Scientists and health officials are seriously concerned about a new COVID-19 variant called B.1.1.529, detected this week in South Africa. The World Health Organization has called an emergency meeting for Friday to discuss the variant and develop guidelines on how to deal with it.
According to Soumya Swaminathan, the chief scientist of the WHO, the new variant had “a number of worrying mutations in the spike protein”. Tulio de Oliveira, the director of the Centre for Epidemic Response and Innovation in South Africa, told the Financial Times that there were traits present in the new variant that have previously been associated with high transmissibility.
Scientists are working overtime (!) to analyze the virus and the data arriving from around the world to determine its properties and develop public health guidelines and possible countermeasures, if needed.
Preliminary analysis of the genetic sequence and observational data from S. Africa suggest high transmissibility of the virus. Its ability to evade existing vaccines is not known although theoretical analysis suggests a good likelihood of it doing so partially.
The total number of identified cases is relatively small so far. One case each has reached Hong Kong and Belgium. It s quite likely that it has already reached other countries undetected.
The U.K and Israel have banned flights from S. Africa and 5 other African nations. Financial markets around the globe are reacting negatively to the news.
The new variant will most likely be named after the Greek letter Nu, pronounced "Nee".
Here is a summary of the variant from the National Institute for Communicable Diseases (NICD), the national public health institute of South Africa -
The rapid spread of B.1.1.529
As reported by multiple sources, B.1.1.529 has spread rather rapidly in S. Africa in the past few days, crowding out the Beta and Delta variants, as shown below.
But John Burn-Murdoch also points out that this new wave in S. Africa is starting with a very low base and the absolute number of cases is still small, although the rise in cases is alarmingly rapid. The number of news cases on Thanksgiving day was 2,465, an increase of 333% from a week ago.
Tulio de Oliveira, the director of the Centre for Epidemic Response and Innovation in South Africa estimates that about 90 per cent of new cases in the South African region of Gauteng, which includes Johannesburg, were caused by the new variant.
B.1.1.529 Discovery
The variant was first reported by virologist Tom Peacock, earlier this week -
It was first sequenced by Dr. Sikhulile Moyo and his colleagues in South Africa -
Some info on how this variant as detected and the speed of the response by South Africa -
Some technical data on B.1.1.529
Preliminary assessment by Bloom Lab, based on deep-mutational scanning experiments, indicate that the Nu variant has lot of antigenic change and many mutations at peak escape sites, especially E484, G446, K417, & Q493.
Additional info from the thread -
Importantly, this does *not* mean Nu variant will fully escape vaccine- or infection-elicited antibodies. @PaulBieniasz @theodora_nyc have shown takes many many mutations to fully escape neutralization (https://nature.com/articles/s41586-021-04005-0…), & there are also T-cells, non-neut Abs, etc.
But I'd expect the Nu variant to cause more of a hit on vaccine- and infection-elicited antibody neutralization than anything we've seen so far.
We can also look at some key monoclonal antibodies. the REGEN-COV cocktail is likely to take a hit for the Nu variant, especially the REGN10987 component.
The early Eli Lily antibodies like LY-CoV555 (bamlanivimab) and LY-CoV016, which were already in trouble with current variants, aren't going to do any better against the Nu variant.
However, it appears the AstraZeneca AZD7442 cocktail and Vir's S309 are likely to hold up better against the Nu variant.
Also note large antigenic change does not mean Nu will necessarily spread & outcompete other variants. That will also depend on its transmissibility, which has been discussed by @Tuliodna & others (eg, https://twitter.com/Tuliodna/status/1463911571176968194…) and for which data remains preliminary.
This assessment is based on genomic analysis. It remains to be seen how the virus will behave in the human body. But the sheer number of mutations and the specific mutations, which have been studied before, has scientists worried.
How did so many mutations appear together so abruptly? A possible explanation provided by virologists is that virus evolved in a single immuno-compromised patient with a long duration infection.
B.1.1.529 Testing
This variant does not affect the ability of existing PCR tests to detect the virus. Additionally, B.1.1.529 has a deletion (△69-70) within the S gene, which allows existing PCR tests to identify this variant. www.nicd.ac.za/…
COVID in Africa
S. Africa, like many other Africa nations, is far behind in vaccination rates, primarily due to vaccine hesitancy and due to the poorly funded health systems. S. Africa is about 24% fully vaccinated, other African nations have significantly lower rates (average 7%). Low vaccine supply also plays a role in many African nations. However, S. Africa has been at the forefront in rapidly sequencing virus samples and sharing information on mutations and variants; this genomic surveillance might be the reason this variant was detected in S. Africa.
It is in the world’s interest to arrest the spread of COVID globally, not just in rich nations. Here is a plea for help for Africa from the Director of CERI: Centre for Epidemic Response & innovation, South Africa -
Vaccine escape?
This data point implies that vaccines are working and preventing hospitalizations in S. Africa. Let’s hope that this result holds good for larger samples.
Travel restrictions
The U.K. and Israel have implemented travel bans from 6 African countries. We can expect the list of such countries to grow today.
This may appear to be over-reaction to some, but many healthcare experts believe that it is best to err on the side of caution at this point until more data becomes available.
But travel bans can be counter-productive, as explained by Dr. Craig Spencer and others.
Some expert opinion
Overall, there is genuine concern, but not alarm bells yet. The scientific community is gearing up to generate more data and analysis. Vigilance and precautions are recommended.
Some precautions against over-interpreting the case graphs -
Some other hopeful alternative possibilities -
A concise synopsis of the situation from the WHO and a plea to get vaccinated.
Epilogue
The COVID pandemic is hardly over, as we are reminded every day; nor is the ability to virus to evolve. Even without this variant, a new wave seems to be forming in Europe and the USA as winter approaches. Anti-vaxx sentiments, pushed by the right in many countries, is making things worse, so is waning immunity from vaccines. The probability of new variants arising remains high so far as the virus circulates in a large section of the population.
The B.1.1.529 variant may create new challenges or it may fizzle out, we do not know yet. It may have vaccine escape properties, but vaccines could still provide protection against severe disease.
A little over-precaution at this point will not hurt. Best case scenario — it will fizzle out like some other variants. Worst case scenario — it is more virulent, but we manage to contain it and develop countermeasures and vaccine variants.
In any case, rich countries need to do to more to vaxx the world. It is in everyone’s interest to help every country achieve herd immunity.
Also, let’s be thankful to the thousands of scientists and healthcare specialists who have dedicated their lives to helping humanity solve this crisis.
What we can do is stay vigilant, get the booster shot if we have not already done so, keep practicing masking and social distancing protocols, encourage others to do so and keep an eye on the news from reliable sources. In any case, to quote Douglas Adams — Don’t panic!