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His argument is fallacious. He's saying that since there all other variants we're susceptible to the vaccine, it's unlikely that this one is. ...and goes on t

His argument is fallacious. He's saying that since there all other variants we're susceptible to the vaccine, it's unlikely that this one is. ...and goes on to list the high number of different markers the vaccines target. Unfortunately, vaccines largely target the spike proteins, and sequencing of omicron is demonstrating that every single protein marker on the spike is changed. Vaccines will likely have a very small effect on this variant. There are also two other mutations of concern that have never been seen together that each increase binding to ACE2 for cell entry. This all needs to be formally confirmed, but this is probably BAD.

dnautics 5y ago
We also don't know what the mortality rate is. Suppose it has 100% vaccine escape but 0% mortality. Would it be "BAD"?
- WithinReason 5y ago
  I think a 0% mortality strain displacing delta would be an extremely good outcome. One way pandemics stop is the virus mutating to harmlessness.
  - gandutraveler 5y ago
    That is exactly what I thought of too. So far the symptoms appear to be very mild and this could be a good way to scale immunity
    - sharken 5y ago
      The media is extremely focused on the number of infected and how infectious a new variant is. Somehow the low number of new hospitalizations is not newsworthy. Here in Denmark the hospitalizations have been steady at around 45% of the numbers we had when there was no vaccine. It's also 45% of the numbers we had in 2017/2018 with the flu back then. But that fact is not being used much to put things into perspective.
Kye 5y ago
Chise is a she/her-shaped creature as far as I know.
fartattack 5y ago
Your argument is fallacious. You clearly lack even an elementary education in immunology. Exposure to the antigen teaches your immune memory cells what the antigen looks like. Quit your job, stay home, live in fear. The rest of society doesn't need cowards like you. The pandemic is over, except for paranoid people. There will be endless variants. It's an RNA virus. No amount of vaccination will be perfect, but life will go on. Get vaccinated and go expose yourself to the existing endemic variants; it's the best defense there is. Live your life. If you think you can wait until there are no more variants, you'll be locked inside wearing a mask forever. Some of us have lives to lead.
f38zf5vdt 5y ago
A study in Nature had previously shown that >= 20 amino acid mutations on the spike protein was sufficient to cause immune escape from the vaccine or previous infection, but that individuals who were both previously infected and vaccinated were still able to neutralize the mutant virus. [1] The omicron variant has >30 AA mutations on the spike protein, so it remains to be seen how effective vaccines are in response to it. Even if it is unable to prevent infection, it's still likely that the vaccines will provide some attenuation of severity, especially with a booster. We also now have pharmaceutical means to treat infections, so any notions that this will bring us back to March 2020 seem unrealistic. https://www.nature.com/articles/s41586-021-04005-0 https://www.nature.com/articles/s41586-021-04005-0
- naasking 5y ago
  > individuals who were both previously infected and vaccinated were still able to neutralize the mutant virus. Mainly because of the infection, not the vaccination. Infection trains your immune response to detect multiple factors of the virus, the mRNA vaccines are only for the spike protein which has considerable mutations in later variants like this one. Arguably, traditional dead-virus vaccines might provide better long-term protection for this reason, but we went all-in on the new tech.
  - lamontcg 5y ago
    Somatic Hypermutation works on vaccine antigens as well, and diversifies B-cells so that the B-cells will recognize many spike mutations. Anyone who has been vaccinated or recovered probably has some B-cells which match this spike, even if they're not amplified and expressed into circulating neutralizing antibodies. T-cells on the other hand don't diversify as much but they recognize primarily the host MHC section of the MHC-antigen complex, so they're already somewhat insensitive to mutations in the protein. The T-cells stimulated by vaccine or virus aren't special in that regard. Arguably it doesn't really matter. If you get infected with this spike it is still going to have pretty much the same shape as the spike in the vaccine (after all even the mutated versions still need to bind to ACE2 and can't vary that broadly) and your vaccine-trained T-cells will still bind fine to the antigen-MHC complex that the spike forms. There's this idea that antibodies and immune responses are like a key fitting perfectly into a lock where any pin being wrong doesn't unlock the lock, and that's just false. The immune system has a need to fuzzy match against antigens because it evolved against adversaries which mutate and attempt to reinfect. You're pushing a narrative that spike-only vaccines are worse in the face of mutation, and there's just no evidence of that. On the other hand mRNA spike-only vaccines allow creating a very strong humoral response to the spike protein in the absence of significant side effects and their efficacy has been so far across the board superior to inactivated virus or viral-vector vaccines.
op00to 5y ago
No. If every single “protein marker” on the spike protein was changed, there wouldn’t be a heck of a lot of chance for the virus to attach to a cell. There still needs to be basic compatibility with the cell and the spike to get inside.
- chii 5y ago
  > there wouldn’t be a heck of a lot of chance for the virus to attach to a cell. but there isn't just a single shape that could be used to attach to a cell. Another shape could be compatible, but is not targeted by the vaccine of today. I'm guessing that this makes the virus a different virus - but isn't that what mutations are? they are slowly causing the virus to change and at some point, it becomes a different virus.
  - mbreese 5y ago
    What you’re talking about is a different form of evolution where there are effectively “multiple answers to the same problem”. A common example is if there are two bird species eat the same nut, they might have two very different beak shapes that both open that nut. But that’s not how the type of evolution in a single virus works[0]. Within a single organism/virus, the evolution is more like finding a local minima. There certainly could be a more effective design with a different shape. But it is very difficult to break out of a local minima through mutation and natural selection. You still have to maintain the function of a protein while simultaneously mutating it. So, breaking out of a local minima is really difficult. As you said, evolution is a slow process, so you wouldn’t expect to see dramatic changes in a shape and keep the same function. [0] I’ve deliberately left out things like horizontal gene transfer, transposons, and gene duplication, all of which can involve hyper mutation or gain of function without being under selective pressure.
bawolff 5y ago
If the variant is already on the rise couldn't we figure this out by looking at the demographics of who is infected (are most of the cases vaccinated people? Are people previously having covid getting this variant). I don't know anything about the field, but it seems like we shouldn't need that high an infection rate before we can start verifying these concerns empirically, especially when a large majority of the population is vaccinated.
IAmGraydon 5y ago
The person you’re claiming is incorrect worked on developing the MRNA vaccines. What are your qualifications?
- freemint 5y ago
  I don't think parent said this person is incorrect. It said that the arguement is falliscious. Whether the value judgement of it being holds we don't know but infection numbers look bad
  - dnautics 5y ago
    You're right that the argument is fallacious, but you ALSO can't say that the high number of mutations make escape almost certain. Fact of the matter is, we don't know, and it's hard to say. For there record, I'm predicting it would escape, but I'm far from certain about it, I'd put like a 75% prior.

dnautics 5y ago

We also don't know what the mortality rate is. Suppose it has 100% vaccine escape but 0% mortality. Would it be "BAD"?

WithinReason 5y ago
I think a 0% mortality strain displacing delta would be an extremely good outcome. One way pandemics stop is the virus mutating to harmlessness.
- gandutraveler 5y ago
  That is exactly what I thought of too. So far the symptoms appear to be very mild and this could be a good way to scale immunity
  - sharken 5y ago
    The media is extremely focused on the number of infected and how infectious a new variant is. Somehow the low number of new hospitalizations is not newsworthy. Here in Denmark the hospitalizations have been steady at around 45% of the numbers we had when there was no vaccine. It's also 45% of the numbers we had in 2017/2018 with the flu back then. But that fact is not being used much to put things into perspective.

Kye 5y ago

Chise is a she/her-shaped creature as far as I know.

fartattack 5y ago

Your argument is fallacious. You clearly lack even an elementary education in immunology. Exposure to the antigen teaches your immune memory cells what the antigen looks like. Quit your job, stay home, live in fear. The rest of society doesn't need cowards like you. The pandemic is over, except for paranoid people. There will be endless variants. It's an RNA virus. No amount of vaccination will be perfect, but life will go on. Get vaccinated and go expose yourself to the existing endemic variants; it's the best defense there is. Live your life. If you think you can wait until there are no more variants, you'll be locked inside wearing a mask forever. Some of us have lives to lead.

f38zf5vdt 5y ago

A study in Nature had previously shown that >= 20 amino acid mutations on the spike protein was sufficient to cause immune escape from the vaccine or previous infection, but that individuals who were both previously infected and vaccinated were still able to neutralize the mutant virus. [1] The omicron variant has >30 AA mutations on the spike protein, so it remains to be seen how effective vaccines are in response to it. Even if it is unable to prevent infection, it's still likely that the vaccines will provide some attenuation of severity, especially with a booster. We also now have pharmaceutical means to treat infections, so any notions that this will bring us back to March 2020 seem unrealistic. https://www.nature.com/articles/s41586-021-04005-0 https://www.nature.com/articles/s41586-021-04005-0

naasking 5y ago
> individuals who were both previously infected and vaccinated were still able to neutralize the mutant virus. Mainly because of the infection, not the vaccination. Infection trains your immune response to detect multiple factors of the virus, the mRNA vaccines are only for the spike protein which has considerable mutations in later variants like this one. Arguably, traditional dead-virus vaccines might provide better long-term protection for this reason, but we went all-in on the new tech.
- lamontcg 5y ago
  Somatic Hypermutation works on vaccine antigens as well, and diversifies B-cells so that the B-cells will recognize many spike mutations. Anyone who has been vaccinated or recovered probably has some B-cells which match this spike, even if they're not amplified and expressed into circulating neutralizing antibodies. T-cells on the other hand don't diversify as much but they recognize primarily the host MHC section of the MHC-antigen complex, so they're already somewhat insensitive to mutations in the protein. The T-cells stimulated by vaccine or virus aren't special in that regard. Arguably it doesn't really matter. If you get infected with this spike it is still going to have pretty much the same shape as the spike in the vaccine (after all even the mutated versions still need to bind to ACE2 and can't vary that broadly) and your vaccine-trained T-cells will still bind fine to the antigen-MHC complex that the spike forms. There's this idea that antibodies and immune responses are like a key fitting perfectly into a lock where any pin being wrong doesn't unlock the lock, and that's just false. The immune system has a need to fuzzy match against antigens because it evolved against adversaries which mutate and attempt to reinfect. You're pushing a narrative that spike-only vaccines are worse in the face of mutation, and there's just no evidence of that. On the other hand mRNA spike-only vaccines allow creating a very strong humoral response to the spike protein in the absence of significant side effects and their efficacy has been so far across the board superior to inactivated virus or viral-vector vaccines.

op00to 5y ago

No. If every single “protein marker” on the spike protein was changed, there wouldn’t be a heck of a lot of chance for the virus to attach to a cell. There still needs to be basic compatibility with the cell and the spike to get inside.

chii 5y ago
> there wouldn’t be a heck of a lot of chance for the virus to attach to a cell. but there isn't just a single shape that could be used to attach to a cell. Another shape could be compatible, but is not targeted by the vaccine of today. I'm guessing that this makes the virus a different virus - but isn't that what mutations are? they are slowly causing the virus to change and at some point, it becomes a different virus.
- mbreese 5y ago
  What you’re talking about is a different form of evolution where there are effectively “multiple answers to the same problem”. A common example is if there are two bird species eat the same nut, they might have two very different beak shapes that both open that nut. But that’s not how the type of evolution in a single virus works[0]. Within a single organism/virus, the evolution is more like finding a local minima. There certainly could be a more effective design with a different shape. But it is very difficult to break out of a local minima through mutation and natural selection. You still have to maintain the function of a protein while simultaneously mutating it. So, breaking out of a local minima is really difficult. As you said, evolution is a slow process, so you wouldn’t expect to see dramatic changes in a shape and keep the same function. [0] I’ve deliberately left out things like horizontal gene transfer, transposons, and gene duplication, all of which can involve hyper mutation or gain of function without being under selective pressure.

bawolff 5y ago

If the variant is already on the rise couldn't we figure this out by looking at the demographics of who is infected (are most of the cases vaccinated people? Are people previously having covid getting this variant). I don't know anything about the field, but it seems like we shouldn't need that high an infection rate before we can start verifying these concerns empirically, especially when a large majority of the population is vaccinated.

IAmGraydon 5y ago

The person you’re claiming is incorrect worked on developing the MRNA vaccines. What are your qualifications?

freemint 5y ago
I don't think parent said this person is incorrect. It said that the arguement is falliscious. Whether the value judgement of it being holds we don't know but infection numbers look bad
- dnautics 5y ago
  You're right that the argument is fallacious, but you ALSO can't say that the high number of mutations make escape almost certain. Fact of the matter is, we don't know, and it's hard to say. For there record, I'm predicting it would escape, but I'm far from certain about it, I'd put like a 75% prior.