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
Should bans have happened now, when we still have many unknowns about the new variant?

This is a difficult balance. The last 2 days, Dr Michael Ryan speech at WHO has been in my head: “If you need to be right before you move, you will never win."

4/10

Clearly, we need balance. ⚖️

Act too soon with too little info and you generate panic without evidence - damaging economy, livelihoods & trust.

But wait too long, & you could miss a vital window when we have the chance to have the most effective response.

5/10
What should we be doing in the meantime?

Travel bans within Europe can't continue indefinitely. Countries with them should be using this time to act locally & make a plan.

6/10
Act:
- Ramp up test & trace
- Special attention to areas with high UK travel/tourism
- Develop targeted PCR to initially detect currently present cases quickly
- Ramp up sequencing to confirm new variant cases, see how they're linked, & monitor for other variants too

7/10
Plan: how to handle traffic from UK?
Some options:
- Restrict travel allowed
- Quarantine (remember, may not work in practice as well as hoped!)
- Test all arrivals from some areas (but remember false negatives in early infection & need way to tell if new variant or not)

8/10
2 things will help detecting the variant in other countries:
- PCR developed to pick up the variant specifically could allow high-throughput testing - likely need sequence confirmation initially
- Ramp up sequencing to detect reliably & to monitor other & emerging variants

9/10
We have unfortunately had a 'curse' with #SARSCoV2: to wait & see if what happened elsewhere happens here too. The answer has been yes.

I hope this time we can break this curse with caution & coordination! 🤝

10/10

As before, you can find some more information on the new variants in the news this week here:

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More from @firefoxx66

20 Dec
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…
Read 5 tweets
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
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
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
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
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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