WHO Closely Monitoring New Variant BA.2.86 - US, Denmark, UK Report Cases - UKHSA Risk Assessment

[Michael Coston]

WHO Closely Monitoring New Variant BA.2.86

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#17,621


For the past couple of days virologists around the globe have been examining three similar COVID sequences (2 from Denmark, 1 from Israel) recently deposited at GISAID that carry > 30 mutations in their spike protein.

At this point, there isn't enough information to even begin to quantify the risk. We don't know how well it transmits, or how stable it is, or whether it is more - or less - dangerous to humans.​

But there is a lot of interest because 20 months ago, we saw a similar report from South Africa (see NICD Statement On B.1.1.529 Variant) on a variantwhich also carried an unusual number of mutations. That turned out to be the start of the Omicron lineage of COVID, which while milder than Delta, was far more transmissible.

This new variant has been dubbed BA.2.86, and it appears to be a descendant from the BA.2 variant which peaked in the United States over a year ago, and as of the last CDC Nowcast, was estimated at between 0.0% and 0.1% of US cases.​

Yesterday Denmark's SSI posted on Twitter/X:



Today they followed up with:



Today the WHO officially added BA.2.86 to their list of Currently circulating variants under monitoring (VUMs) (as of 17 August 2023)



Whether BA.2.86 turns out to be a brief flash in the pan, or the start of a new phase of COVID, remains to be seen. A large number of mutations in the spike protein is concerning, but it could just as easily undermine the virus's `fitness'.

Time will tell.​

In the meantime, EG.5 is on the upswing globally, and in the United States, and regardless of the trajectory of BA.2.86, we will have to deal with that in the near term.

https://afludiary.blogspot.com/2023/08/who-closely-monitoring-new-variant-ba286.html
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[Michael Coston]

Denmark SSI: 3rd Case Of BA.2.86 Detected In Denmark

#17,623

Over the past 3 days a newly discovered COVID variant, BA.2.86 has made headlines, sporting no less than 30 mutations in its spike protein. First reported in July, only 3 cases (2 in Denmark, 1 in Israel) had been reported.

But over the past 24 hours the United States and the UK have both reported cases, and Denmark has now reported a 3rd case. Detection in 4 countries suggests this virus has been spreading, under the radar, for some time.​

The (translated) statement from Denmark's SSI follows:

Three cases of BA.2.86 have been detected in Denmark


Statens Serum Institut has detected another case of the new subvariant of omicron, B.2.86.​

Updated 18 August 2023

A new corona variant, which has been named BA.2.86, was found in Denmark this week, and now Statens Serum Institut (SSI) has detected another case. Isolated cases with the same variant have also been detected in Israel, the United States and the United Kingdom.

The subvariant differs significantly from the other omicron variants that have been seen in the past, and it is designated as ‘Variant under monitoring’ by the WHO.

"It is unusual for corona to change so significantly and develop 30 new mutations. The last time we saw such a big change was when omicron appeared", says senior researcher at SSI, Morten Rasmussen.

The three cases in Denmark are from different parts of the country, and do not appear to have had contact with each other.

SSI grows viruses and analyzes vaccine efficacy

It is still too early to say anything about the severity and contagiousness of the new variant. SSI is in the process of researching and growing the virus variant to test it against antibodies.

"It is clear that we react when we see something completely new, that is the job. But none of the three preliminary cases have had symptoms other than those normally seen in the course of covid-19. We also have a strong expectation that the vaccines - also with this variant - will provide good protection against serious disease", says Tyra Grove Krause, Executive Vice President for Epidemiological Infectious Disease Preparedness, SSI.

There is a lot of international attention to the findings, and therefore SSI continuously shares information about the cases detected in Denmark with the international researchers and health authorities.

Read more about the virus variant BA.2.86​

Overnight the CDC posted the following on Twitter/X.




The CDC should updated theirCOVID Nowcast today, but it may take some time before enough cases are detected for BA.2.86 to register

https://afludiary.blogspot.com/2023/08/denmark-ssi-3rd-case-of-ba286-detected.html​

 

[Michael Coston]

UKHSA Risk Initial Risk Assessment & Update on BA.2.86

#17,624


While there is much we still don't know about the emerging BA.2.86 variant (most importantly, how much of an impact it will have on infections, hospitalizations, or deaths), it is fair to say it represents the largest genetic leap in the SARS-CoV-2 virus since Omicron arrived in late got 2021.

Within a few of months of its detection (Nov 2021), Omicron had all but supplanted the dominant Delta variant - sparking a massive global surge in cases - but was thankfully less deadly (at least, in a largely vaccinated population) than its predecessors.​

Omicron's arrival also changed the way SARS-CoV-2 evolved; instead of hugely dominant waves (like Alpha & Delta) that lasted for 6 months or longer, we've experienced a jumbled parade of rapidly rising and falling Omicron variants (including BA.1, BA.1.1, BA.2, BA.4/5, followed by XBBs, etc.).

As a result, the CDC is currently tracking more than 2 dozen variants in the United States in their latest Nowcast (note: BA.2.86 isn't even on this list yet).



All of these Omicron variants remain fairly closely related; separated by only a few significant mutations. They may differ slightly in their degree of immune escape or transmissibility, but none have (thus far) demonstrated significant changes in their virulence.

As a result, the world has decided the COVID threat is over, and for the most part has stopped reporting on cases, hospitalizations and deaths. Equally troubling, testing for variants has declined significantly both here in the United States (see Nowcast map below), and around the world.
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For now, it remains unknown how disruptive BA.2.86 will become in the months ahead. It may be a flash in the pan, and end up being trampled by the crowded viral field. Or it could be - like Omicron before it - the start of a new phase for COVID.

Only time will tell.​

But it does answer one very important question. New, and radically different COVID variants can still emerge. Which means we dismantle our surveillance and reporting systems at our own peril.

Over the past three days we've seen statements from the WHO and Denmark's SSI on BA.2.86. Late yesterday afternoon, the UK's Health Security Agency issued the following two reports.

UKHSA publishes risk assessment for BA.2.86


The UK Health Security Agency (UKHSA) has published an initial risk assessment of the SARS-CoV-2 variant BA.2.86. This variant was detected in the UK on Friday 18 August, and has also been identified in Israel, Denmark and the US. It has been designated as V-23AUG-01 for the purpose of UKHSA monitoring.

The newly identified variant has a high number of mutations and is genomically distant from both its likely ancestor, BA.2, and from currently circulating XBB-derived variants. There is currently one confirmed case in the UK in an individual with no recent travel history, which suggests a degree of community transmission within the UK. Identifying the extent of this transmission will require further investigation.

There is currently insufficient data to assess the relative severity or degree of immune escape compared to other currently-circulating variants.

Dr Meera Chand, Deputy Director, UKHSA said:​

V-23AUG-01 was designated as a variant on 18 August 2023 on the basis of international transmission and significant mutation of the viral genome. This designation allows us to monitor it through our routine surveillance processes.​

We are aware of one confirmed case in the UK. UKHSA is currently undertaking detailed assessment and will provide further information in due course.​

UKHSA will continue to monitor the situation closely and will publish the results of our analysis when they are available.​

Research and analysis
Risk assessment for SARS-CoV-2 variant V-23AUG-01 (or BA.2.86)

Updated 18 August 2023

Part 1. Context and UK case

As of 3 pm, 18 August 2023, 6 unrelated cases of a new variant BA.2.86 have been identified in 4 countries. This variant is notable due to a high number of mutations.

Israel published the first genome on 13 August 2023. Subsequently Denmark has identified 3 cases, and a single case has been identified in both the US and the UK.

The UK case was identified in a patient tested at a London hospital on 13 August 2023, with no recent travel history. The sample was sequenced routinely as part of local hospital based genomic research.
Part 2. Variant technical group assessment

Meeting and assessment 1 pm, 18 August 2023.

1. The newly identified variant BA.2.86 has a high number of mutations and is distant from both its likely ancestor BA.2 and also currently circulating XBB-derived variants.
2. Despite the small number of sequences, the appearance of the variant rapidly in multiple countries which are still operating genomic surveillance, in individuals without travel history, suggests that there is established international transmission.
3. The sequences are similar across the world, potentially suggestive of a relatively recent emergence and rapid growth, but this is a low confidence assessment until further sequences are available.
4. The UK case has no recent travel history, also suggesting a degree of community transmission within the UK. This clinical site sequenced data rapidly locally, and data from surveillance systems from the same period is likely to follow, thus a more complete assessment of UK transmission will be possible in 1 to 2 weeks.
5. It is unreliable to attempt to predict the combined effect of the large number of mutations, however there is sufficient information to expect significant antigenic change. There are also mutations in spike which may be associated with changes in other viral properties.
6. At present the UK Health Security Agency (UKHSA) has designated this a variant for the purposes of tracking and assessment (V-23AUG-01). We will consider as signals of escalating concern the presence of phenotypic data confirming significant immune escape, other relevant phenotypic data, and signals of rapidly changing epidemiology in the UK or other countries where the variant has been detected.
7. UKHSA will share data from surveillance systems, variant growth rates, and phenotypic laboratory data when available. It is not possible to assess comparative severity by variant based on UK surveillance at present.

We should know a lot more about BA.2.86 in the next week or two, now that it has captured the world's attention. Hopefully, this is much ado about nothing.

But even if we get lucky, COVID still has the ability to deliver new surprises.​

Stay tuned.


​https://afludiary.blogspot.com/2023/08/ukhsa-risk-initial-risk-assessment.html

 

[gsgs]

“The last time we saw such a big change was when Omicron appeared” -
Morten Rasmussen, Statens Serum Institut Denmark
BA.2.86 has 34 new mutations vs BA.2, 36 more than XBB.1.5.
Dr Bloom calls it evolutionary jump. Its clinical abilities are unknow
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[Pathfinder]

“The last time we saw such a big change was when Omicron appeared” -
Morten Rasmussen, Statens Serum Institut Denmark
BA.2.86 has 34 new mutations vs BA.2, 36 more than XBB.1.5.
Dr Bloom calls it evolutionary jump. Its clinical abilities are unknow
​

Three cases of BA.2.86 have been detected in Denmark

Statens Serum Institut has detected another case of the new subvariant of omicron, B.2.86.

Updated 18 August 2023

A new corona variant, which has been named BA.2.86, was found in Denmark this week, and now Statens Serum Institut (SSI) has detected another case. Isolated cases with the same variant have also been detected in Israel, the United States and the United Kingdom.

The subvariant differs significantly from the other omicron variants that have been seen in the past, and it is designated as ‘Variant under monitoring’ by the WHO.

"It is unusual for corona to change so significantly and develop 30 new mutations. The last time we saw such a big change was when omicron appeared", says senior researcher at SSI, Morten Rasmussen.

The three cases in Denmark are from different parts of the country, and do not appear to have had contact with each other.

SSI grows viruses and analyzes vaccine efficacy

It is still too early to say anything about the severity and contagiousness of the new variant. SSI is in the process of researching and growing the virus variant to test it against antibodies.

"It is clear that we react when we see something completely new, that is the job. But none of the three preliminary cases have had symptoms other than those normally seen in the course of covid-19. We also have a strong expectation that the vaccines - also with this variant - will provide good protection against serious disease", says Tyra Grove Krause, Executive Vice President for Epidemiological Infectious Disease Preparedness, SSI.

There is a lot of international attention to the findings, and therefore SSI continuously shares information about the cases detected in Denmark with the international researchers and health authorities.

Read more about the virus variant BA.2.86

...​

https://en.ssi.dk/news/news/2023/three-cases-of-ba-2-86-have-been-detected-in-denmark

 

[Pathfinder]

Translation Google

Covid-19: a first case of the BA.2.86 variant, known as “Pirola”, detected in France

PARISIAN INFO. This new strain, whose Spike protein differs greatly from those of the variants currently circulating the most, has been detected in around fifteen countries around the world.

By Nicholas Berrod
August 31 , 2023 at 5:51 p.m.

It was surely already there, but it still had to be identified. A first case of the new Omicron BA.2.86 variant was finally officially identified this Thursday, August 31 in France, according to our information. The positive sample passed to sequencing, that is to say the complete analysis of the genome, dates from August 21 and concerns a person tested in the Aube department (Grand Est region). It appeared this Thursday at the end of the day in the Gisaid database, used by scientists around the world.

France therefore joins the fifteen countries (United States, Denmark, Sweden, etc.) having detected at least one case of this variant, which is distinguished by the thirty additional mutations in its Spike protein compared to the strains currently dominant. This very specific profile led to it being very quickly placed “under surveillance” by the World Health Organization, although we do not yet know what implications these mutations may have on its transmissibility and virulence.

“Some of the antibodies will always cling to the Spike”

BA.2.86, nicknamed "Pirola" on social networks, could also partially escape the immunity conferred by previous infections or vaccination. Antibodies that target the Spike protein may misrecognize it.

"Even if areas in the Spike protein have mutated, some of the antibodies will still cling to it", thus limiting the infection, reassured on August 20 Étienne Simon-Lorière, head of the RNA virus evolutionary genomics unit. at the Pasteur Institute. "Proven cases do not show atypical symptoms and the world's population has mostly acquired some form of immunity against severe forms, through vaccination and/or infection", he added then.

The arrival of this new variant has, all the same, led England to schedule its new vaccination campaign against Covid-19 from September 11, several weeks earlier than initially planned.


https://www.leparisien.fr/societe/s...nce-31-08-2023-WGG7NPQ7BFBNNMUUFLR4HX6KYY.php

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[Pathfinder]

Translation Google


COVID-19: a first case of the BA.2.86 variant detected in France

As part of the genomic surveillance of SARS-CoV-2, led by Public Health France with the CNR Virus des Infections Respiratoires, and the activities of the EMERGEN consortium, a case of the BA.2.86 variant was detected in the Grand Est, at based on samples from the last weekly Flash survey of 21/08/23. Investigations are underway to gather additional information on this first case.

Posted on September 1, 2023



What do we know about this new BA.2.86 variant?

BA.2.86 is a new variant of the Omicron family and has been classified as Variant Under Monitoring -VUM- by the World Health Organization. It is the subject of particular attention at the international level because of its atypical genetic profile and the large number of mutations it presents.

As of 08/31/2023 at noon, there were 25 sequences of this sub-lineage in the world, distributed in several countries: ten sequences in Denmark, four in the United States, four in Sweden, two in South Africa, two in Portugal, one in the United Kingdom, one in Israel and one in Canada; to these 25 sequences is added that detected for the first time in France on 08/31/2023 by the CNR Virus des Infections Respiratoires from a sample taken from a city laboratory in the Grand Est region and from the last Flash survey of 21/08/23.

At this stage, the emergence of the BA.2.86 variant is still too early to be able to assess its characteristics and its impact. However, the immune status of the world's population is very different from what it was when Omicron emerged, with a large proportion of people vaccinated or having been infected by different successive variants, allowing some protection to be maintained, in especially against severe forms.
TO KNOW MORE

RISK ANALYSIS RELATED TO EMERGING VARIANTS OF SARS-COV-2 (31/08/23)


Genomic surveillance: a pillar for detecting emerging variants

Genomic surveillance of SARS-CoV-2 is now one of the pillars of the fight against the COVID-19 pandemic nationally and internationally. The sequencing of the complete genome of the virus remains the only technique which makes it possible to confirm them, to detect emerging variants, and to specify the mutations which characterize them.
In France, this surveillance falls under the missions of the National Reference Center (CNR) Respiratory Infection Virus (Hospices Civils de Lyon) and its associated laboratories (Institut Pasteur, Institut Pasteur de la Guyane and CHU de La Réunion); it is conducted in close collaboration with Public Health France and its partners in the EMERGEN consortium.

EMERGEN in a nutshell

The EMERGEN project, coordinated by Public Health France and ANRS|MIE, was launched in January 2021 in the context of the COVID-19 pandemic following the emergence of the first worrying variant of SARS-CoV-2 (Alpha, first detected in the UK in November 2020). Its first mission was to deploy a SARS-CoV-2 genomic surveillance system throughout the national territory in order to more reactively monitor the emergence and/or introduction of worrying variants.

Since its creation, the EMERGEN project has been based on a multidisciplinary consortium bringing together complementary expertise: sample collection, preparation and sequencing of samples, bioinformatics analysis of genomes, publication of sequencing results in national and international databases, analysis for monitoring purposes ( Flash surveys) or risk analysis (classification of variants as worrying, to be monitored or under evaluation), possible discovery and functional characterization of new variants, research work on their epidemiological and functional impact. In 2023, the consortium's activities will continue on SARS-CoV-2, calling primarily on the sequencing capabilities of the CNR Respiratory Infection Virus. Work is underway to gradually expand its surveillance and research activities to other emerging infectious diseases (viral, but also bacterial, fungal or parasitic). ​

​https://www.santepubliquefrance.fr/...mier-cas-de-variant-ba.2.86-detecte-en-france

 

[sharon sanders]

Dr Claire Taylor
@drclairetaylor
Not good reading about Ba 2.86 (pirola) and also EG 5.1 ( Eris) All vaccine Sera tested showed NO neutralising activity. Monoclonal antibodies didn’t work at all. Literally the tools we have been told to rely on for living with Covid, in the lab, do not appear to work.
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The Sato Lab (Kei Sato)
@SystemsVirology
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2h
BREAKING A new study from G2P-Japan is out! The preprint will be out so soon, but first we show our results on BA.2.86 - transmissibility, infectivity and immune resistance. This would be the 4th non-peer-reviewed, but includes some new stuff. Please retweet/repost 1/
7:09 AM · Sep 7, 2023
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Dr Claire Taylor
@drclairetaylor
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Vaccines

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Dr Claire Taylor
@drclairetaylor
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Monoclonal antibodies

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Dr Claire Taylor
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Previous infection with XBB

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Dr Claire Taylor
@drclairetaylor
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Not surprised. Saw it coming like a train ages ago. Now is time to act
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Dr Claire Taylor
@drclairetaylor
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Of course, real life can differ from the lab. So caution in interpreting. However, I would see this paper as a red flag

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[sharon sanders]

Please also see:

Sato Lab Preprint: Transmissibility, Infectivity, and Immune Resistance of the SARS-CoV-2 BA.2.86 Variant​

UKHSA To Move COVID/Flu Jabs Forward Due To Concerns Over BA.2.86 - UKHSA Assessment (Sept 8th) - Large Care Home Outbreak (n=28)​

 

[Pathfinder]

Related to:

Euro Surveill . First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023
https://flutrackers.com/forum/forum...t-cases-of-sars-cov-2-ba-2-86-in-denmark-2023


Description og the first cases of SARS-CoV-2 variant BA.2.86 from Denmark published

BA.2.86 is a new variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged recently at global level. When a new variant of a pandemic pathogen emerges, quick initial assessment and sharing of information are of high importance. Statens Serum Institut has in collaboration with regional departments of clinical microbiology published a scientific Rapid Communication article describing the first ten cases that were detected in Denmark.

Updated 11 September 2023

BA.2.86 is a new variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged recently at global level. When a new variant of a pandemic pathogen emerges, quick initial assessment and sharing of information are of high importance.

BA.2.86 has many spike gene mutations and was classified as a variant under monitoring by the World Health Organization on 17 August 2023.

The article describes the first 10 human infections with BA.2.86 that were detected in Denmark between 26 July and 21 August 2023. The infection has also been detected in several other countries, including Israel, South Africa, UK and USA.

”It is not every day that we observe variant so distinct from the other circulating variants, and that is why it catches our attention. Due to the effective Danish genomic surveillance system and the collaboration with regional hospitals, we have the opportunity to address many of the pressing questions of not only of national but also of international importance that a new variant like this one raises.” Morten Rasmussen​

The first cases of infection with the new variant BA.2.86 did not stand out from previous COVID-19 cases seen in 2023. All cases had received the recommended baseline vaccinations against COVID-19, and some had received the updated vaccine as their fourth vaccination. Half the cases had had COVID-19 previously. The symptoms were similar to those seen with other variants, however the current data are insufficient to conclude generally about the ability of BA.2.86 to cause severe disease.

Denmark retains active genomic surveillance for emerging variants. The work showcases the usefulness of complementary surveillance systems. Wastewater surveillance allowed the team to assess the general level of circulation and spread across the country, and a surveillance project at workplaces contributed with samples from individuals with mild symptoms.

”The quick gathering of relevant data was possible thanks to excellent multidisciplinary collaboration across departments at Statens Serum Institut and regional departments of clinical microbiology.” Pikka Jokelainen, Head of Section, Infectious Disease Preparedness, Statens Serum Institut​

Read the article in Eurosurveillance.​
​

https://en.ssi.dk/news/news/2023/description-of-ba-2-86