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Moritz Gerstung Profile picture
Moritz Gerstung
@MoritzGerstung
Division head @dkfz, professor @UniHeidelberg, visiting group leader @EMBLEBI. Previously @sangerinstitute and @ETH_en. We build AI to study cancer. Now at 🦋.
Jan 21, 2023 • 12 tweets • 5 min read
There are some signs now that XBB.1.5 is loosing steam as it spreads through the wider population.

The share of cases has increased more slowly in the US and UK, recently.

A speculative thread why this might be. In slowing down XBB.1.5 follows a pattern that has been noted also for BQ.1.1 or XBB.1.1.

Their initial fitness (daily increase of variant share) was higher than their long term advantage in a multi-lineage model with constant differences between variants (coloured lines).
Jan 3, 2023 • 10 tweets • 4 min read
A global look at the XBB.1.5 SARS-CoV-2 variant, which has spread rapidly in the US. In the US its share doubled every ~8 days during the past 2.5 months and is now estimated to contribute more than 30% of cases.

Across the globe XBB.1.5 is still comparably rare (<5%).
Nov 27, 2022 • 12 tweets • 6 min read
A closer look at SARS-CoV-2 variants across countries and continents:

- The competition between BQ.1*, XBB*, and BA.2.75.* inc. BN.1 & CH.1.1 remains open

- BQ.1* is more prevalent in the Western, and XBB* & BA.2.75.* in the Eastern hemisphere. Europe and North America see high frequencies of BQ.1*.

So far there hasn’t been a major upswing of cases.

Europe saw a wave of BA.5.2 in September which stalled the spread of BQ.1*.
Nov 17, 2022 • 10 tweets • 5 min read
Some musings on SARS-CoV-2 evolution

TLDR: The share of the variant zoo increased further with BQ.1* and XBB* at the top.

But there are interesting patterns underneath which can be illustrated by one exotic lineage: CH.1.1.

It’s rare, but it rises as fast as BQ.1.1. Why? ImageImage Background: There is a whole zoo of omicron sublineages, often defined by a range of mutations enabling partial immune escape.

Looking at the crude global increase over the past 28d CH.1.1 is one that has increased at the upper end of the flock. Image
Nov 4, 2022 • 7 tweets • 4 min read
The current SARS-CoV-2 variant situation in Germany:

* BQ.1 prevalence ranges between 5 to 12% across states,
* BQ.1.1 ranges from 5 to 15%.

The total share is around 18%. ImageImage In line with international observations BQ.1.1’s growth advantage to other lineages is slightly lower than initial estimates suggested.

Image
Nov 4, 2022 • 7 tweets • 3 min read
A brief update on global SARS-CoV-2 variants:

* BQ.1.1 spreads, albeit at the low end of expectations
* XBB* and BQ* lineages are the most widespread
* Further new variants have been defined, including CK.2.1.1 leading to complex patterns While the initial estimates of BQ.1.1's growth advantage to BA.5 were between 10-15%, the estimate has come down to ~10% more recently.

As other more transmissible variants such as BF.7 have also spread the current fitness is lower, around 6-7%.
Oct 18, 2022 • 7 tweets • 4 min read
The next few months may be a tight race between the BQ.1.1 and XBB.1 SARS-CoV-2 variants.

- Globally BQ.1.1 grew ~12% faster than BA.5, ranging from ~10% in Belgium to ~15% in Germany.

- XBB.1 grew >20% faster than BA.5 in Singapore, ~13% in the U.S., but only ~7% in Denmark. Brazil’s estimates are highly uncertain due to sparse rece The current uncertainty of XBB.1’s growth rate makes it an open race.

- XBB.1 dominance in Asia seems given.

- BQ.1.1 is widespread in Europe and North America, so it is likely that it will keep its higher share.

- The rest of the world could see either outcome I think.
Oct 13, 2022 • 15 tweets • 5 min read
What does your medical history tell you about future cancer risk?

And how much can be learned from knowing the medical history of an entire nation?

New preprint from the lab. 🧵

medrxiv.org/content/10.110… Background:

- Cancer is one of the leading causes of mortality in the Western world.
- Tumours develop over a long time before becoming detectable.
- Early detection improves survival rates, but current screening is limited to few cancer types.

cancerresearchuk.org/about-cancer/c…
Oct 12, 2022 • 5 tweets • 3 min read
An update on BQ.1.1 and other SARS-CoV-2 variants in Germany with fresh variant classification in @rki_de’s latest variant release.

There have been n=69 BQ.1.1 cases detected in Germany. Together with BQ.1 (n=124) it is estimated to contribute ~5% of cases on Oct 10. Image BQ.1.1 remains the fastest spreading variant in agreement with last week’s estimates.

BQ.1 and BN.1 (n=36) — a derivative of BA.2.75.5 — are spreading at somewhat lower rate (likely because BQ.1.1 has an additional immune escape mutation). Image
Oct 5, 2022 • 10 tweets • 4 min read
What’s behind the recent rise of covid cases are in Germany?

It’s not the new variants — yet. Image A number of variants possessing immune evasion mutations have been observed — BA.4.6, BF.*, BA.2.75.*, BQ.1.*

These variants make up around 20% of cases in Germany by Oct 1 — BF.7 (15%), BA.4.6 (3%), as well as other BF.*, BA.2.75.* variants and BQ.1.* (each <1%). Image
Feb 2, 2022 • 12 tweets • 4 min read
Behind the scenes of the Omicron waves there are interesting lineage dynamics.

Omicron can be split into two main branches BA.1&2, and BA.1.1, an offshoot of BA.1.

BA.1 is most prevalent in the UK, but BA.1.1 is catching up. All BA lineages have a growth advantage s over Delta/B.1.617.2*.

The advantage varies by lineage, over time and between countries.

BA.2 is fastest followed, by BA.1.1 and BA.1.

The growth advantage sets the slope at which the relative proportion of each lineage develops.
Dec 17, 2021 • 18 tweets • 7 min read
Der Omicron-Tsunami hat England erreicht und die Fallzahlen sind sprunghaft gestiegen.

Ist Deutschland im Vergleich gut gerüstet?

Kurz: Deutschland muss bei den Erstimpfungen und Boostern für Ältere nachlegen und eine Überlastung der Krankenhäuser verhindern. Hintergrund: Omicron ist nicht nur hochansteckend, sondern kann auch Geimpfte und Genesene infizieren.

Diese erkranken zwar eher leicht, tragen allerdings zur Verbreitung mit bei.

Die Fallzahlen drohen in bisher unbekannte Höhen zu steigen.
Nov 26, 2021 • 10 tweets • 3 min read
Some thoughts about the punctuated evolution of variants of concern including B.1.1.529 in Southern Africa. 🧵

A shared characteristic of all known VOCs is that they appeared suddenly with a large number of mutations, many more than the incremental changes we see normally. These mutations recurrently cluster in certain functional sites of the virus’ genome.

This is the signature of selection — while mutations occur more or less randomly, we preferentially see the subset that makes the virus fitter.

But why so many concomitant mutations at once?
Nov 25, 2021 • 6 tweets • 2 min read
🧵 zur neuen B.1.1.529 SARS-CoV-2 Variante, die vor einigen Tagen von Wissenschaftlern in Südafrika entdeckt wurde.

TL;DR: Die Variante bringt nahezu alle besorgniserregenden Merkmale mit sich, die wir in den letzten 1-2 Jahren gesehen haben.

1. B.1.1.529 hat mehr oder weniger alle Mutationen, die wir aus Alpha, Beta, Gamma und Delta kennen, gleichzeitig und noch weitere dazu.

Nov 18, 2021 • 13 tweets • 7 min read
An update on 🦠 SARS-CoV-2 variants in England.

Today: AY.4.2.1, AY.98 and other introductions.

TLDR: It seems to be ok. Background: The list of Delta sublineages has gotten longer – more than 121 AY.x lineages + sublineages.

This is thanks to the virus hunters @PangoNetwork spotting epidemiologically relevant variants across the 🌍.

These appear as colored branches at cov2tree.org
Oct 14, 2021 • 27 tweets • 11 min read
Just out - the rise and fall of SARS-CoV-2 lineages in England.

In the last 1.5yrs the UK has been a bell weather for SARS-CoV-2 evolution and genomic epidemiology thanks to the data sequenced by @CovidGenomicsUK and @sangerinstitute.

Let's recap. >>
nature.com/articles/s4158… As any virus, SARS-CoV-2 accumulates mutations and undergoes an evolutionary journey where fitter variants succeed. Most mutations are neutral and enable us to define lineages, which derive from a single ancestor and share all its mutations. By now there are >1000 lineages. >>
Sep 26, 2021 • 26 tweets • 6 min read
It’s election day in Germany.

A long 🧵 about what’s happening and some anecdotes for my friends abroad.

TLDR: It’s almost spooky how little has changed in the 9 years when I was away. Time for a fresh start, see leader below.

economist.com/leaders/2021/0… The areas where I feel Germany has to catch up compared to other countries where I lived and worked in the last 13 years are: climate, digitisation and bureaucracy.

I’d also think that it needs to take more responsibility in Europe and sort out its domestic demographic problems.
May 26, 2021 • 14 tweets • 6 min read
What have we learned from analysing 200,000 SARS-CoV-2 genomes from genomic surveillance in England in the last 9 months?

These data provide important context for the current situation related to B.1.617.2.

Here’s a summary of the preprint. medrxiv.org/content/10.110… @harald_voeh has developed a model that tracks 62 different lineages across 315 local authorities in England. His model estimates total and lineage-specific incidence and growth rates.
Apr 17, 2021 • 9 tweets • 5 min read
Want to *see* how a tumour has evolved and grown? And also how different clones acquired characteristic transcriptional and histopathological features?

Hold on, that's magic.

No, it's our new preprint by @LucyYat47076319 and @MatsNilssonLab 1/9

biorxiv.org/content/10.110… Jessica Svedlund developed a base-specific extension of the in situ sequencing protocol (BaSISS) to detect somatic mutations on a microscopy slide with fluorescently tagged padlock probes. 2/9
Dec 30, 2020 • 10 tweets • 4 min read
Did the new SARS-CoV-2 B.1.1.7 lineage spread during the English national lockdown? Rising numbers and estimated higher R value suggest so. Together with our colleagues from COG-UK we took a closer look. >> virological.org/t/lineage-spec… Fitting lineage-agnostic daily PCR test and viral genome data from COG-UK to 382 local authorities we find evidence that B.1.1.7 has spread in a staggering 200/246 of affected LTLAs during the November lockdown (R>1) while at the same time other lineages contracted (R<1). >>
Jul 27, 2020 • 9 tweets • 4 min read
Can you see mutations in cancer cells? Kind of.

We trained a neural network on 17k tumour slides with known genomics transcriptomics to assess how histopathology, molecular tumour characteristics and survival correspond. 1/8 nature.com/articles/s4301… This analysis discovered histopathological patterns of 167 different mutations ranging from whole genome duplications to point mutations in cancer driver genes - about 1/4 mutations tested. 2/8