On this Christmas Eve, I would like to spare a thought for the many scientists, researchers, & lab technicians & assistants who have been 'called up' thanks to the new #SARSCoV2 variants.
It's been a tough year & many of us had hoped this week might be a well-earned break.

1/6
Academia/science is rarely a 9-5 job, & we're a bit famous for our tendency to overwork, but it's a rare year when evolutionary biology & phylogenetics are so urgently needed that we can't slip away for a few quiet days over Christmas!

2/6

(see alt text for the ornament shop!) https://www.etsy.com/listing/883890228/plush-virus-in-face-m
I imagine many, like myself, are humbled & proud that we can contribute to the efforts against #COVID19 #SARSCoV2.
But it's been an incredibly long, hard year for many of us, compounded by the same restrictions, loss, & loneliness that so many have felt.

3/6
So I'm sending out strength & peace today to all my science-y colleagues who will have 1 ear on the inbox, 1 hand on the keyboard, & half a brain on the latest news this week, rather than the full 'unplugging' we might have hoped for this time of year.

4/6
As I am for the millions of essential workers & healthcare workers, who work through Christmas *every* year but will no doubt be feeling extra strain after a year of carrying so much of the load of 2020 & the sadness & desperation it has brought so many.

5/6
Be kind to yourself the next few days. Take time to enjoy a glass of something warm (or something strong!). Unplug as much as you can. Zoom with family and friends. Laugh. Spend a quiet evening enjoying beautiful lights.

Stay warm. Stay healthy. Stay strong.
🧣🎁🎄❄️

6/6

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More from @firefoxx66

24 Dec
Merry Christmas! 🎄 The latest focal S:N501 build is now up.

Zooming in on 20B/501Y.V1 (SE England variant), we can see new sequences in Europe from the Netherlands.

1/4

#Newcoronavirusvariant #SARSCoV2 #ChristmasCovid

nextstrain.org/groups/neherla… Image
Zooming in on this further, and switching to divergence view (showing mutations rather than time), we can see they share 1 unique mutation & then have 1 unique mutation each, suggesting 1 introduction, possibly from the UK, & onward transmission.

2/4

nextstrain.org/groups/neherla… Image
We can take a similar look at the Danish sequences. They too, share one unique mutation, & some further unique mutations, suggesting a single introduction & onward transmission.

3/4

nextstrain.org/groups/neherla… Image
Read 4 tweets
23 Dec
A case of the '#SouthAfrica' variant has been detected in the UK. There's also talk about a 501Y mutation in Wales.
It's getting confusing!

First: all 3 of these 501Y mutations are independent. It's appeared a few times, separately.

#Newcoronavirusvariant

1/10
We can see this because the 3 variants (UK=1, Wales=2, SA=3) are not next to or inside each other in the tree below. In fact, we need to trace back to before March to find their common ancestors:

2/10

nextstrain.org/groups/neherla…
Are the UK and South Africa variants the same? No. See this thread for more info:

Critically, the SA variant does not have the 69/70 deletion we see in the UK variant.

3/10

Read 10 tweets
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
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

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