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
4/ The first tweet in this thread was meant to be a quote-tweet of @erwinheim's always-excellent figures. Apologies that it went missing somehow.
As usual, see his full thread for a great breakdown of numbers.

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More from @firefoxx66

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.

ssi.dk/-/media/arkiv/…

1/21
*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.

2/21
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 30 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

1/6
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.

2/6
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.

3/6
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: medrxiv.org/content/10.110…

1/16
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!

2/16
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:

nextstrain.org/groups/neherla…

3/16
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!

1/9
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!

2/9
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.

3/9
Read 9 tweets
23 Oct
I've lost my vacuum cleaner.

I set the Roomba going on its little job & a little while later I heard it give its musical "I'm stuck!" alarm (in French, as I can't figure out how to change the language).

....And I can't find it 🙃🤦🏻‍♀️

#HowsYourFridayGoing?
Good news - I have found the Roomba. It made itself a little nest under a low cupboard, behind some boxes, & over some thick cables (didn't know it could crawl over those). It now has a dead battery & is being grumpy at me (in French).
Roomba & I have a strained relationship at times. I bought it second-hand & I think it has abandonment issues

Me: *pointing* I would actually really appreciate it if you'd do the kitchen floor now please
Roomba: *heads off to vacuum random corner by front door for the 17th time*
Read 5 tweets
14 Oct
We do not have to choose between lives & livelihoods when fighting #SARSCoV2 - through effective #TestTraceIsolate & suppression, we can allow *everyone* to take part in an open society.

Join myself & more than 80 other #COVID19 scientists & experts - sign the #JohnSnowMemo
Why 'John Snow'? It's not just because winter is coming! John Snow is considered one of the founders of epidemiology - he traced a cholera outbreak in London to a water pump & removed the handle to curb transmission. Quick effective action saves lives!

en.wikipedia.org/wiki/John_Snow
The letter says it best, but why do we stand against 'targeted shielding' & 'natural herd immunity'?
1. We do not fully understand immunity to #SARSCoV2 - we don't know how effective it is, or how long it lasts. It's irresponsible to lean on something we don't know will work.
Read 12 tweets

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