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BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

investors.biontech.de

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Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#11

Post by axg11 »

mlindner wrote: post #10
axg11 wrote: post #3

Impressive if true, although I am very sceptical of the results. The real test is to put their neck on the line and predict/warn of the next significant variant. If the authors are not willing to do this, I doubt that the algorithm is useful. As a side note, the first author on this paper is the CEO of InstaDeep. I see it as a red flag that the CEO of a 150+ person company would put themselves as first author on this…

> As a side note, the first author on this paper is the CEO of InstaDeep. I see it as a red flag that the CEO of a 150+ person company would put themselves as first author on this paper. Perhaps I'm unfairly judging and the CEO really was the lead contributor to the study. Authors on scientific papers are ordered by name, so whoever's name is first is pure coincidence.

This isn't true for the field of biology or medicine. If you take a look at the order of authors on the paper in question you can also see that the ordering is not alphabetical.

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#12

Post by WJW »

fasteddie31003 wrote: post #5

I'm all for stopping new variants of COVID. Why in the world do we have a treatment for COVID that intentionally creates mutations in COVID https://en.wikipedia.org/wiki/Molnupiravir ? I'm not a doctor but it seems pretty clear to me that Molnupiravir creates a great environment for new variants to arise (along with cancer, but that's another issue).

From the wikipedia page you linked:

> Molnupiravir is indicated for the treatment of mild-to-moderate coronavirus disease (COVID-19) in adults with positive results of direct SARS-CoV-2 viral testing, and who are at high risk for progression to severe COVID-19.[1][5]

So after the risk of creating mutations in the Covid virus has been assessed and weighed against the chances of patients just outright dying due to not having this medicine available, the board full of medical professionals trained in this matter voted 13 to 10 that they thought the risk was acceptable.

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#13

Post by dopylitty »

Given that we still don’t know the mechanism by which variants achieve their increased fitness I’m a little suspicious of claims of using “AI” to identify new variants.

Claims that spike affinity for ACE2 (or indeed changes to the spike protein at all) haven’t been conclusively proven to increase fitness as far as I know. It’s possible that this tool is simply overfit to the known variants and wouldn’t detect a new one.

I’d be interested to hear what real virologists think of this.

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#14

Post by gpm »

mlindner wrote: post #10
axg11 wrote: post #3

Impressive if true, although I am very sceptical of the results. The real test is to put their neck on the line and predict/warn of the next significant variant. If the authors are not willing to do this, I doubt that the algorithm is useful. As a side note, the first author on this paper is the CEO of InstaDeep. I see it as a red flag that the CEO of a 150+ person company would put themselves as first author on this…

> As a side note, the first author on this paper is the CEO of InstaDeep. I see it as a red flag that the CEO of a 150+ person company would put themselves as first author on this paper. Perhaps I'm unfairly judging and the CEO really was the lead contributor to the study. Authors on scientific papers are ordered by name, so whoever's name is first is pure coincidence.

The order of authors varies by field. I believe in biology it usually starts with the person who did most of the work (or people, but if more than one it's explicitly noted), everyone who contributed in the middle, principal investigator (i.e. head of lab) last.

In this case I notice that they first sorted all the instadeep people to the front, and biontech people to the end... not sure what I'm supposed to take away from the ordering, but it's not random.

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#17

Post by est31 »

alexwg wrote: post #2

Preprint: https://www.biorxiv.org/content/10.1101/2021.12.24.474095v1

Pretty cool stuff!

> When using a weekly watch-list with a size of 20 variants (less than 0.5% of the weekly average of new variant sequences), EWS flagged 12 WHO designated variants out of 13 (Fig. 4.A), with an average of 58 days of lead time (i.e two months) before these were designated as such by the WHO (Table S.4).

> Our system however does not accurately pinpoint the emergence of the B.1.617.2 Delta family of variants. Delta is known to be neutralised by vaccines24 and its global prevalence can be attributed to other fitness-enhancing factors [than immune escape]. These factors, such as P681R mutation, which abrogates O-glycosylation, thus further enabling furin cleavage, are outside of the scope of our approach.

> Specifically, the EWS identified Omicron as the highest immune escaping variant over more than 70,000 variants discovered between early October and late November 2021.

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#18

Post by spuz »

> More than 10,000 novel variant sequences are currently discovered every week and human experts simply cannot cope with complex data at this scale

This is interesting. I think the Greek alphabet naming system would lead some people to believe the virus only mutates once every few months. Of course, the reality is that every infected individual will produce hundreds of mutations within their body. I think there's a gap in the public messaging here which if addressed could help people understand what the future direction of the pandemic might be.

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#19

Post by meepmorp »

gpm wrote: post #14
mlindner wrote: post #10

Earlier quoted context omitted.

> As a side note, the first author on this paper is the CEO of InstaDeep. I see it as a red flag that the CEO of a 150+ person company would put themselves as first author on this paper. Perhaps I'm unfairly judging and the CEO really was the lead contributor to the study. Authors on scientific papers are ordered by name, so whoever's name is first is pure coincidence.

The order of authors varies by field. I believe in biology it usually starts with the person who did most of the work (or people, but if more than one it's explicitly noted), everyone who contributed in the middle, principal investigator (i.e. head of lab) last. In this case I notice that they first sorted all the instadeep people to the front, and biontech people to the end... not sure what I'm supposed to take away…

Or sometimes PI first, depending on the scope of the PI's ego

Re: BioNTech-InstaDeep Early Warning System to Detect High-Risk SARS-CoV-2 Variants

#20

Post by aftbit »

fasteddie31003 wrote: post #5

I'm all for stopping new variants of COVID. Why in the world do we have a treatment for COVID that intentionally creates mutations in COVID https://en.wikipedia.org/wiki/Molnupiravir ? I'm not a doctor but it seems pretty clear to me that Molnupiravir creates a great environment for new variants to arise (along with cancer, but that's another issue).

Because it helps keep people alive and the risks are judged to be worth the cost in high-risk patients. Hopefully Paxlovid will obsolete this one soon enough though.
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