The new #SARSCoV2 variant we identified recently, 20A.EU1, has jumped to New Zealand a few times (& been caught in quarantine) - but this interesting preprint shows how it seems to have transmitted in-flight, from individuals originating in Switzerland:…
Just for the avoidance of all doubt (I know I've been covering a lot of stuff lately!) this isn't linked to mink/Denmark, but the variant that's currently most prevalent in Europe, spread through summer travel. You can read more about it here:
This preprint was made possible by a long list of great people - unfortunately I do not know twitter handles for them all - but it was led by Tara Swadi & Jemma Geoghegan & involved @hamesjadfield @alexeidrummond @edwardcholmes & @Joepdl
This paper also highlights a critical point: while 20A.EU1 may have originally expanded in Spain, it has certainly spread from other European countries since then.
If you can't cut the transmission chain of a variant in your own country, you become the next 'source'.

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More from @firefoxx66

20 Nov
Gentle reminder that in Switzerland we are still feeling our way in the dark: with a #SARSCoV2 test positivity this high, the # of cases we report is largely linked to the # of tests we do.
While there are other signs cases are going down, we have a poor grasp on how much.

You can see this in this great cantonal graph by @gust_avius.
While tests & cases will always be linked somewhat, it's a bad sign when every jitter in testing is reflected perfectly in cases. It means we can't see exactly how case # are changing.


It's an even worse sign for places like Basel-Stadt, Schaffhausen, & Zug, where a decline in tests hasn't seen a same-size decrease in cases - in some cantons cases have even risen or plateaued despite the decrease in tests.

3/5 Image
Read 5 tweets
4 Nov
Recently reported #SARSCoV2 #COVID19 '#mink mutation' in #Denmark is getting a lot of attention right now, but officially we know almost nothing about the variants/mutations in question.
From an SSI report from Sept, here is a little info.…

*Very important caveat* here that I'm working with very limited information, but trying to make some sense of something that's getting a lot of attention, with the little info I can find. However, this should be taken as a tweet thread, not a preprint or anything similar.

On page 8, the document describes 2 variants, defined by mutations A22920T & a 2 amino-acid deletion from 21766-21771. Both are changes in the Spike protein.

3/21 Image
Read 58 tweets
4 Nov
1/ Very important to keep in mind that we've essentially reached #SARSCoV2 #COVID19 testing capacity in #Switzerland. Tests have plateaued but positivity is still >20%.

This makes it *very difficult* to read anything into the case numbers. I would urge caution with all analyses.
2/ There has been talk about hoping we can see signs of measures working by end of this week.

But, many cantons are restricting tests, lines are very long in places, & overall Switzerland can't really test more.

This makes it difficult to see whether restrictions are working.
3/ In the analogy where #SARSCoV2 testing is 'switching on the light' to fully understand the scope of the pandemic, #Switzerland has walked to the edge of where our lightbulb can illuminate.

At the cusp of darkness it's hard to see. Let's not make a leap of faith. #TestTestTest
Read 4 tweets
3 Nov
Looking back as we face a daunting #COVID19 winter: where did it all go wrong?

- We acted like we had an endless summer: didn't scale up #TestandTrace or plan ahead
- When cases rose, we hesitated. Priority on economy & freedom rather than lives means we're losing all three

We live in a world where a lot of things - politics & the economy in particular - are swayed by feelings & confidence. Politicians are used to being able to 'say things until they're true'.

Sadly, this doesn't work for viruses. Most leaders have not adjusted accordingly.

A lot of breath has been wasted on rhetoric:
'#COVID19 cases WILL come down'
'The economy WILL recover'
'Schools WILL stay open'

#SARSCoV2 cares little for words. Communication & messaging is important, but it is only /action/ that saves lives & livelihoods.

Read 5 tweets
29 Oct
Why is #COVID19 sequencing important? For one thing, it is the only way we can detect & track new variants.

In our latest preprint, we describe a novel #SARSCoV2 variant that has spread across Europe this summer & what it can tell us.

Read it here:…

This work was a fantastic joint effort with @MoiraZuber @SarahNadeau19 @TanjaStadler_CH & @richardneher in Switzerland & brilliant collaboration with @icoes & @fgonzalezf from SeqCOVID-Spain consortium.

Huge effort in getting this out quickly!

The 20A.EU1 variant is characterised by spike mutation A222V & accounts for >20% sequences circulating in Europe currently. Another variant, 20.EU2 has the mutation S477N and is about 15% of sequences.

We focus on 20A.EU1 - you can see both here:…

Read 18 tweets
27 Oct
3 years ago today I took my kitty under 1 arm & my bike under the other & boarded the plane to Basel

Today is another bittersweet day: I turned in my paperwork for the end of my time at @UniBasel @biozentrum

Monday, I start a new adventure w @C_Althaus @unibern @ISPMBern!

My time at the @biozentrum @UniBasel has been wonderful. I have been empowered & supported to do great research as part of a great community. The sense of community is strong- not always so easily found in academia!
And I am grateful to have benefitted from @antelope_unibas!

It seems like a small and obvious thing, but during my time here one of the things that sticks with me is that I have been able to *focus on doing my job* - because admin & support staff are clearly on my side! I haven't had to battle bureaucracy or beat against walls.

Read 9 tweets

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