Cornelius Roemer Profile picture
Bioinformatics 👨🏻‍💻 Viral 🦠 Evolution 🧬 with @richardneher @biozentrum Physicist 🔭👨🏻‍🔬 educated @Cambridge_Uni @MIT @KU_Leuven @MRC_LMB
Κασσάνδρα Παρί پری Profile picture Olivier Duquesne aka @daffyduke@mamot.fr🔻🐧🦆🇺🇦 Profile picture .... Profile picture 😷 Daniel Brockmann 💉💉💉 Profile picture J Doe (they/them) Profile picture 11 added to My Authors
Aug 2 5 tweets 3 min read
Monkeypox case rates are slowly decreasing in Germany (as they've been in Portugal).
Meanwhile, US pop adjusted incidence still looks pretty exponential, overtaking Germany (note: log plot)
Sustained exponential growth is unlikely to be driven purely by testing expansion. 1/ Image I'm showing Germany and the US here because they publish the most consistent and smooth data.
See here for the German data on linear axes. 2/ Image
Jul 23 14 tweets 4 min read
Quick explanation why BA.4 and BA.5 descend from BA.2 as opposed to B.1.1.529 in this figure:
The evolutionary history of BA.4/5 is unsolved.
BA.4/5 are so similar to BA.2 that in the big picture it makes sense to have them branch off from ~BA.2 (note the ~). 1/ When the Pango committee gave the names BA.4/5 a name BA.2.X would have been also justifiable.
Pango naming decisions need to be made quickly, without the benefit of hindsight and with limited data.
In the end, names are just names, don't attach too much meaning. 2/
Jul 17 12 tweets 5 min read
Seit ich wissenschaftlich an Virusevolution arbeite, habe ich besseres zu tun als mich mit fragwürdigen Experten auseinanderzusetzen.
Weil ich es aber schwer aushalte, dass Stöhr trotz aller Desinformation immer noch von vielen Medien hofiert wird, mache ich hier eine Ausnahme. Hier ein Faktencheck der Aussagen.
Behauptung: Stöhr tweetet am 31. Mai, dass 5k Dosen völlig ausreichend seien, kritisiert Bestellung darüber hinaus.
Fakt: Allein Berlin hat bereits 8k Dosen erhalten - und wird sie sicherlich komplett verimpfen. 2/
aerzteblatt.de/nachrichten/13…
Jul 16 4 tweets 1 min read
Thought experiment in favor of giving (at very least) all dominant variants names:
What if we were super lucky and got a very transmissible Omicron variant that was super mild?
Would we call this Omicron or not name at all?
After all, it would be a variant of hope not of concern As soon as the level of alert determines variant names we are getting ourselves into deep trouble.
Because names should not change once given. Whereas evidence will change.
Naming must be as much as possible distinct from any degree of concern/alert/alarm. 2/
Jul 15 6 tweets 2 min read
Here's yet another argument for giving (at the very least) wave causing variants a name:
It makes it more obvious that we need strain adapted vaccines.
If it stayed Omicron forever, it's not obvious that Omicron is not equal to Omicron. 1/ Soon there will be BA.4/5 vaccines out there as well as BA.1
So it will no longer sufficient to tell your doctor you got an Omicron-adapted booster. To be precise, you will need to say, I got a BA.1 or BA.4/5 booster.
Wouldn't it be nicer to say: Omicron or Sigma (hypothetically)
Jul 12 7 tweets 6 min read
Cautiously optimistic news from Germany on #monkeypox containment
Not only has case growth slowed but 7d case averages seem to drop for the first time.
More than half of all German cases have been reported in Berlin despite it accounting for just 3m out of 80m inhabitants. 1/ Here you can see distribution by state (unfortunately lacking population adjustment for now, I think @theochemiker is working on it) and age distribution.
Kudos for publishing data at such granularity (even by county!) @rki_de. Data on sex/gender seems not available, sadly. 2/
Jul 5 6 tweets 2 min read
This is just not how this works.
These R0 estimates falsely assume there is no population immunity. But especially Omicrons have mostly thrived due to immune escape since there are very few unvaccinated, uninfected people left.
Omicron R0s are unlikely to be higher than Delta's. So just for context   Wuhan... It's not at all trivial to measure R0 in populations that have almost no naive individuals left.
The closest we can maybe is unvaxxed household secondary attack rate, but even then - chance is that someone will have been infected in the past.
Jun 19 8 tweets 3 min read
Putin has obviously timed gas cuts to Germany very carefully.When:
- German public is getting numb to the war
- there's less time to prepare for winter shortage
- respected non-expert opinion journalists start doubting Ukrainian ability to defeat Russia even with more weapons 1/ Not boycotting Russian gas immediately has made Germany blackmailable
Putin can tune the amount of pain he wants to inflict on Germany.
When Scholz appeases, he'll send more gas, when he is displeased (by e.g. weapons deliveries) he'll turn the gas off.
Perfect torture device 2/
Jun 18 10 tweets 6 min read
It's essential to normalize epidemiological case data relative to countries' population size.
I created a Google Sheet to do just that for monkeypox, based on the fantastic @globaldothealth dataset.
Here's the result visualized with @Datawrapper:
datawrapper.de/_/J70fo/ 1/ It would be great if @globaldothealth implemented this directly inside the "Cases by Country" sheet. Maybe this thread can serve as motivation for how useful that feature would be.
Absolute comparison when inappropriate is a major pet peeve of mine. 2/
Jun 17 5 tweets 2 min read
A German monkeypox patient has written an informative 23 tweet thread (not an actual thread, so navigate to their profile for the list of threads)
First misdiagnosed as syphilis. Here's another thread from a different German patient.
Hats off for sharing your experiences.
Jun 3 4 tweets 5 min read
Phylogenetic tree of the West African clade with new US outbreak sequences (Virginia, Florida): nextstrain.org/monkeypox?c=co…
The tree is built using a @nextstrain build, using @CDCgov @CrystalGigante et al's sequences via @NCBI, pre-processed with @GenSpectrum
Open data at its best Here are pictures from the current outbreak, so you know what to look out for
Sources:
eurosurveillance.org/content/10.280…
eurosurveillance.org/content/10.280…
Here are two more @Eurosurveillanc papers worth reading:
eurosurveillance.org/content/10.280…
eurosurveillance.org/content/10.280…
May 30 4 tweets 3 min read
Post on virological by @AineToole and @arambaut discussing the APOBEC3 hypothesis to explain the unexpectedly large evolution rate for #monkeypox observed since 2018.
virological.org/t/initial-obse… Key part:
"We therefore suggest that the pattern we see in these MPXV genomes since 2017 is indicative of replication in humans and the inheritance of the specific changes [...] means that there has been human to human transmission since at least 2017."
May 30 11 tweets 7 min read
The @biozentrum PhD fellowships are particularly for those who want to explore a number of labs/groups during rotations before picking their group.
In addition to wet labs, there are a number of computational & systems biology groups. 1/
Overview: biozentrum.unibas.ch/research/resea… In @richardneher's group, we work on a broad range of topics in Viral and Bacterial evolution, well beyond @nextstrain - though this is what I mostly work on with amazing full stack dev @ivan_aksamentov (we love Rust/React/Typescript/WASM/Python 🦀) 2/
biozentrum.unibas.ch/research/resea…
May 29 19 tweets 8 min read
With now some 30 monkeypox sequences available, it is possible to analyse what's going on. There's already a surprise: while monkeypox usually has a low evolutionary rate, in the last few years the rate has been much higher, maybe ~10x higher. There are hypotheses why 1/ There's strong evidence of a very specific pattern of mutation in almost all mutations that have been acquired since this virus' ancestor (or at least its genetically identical twin) happened to be sequenced in 2018 in the UK. 2/
May 26 5 tweets 2 min read
The growth advantage that BA.4/5 has over BA.2* is remarkable. In the UK (chosen because of consistent sequencing), the rel advantage is on the order of 15% per day, i.e. rel share doubles every 5 days.
UK is estimated to hit 50% BA.4/5 share this week. 1/
cov-spectrum.org/explore/United… What astonishes me is how few mutations were necessary to produce this large growth advantage.
S:452R on its own does not seem to provide any advantage to BA.2, it must be the other 2: S:486V and S:Q493R reversion or alternatively some interaction (epistasis) between them. 2/
May 25 4 tweets 2 min read
Based on the size of this #monkeypox outbreak, I think there's a non-zero risk it will become endemic in at least some new regions.
Countries with good containment will get it to (near)-zero, but not all will manage.
Hopefully we'll have a vax in a year to start eradicating it 1/ I don't think the narrative that #monkeypox is mild is helpful. Yes we shouldn't panic. But we need people to cooperate, change behaviour to contain it
If they think it's mild, why should they cooperate if inconvenient?
You really don't want to get it. Even if it doesn't kill you Image
Apr 14 8 tweets 5 min read
Warum zitiert @ZDFheute Vad als seriösen Militärexperten?
Hat den noch niemand gegoogelt?
1. Vad hat anscheinend neurechte bis rechtsextreme Verbindungen: Merkel-Berater im Abseits
2. Hat er Anfang des Krieges überall verlautbart dass der Krieg sicher in wenigen Tagen vorbei sei Das zitierte Welt-Interview ist echt irre.
Die USA und andere EU-Staaten liefern massiv Waffen. Aber wenn Deutschland gepanzerte Infanterie-Fahrzeuge schickt, dann führt das in den dritten Weltkrieg?
Amerikaner bilden in wenigen Tagen an Radar aus. Vad sagt das dauere Jahre. 🤔
Apr 14 5 tweets 3 min read
I wouldn't worry about BA.2.12.
Only the daughter lineage BA.2.12.1 has S:L452Q which seems to be the main driver of the growth advantage.
Also, please _always_ quote growth advantage with units. Per day? Per week? It's night or day! 1/
@apoorva_nyc @nyttypos_typos Please don't lump the two together. Their growth advantage differs a lot.
BA.2.12 has probably almost none over BA.2
Also, I'm not a fan of the wording "even more contagious".
It's possibly mostly immune escape. Not higher R0. 2/
nytimes.com/live/2022/04/1…
Apr 13 7 tweets 3 min read
I see a lot of public worry around BA.4/BA.5 that I don't consider justified.
BA.4/5 only differ from BA.2 by 3 Spike substitutions and 1 deletion.
BA.4/5 are much closer to BA.2, than BA.2 to BA.1
They probably just have more immune escape.
Intrinsic severity likely similar. 1/ Image BA.4/BA.5 may well replace BA.2 but this will be more like BA.2 replacing BA.1 (prolonging Omicron waves) but won't be as drastic as when Omicron first appeared and sent case numbers shooting up.
There may be other BA.2 lineages around that are similarly fit as BA.4/BA.5 2/
Apr 11 6 tweets 4 min read
Here are @covSpectrum queries to track BA.4 and BA.5 as they get sequenced around the world.
The queries aren't perfect but they should be pretty sensitive and specific (>95%)
Here's BA.4 and where it has been sequenced:
🇿🇦 73
🇩🇰 5
🇬🇧 2
🇧🇼 2
🇧🇪 1
cov-spectrum.org/explore/World/… 1/ Image And here's BA.5:
🇿🇦 31
🇩🇪 5
🇦🇹 1
cov-spectrum.org/explore/World/… 2/ Image