Covid Scotland: Omicron BA.2 - how worried should we be?

Denmark's top infectious disease authority, the Statens Serum Institut (SSI), estimated this week that the strain currently known as BA.2 is around one and a half times more transmissible than the original version of Omicron - BA.1 - which exploded in southern Africa at the end of last year.

To put that into context, the currently dominant version of Omicron in the UK (that is, BA.1) is already around three to four times more transmissible than Delta.

In Denmark, BA.2 already accounts for more than half of the cases being sequenced and it has been detected in around 40 countries worldwide, including the UK, US, Australia, Singapore and India.

The BA.2 type of Omicron has spread rapidly in India and Denmark, and is on the rise in the UK

On Thursday, Dr Sujeet Kumar Singh, director of India's National Centre for Disease Control, said BA.2 had now become his country's dominant strain.

Globally, the BA.1 lineage continues to make up around 98 per cent of all known Omicron cases, and prevalence of BA.2 remains low - but climbing - in the UK, where it was identified on December 6.

In the UK, 426 cases of the BA.2 have been confirmed so far, mostly in London and the south-east of England, with no data yet available on the extent to which it is being picked up in any of the devolved nations including Scotland.

The UK's Health Security Agency has officially designated BA.2 as a 'variant under investigation' (VUI), a sort of watchlist for emerging strains.

It will only be escalated to a 'variant of concern' (VoC) if its mutations - it is estimated to have around 27 unique markers distinguishing it from BA.1 - confer specific advantages, such as substantially increased virulence, transmissibility, or immune evasion.

Some scientists are pushing for it to be given its own Greek alphabet name by the World Health Organisation, identifying it as a distinct variant. Pi is next in line.

Only key workers, such as NHS and social care staff, and those with symptoms are being asked to book appointments for a Covid PCR test at community sites, meaning fewer swabs overall will be available for sequencing. Previously asymptomatic people with a positive LFD were also tested

“I think the responsible thing to do is to relate to BA.2 as a completely different variant, outcompeting BA.1,” tweeted Shay Fleishon, a researcher affiliated with the Israeli government's Central Virology Laboratory.

Not everyone is agreed, however.

Tom Peacock, a virologist at Imperial College London, describes is as a "sister lineage" and compares it to a "more extreme version" of the so-called 'Delta-plus' strain, AY.4.2 , a faster-spreading cousin of Delta which briefly triggered alarm bells but never made the VoC grade.

"Even with slightly higher transmissibility this absolutely is not a Delta [to] Omicron change and instead is likely to be slower and more subtle," he tweeted.

"That said I wouldn't be that surprised if BA.2 slowly replaces BA.1 over the coming months with a slightly 'optimised' mutational profile. That said this is just a prediction and could be quite wrong."

The precise significance of BA.2 is difficult to gauge right now.

Tyra Grove Krause, the SSI’s technical director, told a press conference in Copenhagen that evidence it is "more contagious" than BA.1 means the peak of Denmark's Omicron wave is likely to stretch further into February than previously forecast.

Should it take over in the UK as well it would probably mean a similar prolonging of the virus at higher rates.

Denmark's current case rate is more than 10 times higher than its previous Covid peak, and five-fold higher than levels currently are in the UK.

Denmark, where the BA.2 strain is now dominant, has experienced an extremely steep rise in Covid rates, far outstripping the UK where BA.1 is the main form of Omicron

On the plus side, Krause stressed that Denmark is not seeing "any difference" so far in terms of hospitalisation and death rates associated with BA.2 - though he stressed that it is early days.

Preliminary data for England from the UKHSA, published on Thursday night, indicates that vaccine efficacy in terms of preventing symptomatic Covid infections "remains unchanged" with BA.2, with boosters providing very strong protection of around 95% against death from Omicron BA.1 infections.

There has been some concern that BA.2 is harder to spot - hence its nickname 'stealth' Omicron.

This does not mean it cannot be detected by PCR testing, however. It simply means that its mutations have removed the S-gene dropout marker found in BA.1 which enabled scientists to distinguish Omicron from Delta.

A second concern is that since asymptomatic individuals are no longer going for PCR tests - necessary for sequencing variants - tracking the spread of BA.2 could be hampered.

This is possible, though all hospital patients continue to be tested and a large amount of random surveillance is still ongoing.

New variants are normal, and they will keep coming.

There is even a third lineage of Omicron - BA.3 - though so far this accounts for only a few hundred known cases globally.

All three seem to have originated from an Omicron 'parent' traced back to around March 2021.

The question is how much we need to worry about any future variants?

The sheer transmissibility of Omicron, coupled with its greater ability - compared with Delta - to sidestep immune defences, triggered a rapid surge in infections wherever it took hold.

But boosters held up against severe disease and, in Scotland, hospitalisations peaked around 20% below last January's high despite cases peaking three times higher.

Covid hospital admissions during the Omicron wave in Scotland remained below the levels seen during January 2021, despite a much higher number of cases being confirmed. This is largely due to the effect of vaccinations, but Omicron also appears to cause less severe disease

Maria Van Kerkhove, the World Health Organization’s technical lead on Covid-19, warns that future variants will inevitably be more transmissible in order to overtake "what is currently circulating"; otherwise like Lambda, Mu and all the other also-rans, it would just fade into the background.

“The big question is whether or not future variants will be more or less severe,” she said.

As Andrew Rambaut, an evolutionary biologist at Edinburgh University, told Nature, it is "a bit of a myth" that viruses evolve to become milder.

Most people infected with Covid will spread it before symptoms emerge, and before they become sick, so there is no evolutionary gain in it becoming less lethal. But the reverse is also true.

Some scientists believed Covid had reached its evolutionary peak with Delta; they were wrong.

What happens next is anyone's guess.