Analysis by Dr Nicholas Davies of the London School of Hygiene and Tropical Medicine (LSHTM) suggests that there were already around 60 cases in England as of November 28, but only 22 have been reported by the UK Safety Agency sanitary (UKHSA).
The data, provided to LSHTM by NHS Test and Trace, shows that the number of samples likely to be omicron dropped from around 0.1% to 0.3% in five days.
Figures are based on infections detected by positive polymerase chain reaction (PCR) tests. About half of laboratories in England use some type of PCR test that can give an early indication that the infection is omicron.
The test looks for three genetic targets found in the coronavirus, but in omicron the virus has mutated so much that one of the targets is missing, known as s gene target failure (SGTF).
Dr Davies, who is a member of SPI-M, said on social media: “Since omicron causes SGTF, while the otherwise globally dominant delta variant does not, these” excess’ of SGTF are most likely cases of omicron, at least some of which have yet to be confirmed by sequencing.
“By the way, these SGTF cases are concentrated in areas of England similar to the omicron cases that have been confirmed so far.
“It’s not a perfect signal. Some rare lines carry SGTF without being a new variant, and sometimes SGTF can occur simply because the viral concentration on a swab is low. So, in the graph above, the low level of SGTF between August and mid-November is just background noise.
“But over the last five days (November 24 – 28), SGTF’s level has gone from its usual level of 0.1% to around 0.3%. That’s not a huge number of cases – it’s about 60 more cases of SGTF than we would expect to see in this data given the background prevalence of around 0.1%. ”