Scientists have identified a “stealth” version of Omicron which cannot be distinguished from other variants using the PCR tests that public health officials deploy to gain a quick picture of its spread around the world, scientists have said.
The stealth variant has many mutations in common with standard Omicron, but it lacks a particular genetic change that allows lab-based PCR tests to be used as a rough and ready means of flagging up probable cases.
The variant is still detected as coronavirus by all the usual tests, and can be identified as the Omicron variant through genomic testing, but likely cases are not flagged up by routine PCR tests that give quicker results.
Researchers say it is too early to know whether the new form of Omicron will spread in the same way as the standard Omicron variant, but that the “stealthy” version is genetically distinct and so may well behave differently.
The stealth variant was first spotted among Covid virus genomes submitted in recent days from South Africa, Australia and Canada, but it may already have spread more widely. Among the few dozen cases identified so far, none are in the UK.
The discovery came as the prime minister told the cabinet that Omicron appeared more transmissible and officials conceded this would have consequences for its impact, and the likelihood of further restrictions being needed.
The UK Health Security Agency said a further 101 confirmed cases of the Omicron variant had been reported in the UK on Tuesday. This brings the total number of UK cases to 437. Of the 101 new cases, one was confirmed in Wales while there have been no new cases reported in Northern Ireland.
At the cabinet meeting on Tuesday morning, also attended by the government’s chief scientific adviser, Patrick Vallance, and England’s chief medical officer, Chris Whitty, Johnson told ministers the “early indications” were that Omicron was more transmissible than the existing dominant variant, Delta, a No 10 statement said.
Johnson’s spokesperson said the next contingency step remained the potential imposition of the so-called plan B, which would introduce vaccine certification and instructions to work from home where possible.
While the government would “want to make sure that parliament has its say” on any new rules, the spokesperson said, ministers had the existing powers to impose plan B restrictions unilaterally, for example if they were needed during the Commons Christmas recess.
Despite such considerations, the spokesperson confirmed that for now, official advice remained that people should return to workplaces if they could, albeit with consideration of mitigations such as ventilation and testing. He said: “We are encouraging businesses to bring back people into the office, in line with the guidance.”
The discovery of the new form of Omicron prompted researchers to split the B.1.1.529 lineage into standard Omicron, known as BA.1, and the newer variant, known as BA.2. Prof Francois Balloux, director of the University College London Genetics Institute, said that 42 or roughly 6% of the 709 Omicron genomes submitted to the Gisaid genome database were BA.2.
“There are two lineages within Omicron, BA.1 and BA.2, that are quite differentiated genetically,” he said. “The two lineages may behave differently.”
Scientists use whole genome analysis to confirm which variant has caused a Covid infection, but PCR tests can sometimes give an indication. About half of the PCR machines in the UK look for three genes in the virus, but Omicron (and the Alpha variant before it) test positive on only two of them. This is because Omicron, like Alpha, has a genetic change called a deletion in the “S” or spike gene. The glitch means that PCR tests that display so-called “S gene target failure” are highly suggestive of Omicron infections.
Informally, some researchers are calling the new variant “stealth Omicron” because it lacks the deletion that allows PCR tests to spot it.
One major unknown is how the new variant emerged. While it falls under Omicron, it is so genetically distinct that it may qualify as a new “variant of concern” if it spreads rapidly. To have two variants, BA.1 and BA.2, arise in quick succession with shared mutations is “worrying” according to one researcher, and suggests public health surveillance “is missing a big piece of the puzzle”.