Thursday, November 25, 2021

South African NICD Statement On B.1.1.529 Variant

Credit NICD


Thanksgiving is normally a slow news day, so it isn't surprising that many major media outlets are leading this morning with worried reports of a new COVID variant - B.1.1.529 - detected in South Africa, which boasts an unusual number of mutations. 

While potentially a serious emerging threat, we've seen previous claims about new variants (see here and here) that have not - as yet - proved to be pandemic game changers.

The caveat being, of course: it just takes one.

South Africa's NICD (National Institute of Communicable Diseases) has issued the following statement on this recently identified variant, after which I'll have some early expert reaction from the Science Media Centre.


25 November , 2021

The National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, confirms that through collaborative efforts with private laboratories and the NGS-SA members, a new COVID-19 variant, B.1.1.529, has been detected in South Africa. Twenty-two positive cases of variant B.1.1.529 have been recorded in the country following genomic sequencing collaborations between the NICD and private laboratories. In addition, other NGS-SA laboratories are confirming more cases as sequencing results come out.

“It is not surprising that a new variant has been detected in South Africa,” comments Prof Adrian Puren, NICD Acting Executive Director. He adds that, “Although the data are limited, our experts are working overtime with all the established surveillance systems to understand the new variant and what the potential implications could be. Developments are occurring at a rapid pace and the public has our assurance that we will keep them up to date.”

Detected cases and percent testing positive are both increasing quickly, particularly in Gauteng, North West and Limpopo. Dr Michelle Groome, Head of the Division of Public Health Surveillance and Response at the NICD says that provincial health authorities remain on high alert and are prioritising the sequencing of COVID-19 positive samples. She stresses that regardless of the emergence of new COVID-19 variants, the importance of non-pharmaceutical interventions remains unchanged and the public are urged to be responsible. “This means that individuals should get vaccinated, wear masks, practice healthy hand hygiene, maintain social distancing, and gather in well ventilated spaces.” She concludes with, “Individual compliance to preventative measures can have a great collective impact in limiting the spread of the new variant.”

From the UK Science Media Centre, we get the following early reaction on the B.1.1529 lineage in Botswana from Prof Francois Balloux, Professor of Computational Systems Biology and Director, UCL Genetics Institute, UCL, said:

B.1.1529 is a new lineage that has been found in Botswana that carries an unusual constellation of mutations. Given the large number of mutations it has accumulated apparently in a single burst, it likely evolved during a chronic infection of an immunocompromised person, possibly in an untreated HIV/AIDS patient.

“It is difficult to know what to make of the carriage of both P681H and N679K. It is a combination we see only exceptionally rarely. I suspect it is generally not ‘stable’, but it might be so, in combination with other mutations/deletions.

I would definitely expect it to be poorly recognised by neutralising antibodies relative to Alpha or Delta. It is difficult to predict how transmissible it may be at this stage.

“So far, four strains have been sequenced in a region of Sub-Saharan with reasonable surveillance in place. It may be present in other parts of Africa.

“For the time being, it should be closely monitored and analysed, but there is no reason to get overly concerned, unless it starts going up in frequency in the near future.

          (Continue . . .  )

(Note: The SMC post refers to B.1.1529, while the NICD refers to B.1.1.529. For now, I've gone with the NICD announcement's nomenclature).

Bombastic headlines aside, it will take some time before we can know if B.1.1.529 has the ability to take on the juggernaut that is the Delta Variant; probably months.  But the history of COVID has been one of new variants emerging, and one eventually supplanting, older strains. 

So Delta's days may well be numbered, even if B.1.1.529 doesn't manage to sweep the world. 

What comes after Delta may be more, or possibly, less dangerous than our current strain.  Change isn't necessarily bad. As disruptive as the 2009 H1N1 pandemic was, it replaced an increasingly antiviral resistant H1N1 virus, and that likely saved lives over the long run. 

The take-away from today's report isn't that a new pandemic threat has appeared, only a reminder that evolution is a process, and another global public health threat will emerge at some point. 

It's just a matter of time.