People calling it “stealth Omicron” because it doesn’t have the deletion that PCR tests can use to find it.

In analyses from South Africa, Australia, and Canada, a novel variant of the strain was discovered. However, it is possible that it has already spread to other countries.

Scientists claim to have discovered a “stealth” strain of Omicron that cannot be recognized from other strains using the PCR testing that public health professionals use to get a fast picture of the virus’s global spread.

The stealth strain shares many mutations with ordinary Omicron, but it lacks a specific genetic alteration that enables lab-based PCR testing to be utilized as a rough and ready method of flagging up potential infections.

The new type is still recognized as coronavirus by all standard tests and can be defined as the Omicron variant through genomic testing, but probable cases are not found by ordinary PCR assays that provide faster findings.

According to scientists, it is too soon to tell if the new form of Omicron will spread in the same way as the typical Omicron type, but the “stealthy” copy is genetically separate and may behave differently.

The stealth mutant was discovered in recent Covid viral genome submissions from South Africa, Australia, and Canada, although it may have already spread to more countries.

The finding of the novel type of Omicron prompted scientists to separate the B.1.1.529 lineage into two parts: normal Omicron (BA.1) and the newer version (BA.2).

“There are two lineages within Omicron, BA.1 and BA.2, that are quite differentiated genetically,” said Prof Francois Balloux, the director of the University College London Genetics Institute.

“The two lineages may behave differently.”

Whole genome analysis is done by scientists to determine which variant caused a Covid infection, but PCR tests can sometimes provide a hint. Approximately half of the PCR machines seek for three genes in the virus, but Omicron (and the Alpha variant before it) only test positive on two of them. This is due to the fact that Omicron, like Alpha, has a genetic alteration known as a deletion in the “S” or spike gene. Because of its bug, PCR tests that show “S gene target failure” is very predictive of Omicron infections.

The origins of the new strain remain a mystery. While it is classified as Omicron, it is genetically unique enough to be considered a new “variant of concern” if it spreads quickly. According to one researcher, the emergence of two variants, BA.1 and BA.2, in short succession with shared mutations is “worrying,” and shows that public health surveillance “is missing a key piece of the puzzle.”

And as it lacks the deletion that permits PCR testing to detect it, some researchers have dubbed the new type “stealth Omicron.”

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