Rapid Increase of Highly Mutated B.1.1.529 Strain in South Africa

post by dawangy · 2021-11-26T01:05:49.516Z · LW · GW · 15 comments

I'm sorry to ruin your holidays. The video above is my only source for this information. I will summarize the key findings here.

A cluster of cases among students in Gauteng was recently sequenced. A new variant, B.1.1.529 was found. The mutation profile of this variant looks horrendous:

Each of the vertical black lines is a mutation from the original strain. For comparison, here is what the Delta variant looks like:

Some of these mutations have known phenotypic impact (effect on transmissiblity and immune evasion), while others are brand new. 

As you may be quick to point out, more mutations does not equal bad. However, the proportion of sequenced cases comprised of this new variant is rapidly rising:

One might be tempted to say that this just the founder effect from the new cluster in Gauteng. However, while there has not been much full sequencing in other provinces, we can see that the lack of the "S-gene" in PCR tests, which the authors here are using as a signal that an infection may have been caused by this variant, is in fact rising rapidly in most provinces of South Africa.

Given that this is the most mutated strain of the coronavirus yet, we may be in for a rough time. The C.1.2 variant, seen in the image "Variant proportions in South Africa" above, was the strain with the most mutations until recently. C.1.2 never really took off the way that B.1.1.529 is taking off, though. 

I expect that we will be hearing about this variant more. I think there is strong reason to believe that the high number of mutations in the spike protein will have a very negative impact on vaccine efficacy against this variant.

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