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Cornelius Roemer Profile picture
@CorneliusRoemer
Aug 11 • 8 tweets • 3 min read Twitter logo Read on Twitter
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/
While the name EG.5 may sound very different from XBB, it is important to know that this is just due to naming - EG.5 is the short form of XBB.1.9.2.5. 3/
While EG.5 does increase in frequency worldwide, it does so much slower than Alpha, Delta, BA.1, and BA.5 did when they spread around the world.
The growth of EG.5 represents gradual evolution, antigenic drift, as opposed to larger evolutionary jumps that were seen in the past 4/
EG.5's growth advantage is not enough to cause waves on its own, in contrast to past variants like Delta and Omicron.
Given EG.5's modest growth advantage, if it causes waves it will be only one factor along others like titer waning or environmental and behavioral changes. 5/
One interesting fact about the 456L mutation:
EG.5 is by far not the first XBB lineage to have acquired this mutation. The first was XBB.1.5.10 in February, see in the figure below which shows all XBB lineages with 456L colored by designation date
6/ https://t.co/M6mKx2RE5Hnextstrain.org/staging/nextcl…
Image
It appears that initially 456L did not provide a significant benefit. The growth advantage seems to have grown as population immunity against XBB increased. This matches with what @yunlong_cao et al already predicted in their impressive work in May: 7/
This analysis is only possible due to the continued sequencing work by thousands of people around the world 🙏
If you want to read more systematic discussions of the evolving variant landscape, you can find monthly report that I write here on Github: 8/github.com/neherlab/SARS-…

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More from @CorneliusRoemer

Cornelius Roemer Profile picture
Apr 10
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.
GISAID should still be able to integrate the data in their platform (unless the license prohibits it, if it's Genbank-like then GISAID can pull the data as they've done with Genbank-only published sequences).
Read 6 tweets
Cornelius Roemer Profile picture
Nov 28, 2022
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/
We have by now seen multiple second generation BA.2 variants evolve independently: BA.4/5 in Southern Africa, BA.2.75 in South Asia, BA.2.3.20 in the Philippines, BS.1 in South East Asia. 3/
Read 9 tweets
Cornelius Roemer Profile picture
Oct 14, 2022
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.
It's hard to think of a better way of solving this problem.
Copilot chose a very pythonic solution.
There's a good chance handwritten solutions by many developers would be less idiomatic and more confusing.
Read 6 tweets
Cornelius Roemer Profile picture
Oct 13, 2022
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/
Here are the mutations that only occur in one of the two variants:
XBB only: S:V83A, S:Y144-, S:H146Q, S:Q183E, S:V213E, S:G339H, S:R346T, S:L368I, S:V445P, S:G446S, S:F486S, S:F490
BQ.1.1 only:
S:H69-, S:V70-, S:V213G, S:G339D, S:K444T, S:L452R, S:F486V 3/
Read 7 tweets
Cornelius Roemer Profile picture
Oct 12, 2022
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/
Even if a variant made a particular symptom 10x more likely (huge effect, much bigger than what's likely to happen), if the variant is only at 1% of all cases, it would only increase overall prevalence of that symptom by 10%! Far below where anecdata would allow detection. 3/
Read 6 tweets
Cornelius Roemer Profile picture
Oct 7, 2022
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.
Mittlerweile sind Varianten bekannt geworden, die eher Szenario 2 als 1 entsprechen.
Sowohl der beobachtete Wachstumsvorteil als auch die im Labor gemessene Immunflucht von BQ.1.1 & co sind auf einem Niveau vergleichbar mit den Unterschieden von BA.4/5 gegenüber BA.2. 3/ Image
Read 9 tweets

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