If Omicron is the dominant variant in UK, why is the number of confirmed cases so low?
The headlines have been unambivalent: Omicron is now the dominant variant in the UK and has been for close to a week.
By contrast, the number of confirmed Omicron cases seems extraordinarily low: the UK Health Security Agency (UKHSA) reported 15,363 new Omicron cases across the UK on 20 December, equivalent to just 17% of the cases reported by government the same day.
So with all the fears around this new variant and its potential affects on the health system, why is the total number of confirmed cases so low?
Confirmed Omicron cases are a sample of an already incomplete figure
The UK reported an average of 88,000 Covid cases each day in the past week (to 21 December). However, only a subset of those cases are being picked up through PCR tests – the type carried out in an NHS walk-in centre – and it is only PCR tests that allow labs to check what kind of variant a person has.
What is more, not all UK laboratories have the capability to carry out these checks. Just four provide the UKHSA with data on variant types.
In the seven-day period to 15 December about 60,000 positive PCR checks were being processed each day, with roughly half making their way to these four labs for sequencing.
What do the scientists look for? Laboratories target three genes contained within the virus, the S-gene and two others (the nucleocapsid, or inner area, gene or N2-gene and the envelope, or outer shell, labelled the E-gene).
Omicron’s S-gene has a small deletion in it that makes the S-gene undetectable. So when testing for Omicron, the PCR tests that make it to the lab floor are genome sequenced to see if the S-gene can be picked up. Samples where the S-gene is not detected, known as S-gene dropout or Sgene target failure are currently being treated as a proxy for Omicron cases, according to a spokesperson for the UKHSA.
The latest available data, which covers all partially sequenced data to 18 December, indicates that just over 16,000 tests of a total of almost 22,500 sequenced lacked the S-gene: indicating that 72% were caused by Omicron.
Although it is very likely these cases are indeed Omicron, a further process has to be undertaken to confirm this. But that can take up to 10 days, meaning the confirmed figure is smaller than the proxy and far smaller than the true level of cases.
How fast is the situation changing?
The proportion by which the variant makes up the majority of the sample tested has risen rapidly in recent weeks.
On 1 December 0.5% of a sample of PCR tests were found to lack the Sgene, the first indication of Omicron. Within 10 days these cases were making up 20% of the sample, rising to more than half the sample on 14 December. The latest figures put that closer to three-quarters.
Are the cases spread evenly across the regions of the UK?
When looking at a regional level, the prevalence of the variant, where Sgene dropout has been detected, varies dramatically. As of 18 December, in London, 89.7% of PCR test samples had S-gene target failure, compared with 47.7% in the north-east.
The trouble is, given the uneven geographic spread of the labs that can carry out the required sequencing, there are a number of blind spots that mean we do not have a full understanding of the spread.
According to Dr Simon Clarke, an associate professor in cellular microbiology at the University of Reading, the existence of regional “cold spots” means it is hard to tell the true prevalence of Omicron.
“The labs that are not doing the test to pick up a S-gene target failure won’t be able to tell you in that geographical region what the proportion of Omicron is.”
What does the data indicate about the true level of Omicron in the UK at present?
Because not every test is sequenced and there are potential holes in the geographic spread, it is not possible to give a true indication of Omicron in the UK at present.
All we can do is make an educated guess based on other available data we have to hand.
The latest government figures show that, since 1 December, 2.3m Covid cases have been detected in the UK, not just through PCR tests but all test types.
If we apply the percentage of daily sampled cases, which the UKHSA thinks likely to be Omicron, then the true number of Omicron cases recorded in the UK to date would be in the region of 400,000, a far cry from the official “confirmed” tally of 60,508.
However, even that may be an underestimate as it excludes any Covid cases that have not been picked up by the UK’s testing regime including asymptomatic cases or unreported lateral flow tests.
However, all such estimates are just that, due to the small number of labs in the UK undertaking these tests and the geographical uncertainty.
“Assuming that the testing labs haven’t switched to doing more S-gene target failure type stuff, it tells us that it is an inaccurate picture. The amount could be overestimated, just as much as it could be underestimated,” Clarke added.