Ulrich Elling Profile picture
Dec 16 13 tweets 6 min read
🇦🇹 Representative genomic surveillance of SARS-CoV-2 in Austria. This is our analysis run number 100, so I would like to start by thanking the entire SARSeq team. One hundred successful analysis rounds straight is an amazing achievement, congratulations to everyone!
1/ Image
With @LCochella and @yelagandula_ram we initiated the task of nationwide surveillance of SARS-CoV-2 in an academic setting in response to the Alpha variant. A great collaboration between #AGES @agesnews, @IMPvienna and @IMBA_Vienna/@oeaw. And a big responsibility!
2/ Image
This collaboration of health authorities and academia showcases the innovative power and value of academic institutions that stepped in in response to the pandemic. Globally such solutions were rather the rule than the exception, so big shoutout to all my colleagues worldwide!
3/
Let’s get to the data of analysis week 50. The new variants are taking over fast. Currently we see ~33% BA.5 including BF.7.
BQ.1* lineages are dominant now at ~50%, and the BA.2.75-derived lineages make up for ~11%. In addition, we see recombinants XAY*, XBB*, XBC.
4/ Image
There is really a soup of expanding lineages currently, shown here extrapolated to absolute reported cases. Needless to say: The extrapolation to officially reported cases is a gross underestimation.
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However, it should be mentioned that also sewage monitoring notices a flattening of the curve recently. Viral interference -directly or indirectly- by people (kids!) being sick at home with RSV, Influenza, and Rhino?
abwassermonitoring.at/dashboard/
6/ Image
Of the BQ.1 lineages the fastest growth is observed for BQ.1.1 with a deletion of spike 144 (BQ.1.1.10/20). This is likely because in near-complete immune evasion of the receptor binding domain this mutation helps immune evasion of the N-terminal domain of spike.
7/ Image
In fact, if you go back to the plot above you will notice that there was no lineage since BA.5 that displayed such a rapid expansion. The faster the growth relative to previous lineages, the more total cases a lineage can produce once it is dominant.
8/ Image
Of the BA.2.75 daughters CH.1.1 grows the fastest and within Austria with a head start in the region of Vorarlberg (shown are cases relative to total cases). Both fast lineages therefore seem to be coming from the West. But CH.1.1 is not quite as fast as BQ.1.1+144del.
9/ Image
There is something else to say about CH.1.1: We continue to detect Spike_P681R in it. This position is important for cell-cell fusion and thus tissue damage, amino acid “H” in Omicron made the virus “milder” the “R” in Delta made things worse. Now we see “R” in Omicron.
10/ Image
Let’s hope it will not expand significantly and/or not show worse disease. (These data are missing.) But Spike_P681R has shown up in neighboring regions now either in single cases or in sewage. github.com/cov-lineages/p…
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Expectedly, also the rate of Influenza A positive Covid patients in on the rise. Currently we are seeing ~0.9% of Covid patients with an Influenza A superinfection. We do not monitor RSV.
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Next week will be the last report for 2022, then we are taking a break until 2023. Thank you for your continuous interest!
13/

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More from @EllingUlrich

Nov 24
Important work on the wild reservoirs of SARS-CoV 1 and 2 and a new SARS-CoV-SARS-CoV-2 recombinant in a paper that just went online summarized here 🧵:
biorxiv.org/content/10.110…
1/11
Yunnan Province at the southern tip of China is a hotspot for bats and bat viruses. Closest relatives of SARS-CoV as well as SARS-CoV-2 are found here and different bat species are living in caves together.
2/11
In this important work, researchers analyzed 149 bats individually to study what virus they carry and found 41 different ones, 70 bats were positive for at least one virus (47%), amongst them 1.5 viral species were found on average per individual.
3/11
Read 11 tweets
Oct 21
🇦🇹 Representative genomic surveillance of SARS-CoV-2 in Austria in week 42 across all regions. Nowcasting in dashed box shows the current situation. A collaboration of #AGES @agesnews and @IMBA_Vienna/@oeaw.
1/6 Image
BA.5 with R346T has reached ~25% now. New variants such as BQ.1(.1) and XBB show clear growth. BQ.1(.1) currently at ~8%, XBB<1%.
2/6 Image
Due to the good weather (see journals.plos.org/ploscompbiol/a…) and declining case counts of BA.5 we currently observe a strong reduction in absolute numbers.
3/6 Image
Read 6 tweets
Oct 13
🧵To mask or not to mask, this is the question again.

With winter starting in the northern hemisphere, masks are discussed many places. Some thoughts within the range of realistic options:

A.For societies
B.For individuals Image
A. Any form of enforced mask mandate as seen in some countries previously of course is a stress test for societies and generally disfavoured by most, but also requested by many. Some arguments for society level reactions:
A.1 One might argue that dampening one wave with masks just means the next wave is higher. Connected vessels. Only true however if we assume that one wave generates immunity against the next, this was neither true always in the past nor is it projected to be the case this winter. Image
Read 15 tweets
Sep 23
Currently there is a trend towards convergent evolution in SARS-CoV-2. But is that the whole picture? All roads to Rome and that’s it? Or where do we go from here?

My 2 cents in an illustrated 😊 thread….
1/
We have built a polyclonal B-cell immunity to counteract a SARS-CoV-2 infection, that we all cherish. But as we get closer to the edge of it, mutations in the spike protein gain more advantage to escape that defense.
2/
With the initial variant this was less likely to occur, but with BA.1 and even more so BA.2 there is more immune erosion and drops get more frequent. Modified from this wonderful study.
biorxiv.org/content/10.110…
3/
Read 18 tweets
Sep 17
Looking like with the latest turn of direction the virus has managed to escape our immune system efficiently yet again.

There is an unprecedented number of highly diverged variants coming up and two brand-new studies shed light on this concerning situation.

Amazing work!
1/
In one study, Ben Murrell and colleagues show five-fold escape from serum neutralization by BA.2.75.2 in pseudovirus assay.
biorxiv.org/content/10.110…
2/
In another very impressive study, Xiaoliang Sunney Xie and colleagues study many current sub-sub variants comprehensively.
3/
biorxiv.org/content/10.110…
Read 14 tweets
Sep 12
Mutational differences between important SARS-CoV-2 lineages within the antibody binding regions of the spike protein. Shown is NTD (defined here as amino acid 1-300) and RBD (301-600) separate and together.
1/4
This rainbow-painted spike (blue to red) shows the N-terminal domain in shades of blue followed by RBD in shades of green for comparison.
2/4
Mutation space differences must not be confused with immunological distance, but do hint towards vaccine efficiency. The upcoming lineages BA.2.75.2 and BJ.1 are 33/36 mutations away from WT, 31/28 from BA.1, and 13/17 from BA.5.
3/4
Read 4 tweets

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