Thread by @firefoxx66

Lots of headlines about B.1.1.529 today.

Thoughts: Yes, this variant has a high # of spike mutations, & a few known to cause changes. But, we've seen previous variants that looked worrying & never took off. We should watch & wait for more data to estimate how concerning this is.

As a catch-up for those who haven't seen said headlines, I think this @guardian article on it gives a fair summary, with some level-headed quotes from scientists.
theguardian.com/world/2021/nov…

We got some additional information this afternoon from a press conference with @Tuliodna & @rjlessells. You can watch it below. A brief touch on some of the new information.

- There are more cases detected now, & over 80 with genomes
- Some mutations in spike mean the variant can be detected through S-gene dropout by PCR
- Likely cases have been detected in provinces outside of Gauteng, where originally detected

You might remember 'S-drop-out' (also called SGTF) from other variants, particularly Alpha. This means that some PCR tests fail to detect one of their targets (they use more than 1, so the test doesn't fail overall), which can be used to quickly ID the variant.

This means even in areas where there aren't sequences, you have a proxy by which you can track the variant. Here, we can see S-drop-out across provinces in SA, with a recent increase noticeable for many of them.
This implies B.1.1.529 may be more widespread than 1st thought in SA

What do we know about the mutations we see in this variant? We know about some of them from previous variants & prev studies. However, important to keep in mind that mutations often work together - we can't perfectly predict what this combination may mean. Wait for lab work.

South Africa has had fairly low case numbers recently, but there's a very recent spike. This may be associated with the new B.1.1.529 variant.

Important thing to keep in mind:
- We cannot perfectly predict virus behaviour from mutations. Even lab work doesn't perfectly mirror what happens in complex, whole-body real-life. Other, alarming variants have failed to spread very far in the past. We need more data.

Important thing to keep in mind:
- SA has recently had relatively low cases - this may leave a void which a new variant can spread into more easily - it likely hasn't had to compete with Delta. In other places, where Delta rages, it may not be as fit.

Important thing to keep in mind:
- We don't know what other factors may be helping spread, for example, an event or recent behaviour change
- SA has a low vax rate - 28% 1dose, 24% 2dose. Immune evasion may not be needed to spread. Fitness could differ in higher-vax countries.

The additional information today helps us: we can track this variant with PCR tests, & we know how to look for it. We can step up monitoring, & we should.

However, what fitness advantage(s) it may have are still unclear, esp outside of initial spread. More data needed.