not that infectious” because the levels of the virus were likely to be lower.

Dr Edwards said: “Even if they have the virus, they’re probably not shedding a lot, so they’re probably not infectious.”

Can Omicron evade PCR nasal swab tests?

LFTs are not the only tests whose effectiveness appears to be affected by the emergence of Omicron.

While the WHO said at the end of November that “the widely used PCR tests continue to detect infection, including infection with Omicron”, subsequent analysis has found exceptions.

The FDA identified certain tests that are likely to fail to identify a positive case when the person is infected with Omicron. This is because the part of the virus’s genetic material that these particular tests look for has changed.

In an online update released this week, the FDA highlighted a PCR nasal swab test called Revogene Sars-CoV-2, produced by Meridian Bioscience, as “being expected to fail to detect Omicron”.

This is because the test has a single target in the genetic material of the coronavirus, some of which has been deleted in Omicron. The FDA recommends that this test not be used until the problem is resolved. Its guidance is specifically for tests for which it had previously authorised use.

Another test, produced by Tide Laboratories, had the same issue, but modifications so that there is more than one genetic target mean that it should now be able to detect Omicron.