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Dr Emma Hodcroft Profile picture
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20 Dec, 5 tweets, 3 min read
From the latest data available on GISAID this morning, an updated S:N501 #SARSCoV2 build is available.

We now have a clade label for the South African variant (20C.501.V2) & will add one for the UK variant soon.

No major additions to the tree.

1/4
nextstrain.org/groups/neherla…
The latest data identified additional sequences in S:501 mutant variants from the UK, Denmark, Australia, & South Africa, but no additional countries.

(!This table does not distinguish variants & some countries listed haven't seen 501 in months!)

2/4
github.com/emmahodcroft/c…
From the plot of variants frequency in sequences, per country, we can see that the 501Y variant (pink) is expanding in the UK (the last data point represents incomplete data & will likely change in future).

3/4
github.com/emmahodcroft/c…
Seeing no new countries in sequences isn't at odds with media reports: our analysis is based only on sequences which are made available to scientists through GISAID. Countries can analyse their own sequences faster, so they may be detecting cases we do not have samples for.

4/4
For more information on the new UK and SA variants, check out my thread from yesterday:

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More from @firefoxx66

Dr Emma Hodcroft Profile picture
21 Dec
Switzerland has now banned flights from the UK - following on from an increasing number of other countries.

If the new UK variant may already be in more countries across Europe, why are countries stopping flights from the UK?

#SARSCoV2 #COVID19

1/10

In short: numbers matter.

The number of people with the new variant in continental Europe is likely still small: with testing, tracing, identification & restrictions, we might be able to prevent them from passing the virus on. That's easier with 10 people than 1000.

2/10
However, border closures make the most sense when coupled with fast action *inside* countries as well.

Even a few cases can become a few thousand quickly, if there's nothing to stop them. So as well as border controls, countries need to be stepping up measures within.

3/10
Read 11 tweets
Dr Emma Hodcroft Profile picture
19 Dec
Is the new UK variant the same as the new South African variant (501Y.V2)?

No.

They both share the same mutation in spike: N501Y (N->Y at position 501). However, the 2 variants have arisen separately.

1/N
nextstrain.org/groups/neherla…
In the tree below, the UK variant is in green at the top. The SA variant is the one with large yellow circles nearer the bottom.

Though it's a bit hard to see in this tree, they are quite distant genetically: they have many mutations they do not share!

2/N
S:N501Y has occurred multiple times around the world. Not all of these have risen & become prominent. So the role of 501Y is probably more complex.

UK variant & SA variant both have many other mutations that are being investigated.

3/N
Read 15 tweets
Dr Emma Hodcroft Profile picture
17 Dec
Two new variants are now up on the #SARSCoV2 #COVID19 Mutations of Interest site! 🎉

Added
- Spike 69 deletion (S:H69-)
- Spike V1122L (S:V1122L) - primarily circulating in Sweden.

(More detail on each on the site coming soon - but thread below!)

1/9
github.com/emmahodcroft/c…
S:H69- is of particular interest, as it's part of a double-deletion (also position 70) that's appeared at least 3 times independently in conjunction with receptor binding domain (RBD) mutations: N501Y, N439K, & Y453F.

2/9
nextstrain.org/groups/neherla…
Below, the yellow is N439K, the orange is Y453F associated with Denmark (we see Y453F mutation multiple times) & the red is N501Y (again, we see N501Y mutation multiple times). Each of these RBD mutations also exists without the 69/70 deletion.

3/9
nextstrain.org/groups/neherla…
Read 10 tweets
Dr Emma Hodcroft Profile picture
15 Dec
Large blue circles below are samples that carry S:N501Y, but unlike the new variant in England, do not have the 69/70 deletion (that's in the green ones). These samples are primarily from Wales. @CovidGenomicsUK may have more information here!

21/N Image
Zooming in on the tree a bit, a small cluster in yellow carries a different mutation at the same position: S:N501T.

These are relatively recent samples, mostly from the North/North Eastern USA & eastern Canada (yellow on map).

22/N Image
Important to remember: these clusters I highlight above are separate from the 'new' UK one. However, they can give us information about mutations at the S:N501 position!

And they highlight the importance of sequence sharing: the only way to see these connections! 🤝

23/N
Read 7 tweets
Dr Emma Hodcroft Profile picture
15 Dec
There are many, many #SARSCoV2 #COVID19 variants out there! A few have caught the attention of scientists in Europe - we're trying to monitor them!

I'll be maintaining updated information here:
github.com/emmahodcroft/c…

#newvariant

1/7
This site includes a bit about what we know about specific mutations/clusters, including counts of sequences, some graphs, and links to dedicated @nextstrain runs (maintained by @richardneher Lab & myself) focused on each mutation

2/7
You can also check out graphs of the prevalence of the clusters in various countries:

3/7
github.com/emmahodcroft/c…
Read 7 tweets
Dr Emma Hodcroft Profile picture
14 Dec
As far as I know, the #SARSCoV2 variant identified by Hancock today is defined by a spike mutation at position 501 N->Y & a double-deletion at positions 69/70.

You can see it in orange in the dedicated Neher Lab S:N501 @nextstrain build below
nextstrain.org/groups/neherla…

1/N
I do not have more information about why scientists in the UK believe this variant may have increased transmission.
However, it does appear the proportion of UK sequences containing S:N501 mutations has increased recently (sorry, hard to see)

github.com/emmahodcroft/c…

2/N
This build is from last week (I'll try to update soon), but from this information, it seems like this particular variant has so far only been detected in the UK and Denmark. However, we may simply not have samples from other countries.

nextstrain.org/groups/neherla…

3/N
Read 19 tweets

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