″The B.1.1.529 (omicron) Spike looks a whole lot like a ‘polymutant’ Spike experimentally generated to evade antibody responses from infection or vaccination, as noted by @theodora_nyc
> “I wish I was as optimistic @jbloom_lab Our polymutant spike has 20 aa substitutions and is almost completely resistant to neutralization by almost all vaccinated and convalescent plasma we tested. This new one has more in overlapping regions.”
I don’t have a great method for estimating exactly how effective existing vaccines will be against symptomatic infection but I’d give 95% odds they perform worse against Omicran than Delta. If I had to give a point estimate, I’d guess that your protection against symptomatic infection by this variant from being triple vaxxed will be 40%. But my error bars are very wide: a 95% confidence interval from 10% protection to 90%.
On a side note: it’s pretty scary to me that scientists are running experiments where they mutate coronaviruses to specically evade vaccines. Haven’t we learned our lesson here from the experiments that were going on in Wuhan? Even if the lab leak theory turns out to be false (which is looking less likely every month), it’s very clear that these experiments have tremendous potential to do harm. Why are we still doing this? It just seems totally nuts to me.
I’m going to put on my tinfoil hat here for a second: what are the odds that Omicron was created by a lab doing experiments on SARS-CoV-2? I keep going back to that tweet from Michael Woroby:
> “The B.1.1.529 (omicron) Spike looks a whole lot like a ‘polymutant’ Spike experimentally generated to evade antibody responses from infection or vaccination”
If the spike looks a lot like one that was experimentally generated to evade antibody responses, what are the odds that Omicron was created through such experiments? How many labs are doing the types of experiments that are being done at Theodora’s lab? If the number is high enough it seems likely that there will be a leak at some point given what we know about the history of such incidents at even the highest BSL facilities. Anyone have thoughts about how to more rigorously constrain the odds that this variant was accidentally released from a lab doing gain of function research?
“The B.1.1.529 (omicron) Spike looks a whole lot like a ‘polymutant’ Spike experimentally generated to evade antibody responses from infection or vaccination”
At this point I have to wonder about the existence of antinatalist virologists.
If the spike looks a lot like one that was experimentally generated to evade antibody responses, what are the odds that Omicron was created through such experiments?
The research in question seems to be described in this Nature paper, where the authors say (emphasis mine):
To more precisely map the targets of polyclonal neutralizing antibodies in individuals who are convalescent, we passaged a recombinant vesicular stomatitis virus (rVSV)/SARS-CoV-2 chimeric virus1,5 in the presence of each of the RU27 plasmas for up to six passages. rVSV/SARS-CoV-2 mimics the neutralization properties of SARS-CoV-2 (refs. 1,5) but obviates the safety concerns that would accompany such studies with authentic SARS-CoV-2.
So, regarding safety, it seems the place to start would be understanding the properties of this rVSV/SARS-CoV-2 construct. Further details are here.
Do you know what kind of research Theodora’s lab is actually doing? (She doesn’t have a surname on Twitter so I can’t find her). But I imagine research into spike protein mutants could just involve synthesising spike protein that has mutations and assaying the binding affinity of antibodies to the synthetic spike protein – not necessarily creating mutated viruses.
(undergrad biochemistry was a long time ago. I could well be wrong)
“The B.1.1.529 (omicron) Spike looks a whole lot like a ‘polymutant’ Spike experimentally generated to evade antibody responses from infection or vaccination”
If the spike looks a lot like one that was experimentally generated to evade antibody responses, what are the odds that Omicron was created through such experiments?
Alternatively, gain of function research is useful and gives us advanced warning of natural mutations. I don’t know if that is the one true narrative , but I’m not ruling it out.
That’s certainly the argument its proponents make, and perhaps it’s true in some circumstances. But after looking at some of the research grants made to the Wuhan Institute of Virology in the years leading up to the outbreak, it’s clear to me that there really is dangerous research out there whose theoretical benefits are vastly outweighed by the costs.
For example, there was some really dangerous gain-of-function research happening in a BSL-2 facility, which are just not designed to contain dangerous pathogens.
But we inherently need international agreements to deal with these problems. I believe the US banning gain of function research in 2015 was one of the driving factors that pushed the research overseas into Wuhan.
But we inherently need international agreements to deal with these problems. I believe the US banning gain of function research in 2015 was one of the driving factors that pushed the research overseas into Wuhan.
That seems doubtful to me. It seems to me like as part of wanting world class scientists this is something the Chinese wanted regardless of US research policy as long as the research is held at high esteem by the international scientific community.
Alternatively, gain of function research is useful and gives us advanced warning of natural mutations.
Even if it would produce useful information, that might still be the case that Omicron exists for those reasons. It’s strange to use the word alternatively hear when any information gained doesn’t negate the cost of potentially producing variants like Omicron.
To the extend that you believe that there’s useful information, can you give any example of anything useful coming out of it?
Whether or not something provides valuable information is orthogonal from it being dangerous. The two aren’t alternatives. Something can be valuable&dangerous.
I think you are likely underweighting the possibility that Omicron could significantly decrease vaccine efficacy.
Omicron has 50 mutations including 30 in the spike protein. I believe Delta had 9. https://twitter.com/EricTopol/status/1464410605402480641
https://twitter.com/MichaelWorobey/status/1464325657861574659
″The B.1.1.529 (omicron) Spike looks a whole lot like a ‘polymutant’ Spike experimentally generated to evade antibody responses from infection or vaccination, as noted by @theodora_nyc
And at long last, here’s the tweet I read two days ago and have been looking for ever since. https://twitter.com/theodora_nyc/status/1464257411582148608
> “I wish I was as optimistic @jbloom_lab Our polymutant spike has 20 aa substitutions and is almost completely resistant to neutralization by almost all vaccinated and convalescent plasma we tested. This new one has more in overlapping regions.”
I don’t have a great method for estimating exactly how effective existing vaccines will be against symptomatic infection but I’d give 95% odds they perform worse against Omicran than Delta. If I had to give a point estimate, I’d guess that your protection against symptomatic infection by this variant from being triple vaxxed will be 40%. But my error bars are very wide: a 95% confidence interval from 10% protection to 90%.
On a side note: it’s pretty scary to me that scientists are running experiments where they mutate coronaviruses to specically evade vaccines. Haven’t we learned our lesson here from the experiments that were going on in Wuhan? Even if the lab leak theory turns out to be false (which is looking less likely every month), it’s very clear that these experiments have tremendous potential to do harm. Why are we still doing this? It just seems totally nuts to me.
I’m going to put on my tinfoil hat here for a second: what are the odds that Omicron was created by a lab doing experiments on SARS-CoV-2? I keep going back to that tweet from Michael Woroby:
> “The B.1.1.529 (omicron) Spike looks a whole lot like a ‘polymutant’ Spike experimentally generated to evade antibody responses from infection or vaccination”
If the spike looks a lot like one that was experimentally generated to evade antibody responses, what are the odds that Omicron was created through such experiments? How many labs are doing the types of experiments that are being done at Theodora’s lab? If the number is high enough it seems likely that there will be a leak at some point given what we know about the history of such incidents at even the highest BSL facilities. Anyone have thoughts about how to more rigorously constrain the odds that this variant was accidentally released from a lab doing gain of function research?
At this point I have to wonder about the existence of antinatalist virologists.
The research in question seems to be described in this Nature paper, where the authors say (emphasis mine):
So, regarding safety, it seems the place to start would be understanding the properties of this rVSV/SARS-CoV-2 construct. Further details are here.
To me the most remarkable thing about the Nature paper is that the word biosafety or BSL doesn’t appear in it.
Saying they obviated the need of safety concerns and then doing the experiments without any biosafety protocols seems crazy.
Do you know what kind of research Theodora’s lab is actually doing? (She doesn’t have a surname on Twitter so I can’t find her). But I imagine research into spike protein mutants could just involve synthesising spike protein that has mutations and assaying the binding affinity of antibodies to the synthetic spike protein – not necessarily creating mutated viruses.
(undergrad biochemistry was a long time ago. I could well be wrong)
Alternatively, gain of function research is useful and gives us advanced warning of natural mutations. I don’t know if that is the one true narrative , but I’m not ruling it out.
That’s certainly the argument its proponents make, and perhaps it’s true in some circumstances. But after looking at some of the research grants made to the Wuhan Institute of Virology in the years leading up to the outbreak, it’s clear to me that there really is dangerous research out there whose theoretical benefits are vastly outweighed by the costs.
For example, there was some really dangerous gain-of-function research happening in a BSL-2 facility, which are just not designed to contain dangerous pathogens.
But we inherently need international agreements to deal with these problems. I believe the US banning gain of function research in 2015 was one of the driving factors that pushed the research overseas into Wuhan.
That seems doubtful to me. It seems to me like as part of wanting world class scientists this is something the Chinese wanted regardless of US research policy as long as the research is held at high esteem by the international scientific community.
Even if it would produce useful information, that might still be the case that Omicron exists for those reasons. It’s strange to use the word alternatively hear when any information gained doesn’t negate the cost of potentially producing variants like Omicron.
To the extend that you believe that there’s useful information, can you give any example of anything useful coming out of it?
If you want to determine the balance of evidence, by all means do so, but you can’t do that by completely disregarding the alternative explanation.
There was a time when thus place was all about the avoidance of bias.
Whether or not something provides valuable information is orthogonal from it being dangerous. The two aren’t alternatives. Something can be valuable&dangerous.
If the value is in saving lives, then the two are not orthogonal.