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Cornelius Roemer Profile picture
Cornelius Roemer
@CorneliusRoemer
Studying SARS-CoV-2 evolution @nextstrain @biozentrum Studied Physics @Cambridge_Uni, then learned about computers @corneliusroemer.bsky.social
Κασσάνδρα Παρί پری Profile picture @daffyduke@mamot.fr Profile picture Jörg 🌻 @j_honegger@swiss.social Profile picture Guus Brugman 💙 Profile picture .... Profile picture 16 subscribed
Aug 21, 2023 • 14 tweets • 3 min read
Here are counts of BA.2.86 and overall sequence submissions to GISAID
Note that the English sample included in week 2023-08-07 likely got expedited, so it may be best to exclude from this analysis. 1/ Image In my very rough reading, there's not enough data yet to pin down growth advantage. It could be small or non-existent, or it could be sizeable, e.g. doubling every week.
Bear in mind that due to constant antigenic drift, there are always lineages with decent growth advantage. 2/
Aug 11, 2023 • 8 tweets • 3 min read
EG.5 (and EG.5.1) has recently got attention due to being highlighted by @UKHSA and @WHO.
EG.5, which is an alias for XBB.1.9.2.5, is a sublineage of XBB characterized in particular by Spike RBD mutation F456L. 1/ EG.5 is one of the fastest growing XBB sublineages, particularly common in China where it appears to be dominant.
As EG.5 has only one RBD difference compared to the upcoming vaccine strain XBB.1.5 vaccine protection is expected to be good. 2/
Apr 10, 2023 • 6 tweets • 2 min read
It appears that China has stopped uploading SARS-CoV-2 sequences to GISAID and now shares via its own version of Genbank: Genbase
github.com/yatisht/usher/… I don't yet fully understand the terms under which China shares the sequences - I assume (and hope_ they are just as open as Genbank.
In that case this is a great development towards having as much SARS-CoV-2 data being free of usage restrictions as possible.
Nov 28, 2022 • 9 tweets • 2 min read
I'm seeing quite a bit of discussion about the potential impact of a big wave in mainland China on variant evolution.
I do not think a big wave in mainland China would have major consequences outside of China. 1/ While China is a big country, it has less than 20% of the global population. The rate at which new variants evolve would only increase slightly as a result of fractionally more infections worldwide. 2/
Oct 14, 2022 • 6 tweets • 3 min read
For straightforward problems, @github Copilot really rocks.
Yes, as a Python dev, I could code this up myself in less than a minute
But why spend mental energy on this if it can be auto-generated?
As a beginner, this could have easily taken me a few minutes. Now it's just seconds And the only unnatural about this example is that I deleted the output generated by copilot before recording.
Everything else is exactly as it was when I did it.
Nothing contrived, very natural usage pattern.
Oct 13, 2022 • 7 tweets • 4 min read
BQ.1* and XBB have different geographic foci
BQ.1* is mostly in Africa, Europe and North America
XBB in South (East) Asia
3 countries with similar levels worth watching for comparison and potential co-circulation are:
- Japan
- Australia
- South Korea
cov-spectrum.org/explore/World/… 1/ ImageImageImage BQ.1.1 and XBB have quite a lot of spike differences and seem to have similar growth advantages - this makes them candidates for co-circulation.
We may only be able to know once we see how the variants do in countries that had a wave with the other one. 2/
Oct 12, 2022 • 6 tweets • 1 min read
A general point why one should be extremely skeptical about stories proposing a causal relation between a new lineage/variant and particular symptoms (right now diarrhea):
New lineages always start very rare.
BQ.1.1 makes up at most a few % of infections in recent weeks. 1/ The people speculating that a variant may be responsible don't seem to understand this.
They think "there's news of a new variant, maybe that's what's driving X"
This is flawed. New variants at low percentage are neither responsible for case growth (yet) nor new symptoms 2/
Oct 7, 2022 • 9 tweets • 3 min read
Ich freue mich, dass verschieden Forschungsgruppen die Auswirkungen verschiedener Virusevolutionsszenarien modelliert haben.
Leider enthält das Papier Aussagen die über Modellierung von Szenarien hinausgeht und die in meinen Augen nicht mehr haltbar sind. 1/ Image In der Veröffentlichung & zugehöriger Pressemeldung steht, dass es momentan nicht möglich sei zu prognostizieren welches Szenario eintritt.
Das stimmt leider nicht. Während es in der Tat vor 2 Monaten nicht klar war wie groß der Variantenimpact sein würde hat sich dies verändert.
Oct 6, 2022 • 14 tweets • 8 min read
With 3 more days of data, here's a look at how far various collections of immune escape variants have progressed so far.
I now count S:493 as a key mutation, so what used to be >=5 (Pentagon) is now >=6.
The more RBD mutations, the faster the growth.
cov-spectrum.org/explore/World/… 1/ Image Looking at the data like this, we reduce the complexity behind numerous emerging variants into 4 buckets of increasing escape. This is not perfect as what's in a bucket is not totally the same, but it solves the problem of having to remember BQ.1.1, BA.2.75.2, XBB etc. 2/ Image
Oct 5, 2022 • 5 tweets • 3 min read
The best way to monitor the impact of new variants for will be not to consider individual lineages but a collection of lineages with similar properties.
Each lineage may make up only a fraction of the swarm. But together they are already more prevalent. 1/
cov-spectrum.org/explore/United… In the example above, for the US, BA.2.75* lineages make up 40%, BQ.1 makes up 30%, and other lineages make up the other 30%.
This is a challenge for dashboards like the CDC's, that only list individual lineages when they are at above 1% individually. 2/
Oct 2, 2022 • 18 tweets • 7 min read
With 11 days more data, it is becoming quite clear that BQ.1.1 will drive a variant wave in Europe and North America before the end of November
Its relative share has kept more than doubling every week
It has taken just 19 days to grow 8-fold from 5 sequences to 200 sequences 1/ A week ago, @TWenseleers estimated a growth advantage of ~14% per day for BQ.1 over BA.5
This may be a slight overestimate. But note this was for BQ.1 not BQ.1.1 which has a few extra % pts
Evidence quite strong that BQ.1.1 will have >10%/day advantage. 2/
Sep 21, 2022 • 5 tweets • 2 min read
Ich hab über das Baden-Württembergische Impfterminportal einen Impftermin gebucht
Jetzt bin ich in der Praxis und die Praxishelfenden sagen mir ich darf nicht geimpft werden, ich hätte schon 3 Impfungen und sei viel zu jung. Der Impfstoff sei nur zugelassen für Ü60
So ein Quatsch Ich versuche zu erklären dass sie vermutlich die STIKO-Empfehlung meinen, nicht die Zulassung. Und dass der Impfstoff sehr wohl zugelassen ist für mich.
Die EMA ist da ganz klar.
Helfenden sagen sie hätten strikte Anordnung.
Ich sage dann möchte ich mit der Ärztin sprechen. Image
Sep 8, 2022 • 9 tweets • 5 min read
There is no mystery. Let me try to explain.
BA.5 is not equal to BA.5 - there are many sublineages
BA.5 that have acquired S:346T are growing consistently
You don't see that if you don't separate it.
The other 10% are mostly BA.4.6 (BA.4 + S:346T).
Graphs in thread 1/ Image BA.4.6 has slowed in growth because BA.5 + S:346T is fitter than BA.4 + S:346T (we have much more BA.5 now than BA.4)
That's the explanation why it looks like nothing is happening if you only break out:
BA.5 and BA.4.6 and ignore the richness in BA.5* lineages. 2/ ImageImage
Sep 6, 2022 • 4 tweets • 1 min read
Ich experimentiere mal mit verschiedenen Fragestellungen um zu sehen wie groß der Unterschied ist. Bitte Fragen genau lesen und alle Umfragen im folgenden Thread ausfüllen
Ich fange die Umfrage bewusst im nächsten Tweet, weil sonst Zahl der Antworten im ersten Tweet viel höher 1/ Wie häufig haben Sie sich PCR-bestätigt infiziert?
Wichtig: Nur echter PCR zählt in dieser Frage. 2/
Aug 21, 2022 • 8 tweets • 2 min read
Even if no wildcard variant arises, it's quite hard to predict which variant is going to be dominant in ~2 months from now.
The most likely candidates look like
- BA.5 + S:346T (e.g. BF.7)
- BA.2.75
Interesting about BA.2.75 is that it already has lots of interesting lineages 1/ Various BA.2.75 lineages have already acquired a variety of RBD mutations e.g. at S:486, S:490, S:452
There are also lineages with mutations S:346T and S:356T. In some of the lineages more than one extra Spike mutation is present. 2/
Aug 2, 2022 • 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, 2022 • 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, 2022 • 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, 2022 • 6 tweets • 2 min read
Fascinating So many amazing videos there, thanks @caceypeters
Jul 16, 2022 • 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, 2022 • 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)