Thread by @kakape

There’s a lot of concern and confusion right now about the new #sarscov2 variant identified in UK. I’ve spent today and yesterday talking to a dozen people working on this. My story is here: sciencemag.org/news/2020/12/m…
Thread to come (may be long and slow)

There are a ton of things to explain, dozens of questions to discuss and I won’t be able to cover more than a tiny part here now. So three general things up front:
1. Expect more threads and stories on this from me

2. A lot of scientists are working on this. You can follow @firefoxx66, @arambaut, @K_G_Andersen, @GuptaR_lab, @pathogenomenick, @EvolveDotZoo, @jbloom_lab, @Tuliodna for starters.

@firefoxx66 @arambaut @K_G_Andersen @GuptaR_lab @pathogenomenick @EvolveDotZoo @jbloom_lab @Tuliodna 3. This is a really complex topic. There are no easy or fast answers, so be wary of anyone who pretends to have them.
It also means a lot of decisions will have to be made and are being made with considerable uncertainty. That is just the way it is I’m afraid.

@firefoxx66 @arambaut @K_G_Andersen @GuptaR_lab @pathogenomenick @EvolveDotZoo @jbloom_lab @Tuliodna Now to the UK variant:
UK scientists in @CovidGenomicsUK have been following changes in this virus more closely than anyone else. In December they looked at viruses from a surge in cases around Kent and found something very weird:

@firefoxx66 @arambaut @K_G_Andersen @GuptaR_lab @pathogenomenick @EvolveDotZoo @jbloom_lab @Tuliodna @CovidGenomicsUK Half the cases seemed to be the same variant (you expect more of a mix). And that variant seemed very distant from the other viruses when you plotted their relationships: There were 17 mutations that led to changes in the make-up of proteins (and some more that didn’t).

@firefoxx66 @arambaut @K_G_Andersen @GuptaR_lab @pathogenomenick @EvolveDotZoo @jbloom_lab @Tuliodna @CovidGenomicsUK Amongst those mutations were two of particular interest:
1. N501Y: previously shown to increase how tightly spike binds to ACE2, the virus' entry point into human cells. And @Tuliodna had reported worries that virus with this mutation appeared to be spreading fast in South Africa

@firefoxx66 @arambaut @K_G_Andersen @GuptaR_lab @pathogenomenick @EvolveDotZoo @jbloom_lab @Tuliodna @CovidGenomicsUK 2. 69-70del: a deletion of two amino acids in spike. This mutation had been found in virus from an immunocompromised patient who later died. Virus with the mutation (and another) appeared to elude the antibodies in convalescent plasma given to the patient. (work by @GuptaR_lab)

@firefoxx66 @arambaut @K_G_Andersen @GuptaR_lab @pathogenomenick @EvolveDotZoo @jbloom_lab @Tuliodna @CovidGenomicsUK It is important to remember that we are dealing with a really complex problem here: A virus competing with other viruses while being attacked by an immune system in a complex human body. What you see in a petri dish does not really tell you what happens in a patient.

@firefoxx66 @arambaut @K_G_Andersen @GuptaR_lab @pathogenomenick @EvolveDotZoo @jbloom_lab @Tuliodna @CovidGenomicsUK And in genomics, just as in journalism, context matters. A mutation may lead to one thing alone but to something else when it comes on the background of other mutations. That is another layer of complexity.
So seeing these mutations in a virus alone tells you little.

@firefoxx66 @arambaut @K_G_Andersen @GuptaR_lab @pathogenomenick @EvolveDotZoo @jbloom_lab @Tuliodna @CovidGenomicsUK But the scientists also saw this particular UK variant increasing in frequency in the south east of England quite rapidly.
That could just be chance, a series of super spreading events for instance that just happen to be with this virus. Or something else.

@firefoxx66 @arambaut @K_G_Andersen @GuptaR_lab @pathogenomenick @EvolveDotZoo @jbloom_lab @Tuliodna @CovidGenomicsUK This summer, for instance, another variant B.1.177 (I know, 🙄) seemed to spread across Europe rapidly. Researchers thought it might transmit better. But it probably just happened to be the strain circulating in Spain where many tourists were that then carried it back home.

@firefoxx66 @arambaut @K_G_Andersen @GuptaR_lab @pathogenomenick @EvolveDotZoo @jbloom_lab @Tuliodna @CovidGenomicsUK The difference now though is that there is already a lot of virus spreading in the UK, so it seems less likely that this kind of thing could explain why the new variant appears to be taking over. But still, as @firefoxx66 told me: Beware of early data, it can be tricky.

@firefoxx66 @arambaut @K_G_Andersen @GuptaR_lab @pathogenomenick @EvolveDotZoo @jbloom_lab @Tuliodna @CovidGenomicsUK The point is that taken together this is concerning: the signs we have of some mutations possibly changing the virus in a meaningful way AND the rapid spread of the variant carrying these mutations.
On a very basic level this is why scientists are more worried this time around.

@firefoxx66 @arambaut @K_G_Andersen @GuptaR_lab @pathogenomenick @EvolveDotZoo @jbloom_lab @Tuliodna @CovidGenomicsUK The other worry, of course, is how the virus acquired all these mutations so fast. And what the implications are for vaccines.
I’ll revisit this tomorrow. It’s late and I’m exhausted. Just wanted to explain why we should take seriously concerns that this variant spreads faster.