Maps show rapid spread of new Covid sub-variant in the United Kingdom

A fortnight ago, the new Omicron sub-variant was practically non-existent in the UK. Now there are hotspots all over the country.

BA. 2 infections in the UK, in the week leading up to January 1, January 8 and January 15, respectively. The darker the colour, the more cases. Picture: The Wellcome Sanger Institute

Maps showing the spread of a new Covid sub-variant in the United Kingdom have added fuel to scientists’ suspicions it is more infectious than Omicron.

BA. 2 is a sub-variant of Omicron, sharing many of that variant’s characteristics, but with several different mutations.

It’s been called “Omicron’s sister”, “Omicron’s brother” and “Omicron’s son”. Whichever family member you prefer, you get the point: it’s closely related to Omicron.

Speaking to Today on Thursday morning, epidemiologist Nancy Baxter went for “cousin”.

“I don’t want to frighten people too much,” Professor Baxter said.

“But there is a variant – they call it the ‘son of Omicron’, but it’s more of a cousin – it’s a variant related to Omicron. It is spreading. We are particularly seeing it in Denmark. We don’t know if it’s going to be a problem yet.

“But it looks like – if people can believe it – it looks like it might be more contagious than Omicron.

“So if it gets here, it may extend our waves, so our wave may take longer to get out of. But we don’t know enough yet.”

The BA. 2 sub-variant has now been detected in more than 40 countries, though it is most prevalent in Europe. It now accounts for almost half of all Covid cases in Denmark, for example, where it has overtaken the original Omicron variant.

That has not yet happened in the UK. But the maps below show it is very much on the rise.

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BA. 2 infections in the UK, in the week leading up to January 1, January 8 and January 15, respectively. The darker the colour, the more cases. Picture: The Wellcome Sanger Institute

The maps were created by the Wellcome Sanger Institute, which has been tracking the spread of Covid variants in the UK.

As you can see, BA. 2 was practically non-existent in the UK at the start of the month. A fortnight later, there are hotspots across much of the country.

The institute estimates there were 186 cases of the sub-variant by January 1, about 1700 in the following week and 4400 in the most recent week of data, ending on January 15.

(Note that these are estimates, not confirmed cases. The official government figures only include several hundred BA. 2 infections so far. But not all cases are detected.)

The original Omicron variant remains dominant for now, accounting for about 98 per cent of all UK Covid cases. But in the week between January 8 and 15, BA. 2 quietly slid into second place, overtaking the older Delta variant.

In that period, the once-dominant Delta dropped from 1.1 per cent of cases to 0.5, while BA. 2 rose from 0.2 to 0.8.

At the moment, those numbers sound tiny. But remember, BA. 2 only arrived in the UK a matter of weeks ago.

On Friday, the UK Health Security Agency (UKHSA) said 426 BA. 2 cases had been detected, with the earliest dating back to December 6.

It said the sub-variant had been formally designated a “variant under investigation”, meaning it will be observed and analysed. According to UKHSA, early indications are that it’s more infectious than Omicron, though further data is needed.

“It is the nature of viruses to evolve and mutate, so it’s to be expected that we will continue to see new variants emerge,” said Dr Meera Chand, the agency’s incident director.

“Our continued genomic surveillance allows us to detect them and assess whether they are significant.”

Health workers at a Covid test clinic in Brisbane. Picture: Dan Peled/NCA NewsWire

Tracking the ‘stealth’ variant

Tracking the spread of BA. 2 is particularly challenging, as it’s missing a key mutation which allows PCR tests to easily identify regular Omicron cases. To be specific, the UKHSA says it “does not have the spike gene deletion at 69-70 that causes S-gene target failure”.

This has led some scientists to label it “stealth Omicron”.

All you need to understand is that the “S-gene target failure” is what easily distinguishes Omicron from other variants, and it’s made Omicron relatively simple to track. In the BA. 2 sub-variant, that S-gene target failure no longer happens.

So, while PCR tests will obviously still detect BA. 2 cases and identify them as Covid, they might appear to be cases of the Delta variant, rather than Omicron.

“It’s not that the test doesn’t detect it. It’s just that it doesn’t look like Omicron,” pathologist Dr Wesley Long told The Associated Press.

“Don’t get the impression that ‘stealth Omicron’ means we can’t detect it. All of our PCR tests can still detect it.”

The good news is that BA. 2 appears to be no more severe than vanilla Omicron, in terms of its potential to cause hospitalisation or death.

“Very early observations from India and Denmark suggest there is no dramatic difference in severity compared to BA. 1 (Omicron),” Dr Tom Peacock, from London’s Imperial College, said last week.

“So how worried should we be? Those working in sequencing/surveillance should definitely be keeping a close eye on BA.2. Personally, I’m not sure BA. 2 is going to have a substantial impact on the current Omicron wave of the pandemic.

“Several countries are near or even past the peak of BA. 1 waves. I would be very surprised if BA. 2 caused a second wave at this point.

“Even with slightly higher transmissibility, this absolutely is not a Delta to Omicron change, and instead is likely to be slower and more subtle.”

In Denmark, BA. 2’s rise to become the prevalent strain has not derailed the government’s plan to lift all remaining Covid restrictions at the start of February.

Health officials there do believe it is more infectious than Omicron.

“There is no evidence that the BA. 2 variant causes more disease, but it must be more contagious,” Denmark’s Health Minister, Magnus Heunicke, said this week.

According to the nation’s infectious disease body, the Statens Serum Institute (SSI), preliminary data suggests BA. 2 is “1.5 times more infectious” than Omicron.

“There is some indication that it is more contagious, especially for the unvaccinated, but that it can also infect people who have been vaccinated to a greater extent, the SSI’s technical director, Tyra Grove Krause, said at a briefing.

Again, the Danish officials stressed that BA. 2 did not appear to be more severe.