Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern
who.int
who.int
A lot of speculation still, but it's not all bad so far.
https://twitter.com/sailorrooscout/status/146422268073182004...
The red portion of the graph on the far right is the new variant.
And this was before Omicron was known.
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.
This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa"
At this point, if you are not immunocompromised and you have the first vaccination and a booster. You should be able to easily recover regardless of the mutation(s). The virus would need to completely diverge from SARS-CoV-2 in order to fully defeat the countermeasures of the current vaccinations.
Pfizer says that if they have to generate a new vaccine for this variant, it will take about 100 days.[2] That's the great thing about this mRNA vaccine technology - given the gene sequence of a virus, a vaccine can be designed. The original Moderna vaccine was designed in two days.
[1] https://www.newsweek.com/omicron-variant-prompts-concerns-ab...
[2] https://www.msn.com/en-ie/news/world/pfizer-release-statemen...
[1] https://www.boston25news.com/news/trending/biontech-will-kno...
“It’s all speculation at this stage. It may be it’s highly transmissible, but so far the cases we are seeing are extremely mild,” she said. “Maybe two weeks from now I will have a different opinion, but this is what we are seeing. So are we seriously worried? No. We are concerned and we watch what’s happening. But for now we’re saying, ‘OK: there’s a whole hype out there. [We’re] not sure why.’”
https://www.theguardian.com/world/2021/nov/26/south-africa-b...
So, like most COVID infections?
And that’s the same as other “mild” COVID infections, yep. The ones where you don’t die. You ignorant dipshit.
If you would please review https://news.ycombinator.com/newsguidelines.html and take the intended spirit of the site more to heart, we'd be grateful.
Just lift measures and let it do its work...
There are already reports of (vaccinated) young people getting seriously ill.
Unlike with other viruses, there is little selective pressure towards being less deadly, because illness/death mostly happen after transmission.
And while I'm not a virologist, it doesn't seem far-fetched that "breeds higher viral loads more quickly" would be correlated not only with transmissivity, but also with "kills more".
Yeah, you shouldnt be making these claims if you don't have specific background or understanding of what you are talking about
All current vaccines target few/couple specific proteins and protein groups on the virus spikes which interact with our cells, if these couple spikes/protein groups change then the vaccines stop being effective, you don't need a complete divergence of the vaccines to stop working as the vaccines don't target the "whole virus" to begin with, just specific parts of it, that was the worry with Delta and is the worry with this new strain
Since you have the specific background and understanding and know what you are talking about can you explain to us how inactivated virus covid vaccines target specific proteins ? I would expect them to target the whole virus.
[1] https://en.wikipedia.org/wiki/Covaxin [2] https://en.wikipedia.org/wiki/CoronaVac
Gives a better breakdown of what we're actually talking about.
Variant21K appears to have arisen in November 2021, possibly in South Africa. Early sequences are predominantly from South Africa, though also detected in Botswana and Hong Kong.
21K is primarily of concern due to the large number of mutations it has in the Spike gene. Many of these variants are in the receptor binding domain and N-terminal domain, and thus may play key roles in ACE2 binding and antibody recognition.
This literally reads like post apocalyptic fan fiction.
I find it incredibly fascinating how fast this virus can mutate in order to throw curveballs around our natural and engineered defenses and become more efficient at killing us.
How is this even possible in such a short amount of time? I thought evolution takes tens of thousands of years. It's not like viruses have giant brains with massive IQs to come up with all this so fast.
Would be cool if someone could ELI5.
Edit: fixed bit about error correction, thanks somewhereoutth!
Long to short, if death prevention is the objective then we need to shift to finding solution that are less specific but still effective. For example, anti virals.
Flu vaccines are also updated on a yearly basis to reflect the strains currently in circultion, so why would the covid vaccines not do the same?
This sounds like an anti-viral subscription service. :)
These bits perform several critical functions: hiding from the immune system, attaching to cells the virus needs to replicate in, etc.
Changing any of these things results in two questions.
(1) Does the change make the virus better or worse at X? (where X is something related to what that bit was doing)
(2) Does the change make the virus more or less visible / resistant to the immune system?
The answer to both of these are independent, and for any one particular change, depends all the way down to chemistry and physics.
It's possible that a given virus design cannot mutate external features without rendering itself ineffective. It's also possible that relatively minor mutations can make it more effective and/or able to avoid antibodies and the immune system.
The mutation space has been studied for SARS-CoV-2, but to put it simply, it's a very complicated problem that involves (among other things) protein folding and molecular simulation. Not easy stuff to brute force.
Sometimes far fewer tries than that, of course, but viruses certainly get a lot of iterations in any given population in any given month.
In the normal case the selective pressure isn't really there, since the virus will get beat back after a week or two anyway and just 1-2 point mutations probably didn't give it any significant advantage is infecting more hosts.
Given how many mutations this variant has compared to its most direct known ancestor, the former is almost certainly what happened in this case too.
See for example: https://www.scientificamerican.com/article/covid-variants-ma...
Mutations on organisms such as viruses depend on the raw amount of virus duplication which happens, not per se "time", if you have a large amount of hosts, and therefore high amounts of duplication that increases the duplication rate making it more likely that mutations will occur, therefore speeding up the mutation rate, and as it happens with large countries still not taking strong measures against covid there's ample amount of hosts which can incubate new mutations....
Also, ought be noted that mutation is entirely random, this is *not* "a consequence to vaccines existing", most mutations will be neutral, others negative to the virus itself, but few might have positive effects on its vitality, or incubation period or others
This is not actually a "goal" of the virus, since dead people cannot move and therefore spread much less of the virus. They seek to become more infectious so they can spread more, and in this process sometimes they also accidentally kill the host.
https://mobile.twitter.com/angie_rasmussen/status/1441416013...
Numerous viruses throughout history have not become less virulent even over the course of thousands of years.
The variants arise randomly and proliferate with the current major strains. The infected population adapts to reduce the transmission of the most virulent/contagious strains. Selective pressure (tug of war between infecting people and people fighting off the infection) increases on the new variants until one or a few maintain or exceed the transmission of the progenitor strain.
That's the problem with the, "I'll get over it/I'm not worried/My segment of the population doesn't die from it" mentality. The more infections - subclinical, asymptomatic, severe, fatal, undetected - the more rolls of the dice. We (humans) are selecting variants that are worse for us, hoping we can snuff out the infection before some key mutation that eludes our immune system and/or testing develops.
Two other thoughts with internal conflicts/points worth mentioning - First, recovered patients should be more resistant to new strains. Their immune systems threw everything at the virus to defeat it, so their response will be more diversified than those with mRNA vaccines targeting a specific protein sequence. (The magnitude and usefulness of the variations in immune response can negate that advantage.) Second, the reasons that a 'novel' virus is dangerous are that we, as a species, don't know if we can (naturally/innately), and we don't know how much the virus can change in protein sequence (to evade our defenses) or our response to infection.
Anyways, I'm rambling. Not a virologist, but a PhD (and as such, I think I know more about stuff than a really do) and that's how I think about it. :)
The vaccines we're currently using don't prevent infection as they do not provide sterilising immunity. To quote[1] Sunetra Gupta[2], infectious disease epidemiologist and a professor of theoretical epidemiology at the Department of Zoology, University of Oxford:
> The vaccines that we currently employ appear to be highly effective in preventing life-threatening illness but do not meaningfully contribute to the maintenance of herd immunity.
> …we find ourselves trapped by the superannuated conviction that vaccines must block infection as well as disease.
Given that, how is contrasting those who've had vaccines with those who haven't of any relevance? We have other comments in the thread (like this one[3]) pointing out that it could be immuno-compromised people that are the main source of new variants. Right now, they're among the least likely people to have been vaccinated.
[1] https://www.telegraph.co.uk/news/2021/11/24/vaccines-never-r...
I believe this to be a very common misconception. Evolution selects variants that are better at replicating. It does not follow that those are the worse for our health.
Imagine a variant that would effectively be very lethal to us: wouldn't it go extinct if the bearers die or even stay home sick before it can spread?
Successful viruses fly below the radar, I guess.
Evolution does not work that way. It is not a conscious decision or process on the part of the organism. It is the result of mutations due to imperfect copying of genetic material. Very likely most of the mutations are useless or harmful to the organism. But once in a while the mutation gives the organism an advantage and allows it and it's progeny to outcompete the other, unmutated organisms.
Even the process of evolution does not make decisions or have a particular direction or goal. It's all randomness and depends on the large number of chances.
As far as becoming more efficient at killing is, most viruses mutate to a state of being less deadly. Not killing the host is an advantage for a virus.
"The Evolution of Bacteria on a “Mega-Plate” Petri Dish" https://vimeo.com/180908160
The original paper about the experiment:
"Spatiotemporal microbial evolution on antibiotic landscapes" https://www.science.org/doi/10.1126/science.aag0822
Some bloke who was the head of Porton Down aka Public Health England when commenting on the London Plague pits found when digging the tunnel for Cross Rail suggested RNA viruses have a single helix so are prone to high levels of mutations unlike DNA which has the double helix checksum to reduce mutations. This is probably the episode. https://www.bbc.co.uk/programmes/b04cnps9
How Messenger RNA vaccines work. https://www.cdc.gov/coronavirus/2019-ncov/vaccines/different...
mRNA is not the only solution, some dietary changes can create a chemical based attack vector as your body has evolved to cope with extremes. This just one example of many different chemical attack vectors. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7413200/
There is also this https://news.ycombinator.com/item?id=12451198
But I cant find the hacker news link on a paper from MIT which also suggested a 3 day fast reset the immune systems "memory" which was a novel way of wiping vaccine triggered immune system responses and probably isnt what you want to do if you believe in the covid vaccines, but if you are an anti-vaxxer forced into having a vaccine, then it could be a way of wiping its effect from your body if the study was accurate.
Now before you go out fasting, just bear in mind you will be depleting your body of many things like the vampire chemical glutathione (NAC, Glutamine & Glycin) which depletes as you age. Its called the vampire chemical because it whitens skin and makes you sensitive to light amongst other things so there might have been some truth to those vampire legends!
I know Vit D is mentioned alot, the Welcome Trust in Cambridge reversed engineered the human genome back a few years back and suggested there were 2776 Vit D receptors, most concentrated around the immune system genes, but the VDR has a zinc finger so you need to take zinc and both A & D will get you closer to hypercalcemia so that brings its risks, but in 1959 the scientific community did work out if you take A & D you need to take K to mitigate the risk of hypercalcemia. And if you are elderly, you should consider taking taurine as this helps the body manage the fats in your diet (bile) amongst other things, which explains why the elderly generally absorb A & D less easily or respond less to supplementation compared to young people. You'll find taurine in some wacky places in the body.
That's a huge part of the pandemic, people are not used to being exposed to that kind of language, so their imagination runs wild.
Really? I wonder how much of this is "it's very easy to spot in the pcr" and we don't have to Redeploy tests..
A: “… Ok so we agree - ‘Nu’ creates all sorts of confusion so we will skip this letter”
B: “Sounds good. What do we have next in the alphabet - ‘Xi’. Oh.”
Pause. Exchange of glances.
A: “So that’s probably no good either right?”
B: “Yeah looks like it”
A: “Because it will be hard to pronounce?”
B: “Right. Yup.”
A: “Alright, ‘Omicron’ it is then.”
B: “Done.”
"Some other variants with Greek letters do not reach those classification levels, and the W.H.O. also skipped two letters just before Omicron — “Nu” and “Xi” — leading to speculation about whether “Xi” was avoided in deference to the Chinese president, Xi Jinping.
"“‘Nu’ is too easily confounded with ‘new,’” Tarik Jasarevic, a W.H.O. spokesman, said on Saturday. “And ‘Xi’ was not used because it is a common last name.”
"He added that the agency’s best practices for naming diseases suggest avoiding “causing offense to any cultural, social, national, regional, professional or ethnic groups.”"
[0] https://www.nytimes.com/2021/11/27/world/africa/omicron-covi...
https://github.com/cov-lineages/pangolin
I'm surprised it has so few stars, watches, and forks given how big a deal it is.
Omicron = o + mikron = small o Omega = o + mega = big o
Bonus points: Nu is the 13th letter of the Greek alphabet, and today is Friday 26 (2*13).
Maybe they wanted to avoid all the lazy puns. A pretty significant part of the world speaks either of those two languages.
Also, both the masculine and feminine forms, “nu” and “nue”, are pronounced exactly the same. “Le variant nu” in French would always be ambiguous.
I speak Portuguese and I can assure you what you’ve written is funny nonsense. No one would care about this when making the 1000th internet meme.
Perhaps there is a second meaning I don't know?
No, what’s it called?
The nu variant
Yeah, does it have a name?
It’s nu
Yeah I know it’s new but what do they call it?
What does who call it?
That’s what I’m asking you! What does WHO call it?
Edit: Stupid math error.
Not sure if you're being hyperbolic, but the death toll just in the US has surpassed 0.23%
World covid deaths = 5.7 million
World population = 7.9 billion
Death toll = 0.07%, rounded up
https://www.google.com/amp/s/www.bbc.com/news/world-asia-ind...
Also, your case mortality rate number seems wrong, by orders of magnitude.
people who suggest that we should "let natural immunity work" are implicitly imagining that they themselves are going to be OK, and would rather have their freedom and activities restored at the cost of lives. Other people dying is "a sacrifice i'm willing to make".
> because flu viruses are constantly changing, the composition of flu vaccines is reviewed annually, and vaccines are updated to protect against the viruses that research indicates will be most common during the upcoming flu season.
10,000,000 times 50,000,000,000 (rough stab at # of virions per infection, range 1 to 100 B), is
500,000,000,000,000,000 opportunities for mutations so far.
You can take it to the bank that the number of mutations is far, far higher than the number that makes it to the press because the strains that end up dominating have already undergone a lot of competitive pressure by the time we notice them, so there will be a lot more strains that we will simply never know about.
Fun fact: the total mass of all virions produced by infected hosts to date is likely less than 10 kg.