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
Needless to say, during the last 9 months that's been even more critical! When our compute cluster had to go down due to malicious activity, @UniBasel IT worked with us to ensure the @nextstrain #SARSCoV2 builds could keep going out!

4/9
@biozentrum @UniBasel have also supported me personally through an unforeseen rocketing in visibility! Even though I'm 'just' a post-doc, they have made me feel valued & supported my media activity - even arranging a socially-distanced photoshoot so I have proper pictures!

5/9
I am incredibly proud of the way that @biozentrum in particular has navigated the #COVID19 pandemic, & believe it has been a shining example in Basel. For example, the messages of support from @schierlab have been clear, open, & exemplary. (I forwarded them to my family!)

6/9
But now I turn a new page: Supported by the @snf_ch on a joint grant btwn @C_Althaus & @richardneher, I'll be continuing my work on #SARSCoV2 & @nextstrain! In particular, we'll be continuing to try to understand how #COVID19 has spread & is spreading in Switzerland & Europe

7/9
I will remain a key part of the @nextstrain team, so don't worry - I'm not going anywhere in that sense!

However, I am excited to join @ISPMBern @unibern with renowned colleagues working on epidemiology & public health! I'm 100% certain great science will come from this!

8/9
As part of @C_Althaus's group, I'll be exploring new ways to integrate epidemiology, modelling, & phylogenetics. Though it'll be #SARSCoV2 focused initially, it's work that will hopefully be useful to more pathogens in future!
So stay tuned - even more science coming soon!

9/9

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More from @firefoxx66

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
7 Oct
Thanks for helping to spread info about phylogenetics @Laurie_Garrett! But it's critical the info is accurate.

Couple of important points:
These great graphics are come from @nextstrain! You can see a tree with full menus here: nextstrain.org/ncov/global
We update every weekday!
Also, those early genomes aren't 1% different. That would be a difference of 300 bases, and they differ by 0-2 bases.

The divergence of the strain you pick out (see it in yesterday's run nextstrain.org/ncov/global/20…) is in number of changes, NOT percent! Much less worrying :)
As @pathogenomenick says, even the longest branches of the tree are incredibly similar - they differ by ~20 bases out of 30,000 - or ~0.07%

Also, the sequence highlighted has 4 amino acid changes, not 6. This isn't unusual, so no need for alarm!
Read 4 tweets
7 Oct
1/ In much of Switzerland, we had a significant drop in temperature about 2 weeks ago. Likely people have come indoors, closed windows, & turned on heaters - all things that increase #SARSCoV2 #COVID19 transmission.

Winter isn't coming - it's here. And it's making things harder.
2/ In #Switzerland we have been teetering over the edge for weeks: a slow but sustained rise in cases. Our actions were slowing transmission, but not stopping it. The thermostat drop may have just given us a gentle push into more effective #SARSCoV2 spread.
3/ Rising #SARSCoV2 cases are bad on all counts:
- More chance of spilling into older age groups (worse outcomes) 👵🏼
- More chance of rare bad outcomes in younger ages 🤒
- And cases beget cases - the more there are, the harder it is to contain them 📈
Read 4 tweets
30 Sep
1/ #SARSCoV2 #COVID19 transmission isn't equal: some cases transmit much more than others. We know that close, crowded, poor ventilated places (esp w loud talking/singing) link to superspreader events.

Minimising these situations will have an outsized effect - without 'lockdown'
2/ We can also reduce *risk* in those situations: make them less crowded (density rules), make them quieter (no singing, turn down music so talking is easier), increase ventilation (open doors/windows, turn up HVAC), reduce aerosols (wear masks if possible).
3/ @AdamJKucharski explains that this uneven transmission also means a person, on average, was infected by someone who infected others too. If we trace *backwards* & find the 'source' - then trace their contacts - we'll identify more cases.
More effective use of tracing efforts!
Read 11 tweets
25 Sep
Is #SARSCoV2 #COVID19 evolving to bypass masks & hand-washing??

Good news - No! These measures physically remove 🧼👏🏼 or trap 😷 the virus so it never reaches you. These basically can't be evolved around. So keep up the mask-waring & hand-washing - it *is* protecting you!
Ah, you'd like more detail? Sure! The 'mutation' referenced is 'D614G' - it arose in Jan (long time ago!) & we've known about it for months. It's actually the variant that most ppl in Europe & many in the US already had!

So why are scientists still looking at it?
There is evidence the D614G mutation *may* slightly increase transmissibility. Studies in cell culture & looking at the virus structure think it might be /better at bonding to cells/.

That means it has to get to a cell before that mutation can have an effect!
Read 4 tweets

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