I'm excited to announce a new paper with @MLReichmuth and @C_Althaus, out now in @PLOSPathogens!

We used phylogenetics & modelling to investigate the introduction & expansion of #SARSCoV2 Alpha & Delta variants into #Switzerland & to simulate different interventions.

1/17 First, we wanted to estimate the number of times Alpha & Delta were introduced into Switzerland before they were dominant.
For this we used sequences: we looked for where Swiss Alpha/Delta seqs descend from non-Swiss sequences - coming to Switzerland from elsewhere.

2/17

Benevolent dictators have no place in academic science.

I don't care if they usually make the right decision. Or if people don't think they've abused their power yet.

Science should not depend on one person being well-behaved.
Balance should be built in, power distributed.

1/5 "If you want to go fast, go alone, if you want to go far, go together" the African proverb says.

Can driven, visionary people start up groundbreaking ideas & cut through barriers to implement them? Absolutely! This 100% is part of science.

2/5

🎉CoVariants.org Update!🎉

23B (XBB.1.16) is now available on CoVariants! It's visible as part of Per Country & Per Variant plots, on the shared mutation page - and of course, has a page of its own.

1/10

#XBB116 #23B #Arcturus
📷 This is in line with the recent addition of 23B (XBB.1.16) as a @nextstrain clade - read more on that below 👇🏻!

2/10

https://twitter.com/nextstrain/status/1650545883480567813

A Q I've seen: "How did this stay quiet so long?"

Quote from the article:
"Many sources who spoke to Science declined to be named out of fear of legal action from Bogner or of losing GISAID access."

Scientists depend on GISAID access. Fear is powerful.

science.org/content/articl… Also from this article:
'Marion Koopmans ... says she has received multiple calls from Bogner“with a rather intimidating tone.” So have colleagues, she adds. “I have heard similar experiences from quite a few.”'

If you're an early career researcher (yes even 'just' a PhD student!) 1 of my biggest pieces of advice would be:
Go claim/create your Google Scholar page!! 👈🏻✍️🏻

I put this off bc I thought I 'didn't have enough on it'. I also generally thought "nobody is looking for me".

1/4 Now that I'm (a little) on the other end, I see how wrong I was.

It's *just fine* to not have "much" in your Google Scholar profile - anyone worth their salt will be evaluating you relative to your career state.
Much more important: to be findable!

2/4

🎉 CoVariants.org Update! 🎉

23A (XBB.1.5) is now available on CoVariants! It's visible as part of Per Country & Per Variant plots, on the shared mutation page - and of course, has a page of its own.

1/9

#XBB15 #23A This is in line with the recent addition of 23A (XBB.1.5) as a @nextstrain clade - read more on that below 👇🏻!

2/9

https://twitter.com/nextstrain/status/1623723987707564034

I've had this question a couple of times:

The recombinant XBB is shown as having mutation S:F486S (inc on CoVariants.org), from parent BM.1.1.1 - but looking at BM.1.1.1* now, it seems to have mostly S:486P!
So did XBB really get 486S?

https://twitter.com/firefoxx66/status/1587762412110974976

1/5 As usual @GenSpectrum helps us dig into this at CoVSpectrum:
cov-spectrum.org/explore/World/…

Looking at "Mutations over time", we can see really nicely that BM.1.1.1* was mostly S:486S earlier, then 486P later - likely a daughter lineage outgrowing 'original' BM.1.1.1!

2/5

Wonderful to be back in #Wengen last night for the @ISPMBern #SwissEpiWinterSchool - to talk about Wengen! Specifically, the Alpha #SARSCoV2 outbreak in Dec 20 - Feb 21 - bringing together 3 different data sources! Alongside @nicolamlow Chris Kosok @JulRiou!
1/4 Thanks to tireless work of many, the #Wengen outbreak was swiftly identified & action was taken. Chris' field observations, cantonal teams of contact tracers, & of course testers & sequencers, mean we're able to bring together sequences, contacts, & observations for analysis!
2/4

Well, after almost 3 years of a dizzy dodging dance - #SARSCoV2 finally got me last week. 🦠🤒 Happy to say I'm on the road to recovery now! 🛣️

It seems many of us 'hold outs' have been caught out in the last few weeks - be safe out there this Xmas!

1/5 I've generally been quite careful, but with the resumption of in-person meetings (& all the activities that go along, like dinners & aperos!), there was always a risk - one I accepted knowingly. I think online working is great TBH, but in-person really is different.

2/5

In spring 2020, I crafted myself 5 rules for how I would engage on Twitter. Generally, I think they've worked well for me:

1. Tweet with intent 🖋️
2. Stay positive 🙂
3. Engage in good faith 🫱🏿‍🫲🏻
4. You don't owe anyone a response 💁🏻‍♀️
5. Never feed the trolls 🧌

1/9 First, a disclaimer: These are the rules I try to follow. But I'm not perfect - I've broken them; I've made mistakes.

But in general, I've stuck to them. I do think they've allowed me to have a better social media experience in the last 3 years than many, & I'm grateful.

2/9

🎉CoVariants.org Update!🎉

22F (XBB) is now available on CoVariants! It's visible as part of Per Country & Per Variant plots, on the shared mutation page - and of course, has a page of its own.

1/9

#XBB #22F This is in line with the recent addition of 22F (XBB) as a @nextstrain clade - read more on that below! 👇🏻

2/9

https://twitter.com/nextstrain/status/1588313824301649920

I got verified when the option arose, to try to make it harder for others to impersonate me & spread pandemic misinformation under the guise of being me. That's all.
I think for that purpose, it's really useful. But I won't pay for it.

1/5 As others have said, I put a lot of work into my tweet threads - sometimes hours. That's time that is already taken away from my 'real' work. Though I consider it privilege to be able to do this public service work, I won't pay to do it.

https://twitter.com/NathanGrubaugh/status/1589004373736460288

2/5

You might be seeing a lot about XBB these days, & we're in the process of adding it to @nextstrain, Nextclade, & CoVariants.org (as 22F).

You might also be hearing it's a 'recombinant' - but what does that mean? Let's take a look.

1/9 We've been hearing of recombinants for a while now (remember 'Deltacron'?). They can sound scarier than they are!
The process itself is likely common, but we only 'see' recombinants when someone is infected with two distinct lineages, with different mutation patterns.

2/9

I'm pleased that case numbers & hospitalizations in many European countries have a downward trend - but hesitant to overinterpret this.

#SARSCoV2 is seasonal & while that isn't entirely due to temperature, some of it is - & this season in Europe has been... quite warm!

1/4 Here are the daily temperatures in Basel, & how they compare to average (black line) from @meteoschweiz. As you can see, we've almost been having 'August temperatures' in October! Much of Europe has enjoyed a similarly mild autumn 🌞🍂🍁

2/4

🗓️CoVariants.org Update🗓️

In preparation for more flexibility in adding variants, CoVariants.org now processes & colours recombinant sequences separately - you can spot them in brown in the Per Country graphs. 🔀🔀

1/5 Previously recombinants weren't included in CoVariants as they presented some unique problems - but now they're included and shown separately. (If any recombinants are designated as variants, they'll show up as their designated variant instead!)

2/5

🎉CoVariants.org Update!🎉

22E (BQ.1*) is now available on CoVariants! It's visible as part of Per Country & Per Variant plots, on the shared mutation page - and of course, has a page of its own.

1/8

#BQ1 #22E

covariants.org/variants/22E.O… This is in line with the recent addition of 22E (BQ.1*) as a @nextstrain clade - read more on that below! 👇🏻

2/8

https://twitter.com/nextstrain/status/1583182554982920193

I've scheduled my #SARSCoV2 COVID-19 bivalent booster! 🗓️💉How about you?

Even with immune-evasive variants, vaccinations can still help boost your protection, especially from bad outcomes! Every little bit might make the difference this autumn - you can help! 😁✊🏻 If, like me, you live somewhere where only the BA.1 bivalent is currently available, I would still recommend it. We don't know what variant may dominate, (but it's likely Omicron, like BA.1), & given how things are looking, I wouldn't wait for 2023 to get boosted.

What should we expect from #SARSCoV2 this autumn?

I think it would be smart to prepare for both an increase in #COVID19 due to seasonal (behavioural) change & a new variant.
As so many others have elegantly illustrated, new lineages of SC2 are sparking interest.

1/17 Up front, I want to give a huge shout-out to @CorneliusRoemer who does a fantastic job keeping an eye on variants, particularly for @nextstrain & #Switzerland. But also for fantastic tireless work by @PeacockFlu @theosanderson @siamosolocani @SolidEvidence & more

2/17

📡CoVariants.org Update📡
This update doesn't impact the visualizations or the data, but @MoiraZuber deserves a public appreciation thread thanks to her tireless efforts & recent refactoring achievements - so here it is!

1/7 CoVariants is a labour of love - I'm always trying to squeeze it in between the million other things I 'should' be doing (which hopefully lead to publications, the hard currency of academia). Because of this, the time I can put into CoVariants is sadly limited 😞⌛️

2/7

Huge thanks to @HopkinsMedicine @AmaryFaln @hmostaf2 for sending along the first #Enterovirus #D68 #EVD68 sequences of 2022! 🙏🏻🚀

You can see them in the full-genome & VP1 builds:
nextstrain.org/enterovirus/d6…
nextstrain.org/enterovirus/d6…

1/5 Note that for the moment I don't have anything but year for these sequences, so month is being inferred by the pipeline - note the wide confidence interval on the date!

However, zooming into the VP1 build, we can see some interesting connections...

2/5

📡#Enterovirus #D68 #EVD68 builds on @nextstrain are now updated 📡

You can check out the VP1 (single-gene) build (nextstrain.org/enterovirus/d6…) & full-genome builds (nextstrain.org/enterovirus/d6…).

I'll give a brief overview of a few things of interest...

1/7

https://twitter.com/firefoxx66/status/1565721872234340352

The VP1 #EVD68 build lets us include the most sequences, so I'll focus on that here - though full-genome has many other advantages!

No 2022 seqs yet (got my 👁️peeled!), but there are some from 2021 - from Europe & N America. These stem from the B3 & A2 clades.

2/7