More Details Emerge On B.1.1.529 - The UK Places 6 African Nations On Travel `Red List'

 

Youtube Briefing By South African Public Health Officials 1-hour 51 mins 

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Yesterday's relatively tepid announcement from South Africa's NICD (see South African NICD Statement On B.1.1.529 Variant) - which directly mentioned only 22 confirmed cases - has been supplanted by a nearly 2-hour briefing (YouTube Link) by South African research scientists which provides considerably more detail, and raises greater concerns, than the initial report on the emerging B.1.1.529 COVID variant. 

Events have moved rapidly over the past 48 hours, as illustrated by the following slide from the South African briefing, which culminates with a requested and approved urgent sitting of WHO TWG (Technical Working Group) on the virus evolution. 

The reason behind this raised concern is a sudden spike in COVID cases in Gauteng, South Africa which is reporting a preliminary (estimated) R0 of 1.93 (see chart below), significantly outpreforming the (predominantly) Delta variant across the rest of South Africa.

Rather than the 22 cases mentioned in yesterday's press release, the number of confirmed cases in South Africa is reportedly now well over 1,000, and rising rapidly.  

Exact numbers via genomic sequencing take time and abundant resources, but this new variant - much like Alpha - carries mutations that produce an ‘S Gene Target Failure’ on many PCR tests, which can give us a rough estimate of its prevalence. 

Overnight the UK announced that starting today,  six South African nations - South Africa, Botswana, Eswatini, Lesotho, Namibia and Zimbabwe - would be placed on their travel `Red list', which will order: 

It appears that at least one of the reasons behind the overnight retreat of European Stock Markets (> 2.5% as of this writing) is due to rising concerns over the transmissibility of this B.1.1.529 variant.  

In stark contrast to yesterday's assessment of B.1.1.529 by Prof Francois Balloux on the UK Science Media Centre website - who counselled that  ". . .   it should be closely monitored and analysed, but there is no reason to get overly concerned . . . ", the tone today, in light of these new revelations, is one of greater concern. 

We still don't know if this new variant produces more severe illness - or worse outcomes - than previous strains, but the higher R0 numbers and rapid spread are concerning. You'll find considerably more discussion today (including from Prof Francois Balloux) on the SMC website, a few excerpts of which you'll find below:

NOVEMBER 26, 2021
Expert reaction to B.1.1.529 variant situation in South Africa; and UK travel restrictions in response

There are reports of the emerging B.1.1.529 variant, predominantly in southern Africa, which have prompted new infection control measures from the UK government, including that travellers arriving in the UK from several southern African countries will have to quarantine, and from 12:00 UK time on the 26th six countries will be added to the red list with flights temporarily banned.

 

Prof Sharon Peacock, Director of COG-UK Genomics UK Consortium, and Professor of Public Health and Microbiology, University of Cambridge, said:

“An important body of evidence on a new SARS-COV-2 variant was released yesterday by the South Africa Ministry of Health and supporting scientists.  This is referred to as lineage B.1.1.529, and the information can be found here: https://www.youtube.com/watch?v=Vh4XMueP1zQ.

“Although case numbers of COVD-19 in South Africa are low compared with the UK daily count, a rapid increase has been observed in the last 7 days.  The number of recorded COVID-19 infections on 16th November 2021 was 273 cases.  By 25th November this had risen to more than 1200 cases.  More than 80% of these were from Gauteng province.  Cases in Gauteng province initially appeared to be clustered, but over time there has been more widespread dispersal of infections across the province.

“An analysis of the R value (a measure of growth rate) is 1.47 for South Africa as a whole, but initial estimates for Gauteng province are 1.93.  Based on this measurement, it indicates that growth rate of cases is considerably higher in Gauteng province than the rest of the country.

“The Ministry of Health and scientists in South Africa acted quickly on this information to target genome sequencing of positive samples from people who were PCR test positive in Gauteng province.  This identified a new variant B.1.1.529, which has a very unusual constellation of mutations and a mutation profile that is different from known variants of concern.  The 1.1.259 variant genome has around 50 mutations, but more than 30 of these are in the spike protein, the region of the protein that interacts with human cells prior to cell entry.  The Receptor Binding Motif (the part that binds to our cell receptor called hACE2) has 10 mutations (greater than previous variants of concern). 

           (SNIP)

“In summary, the full significance of this variant is not known.

“Aspects of concern are: 1. the rapid increase in cases in Gauteng province with a raised R value, linked to the detection of a new variant; 2. the detection of putative cases across numerous provinces in South Africa based on a PCR test with S Gene Target Failure, consistent with the new variant; 3. the variant may be outcompeting the Delta variant, suggesting that it is ‘fitter’; 4. a very large number of mutations are present in the spike protein, some of which have been associated previously with increased transmission and immune evasion.  Many mutations are not familiar to us (not characterised).

“Numerous questions remain unanswered, including disease severity, and immune evasion in lab tests and real life.  Increased transmissibility also needs to be formally assessed.  The evidence so far (or lack of it) would mean that this would not be categorised as a variant of concern today based on established criteria. 

(Continue . . . )

This is a rapidly evolving situation, and our perception of the threat posed by B.1.1.529 will probably fluctuate from day-to-day, and it may be weeks or even months before we'll know if this is the heir apparent to Delta, or simply a flash in the pan. 

But the appealing notion that the COVID pandemic might be on its last legs (see last September's NPR Is The Worst Over? Modelers Predict A Steady Decline In COVID Cases Through March), has always seemed to be predicated more on hope than reality. 

Europe is in the throws of their worst pandemic wave to date, and numbers are slowly increasing again in the United States.  International borders - many closed for more than a year - are opening up again, increasing the potential for spreading new variants. 

And as more and more people are either infected by Delta, or vaccinated, the pressure on SARS-CoV-2 to evolve grows greater, as its supply of susceptible hosts dwindles.  

While we could get lucky, and Delta ends up being COVID's last Hurrah, that is far from the only scenario open to the pandemic.  Not a prediction, of course.  

But we do need to be prepared for surprises.