NHS could roll out all-in-one test for Covid, flu and RSV to ease winter pressures

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The UK is in talks to roll out an all-in-one test that can detect Covid, flu and RSV to help alleviate winter pressures facing the NHS.

It would work in the same way as a current Covid PCR test, with nasal swabs being taken before being sent off to the lab for analysis.

But instead of only looking for signs of the coronavirus, an additional winter panel would simultaneously look for a variety of viruses known to be in circulation.

Thermo Fisher Scientific – an American company based in Massachusetts which specialises in the manufacture and supply of scientific tools, tests and materials – has already made the kit and had it approved.

The firm produces the most popular Covid-19 PCR test in the UK and the winter model was created as an expansion of this.

“We realised we could develop more technology into the same assay,” Mark Stevenson, Executive Vice President and Chief Operating Officer at Thermo Fisher, told The Sunday Telegraph.

‘A three traffic light system’

“With the UK Government, we've been discussing not only having Covid but having flu in there [as well]. We've been talking about a winter panel with RSV, so the UK has been evaluating different assays.”

The UK Health Security Agency (UKHSA) refused to comment on the details of “procurement negotiations”.

Thermo Fisher’s Covid test TaqPath is used for around 60 per cent of swabs in the UK and works by recognising three genes found on the original Wuhan strain of the virus.

“It looks like a three traffic light system,” said Mr Stevenson.

“You get three green lights when all genes are detected. The software then reports a zero, or red light, if nothing was detected.

“It's very simple. If you get two out of three, you know you have Covid, that's how the diagnostic test is set up. If you have all three, that's also good.”

However, one specific mutation, called 69-70del, found on both the alpha and omicron variants, causes one of these probes to fail, so while the test still flags up a positive case, it only shows two of the three markers.

The marker that fails is on the S protein, also known as the spike, and hence the phenomenon is dubbed “S gene target failure” (SGTF), or colloquially, S gene drop-out.

Mr Stevenson said that when the alpha variant first emerged in Kent in late 2020 and this issue was first spotted, there was initial concern.

“[But] once we got the sequence of the alpha strain and we compared it to our assay design, we knew why that probe was failing,” said Mr Stevenson

“There was concern about that but once we confirmed the other two probes would still work, it then became very useful.

“By happenstance, this one mutation deletion causes this S gene drop-out and ours is the only assay that does that.”

As a result, the TaqPath test has been used as an early indicator system for new variants, being deployed in surge testing to speed up identification of new variants in the country as it can take up to two weeks to fully sequence a sample.

On Friday, the UKHSA said in its variant technical briefing: “The likelihood of SGTF depends on whether the Spike 69/70 deletion is common in circulating lineages.

“The dominant lineage in the UK is delta, accounting for 99.8 per cent of cases.

“Over the last 8 weeks (6 October onwards), only 0.056 per cent of sequenced delta genomes had the deletion.”

All tests on suspected omicron cases are TaqPath and any that show the S gene drop-out are provisionally thought to be omicron, and undergo rapid testing to confirm this is the case.

Thermo Fisher actually updated their test, moving away from the hit-or-miss S gene probe, and using eight markers instead of three to enhance reliability.

It is more robust against future mutations than its predecessor, but the UK opted not to upgrade their stocks because it does not have the quirk of being able to act as a de facto variant smoke signal.

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