An interesting read, & reflection on why "moonshot" ideas like testing everyone all the time *are not a silver bullet* on their own. Among other reasons:
"Even a small number of people who willfully break rules 'can cause an extraordinary amount of damage.'"

#COVID19 #SARSCoV2
One of the problems we have with #COVID19 containment is social: "If you don’t help people to see an alternative that is palatable, and if you don’t find ways to create an alternative that is palatable, then they’re going to go back to what they always did" @emilymicheleL
We don't *need* lockdowns & severe restrictions to contain #SARSCoV2 - we know this now. But we do need planning, good execution, & a willingness to be responsive to changing situations - including openness to *some* restrictions. As all our tools work best when cases are low!

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More from @firefoxx66

14 Sep
2000 students from all over Switzerland (& the world?) in a giant room, & not a mask in sight... 😖

Please - if you're inside a room with multiple others - EVEN if you can keep your distance, & EVEN if it's not the rule - mask up! 😷

#COVID19 #SARSCoV2
It pains me a bit to tweet this because generally I think @UniBasel & Biozentrum in particular have had a really good pandemic response.

But the trend in Swiss Unis is that masks can come off when you sit down - & I have to caution against this. I don't think it's wise! 😣
One more clarification - I assumed from the caption that there were 2000 in the room, but this is actually not clear. Could be 2000 starting, but not all present in person.

However, still clearly more unmasked people in that room that I'd like!!
Read 4 tweets
31 Aug
This morning, after 14 wonderful years together all over the world, the most beautiful & wonderful cat in the world, Svara, passed away in my arms. 💔😿

A tiny grey-&-white fluffball, she was the most polite, friendly cat. I want to take a minute to tell the world about her...
Svara was abandoned in early 2006 on a homestead in the Texas countryside when a family took their mobile home & moved on, leaving behind an old washing machine, a bunch of trash, & 3 cats...

We rescued them & brought them to a vet. The little grey-&-white one stole my heart.
I was only 20 yrs old & in my 2nd year at Uni - literally no idea what my future held. I found her name on a baby-name website: it's Hindi and means Goddess of sound.

I didn't know what come, but what a pair we made. We moved together to Ft Worth & TCU in late 2006.
Read 11 tweets
19 Aug
In June, after reopening, #SARSCoV2 #COVID19 cases in Florida began to rise. Hospitalisations & deaths, however, stayed low.

Perhaps it just wasn't so bad after all? Perhaps something had changed?

We see similar trends in Europe now. So what happened in Florida?
Let's see

1/25 Data from vhttps://public.tableau.com/profile/jason.salemi#!Data from https://public.tableau.com/profile/jason.salemi#!/
Something was going on in the new cases in June - noted in the media across much of the US South: new cases were mostly in the young. Note the change in proportion of tests in 20-34 yo (orange) over time

Huh. Why might that be?

2/25 Data from https://public.tableau.com/profile/jason.salemi#!/
@nataliexdean excellently explains 3 options:
1- More & more general testing (more likely to test any less symptomatic young ppl)
2- Elderly people being /more/ cautious
3- Young people being /less/ cautious



3/25
Read 26 tweets
18 Aug
Real-life lessons in phylogenetics... always be aware of your sampling biases. If most of the samples come from countries X & Y, you're very likely going to infer X & Y as the source.

(Note: I do not have the seqs. NZ may have extra info. However, using this as cautionary tale)
The group the New Zealand sequences fall into is marked here in yellow - you can click at the base to zoom in.
nextstrain.org/ncov/global/20…

If we then switch to coloring by country, you can see the diversity of this group: Image
We subsample our builds to balance the # of sequences from each place. Without doing that, the number of UK sequences would totally dominate.

However, while we can 'dial down' countries w/a lot of sequences, we can't 'dial up' countries we have few or no sequences from!
Read 4 tweets
18 Aug
1/ Small point in a big crisis but I'm *very* grateful to @biozentrum @UniBasel for giving postdocs access to Zoom Pro. Far as I can tell, this is not the norm!

But I'd be mortified to have to beg a collaborator, PI, or media contact to set up a Zoom every time I have a meeting.
2/ As post-docs we are working towards independent research - & that should include being able to schedule our own meetings in this social-distant time. It's infantilizing to not trust your post-docs to use Zoom 'properly'.
3/ (And even worse if the calculation was we're 'not worth the money' - postdocs are often the workhorses of research!)

So Unis, why leave postdocs out of Zoom Pro?

It's a small thing, but small things go a long way to making your staff (& they are staff!) feel valued!
Read 5 tweets
13 Aug
Our new paper, out now in @Eurosurveillanc, looks at #COVID19 #SARSCoV2 across Europe eurosurveillance.org/content/10.280…

A major part was reconciling different nomenclatures!

Working with @GISAID & @AineToole, we created a handy reference between @nextstrain, Pangolin & GISAID!

1/8
Using ~39,000 seqs from 35 WHO Europe countries (up to 10 Jul), we found an avg of 40 days btwn sample collection & GISAID submission, with 8% published in 2 wks!

We can breakdown timing by country (worth viewing in manuscript - Supp Fig 2!)

2/8
When we look at clades/lineages over time in Europe, we see 19A, L/V/O, A (Nextstrain, GISAID, Pangolin) dominating initially, concordant w early intros from Asia. However, must be mindful of small # samples from early epidemic & poss bias in who was tested (travellers)

3/8
Read 9 tweets

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