Nu, a variant of real concern

Here is the Eric Topol thread.  Do read it.  Here is the scary graph, based on preliminary data.  Here is Bloom Lab.  Here is a layperson’s take from the Times of London:

When was the variant first discovered?
South African authorities raised the alarm at 2pm on Tuesday of this week, when they found samples with a significant number of worrying mutations.

The samples dated from tests taken on November 14 and 16. On Wednesday, even as scientists were analysing the genome, other samples were found in Botswana and China, originating from travellers from South Africa.

Why were scientists initially concerned by this variant?
The spike protein is the tool a virus uses to enter cells, and the part of it our vaccines are trained to spot. This variant had 32 mutations in the spike — meaning it would look different to our immune system and behave differently when attacking a body. As a virologist at Imperial College put it, it was a “horrific spike profile”.

Why has worry increased over the course of the week?
When geneticists and virologists looked at the mutations they realised there was a high likelihood they could increase its transmissibility or help it evade immunity. But these concerns were still theoretical. However, today South African scientists spotted a quirk in the testing regimen. PCR tests look for three genes in the coronavirus and amplify them. If, however, the virus was this variant they were only able to amplify two.

In the province of Gauteng, where the proportion of tests coming back positive has rocketed to one in three, they found the proportion in which only two genes were amplified has also rocketed.

What does this mean?
There are three options. It is still possible — though unlikely — this is chance, with the variant’s apparently increased spread relating to an unusual cluster. If it does have a genuine advantage, then it is either better able to spread or better able to infect people who have prior immunity — either from vaccination or infection. Or, it is both.

This might come to nothing, but it is definitely a matter of concern.  One more general point is that even if Nu is a non-event, it seems to show that the space for possible significant mutations is largely than we had thought.

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