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Heavily mutated coronavirus variant puts scientists on alert (nature.com)
350 points by abbassi 55 days ago | hide | past | favorite | 419 comments

It's so interesting watching this get picked up by the news.

Many aren't aware but interestingly these variants are identified and designated in the open on GitHub, here is the GitHub issue for this B.1.1.529 designation https://github.com/cov-lineages/pango-designation/issues/343. I've recently started watching this repo as it's quite interesting reading about the different variants popping up across the world.

That’s not quite accurate, they’re identified in GISAID [0] and other platforms, which is where scientists upload sampled genetic sequences. It’s also out in the open and free to access.

This GitHub repo is just about registering the Pango lineage, based on data already collected and published at other locations.

[0] https://www.gisaid.org/

I thought the visualization provided by NextStrain was fairly fascinating, not to mention it is used by the CDC an other organizations:


How to read that branch diagram?

just click on the json link below it?

Wow that's wild would not have thought of that being on GitHub ha

GitHub is being used by many governmental agencies as a repository for information, especially numeric and usable for automation (not just for code). Another contextual example is "how many contagions per district, daily", but you could also have "how many herons observed in that territory", etc.

Whenever you hear news about mutated COVID and how fast it spreads there are a few important things to remember.

1. Viruses are constantly mutating, its kind of their thing.

2. Most mutations do absolutely nothing or are actually harmful to the virus.

3. When a new mutation is noted to be spreading fast its usually because of the nature of super spreader events and not because the new mutation is more or less transmissible.

4. Scientist and health officials should absolutely be keeping an eye on these things.

[0] Vincent Racaniello - SARS-CoV-2 UK variant: Does it matter https://youtu.be/wC8ObD2W4Rk

But Vince from YouTube was of course completely wrong there. At the time they recorded that video, there was overwhelming evidence that the Alpha variant was more transmissive. It was astronomically unlikely that it could have been explained by a founder effect or individual super-spreader events. Unsurprisingly, the evidence was correct while the uninformed pattern-matching from a non-epidemiologist was wrong.

For this new variant it could still plausibly be a founder effect. But that's because the circumstances are different this time (the variant became dominant while cases were surging from almost nothing, not when the cases were already at a high level). Not because that checklist is actually correct.

> But Vince from YouTube was of course completely wrong there.

Claiming Vince was wrong in the video also means the researchers that discovered the variant were wrong. After all he was just parroting their findings in the video.

This article was on the same day as your YouTube video and paints a very different picture. So what's your source that the YouTuber has accurately parroted scientific findings?


Vincent Racaniello is a professor of virology.


17 minutes in, dismissing the R value that the UK scientific advisors calculated based on unpublished data, that we now know was correct: "you can't use epidemiological data to prove a biological effect of an amino acid..."

Yeah, that's a virology point of view all right. That something has to have a proven biological mechanism before it can be taken as fact, or even considered as a risk. That's bad public policy though. With his reasoning there would have been no reason to increase restrictions in the UK in Dec/Jan, but in fact the restrictions were extremely necessary and the variant caused tens of thousands of extra deaths.

The R numbers coming out of UK epidemiology are garbage, Racaniello is right about that. They aren't physically grounded in any way, they're just arbitrary fudge factors brute forced to make their equations plot graphs that look like reported government stats so far. The same model will routinely calculate totally different values of R for different areas of the same country at the same time, without variants or anything like that.

Also the claims about variants being "more infectious" are - when you dig in - hopelessly confounded by seasonal effects that many epidemiological papers were at that time still ignoring.

The seasonal effects are trivially controlled for by comparing the growth rate of the variant to the growth rate of the wildtype at the same time. And that's exactly how the original analysis was done, because the people doing it were not incompetent.

For your seasonal effect explanation to make any sense, the effect would have to have only applied to Alpha but not to baseline Covid at the same time. And then it's not a seasonal effect, is it? It's an actual difference in the behavior of the two variants. The same goes for any other similar confounder that you try to manufacture.

Not the analysis I saw, where Delta's growth rate was compared to Alpha in the same time window, not the start of alpha's own growth period. Because yes, they are totally incompetent. You can look at graphs of the changing proportions to see visually that that's not much difference in how fast they took over.

Professors can be wrong or misunderstand things. They are human too.

Is there any evidence besides an appeal to authority?

An expert in the field is more likely to be right compared to someone who isn't an expert. Their opinion should carry greater weight

The modern issue is that most of experts are with very narrow expertise, which is not carrying that great weight as you might think and such expertise also doesn't mean that much in responsibilities.

My mother at 14 after a car accident was considered as lost cause and by opinion of expert she should be dead, but survived only because her relative with much less medical expertise believed in second opinion and got her in different hospital. Sometimes, these stupid parroted ideas about expert opinions can only be proven wrong by personal experience only. But quite many people do not learn from their own mistakes, so, meh - there is no cure for stupid people, who can't think by themselves.

PS Every covid mutation so far has put scientists on alert...

If a thousand people point to expert A, and a single person points to expert B, does that tell us anything useful about expert A or B?

expert A has thousands of twitter followers, while expert B does not use social media.

Only if they have a good record of predictive accuracy.

Is that the case here?

Are you claiming a professor of virology shouldn't be classed as an expert in viruses?

They are only allowed to be an an expert in 2021 if a majority of anonymous Twitter followers agree with their assessment, and if their stated political opinions for their entire lives lean in the correct direction. Please note those two conditions correlate.

Not saying this is you. Normally your comment is a trope by the right to paradoxically imply how they are such victims in 2021, but the other side are snowflakes and want to cancel every one.

There’s an overlap with hard left and a few other niche political views as well. Though with less victimhood and more consistency at times.

Personally, I care very little for appeal to authority myself. The bias among experts based on their political views is generally going to be very high.

Vince kind of lost his credibility when he allowed David Tuller to post on his blog.

So Vincent wasn't wrong, because he was just parroting the experts.. but Vincent is the expert? Am I understanding the logic correctly?

No you're not understanding the logic correctly. The GP was wondering why he has to trust a YouTuber to accurately parrot a research article and I point out that he's not a random YouTuber. Of course he can still be wrong?

Appeal to authority is a logical fallacy, no? Because that's exactly what the claim is. I understand that it makes him less likely to misunderstand the research (probably) but its not a guarantee and is naive to depend on that fact.

Appeal to authority is not a logical fallacy, although some people argue that it is. Put more correctly: experts know better, but aren't perfect. For example, were I to cite Peter Duesberg, a well known virologist, about HIV transmission, I'd be wrong, even though he's an expert virologist.

I assign higher priors to subject matter experts until I have reason to believe otherwise.

> Appeal to authority is not a logical fallacy, although some people argue that it is.

I mean, it is a logical fallacy. An expert isn't right only because he's an expert, he's right only when the evidence supports his position. Do all experts only make conclusions based on evidence, or do other beliefs factor in? I think the answer is clear, hence the fallacy.

No, it's not a logical fallacy. Nor would the fact that experts don't make conclusions purely on evidence mean their citing their statements fallacious.

For any given scientific question, select two populations. One populaton is enriched in subject matter experts, while the other is selected at random. Have them make blind predictions about scientific facts. It is not fallacious to sdtate that the first group's predictions will have a higher posterior probability.

I've actually studied a lot about logical fallacies, and so I can tell you with certainty that appeal to authority is, indeed, a logical fallacy.

Source: Myself, an authority

Joking aside, you are just misrepresenting what the "appeal to authority" logical fallacy is. An "appeal to authority" is when one argues that "X is correct because <insert some expert> said it was". In really, X is either correct or incorrect, regardless of what any authority has said about it.

So yes, appeal to authority is absolutely a logical fallacy. Changing the definition of those words and then arguing that your definition isn't a fallacy is called a fallacy of equivocation. And yes, a fallacy of equivocation is also a logical fallacy.

What's really going on here is two different meanings of the word "argument". Appeal to authority is indeed a fallacy if you're dealing with a logical argument meant to prove something absolutely and undeniably true.

That's not the only kind of argument that exists though, and we're pretty unlikely to be in that kind of argument on the internet talking about current events. When trying to tell from incomplete facts what's more likely to be true, listening to what an expert says is a pretty good start.

I agree with everything you said. But I still say that “appeal to authority is not a logical fallacy” is a false statement, regardless of whatever shinanigans is going on in this discussion.

Agreed. It's always a true statement, though sometimes irrelevant.

you can't provide anything absolutely and undeniably true, except maybe in math. I mean, I used to do debate and after some time I noticed that none of it was based on truly logical arguments; everything was about persuasive seduction and coming up with the minimum to cast doubt on your opponent's position.

But yeah, I like the way you put this; we're just arguing on the internet about things which are too messy to have a true false dichotomy.

> you can't provide anything absolutely and undeniably true, except maybe in math

Logic is part of math, and logic is where logical fallacies come from.

You really need to look up what "logic fallacy" means. Any invalid logical inference is a fallacy. An appeal to authority is not a valid logical inference because an authority's claim is not necessarily true; the definition of a valid inference rule is if it's result is necessarily true if it's antecedents are true. Therefore an appeal to authority is a logical fallacy, by definition.

Appeal to probability is also another kind of logical fallacy. Don't get me wrong, there's value on knowledge and judgement that resides outside of the logic domain but you don't know what's a logical fallacy.

What does the logic domain have to contribute to human arguments? There is nothing, other than pure math, which follows logic. Nothing in our society is logical in a way that people arguing objective facts could resolve a problem.

A lot. It's the language of pure reason and a tool for abstract thought. It's a pillar of any STEM field like math, computers, physics, engineering, etc. Our society was built on top of it. I think you're misjudging it's value because you're mistaking it for a way to achieve non-falsifiable claims, which it's not as any logical claim only hold as much as it's premises, while ignoring it's value as a framework for though.

Where is the appeal to authority? I made no such claim and have explained what I meant in considerable detail? I have explicitly mentioned several times that he can be wrong. Appeal to authority means authority isn't wrong because authority.

lozenge stated: "So what's your source that the YouTuber has accurately parroted scientific findings?"

To which you replied: "Vincent Racaniello is a professor of virology.


This is an appeal to the authority of Vincent's position as a professor

On its own you can interpret it like that, but this is a bit unfair. I have already explained what I meant with my comment, I even have a comment that predates the one you cite where I explicitly claim that he can be wrong... My point was not to say that he's right because he's a professor. It was to clarify that he's not a random YouTuber.

It seems silly, to me at least, to take external statements to this given thread and apply them as if they were said here. I took your comment at face value, all seven words and the URL. That was the entire statement, there was no mention of "he's an expert but he could be wrong"

When asked for evidence, the ONLY evidence that you provided, was that he IS an expert. Full stop.

At the time the message tree was vastly different. The messages were next to each other. It looked like this:

      Comment.  My 2nd reply with link.
My first reply where I said he could be wrong.

> So what's your source that the YouTuber has accurately parroted scientific findings?

The parts of the video where he literally quotes the original findings.

And then dismisses their findings as "that's a flawed argument and not how we do science" (17 minutes in).

Why does it matter? Researchers are wrong all the time, improving upon that is kind of the point of science.

It's a bit unfair that the GP calls him Vince from Youtube. He's a professor of virology so not just some nobody giving his opinion on Youtube. This doesn't mean he can't be wrong of course.

I did feel a bit bad writing it, but it was for the purpose of countering the appeal to authority. This is a epidemiological question, and being a professor of virology doesn't make you an expert at that. So the outcome was that Racaniello ended up recommending inaction, since he'd only accept evidence from his own field (i.e. lab work).

Thanks dude, now I have to deal with lots of replies that misunderstand what I wrote in response to you. While you knew who he was! :P

But all good. I used to listen to his podcast at the beginning of the crisis but after a while I stopped because I felt they were ignoring reality while waiting for science. Which felt like a strange way of working when reality was what we had to base decisions off of.

I think it matters that he’s wrong because you’ve already given him such a high stature. Him being wrong means a policy that depends on him being right should also be reinspected. But policies aren’t that flexible.

> Why does it matter?

because the science matters. This new SA variant could be more transmissible or it could not be. Lets stick to the actual data and go from there.

The question is: what do you do in the absence of data, or with only very preliminary data? By the time the scientists have had chance to fully investigate the moment for action has often passed.

'... what do you do in the absence of data, or with only very preliminary data?'

Stop shoveling carbs at every meal. Lose 30 pounds. Start to exercise and increase cardio-pulmonary performance. It appears most people in developed countries became couch potatoes and gained fat. To each his own. My body, my choice. Your body, your choice.

One day this totally common sense comment will be the norm.

Probably the same thing as if a new variant didn't exist. Get vaccinated, wear mask, etc.

I think we are misunderstanding each other. I asked why it matters if Vincent being wrong means that the scientists that wrote the article would be wrong. To me it is a natural thing that happens in science. Of course the scientists can be wrong?

because I was getting the impression the person I replied to was trying to frame the situation as a YouTuber vs Scientist argument. That of course wasn't the reality.

But the actual commonsense evidence is that Alpha isn't more transmissive, which makes Vincent right. Alpha, Delta, and every other variant has turned out to be the same when practically speaking as experienced in our actual cities and populations across the world. So Vincent is ultimately correct: the "evidence" based on modeling was lacking, and his second point was that politicians and the media should not be rhetorically distorting the scientific positions that can be taken. There's a difference between taking reasonable precautions and oversimplifying scientific positions in order to "motivate" the public or to make media hype (both of which are TWiV's pet peeve, as anyone who has been watching their videos can see).

Absolutely False.


Delta’s quick growth rate has been especially dramatic, says F. Perry Wilson, MD, a Yale Medicine epidemiologist. Delta was spreading 50% faster than Alpha, which was 50% more contagious than the original strain of SARS-CoV-2, he says. “In a completely unmitigated environment—where no one is vaccinated or wearing masks—it’s estimated that the average person infected with the original coronavirus strain will infect 2.5 other people,” Dr. Wilson says. “In the same environment, Delta would spread from one person to maybe 3.5 or 4 other people.”


“ We found a mean R0 of 5.08, which is much higher than the R0 of the ancestral strain of 2.79.”

Please stop spreading misinformation.

> Alpha, Delta, and every other variant has turned out to be the same when practically speaking as experienced in our actual cities and populations across the world.

This claim is wildly false, and you've already been refuted by someone else.

Remove your false post.

> 3. When a new mutation is noted to be spreading fast its usually because of the nature of super spreader events and not because the new mutation is more or less transmissible.

Mostly true but in some very major cases it was because the variant did spread faster in general. Such as Delta and the British variant before hand.

Yeah by the time fast spreading variants get picked up by the press, they usually are indeed more transmissible, rather than merely founder effects / super spreader events. We've seen this time and time again to the point that the rational evaluation is to assume the new variant is indeed more transmissible. Especially for this variant which is overtaking Delta so quickly that it can't really be explained by super spreader events.

If such a variant was not spreading faster, how would it ever become a dominant new strain? Just because of some unlucky incident on the other side of the world?

I think the initial fast spread can be incidental, a super spreader event. But if it has lasting ability to displace other variants, especially across multiple countries, then it is likely just easier to spread.

Basically superspreader events can artificially boost a variant for a bit -- it is basically noise. You need to look at a longer time frame to be sure.

Viruses sure fail fast, truly fascinating. Tirelessly mutating to spread and (I assume) survive. Do they serve as purely a "cleaning" function of nature, restoring balance... or do they seek global domination... even if it means destroying the host organisms they depend upon? Are they simply mindless, unintelligent organic micro programs or do they have some kind of plan?

They’re the paperclip maximizers of the animal kingdom. All a virus does is make more of itself. If it does, there’s more, if not, it goes extinct. They do it sloppy and mutate. If it does the thing better, there’s more of the new thing. If not, that new thing goes extinct. Once that’s been happening for billions of years some parts of these viruses will look pretty clever.

Isn’t the difference with AI that viruses don’t have a “final goal” baked into them?

I think the process that you’re describing is the process of genetically evolving-by-mutation life forms in general. So not specific to viruses.

Human bodies are the vehicles for our genes to survive and reproduce :-)

"Goal" kinda invokes intentionality, which can't exist at the size viruses are. (Of course it's an open question whether it exists at all but let's leave that aside.)

Viruses don't have goals. If a virus successfully makes more virus, then there is more of the virus. For viruses that don't do that, there are less of them. That's all there is to it.

It so happens that making more virus often requires resources that were previously in use by other organisms. But that's incidental, not by design.

You only see viruses that are good at making more virus because the other ones died out.

It may be very unlikely, but claiming intention is not possible given virus size feels a little short sighted. Simply because we as humans don't know why or how doesn't mean it's not possible.

Is any of that different to other biological organisms except the mutation rate?

Mutation rate and, relatedly, short generations and huge numbers of copies.

Viruses are what viruses do, they don't have any of these properties that you could assign to them, they just do their thing (replicating using some combination of mechanisms provided by other organisms), and if they do it well they get to do it some more. There are no motivations, there is no plan, there is no function and they don't seek anything.

If they're too successful at what they do their host dies before they can be passed on, if they're not successful enough then the infection wave loses momentum and dies out. Effectively we have been helping them for the last year and a half do do this, without our help this particular virus would die out within a couple of weeks. It needs us for transportation and to be brought in contact with new viable hosts. On its own it can't do much of anything.

From what we know, there's no "plan" or designed function for viruses. They're just crafty pieces of information that get copied and spread in living organisms and sometimes wreak havoc on the hosts.

Like humans? :)

As I understand evolution: life has no plan, goal, aim or intention. It’s endless amounts of parallel and random experimentation over billions of years. And this has led to biological structures that have certain tendencies that work well: cells, reproduction, energy consumption, sexual reproduction. On top of that life has evolved to have behaviour and other attributes that work in certain context: immune systems, locomotion, fur, gills, adaptability, use of tools, creative problem solving.

viruses are a natural outcome of a complex information system and a rich energy economy. Don't ascribe "intent" or "meaning" to them.

I would say they have meaning in a different sense - not as a message but their origin as proof. They are fundamentally proof of the "tautological mechanism" of evolution. It isn't a matter of life but that things which can survive over time and are produced over time will have a higher number existing at once than ones which perish and are not produced. This holds regardless of the how and why.

Native copper ore got largely picked up and used by humans rendering such deposits "extinct" from early civilizations and lead to the practice of mining after the low hanging fruit was used up.

Dekhn is correct in ascribing this to complex information systems though, it is the storage, copying, transmission and expression of DNA that gives viruses their opportunity. All of these mechanisms can be hijacked.

Luckily for us, if they kill their host, they will not spread effectively.

Not necessarily, if they kill their host after a couple of weeks they will spread very effectively indeed, the longer the asymptomatic spread period the better for a virus' chances of moving on to a fresh host undetected. During symptomatic spreading there is at least a warning that someone might be contagious so this is a harder way to spread. And for some viruses it is even possible to spread after the host has died. What happens to the host itself after the virus has spread doesn't really matter. If a host dies before spreading and the virus can't be spread from the corpse then that will work against the virus.

Its know that most viruses trend towards increased transmissibility and decreased lethality.

Killing your host is an awful strategy for continued existence if you don't have your own lipid bilayer.

I am not a virologist but it sounds to me that this is an observation and not a law/axiom.

The virus does not decide a strategy, it is random mutation and selection and even if it is less likely it might be that we could have a variant that is super transmissible and super deadly. This effect could be obtain in the delay between transmission and visible effects on human body. Example: virus is transmissible with N days before we can see signs of infection.

Of course we can fight back by testing everyone weekly even if they show no signs.

Mutations which improve transmission and longetivity will, in general, become more prevalent. Proliferation begets proliferation. You cannot transmit a strain if you are at home in bed from its severity.

Help me understand how a virus can replicate without being detected but can also increase its lethality.

We already have an asymptomatic and infectious incubation period. If that kept stretching longer then you are delaying the lytic cycle even longer? Or does propogation and ultimately viral load also happen as a slower burn? Eventually you will have damaged too many cells.

I said “visible effects” which is different than detecting a virus in human body. That mean pre-symptomatic transmission.

I am not up to date with latest research but it seemed to be that SARS-CoV-2 is a virus that can be transmitted before symptoms onset.

Regarding replication without being detected but also increased lethality this you might be right that doing the math maybe the hypothesis I present seems far fetched.

Still I guess that a slight bump in mortality will create a lot of deaths due to its transmission.

Of course like I said I am just expressing an opinion that might be very wrong.

This is false.

No virus has ever done this.

Wasn’t there also some kind of watchlist where they track up to 7000 mutations in a given timeframe? Probably just minor mutations, but still.

Does the flu virus mutate every year?

I'm not sure if you are trolling, or sincere, but yes:


This is why Flu shots are seasonal

I'm wondering why we don't start producing mRNA vaccines targeting this other variant now. Seems like there could be some safety and efficacy protocol put in place to target emerging variants so we don't have to start from scratch in the approval process, requiring 30k-40k adults alone every year.

>I'm wondering why we don't start producing mRNA vaccines targeting this other variant now.

People are developing mRNA vaccines for 'flu now. Moderna, Pfizer and Sanofi all have mRNA 'flu vaccines in clinical trials, and there are a bunch more in the pre-clinical stages.


why the apostrophes?

Flu is short for influenza so perhaps the apostrophes are intended to indicate the existence of missing characters?

Ah yes, but that would be " 'Flu' " would it not?

I'd say that's a good rhetorical question rather than a troll.

It's designed to make a statement, rather than elicit information. (Ref Oxford Languages).

Yeah, that’s why people take a shot every year.

Also why many people don't take it at all. Not worth the constant hassle for something that doesn't bother me in the first place. Flu shot efficacy is usually in the gutter anyway (https://en.wikipedia.org/wiki/Influenza_vaccine#Effectivenes...).

It doesn't bother you yet. Wait until you are say sixty or seventy years old. I am of course making a few assumptions here 8) Flu rarely kills young 'uns in reasonable to good shape with no other indicators or whatever doctors call it. I mean risks associated with a particular individual.

The point of vaccines is not perfection but more like a war of attrition. A vaccine has several potential purposes, some of them are these:

  * Reduce the possibility of infection
  * Reduce the effects of an infection 
  * Reduce the infectiousness of an individual to other people
The first two effects affect you personally and the third one affects society as a whole. The third one is the thing behind the "Don't kill grandma" meme. Your comment implies to me that you may not have considered it. If you have and are happy with that, then that is your prerogative.

Each of those items above have various probabilities associated with them and rather a lot of external factors and so on. A vaccine's stated effectiveness in each area will obviously be some sort of average across a population.

That's the thing: Vaccines inoculate societies as a whole and not just individuals when you look at statistics. The phrase "anecdotes are not data" is particularly true here.

Even a "lol sad" 40% effective (whatever that means) vaccine will slow the spread of the thing across a population and reduce the possibility of individual deaths or other non optimal outcomes. When you start to look at the population as a whole you see huge numbers of people living instead of dying.

With luck, one of those survivors might be you or me one day. This is the only time I will advocate a sort of communist approach to things. By "risking" inoculation, you reduce the possibility that someone else might catch the disease. You also get some additional abilities to fight off the bloody thing too - nice!

The old people in my family usually get the shot. When I'm old, I might start to get it as well. Until then, I don't bother.

The flu didn't bother me 'til it knocked me on my ass for two weeks and I had brain fog for several months afterwards. The cost of a flu shot is a few bucks, a few minutes to get the jab, a sore muscle and mild symptoms for a day. That for 20-50% efficacy chance to avoid that 2-week monster flu? I'm in.

One big issue is that colloquially "the flu" is used to describe bad colds and other illnesses. Almost no one who has "the flu" has influenza. Thus people underestimate how bad influenza actually is

Actually I believe that in itself is a misunderstanding. Flu may be more likely than a cold statistically to hit someone badly, but it's quite possible to get the flu mildly, and it's quite possible to get really, really bad cold. The same way Covid being statistically more dangerous than the flu doesn't mean that every person getting infected by Covid has a worse time than every person getting the flu.

If taking a quick and harmless shot every year gives me up to a ~40% chance of avoiding disease then I’m good with that.

Definitely a better outcome than not getting a flu shot.

when I get the flu shot I typically spend a week with a non-functioning arm and feeling like I'm very sick. However, I still get flu vaccination because it seems likely that this maximizes the overall health of humanity, and I'm more interested in the health of humanity than my own, in the long term.

Good that you get the shot, but I'll just note that the symptom you describe is far worse than most people who get the flu shot. Most years I get it I have no symptoms at all besides slight arm soreness. Maybe one in five years I have a mild fever for a day.

> constant hassle

> something that doesn't bother me

Yeah you've never been unlucky enough to get a bad flu.

I'll absolutely choose the "constant hassle" of getting a flu shot (i.e. a 5 minute pit stop at the drug store once per year).

The flu sucks.

That's why a minority of people take a shot every year.

Yes that's why the effectiveness of the flu-shot differs between years

Yes. The CDC has this to say about flu virus mutation:

How Flu Viruses Can Change: “Drift” and “Shift”

Influenza (flu) viruses are constantly changing. They can change in two different ways.

Antigenic Drift

One way flu viruses change is called “antigenic drift.” Drift consists of small changes (or mutations) in the genes of influenza viruses that can lead to changes in the surface proteins of the virus, HA (hemagglutinin) and NA (neuraminidase). The HA and NA surface proteins of influenza viruses are “antigens,” which means they are recognized by the immune system and are capable of triggering an immune response, including production of antibodies that can block infection. The changes associated with antigenic drift happen continually over time as flu viruses replicate (i.e., infect a host and make copies of themselves). Most flu shots are designed to target the HA surface proteins/antigens of flu viruses. The nasal spray flu vaccine (LAIV) may target both the HA and NA of a flu virus.

The small changes that occur from antigenic drift usually produce viruses that are closely related to one another, which can be illustrated by their location close together on a phylogenetic tree. Flu viruses that are closely related to each other usually have similar antigenic properties. This means that antibodies your immune system creates against one flu virus will likely recognize and respond to antigenically similar flu viruses (this is called “cross-protection”).

However, the small changes associated with antigenic drift can accumulate over time and result in viruses that are antigenically different (further away on the phylogenetic tree). It also is possible for a single change in a particularly important location on the HA to result in antigenic drift. When antigenic drift occurs, the body’s immune system may not recognize and prevent sickness caused by the newer flu viruses. As a result, a person becomes susceptible to flu infection again, as antigenic drift has changed the virus’ antigenic properties enough that a person’s existing antibodies won’t recognize and neutralize the newer flu viruses.

Antigenic drift is an important reason why people can get flu more than one time. Drift is also a primary reason why the composition of flu vaccines for use in the Northern and Southern Hemispheres is reviewed annually and updated as needed to keep up with evolving flu viruses.

Antigenic Shift

Another type of change is called “antigenic shift.” Shift is an abrupt, major change in a flu A virus, resulting in new HA and/or new HA and NA proteins in flu viruses that infect humans. Antigenic shift can result in a new flu A subtype. Shift can happen if a flu virus from an animal population gains the ability to infect humans. Such animal-origin viruses can contain HA or HA/NA combinations that are different enough from human viruses that most people do not have immunity to the new (e.g., novel) virus. Such a “shift” occurred in the spring of 2009, when an H1N1 virus with genes from North American Swine, Eurasian Swine, humans and birds emerged to infect people and quickly spread, causing a pandemic. When shift happens, most people have little or no immunity against the new virus.

While flu viruses change all the time due to antigenic drift, antigenic shift happens less frequently. Flu pandemics occur rarely; there have been four flu pandemics in the past 100 years. For more information, see pandemic flu. Type A viruses undergo both antigenic drift and shift and are the only flu viruses known to cause pandemics, while flu type B viruses change only by the more gradual process of antigenic drift.


I think you're missing the point. As a media event, you need the drama so that you are able to run the script you have planned.

Really simple: If this new variant does nothing more than previous versions to increase mortality, particularly among the increasingly vaccinated population, obsessing over its spread should be considered pointless and absurd. For one thing, it wouldn't work without endless other streams or authoritarian security theater measures (that in any case themselves don't really work most of the time) And for another thing, "stop the spread" is an idiotic notion without heavy qualification. Stop death? Sure, Stop large quantities of hospitalizations? That too, albeit with cost/benefit calculations applied to all measures, but stopping spread itself for its own sake? Absurd paranoia that has no merit the moment the thing spreading stops being a truly widespread threat. We have lived with colds and flus for all our history without obsessing over their spread. COVID among those who are already immunized or vaccinated is comparably dangerous to common flu strains.

Are existing vaccines effective against this new variant?

We simply don't have the data. It's all speculation at this point.

Israel reported one positive case and two suspected, all three vaccinated.

Vaccines only help you not get seriously ill, they don’t seem to help much with preventing covid infection in the first place

don't want to sound smug but I think this is very easy to understand with very basic knowledge about the immune system and some common sense.

I think you're overestimating the average citizen.

At this point those are anecdotes, not data

This again reminds that having all your own population gotten 3rd jab (or n-th jab) won't make the pandemic disappear.

Meanwhile rest of the world hasn't got their first dose of a reliable vaccine.

"South Africa has asked Johnson & Johnson (JNJ.N) and Pfizer (PFE.N) to delay delivery of COVID-19 vaccines because it now has too much stock, health ministry officials said, as vaccine hesitancy slows an inoculation campaign."


If rest of the world don't want it, I'll take it (and did).

South Africa is one of the most developed countries in Africa though. World vaccination rate is something like 40% and it's not 60% anti-vaxxers.

Denmark was able to offer vacines to everybody because Rumania didn't want them.

Variants will continue to to be generated as SARS-CoV-2 is almost certainly endemic. We should be focusing on developing and testing therapeutics and treatment protocols to help as many people as possible, rather than focusing so heavily on vaccinations.

Therapeutics and treatment protocols require a lot more medical staff to implement than a simple jab.

The only way to keep cases to a low enough level to be successfully 'processed' by the health system is to maintain fairly severe social restrictions - and maintain them forever.

Didn't vaccination require huge spending as well? I think governments over-relied on vaccination for their own reasons, even long after it became evident it wasn't going to magically solve the pandemic. At the very least, vaccines should always be combined with some sort of restrictions to prevent the appearance of new variants (since the vaccines themselve create a pressure for the virus towards an escape mutation)

Absolutely - to my mind vaccines should be used to drive infections to very low levels, if not complete eradication, for the reason you state.

I believe that all of our successful vaccination campaigns (against highly contagious viruses) have by necessity resulted in (near) eradication. E.g. Polio, Smallpox, Measles, Rabies (in animals)

Is Nu /ˈnjuː/ (en) /niː/ (cz) a good name? I assume that most people have heard first few letters of Greek alphabet. Yet after Delta they should have switched to Pokemon names. Would be much more robust. I can already imagine all the misspelling in Twitter rants.

> they should have switched to Pokemon names

The slogan "Gotta catch 'em all!" makes that idea even less viable than it first seems.

Maybe colors of PacMan ghosts then?

I wonder if we would eventually reach the Koffing and Weezing variant?

I think the Greek letter Xi is where we'll hit real trouble. "zai", "k'see", and "she" are all likely ways people will pronounce the letter.

I think most Americans have at this point enough exposure to news about China that they'd pronounce it "she", as if it were pinyin. In the fraternity/sorority system, I think most people pronounce it "zai", but my understanding is "k'see" or "ke-see" is closer to classical (and perhaps modern) Greek pronunciation.

I had an analogue control systems professor with a very strong accent (his catch phrase was "Quitch dewice wuh you choose?") who pronounced Xi close to correctly. I presume a huge chunk of the class (about half of the men, and many women at MIT were in fraternities/sororities/independent living groups at the time) probably dismissed his pronunciation of the Greek due to his accent in English and their prior exposure to the Greek alphabet in the "Greek" living system.

There are many covid variants. Nu is simply the next letter in the alphabet

Naming a disease after private intellectual property is a terrible idea. Im not sure what that would accomplish.

Sonic hedgehog (the gene) would disagree with you

The Shiny Charizard Variant would get the kids into it. Sibling post is right about the slogan though..

On the other hand, it may finally give a reason to learn it.

Given the stupefying number of anti-vaxers and rapid viral mutation rates, the only way we get out of this pandemic is by a relatively harmless variant out competing the more deadly ones. Same as with the Spanish Flu.

Fortunately this is the trend for most viruses. I have seen no evidence that the delta variant was more lethal, but that it was more transmissible. I have also seen numbers from my locality sequencing that suggested lethality was significant chunk less than that of alpha.

> I have seen no evidence that the delta variant was more lethal, but that it was more transmissible

Look here then:


Increased risk [compared to non-variant-of-concern SARS-COV-2] with the Delta variant was more pronounced at 108% (95% CI 78%–140%) for hospitalization, 235% (95% CI 160%–331%) for ICU admission and 133% (95% CI 54%–231%) for death.

Alpha falls into the variant of concern classification, and this is contrasting delta with non-VOCs unless I misunderstand.

Just the preceding sentence in the abstract

Compared with non-VOC SARS-CoV-2 strains, the adjusted elevation in risk associated with N501Y-positive variants was 52% (95% confidence interval [CI] 42%–63%) for hospitalization, 89% (95% CI 67%–117%) for ICU admission and 51% (95% CI 30%–78%) for death.

N501Y is alpha

Wasn't that always the case?

Pretty much. The R0 was high from the onset and has only gotten worse with new mutations. This isn't surprising either. To get to herd immunity, we'd need a very high percentage of the population to be immune. The one difference from before the vaccines is that we now know they don't make you immune.

Has any vaccine in known history been truly 100% effective? "Immunity" was never the goal to my understanding.

The Polio vaccine is >99% effective after the full course.

Polio and a few other vaccines really spoiled us in terms of what's realistic when vaccinating against a Coronavirus. Vaccinated != Immune, sadly.

No, but the chance of breakthrough infection with the current vaccines is high enough that it's unlikely to allow good herd immunity at realistic vaccination rates, which sucks.

Immunity is always the goal if you can get it. It's not how you judge success though, you're right.

Thankfully the vaccines do drastically reduce severe illnesses though, so that's something.

The boosters seem to help quite a bit. Perhaps higher effectiveness even than after the second dose.

It's called an endemy and it's totally normal and yes people die occasionally.

Has anyone ever attempted to intentionally spread a less lethal variant of a virus in order to speed up the crowding out of other strains? I could see us trying this if a quick spreading but innocuous strain is found.

Yeah I'm so hoping this will happen. Evolution will favor it of course, because a milder virus we won't fight so hard.

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