Twitter thread from a vaccine developer: https://threadreaderapp.com/thread/1464222680731820043.html
A lot of speculation still, but it's not all bad so far.
A lot of speculation still, but it's not all bad so far.
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.
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.
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.
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.
"Pushing a narrative" is a pretty uncharitable interpretation of a short off-hand comment.
There actually is some evidence that the infected have a stronger immune protection to exposure than the vaccinated, and there are mechanistic reasons this would make sense, so I wouldn't go so far as there's no evidence for it. We'll just have to wait and see.
That argument sounds good in theory, but we have data we can look at to assess — Sinovac is inactivated virus and it's efficacy was 50% against the early strains. Also, work has shown that spike antigen vaccines broaden the range of antibodies produced by previously infected immune system to increase neutralisation against later variants, even though the vaccines were of course based on ancestral spike protein sequence..
What is actually needed and is probably working for previous infection is knowledge about proteins that are generated after entering cells.
Antibodies and cell based immunity against these do not avoid infection but will allow early elimination of the infected cells.
This is again where mRNA vaccines can shine as they can introduce any protein onto cell surface to be recognized by the immune system.
It ignores any benefits that other vaccines or natural immunity might have compared to the mrna vaccines "spike-only" approach.
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.
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.
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.
Whether the value judgement of it being holds we don't know but infection numbers look bad
For there record, I'm predicting it would escape, but I'm far from certain about it, I'd put like a 75% prior.
The red portion of the graph on the far right is the new variant.
And this was before Omicron was known.
https://twitter.com/sailorrooscout/status/146422268073182004...