Covid-19 tests versus Omicron

The new variant might be able to dodge one of the PCR tests authorised in the US, the FDA says.

The FDA yesterday named the first authorised Covid-19 test that might be unable to detect the Omicron variant. The DTPM Covid-19 RT-PCR assay, developed and sold by the small private group Tide Laboratories, looks at only one region of the virus’s N gene, which is mutated in Omicron.

Assays that focus on a single genetic target are logically more vulnerable to evasion by mutated Covid-19 strains. It is not known exactly how many single-target tests the FDA has authorised, but it is very possible that Tide’s might not be the last that the FDA highlights.

The agency has not specifically warned against using Tide’s test. Instead it suggested that healthcare workers consider repeat testing with a different authorised molecular diagnostic – one that uses different genetic targets – if Covid-19 is still suspected after receiving a negative result with Tide’s product.

The assay obtained US emergency authorisation in June 2020, before any mutated variants of concern had been identified. It is not believed to be used for high-volume testing, but the FDA provided a list of the 33 US sites where it is in use. 

Turn on, tune in

Separately, the agency detailed a number of other diagnostics which might be able to distinguish Omicron from the prevalent Delta strain. These tests focus on several genetic targets, one of which is a region of the S gene. In Omicron, but crucially not in Delta, this region is mutated in a particular manner which causes an S-gene drop out, also called an S-gene target failure. 

Consequently, when run on an Omicron sample, these tests will still detect the virus thanks to the other, unmutated targets; the FDA spells out that their overall sensitivity should not be affected. But the drop out means they can pick Omicron out from Delta.

The best known of the tests theoretically capable of this are Thermo Fisher Scientific’s TaqPath PCR tests, but assays from companies including Verily and Helix are also on the FDA’s 27-strong list. The agency identified these diagnostics based on initial bioinformatics analyses, and warned that they may not yet have been directly tested against Omicron in a lab.

It is not clear how sales of these assays have been affected by the publication of this list, which first occurred last Friday. It seems possible that they might become more popular, as labs seek to track the transmission of Omicron.

As for Tide Laboratories, the consequences of its test being specified as potentially unable to detect Omicron would seem to be muted, given that the FDA has not warned against its use. Even so, many labs might opt to use other diagnostics to be on the safe side. This is a distinction other test manufacturers will be keen to avoid.

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