Omicron 'sub-variant' throws up new virus questions

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Omicron 'sub-variant' throws up new virus questions​

BA.2 found in 40 countries, including UK, India, could spread relatively quickly


Reuters
January 22, 2022

Scientists are keeping a close watch on a recently-discovered sub-variant of the Omicron version of the Covid-19 virus to determine how its emergence could effect future pandemic spread.

The initial Omicron variant has become the dominant virus strain in recent months but British health authorities have notably identified hundreds of cases of the latest version, dubbed BA.2, while international data suggest it could spread relatively quickly.

The UK Health Security Agency (UKHSA) identified more than 400 cases in Britain in the first ten days of this month and has indicated the latest variant has been detected in some 40 other countries, accounting for a majority of most recent cases in some nations including India, Denmark and Sweden.

The UKHSA indicated on Friday it had designated the BA.2 sub-lineage as a variant under investigation (VUI) as cases of it were on the increase even if, in Britain, the BA.1 lineage currently remains dominant.

The authority underlined that “there is still uncertainty around the significance of the changes to the viral genome,” which required surveillance as, in parallel, cases in recent days showed a sharp rise in BA.2 incidence notably in India and Demark.

“What surprised us is the rapidity with which this sub-variant, which has been circulating to a great extent in Asia, has taken hold in Denmark,” French epidemiologist Antoine Flahault told AFP.

Scientists must evaluate how the virus, which has engendered the worst global health crisis in a century, continues to evolve and mutate. Its latest incarnation does not possess the specific mutation used to track and compare BA.1 against Delta, the previously dominant strain.

BA.2 has yet to be designated a variant of concern - but Flahault says countries have to be alert to the latest development as scientists ramp up surveillance.

“(France) expected a spike in contaminations in mid-January: It didn’t happen and perhaps that is due to this sub-variant, which seems very transmissible but not more virulent” than BA.1, he observed.

“What interests us is if this (sub-variant) possesses different characteristics” from BA.1 in terms of contagiousness and severity, France’s public health agency said Friday.

To date, only a handful of BA.2 cases have emerged in France - but the country is monitoring developments as they spread across the Channel.

'Comparable severity'

Flahault, director of the University of Geneva’s Institute of Global Health, says the watchword is not panic but “vigilance” as “for now we have the impression (BA.2 case) severity is comparable to” classic variant Omicron cases.
“But there are numerous questions on the table” and a need to monitor properties of the new variant on the block.
“Very early observations from India and Denmark suggest there is no dramatic difference in severity compared to BA.1,” tweeted Tom Peacock, a virologist at Imperial College, London, adding the latest variant should not call into question the effectiveness of existing vaccines.

Peacock stressed that “we do not currently have a strong handle on ... how much more transmissibility BA.2 might have over BA.1. However, we can make some guesses/early observations.”

He added that “there is likely to be minimal differences in vaccine effectiveness against BA.1 and 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-Omicron change and instead is likely to be slower and more subtle,” he forecast.

French Health Minister Olivier Veran said Thursday that BA.2 did not look as if it would prove a game-changer as variants appear on the scene “fairly regularly”. But he indicated he would reserve judgment.

“What we know for now is that (BA.2) more or less corresponds to the characteristics that we know of Omicron” mark one.

 

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Omicron subvariant BA.2 more infectious than 'original':​

The BA.2 subvariant of the Omicron coronavirus variant, which has quickly taken over in Denmark, is more transmissible than the more common BA.1 and more able to infect vaccinated people, a Danish study has found.

The study, which analysed coronavirus infections in more than 8,500 Danish households between December and January, found that people infected with the BA.2 subvariant were roughly 33 per cent more likely to infect others, compared to those infected with BA.1.

Worldwide, the “original” BA.1 subvariant accounts for more than 98pc of Omicron cases, but its close cousin BA.2 has quickly become the dominant strain in Denmark, dethroning BA.1 in the second week of January, according to Reuters.

 

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The highly transmissible Omicron variant now accounts for half of the world's infections.
But Omicron is an umbrella term for several closely related lineages of the SARS-CoV-2 coronavirus, the most common of which is the BA.1 lineage.
Now more countries, particularly in Asia and Europe, are reporting an increase in cases driven by BA.2.
While BA.2 appears to be more transmissible than previous variants, there is no data yet to suggest that it is any more severe.
So how worried should we be about this emerging variant? Here is what we know about it.

What is BA.2?​

As viruses mutate into new variants, they sometimes split or branch off into sub-lineages.
The Delta variant, for example, comprises 200 different sub-variants.

The same happened with Omicron, which includes the lineages BA.1, BA.2, BA.3 and B.1.1.529.
BA.1 accounts for most of the cases. According to the World Health Organization (WHO), nearly 99% of viral DNA submitted to the global GISAID database as of 25 January were identified as this sub-variant.

IMAGE SOURCE,GETTY IMAGES
BA.2 was first detected in the Philippines

While BA.1 and BA.2 are similar, they are 20 mutations apart.

It is not clear where BA.2 originated, but it was first detected in the Philippines in November.

Where is BA.2 spreading?​

The sub-variant of Omicron has been detected in 57 countries now, the WHO says. In some countries, BA.2 accounts for more than half of sequenced Omicron cases, it adds.


In some places, growth in recorded cases of the sub-variant has been sharp.

According to Denmark's Statens Serum Institut (SSI), BA.2 infections rose to account for about half of the country's reported Covid cases in January.

India is another country where BA.2 is rapidly replacing the Delta and Omicron BA.1 variant, according to molecular biologist Bijaya Dhakal.
It is already the dominant variant in several states and likely drove the country's recent third wave of infections.

The BBC is not responsible for the content of external sites.View original tweet on Twitter

The Philippines' Department of Health (DOH) said the BA.2 sub-lineage was already prevalent in samples it received at the end of January.
And in England, more than 1,000 confirmed cases of BA.2 have been identified, according to the UK Health Security Agency (UKHSA). It has been designated a "variant under investigation" by British health authorities, meaning they are keeping a close watch on it, but are not overly concerned by it.
BA.2 infections in Germany are also growing faster than BA.1 and Delta, according to Dr Meera Chand, Covid-19 director at the UKHSA.

Is BA.2 more transmissible?​

A study of 8,500 households and 18,000 individuals conducted by Denmark's SSI found that BA.2 was "substantially" more transmissible than BA.1.

The study also showed evidence to suggest that the BA.2 sub-variant is better able to evade vaccines.

About half of new cases in Denmark are caused by BA.2

However, vaccinated people are still less likely to get infected than unvaccinated individuals, and they are also less likely to pass it on.

A separate UK study also found higher transmissibility for BA.2 compared to BA.1.

But the preliminary assessment found no evidence that vaccines would be any less effective against symptomatic disease for either sub-variant.

Is BA.2 more dangerous?​

There is no data to suggest that BA.2 leads to more severe disease than previous Omicron sub-variants.
"Looking at other countries where BA.2 is now overtaking, we're not seeing any higher bumps in hospitalisation than expected," the WHO's Dr Boris Pavlin says.

Francois Balloux, Professor of Computational Systems Biology and director of the UCL Genetics Institute, said that BA.1 and BA.2 "can be considered as two epidemiologically largely equivalent sub-lineages of Omicron".

As with previous variants, experts believe vaccines will continue to be highly effective against severe illness, hospitalisation, and death.

Dr Chand said: "So far, there is insufficient evidence to determine whether BA.2 causes more severe illness than Omicron BA.1.

"We must remain vigilant and take up vaccinations. We should all continue to test regularly with LFDs [lateral flow devices] and take a PCR [polymerase chain reaction] test if symptoms develop."

 

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Variant that combines Delta and Omicron identified​

Hybrid versions of the coronavirus that combine genes from the Delta and Omicron variants - dubbed "Deltacron" - have been identified in at least 17 patients in the United States and Europe, researchers said.

Because there have been so few confirmed cases, it is too soon to know whether Deltacron infections will be very transmissible or cause severe disease, said Philippe Colson of IHU Mediterranee Infection in Marseille, France, lead author of a report posted on Tuesday on medRxiv ahead of peer review.

His team described three patients in France infected with a version of SARS-CoV-2 that combines the spike protein from an Omicron variant with the "body" of a Delta variant. Another two unrelated Deltacron infections have been identified in the United States, according to an unpublished report by genetics research company Helix that has been submitted to medRxiv and seen by Reuters. On virus research bulletin boards, other teams have reported an additional 12 Deltacron infections in Europe since January - all with an Omicron spike and a Delta body.
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CHICAGO: The highly transmissible Omicron variant of the SARS-CoV-2 virus — the most common form of which is known as BA.1 — now accounts for nearly all of the coronavirus infections globally, although dramatic surges in Covid cases have already peaked in some countries.

Scientists are now tracking a rise in cases caused by a close cousin known as BA.2, which is starting to outcompete BA.1 in parts of Europe and Asia.

Globally, BA.1 accounted for 98.8pc of sequenced cases submitted to the public virus tracking database GISAID as of Jan 25. But several countries are reporting recent increases in the subvariant known as BA.2, according to the World Health Organisation.

In addition to BA.1 and BA.2, the WHO lists two other subvariants under the Omicron umbrella: BA.1.1.529 and BA.3. All are closely related genetically, but each features mutations that could alter how they behave.

Trevor Bedford, a computational virologist at Fred Hutchinson Cancer Center who has been tracking the evolution of SARS-CoV-2, wrote on Twitter on Friday that BA.2 represents roughly 82pc of cases in Denmark, 9pc in the UK and 8pc in the United States, based on his analysis of sequencing data from the GISAID database and case counts from the Our World in Data project at the University of Oxford.

The BA.1 version of Omicron has been somewhat easier to track than prior variants. That is because BA.1 is missing one of three target genes used in a common PCR test. Cases showing this pattern were assumed by default to be caused by BA.1.

BA.2, sometimes known as a “stealth” subvariant, does not have the same missing target gene. Instead, scientists are monitoring it the same way they have prior variants, including Delta, by tracking the number of virus genomes submitted to public databases such as GISAID.

As with other variants, an infection with BA.2 can be detected by coronavirus home tests kits, though they cannot indicate which variant is responsible, experts said.

Some early reports indicate that BA.2 may be even more infectious than the already extremely contagious BA.1, but there is no evidence so far that it is more likely to evade vaccine protection.

Danish health officials estimate that BA.2 may be 1.5 times more transmissible than BA.1, based on preliminary data, though it likely does not cause more severe disease.

In England, a preliminary analysis of contact tracing from Dec 27, 2021, through Jan 11, 2022, by the UK Health Security Agency (HSA) suggests that household transmission is higher among contacts of people infected with BA.2 (13.4pc) compared with other Omicron cases (10.3pc).
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