As we had been predicting, a new variant with many mutations may be the next super variant. The variant, called B.1.1.529, has been detected in South Africa in small numbers.
- South African scientists have detected 32 mutations to the spike protein, the part of the virus that binds to cells in the body, which could have implications for vaccine efficacy and transmissibility.
- The B.1.1.529 variant was first spotted in Botswana.
- WHO is monitoring the new Covid variant, scheduling a special meeting Friday to discuss what it may mean for vaccines and treatments, officials said.
It’s unusual for the WHO to be this quick on the uptake. With mounting cases in Europe and highs in deaths in the U.S. (that is typically 5 weeks behind Europe) we have to be cautiously worrying. The U.K. announced it would ban flights from six African countries, including South Africa, starting midday Friday.
So why is this significant? Delta has been due for a super-variant emergence for quite some time. The B.1.1.529 variant contains multiple mutations associated with increased antibody resistance, which may reduce the effectiveness of vaccines, along with mutations that generally make it more contagious, according to slides presented at the briefing.
Other mutations in the new variant haven’t been seen until now, so scientists don’t yet know whether they are significant or will change how the virus behaves, according to the presentation.
The variant has spread rapidly through the Gauteng province, which contains the country’s largest city of Johannesburg. At this early stage there are fewer than 100 full genome sequences of the new mutation. So if scientists have already sounded the alarm, it must be potentially serious.
With waning vaccine efficacy and increased deaths in poorly vaccinated countries this could be a wake up call for 2022. The B.1.1.529 variant has 32 mutations in the spike protein, the part of the virus that most vaccines use to prime the immune system against Covid. Mutations in the spike protein can affect the virus’s ability to infect cells and spread, but also make it harder for immune cells to attack the pathogen.
Horrific Spike Protein Profile
In terms of deaths the U.S., Russia, Ukraine, Poland, Germany, Romania, Turkey and Hungary seem to be in really bad shape as well as India, where numbers that are accurate are hard to come by.
Dr Tom Peacock, a virologist at Imperial College London, posted details of the new variant on a genome-sharing website, noting that the “incredibly high amount of spike mutations suggest this could be of real concern”, as reported by the Guardian.
In a series of tweets, Peacock said it “very, very much should be monitored due to that horrific spike profile”, but added that it may turn out to be an “odd cluster” that is not very transmissible. “I hope that’s the case,” he wrote.
November 11th Origin Point
The first cases of the variant were collected in Botswana on November 11th, and the earliest in South Africa was recorded three days later. The case found in Hong Kong was a 36-year-old man who had a negative PCR test before flying from Hong Kong to South Africa, where he stayed from October 22nd to November 11th. He tested negative on his return to Hong Kong, but tested positive on November 13th while in quarantine.
Some virologists in South Africa are already concerned, particularly given the recent rise in cases in Gauteng, an urban area containing Pretoria and Johannesburg, where B.1.1.529 cases have been detected.
In a media briefing Prof de Oliveira said there were 50 mutations overall and more than 30 on the spike protein, which is the target of most vaccines and the key the virus uses to unlock the doorway into our body’s cells.
The virus evolution working group will decide if B.1.1.529 will become a variant of interest or a variant of concern, after which the WHO would assign the variant a Greek name, Van Kerkhove said.
Ravi Gupta, a professor of clinical microbiology at Cambridge University, said work in his lab found that two of the mutations on B.1.1.529 increased infectivity and reduced antibody recognition. “It does certainly look a significant concern based on the mutations present,” he said.
Is this the next Delta, the one that replaces what we have today? Zooming in even further to the receptor binding domain (that’s the part of the virus that makes first contact with our body’s cells), it has 10 mutations compared to just two for the Delta variant that swept the world.
The concern is this virus is now radically different to the original that emerged in Wuhan, China. We are slowly getting to the point where our first wave of vaccines may be less effective, although the extent of this is not clear.
Speculation on how these new types evolve is also quite interesting. Prof Francois Balloux, the director of the UCL Genetics Institute, said the large number of mutations in the variant apparently accumulated in a “single burst”, suggesting it may have evolved during a chronic infection in a person with a weakened immune system, possibly an untreated HIV/Aids patient.
There’s a 70% probability that is the variant that replaces Delta, so try to keep yourself informed and stay safe. Prof Ravi Gupta, from the University of Cambridge, said: “Beta was all immune escape and nothing else, Delta had infectivity and modest immune escape. This potentially has both to high degrees.”
There are currently under 100 cases known. Yet scientists are already concerned.
Just spotted: very small cluster of variant associated with Southern Africa with very long branch length and really awful Spike mutation profile including RBD – K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505Hhttps://t.co/kgA9c1hKDa
— Tom Peacock (@PeacockFlu) November 23, 2021