A HIGHLY contagious Covid variant which has spread rapidly in the US is now on the rise in Scotland.

The strain, known as BA.2.12.1, exploded in the states of New York and New Jersey back in April - where it is now responsible for over 80 per cent of infections - and became the dominant Covid variant across the US as a whole in May.

Now data suggests that it is helping to drive the uptick in cases in Scotland, where it appears to be more prevalent compared to the rest of the UK.

"It seems to be increasing more in Scotland than in England and Wales - why, we don't know," said Professor Rowland Kao, chair of veterinary epidemiology and data science at Edinburgh University.

HeraldScotland: An estimated one in 30 people in Scotland had Covid in the most recent weekly surveillance compared to one in 50 in England (Source: Office for National Statistics)An estimated one in 30 people in Scotland had Covid in the most recent weekly surveillance compared to one in 50 in England (Source: Office for National Statistics)

BA.2.12.1 is an offshoot of Omicron BA.2, but it has an estimated 27% growth advantage over its parent.

It is unclear whether it will outcompete the BA.4 and BA.5 variants which are now dominant in England, Wales and Northern Ireland, and on the rise in Scotland.

Like BA.2 - and the more virulent Delta variant which spread from India last summer - BA.2.12.1 is an S-gene positive form of Covid.

The S-gene is one of three coronavirus genes which can be picked up during PCR testing.

READ MORE: Herd immunity and the threat from New York's 'son of BA.2' Covid variant

By contrast, the BA.4/5 Covid variants are S-gene negative, like the original Omicron BA.1 strain.

This enables scientists to track patterns of infection relatively accurately based on the S-gene, without requiring more time-consuming genomic sequencing.

According to the most recent surveillance by the Office for National Statistics, in the week ending June 11 slightly over half of all Covid cases in England, Wales and Northern Ireland were "compatible with BA.1, BA.4 or BA.5" - meaning they were S-gene negative.

The vast majority of these will be BA.4 and BA.5 since BA.1 has all but vanished.

HeraldScotland: In Scotland, S-gene positive Covid strains are on the rise (pointing to the spread of BA.2.12.1) and currently outnumber S-gene negative strains on a ratio of around 2:1In Scotland, S-gene positive Covid strains are on the rise (pointing to the spread of BA.2.12.1) and currently outnumber S-gene negative strains on a ratio of around 2:1

In Scotland, the picture is different.

Here, S-gene positive cases - that is, those "compatible with BA.2" - outnumber S-gene negative ones on a ratio of around 2:1. However, both are on the rise.

Prof Kao said it is probable that BA.2.12.1 is driving the increase in S-gene positive infections in Scotland since it is more transmissible than BA.2, and because genomic surveillance data for the UK as a whole also shows a clear downward trend in BA.2 prevalence.

According to the respected CoVariants.org website, BA.2 has shrunk from making up 77% of all sequenced Covid cases in the UK in the second half of May, to 44% in the first half of June.

HeraldScotland:

HeraldScotland:

HeraldScotland: The percentage of sequenced variants which are BA.2.12.1 is increasing in the UK, along with BA.4/5, while Omicron BA.2 is receding and BA.1 has all but disappeared (Source: CoVariants.org; NB: 21K = BA.1; 21L = BA.2; 22A = BA.4; 22B = BA.5; 22C = BA.2.12.1)The percentage of sequenced variants which are BA.2.12.1 is increasing in the UK, along with BA.4/5, while Omicron BA.2 is receding and BA.1 has all but disappeared (Source: CoVariants.org; NB: 21K = BA.1; 21L = BA.2; 22A = BA.4; 22B = BA.5; 22C = BA.2.12.1)

In contrast, over the same period, BA.4 has gone from 6% to 16% of sequenced cases; BA.5 from 9% to 30%; and BA.2.12.1 from 7% to 13%.

Although testing has been wound down, the UK still sequences thousands of cases a week.

Prof Kao said: "It looks like [BA.2.12.1] may explain the faster increase infections in Scotland, because the overall increase is steeper than in England and Wales and the 'BA.2-compatible' cases are going up faster here, whereas in England they're sort of stable.

"What's happening in Scotland is that [BA.2.12.1] is expanding more rapidly than in the south, for whatever reason."

READ MORE: One in 30 Scots infected as BA.4/5 strains become dominant in UK

Scotland currently has the highest Covid infection rate in the UK, at one in 30, compared to one in 50 in England and one in 45 in Wales and Northern Ireland.

However, Prof Kao said other factors could also be at play.

He said: "Our residual immunity here may be different. Broadly speaking we probably did slightly better vaccination-wise - in that we got boosters out more quickly - and ironically that could mean we have less residual immunity now.

"Covid also spreads better in deprived areas, so there could be an element of greater circulation here in those areas."

There remains uncertainty over what will happen with BA.4, BA.5 and BA.2.12.1 all circulating in a single population.

In the US, where BA.2.12.1 is dominant, BA.4 and BA.5 are only now beginning make inroads, while in Europe the situation is reversed with BA.4/5 - which share similar mutations on their spike protein - only now coming up against BA.2.12.1.

READ MORE: Experts back Covid boosters for all amid warnings of 'quite a surge' in infections

Marc Johnson, a microbiology and immunology professor at the University of Missouri who leads the state’s wastewater surveillance program, told Time magazine that all three variants are “competing for the same people, because they kind of have the same advantage".

His team’s Missouri wastewater surveillance network shows BA.4 and BA.5 causing more cases in some places, while BA.2.12.1 is causing more cases in others. However, the regions dominated by BA.2.12.1 are showing a bigger increase in cases, he added.

In contrast, a recent preprint from researchers in Japan claimed that the BA.4/5 duo had a "clear transmission advantage" over BA.2.12.1.

HeraldScotland: The new variants are spreading at a time when all legal Covid restrictions have been lifted, and routine testing is no longer availableThe new variants are spreading at a time when all legal Covid restrictions have been lifted, and routine testing is no longer available

Prof Kao said it could simply come down to whichever is newest, rather than "any inherent transmissibility advantage".

It comes after scientists at Imperial College London found that people infected with the original BA.1 form of Omicron may have little protection against reinfection by subsequent forms of Omicron, even if they are triple-vaccinated.

He said: "If another type comes in that has a slightly different immune profile, then that one will have an advantage.

"So, if BA.2.12.1 was there first then BA.4/5 will have an advantage because people will already have immune waning, and vice versa.

"Broadly speaking they're all relatively mild compared to [Delta] so it's nothing to worry about from that point of view.

"Except that the longer these things keep circulating the worse off we are in so many other ways."

READ MORE: Two new Covid strains designated variants of concern

The number of people in hospital with Covid in Scotland rose by 27%, to 748, between May 28 and June 12.

The World Health Organisation has also warned that countries are "playing with fire" by cutting back on the testing and sequencing needed to track the emergence of new, potentially more pathogenic, variants.

HeraldScotland: The number of Covid positive patients in hospital increased from 590 on May 28 to 748 on June 12. The figures, which are published weekly, will be updated later todayThe number of Covid positive patients in hospital increased from 590 on May 28 to 748 on June 12. The figures, which are published weekly, will be updated later today

Meanwhile, recent research indicates that while Omicron is less likely than Delta to lead to Long Covid, the eventual toll of Long Covid from the Omicron wave could be far higher due to the sheer number of people infected.