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
As long as our test positivity remains so high, we're at the edge of our knowledge about the #SARSCoV2 epidemic dynamics.
We risk rolling back measures too soon, when we still have a very limited understanding of how case numbers are really behaving
It's also a reminder that Swiss-wide estimates are likely largely reflecting the dynamics of hardest-hit cantons, but may be masking what's happening in other places in Switzerland. We must stay aware of the larger- & smaller-scale picture.
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: research.esr.cri.nz/articles/prepr…
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
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.
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.
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
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
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.
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