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PHealthy t1_jdin3el wrote

We really don't know much about serotype specific waning immunity, it's likely we'll have robust long term immunity from the earlier variants like alpha and delta.

The whole issue of "re-infections" is that new serotypes keep emerging not that people keep getting reinfected with the same variant.

If anyone is interested in infectious disease news: r/ID_News

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yofomojojo t1_jdjj3fe wrote

Just to follow up on the re-emergence question. Here's a fun fact about the original Influenza epidemic we call the Spanish Flu; H1N1: It actually died out, once.

Partially from its own mortality rate, partially from built up immunities over time and evolving variants, but by the time we understood what viruses really were and how to approach them, there was no known surviving sample of it.

Before it died out, though, it passed on, first into the birds as H1N2, swapping out one bit for another, and again into pigs as H3N1, which themselves eventually crossed and produced H3N2, but enough mutations and variations kept the base nodes on infrequent rotation over the years. And eventually they met and hot swapped again, giving us the "Novel" influenza virus we called Swine Flu, H1N1.

And at some point, someone found an inexplicably well preserved vial of blood containing the Spanish Flu from back in the early 1900s, and tested it, confirming suspicions that yes indeed, through a series of exchanged hands, swine flu was a perfect re-assembly of the original Spanish Flu strain of influenza.

Tl;Dr - re-emergence is entirely possible even when the given strain has already gone extinct. Blind mutation and hot swapped component parts can always put Humpty Dumpty back together again.

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im_thatoneguy t1_jdjlrq0 wrote

Out of curiosity if H1N1 Spanish Flu == H1N1 Swine Flu, why was Swine Flu so much less virulent? The Spanish Flu was particularly deadly among younger people and no young people would have been exposed to the extinct Spanish Flu.

(I Had H1N1 and it was awwwwwffullll, but didn't shut the world down like Covid or Spanish Flu).

​

EDIT: They're not the same:

>The Centers for Disease Control and Prevention said Friday the swine flu virus appears to be about as contagious as the average seasonal flu. In examining the virus, it also did not find the genes they think made the infamous 1918 flu so deadly.
>
>https://www.npr.org/templates/story/story.php?storyId=103728922

Edit edit:

>Model to Explain the 1918 Mortality Patterns.
>
>Elderly individuals may have been protected from the 1918 virus by childhood exposure to an H1N1-like virus (5). We estimate that H1 and the H2 + H5 lineage diverged from a common ancestor near the time of the 1830 pandemic (SI Appendix, SI Text and Figs. S13 and S14). Moreover, protection was clearly greatest in those born before 1834 (5) (Fig. 3A), implicating the 1830–1833 pandemic virus, which would have primed the majority of that age group. If an H1-like virus emerged in 1830, it would likely have been positioned near one of the orange stars close to the root of the tree in SI Appendix, Fig. S13. Those primed as children between 1830 and 1889 by this HA lineage would likely have had considerable protection against the 1918 HA, comparable to that exhibited during the 2009 H1N1 pandemic by those born before 1957 (32), based on the similar genetic distances separating the childhood and pandemic virus HA in each case

https://www.pnas.org/doi/10.1073/pnas.1324197111#supplementary-materials

The tree here would indicate that H1N1 like Covid just continued to evolve and become endemic, it didn't die out. Nowhere is it claimed that the genomes are the same. In fact as the CDC mentions, we had a full sequence by 2005 of the 1918 flu and it didn't match.

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hayalci t1_jdjswfg wrote

In addition to r/brown_felt_hat's answer, Spanish Flu was around World War I, ravaged economies, poverty, illness, and a general lack of resources probably would have confounded its effects.

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brown_felt_hat t1_jdjn0u2 wrote

We are definitely a lot better at recognizing and treating illnesses these days. We have drugs to mitigate infection vectors (eg cough syrup prevents coughing, a massive transmission vector, decongestants limit mucus production so you're not sneezing snot everywhere), we have drugs to treat dangerous symptoms (anti pyretic drugs to prevent high fevers, repository drugs to prevent failure), and just much better overall awareness of how viral infections work and spread.

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im_thatoneguy t1_jdjx0hg wrote

So if you didn't take any medication, you had pretty much the experience you would have in 1918--except you would probably take Paracetamol for fever and if your condition worsened you could receive tamiflu and other stronger medications?

Or like the difference between Alpha and Delta Omicron, they're the "same" but probably exhibited substantially different mortality?

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Atechiman t1_jdk1y5e wrote

HXNX is a way of indentfying large families of Orthomyxoviridae in particular alphainfluenza betainfluenza gammainfluenza and deltainfluenza, the four 'families' of bird/mammalian flus (often just called a,b,c,d) I forget off hand the exact proteins it refers to, but all of the viruses have one of four of them so H1N3 viruses tend to behave similar to each other but different from H1N2.

H1N1 is an alpha virus, that different strains have caused several major pandemics including the Swine Flu. It is an avian virus usually, but some strains are endemic in humans and it is often the flu-a vaccine for a year.

1918 flu is an outlier as was the '83? '82? Russian pandemic novel. The 2008 was slightly more lethal than normal but not more contagious.

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byerss t1_jdjw4rg wrote

H1N1/09 did hit younger people harder than older folks. I remember reading that one theory was that for 2009 older folks may have had more natural immunity because they were exposed to flu variants based on Spanish Flu.

Look up the death vs age graphs for swine flu.

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yofomojojo t1_jdk0chr wrote

Re: your edit - I'm open to being rebutted here but, I think that clip might be a bit outdated. H1N1 is Swine Flu and Spanish Flu. If we're doing podcast links, RadioLab covered this topic again during early Covid. Current scientific papers and articles on the topic all seem to understand and accept that H1N1 is the virus in question in both cases.

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im_thatoneguy t1_jdk1ror wrote

https://pubag.nal.usda.gov/download/26795/PDF

That radiolab is discussing the basis of a 2005 paper which included the entire genome. So a 2009 CDC analysis (which NPR cites) should be based on the fully sequenced H1N1-1918 genome from 2005.

Edit:

https://www.pnas.org/doi/10.1073/pnas.1324197111#supplementary-materials

This states that H1N1 didn't go away, it continued to evolve into a seasonal H1N1. And that likely the 1918 H1N1 branched off into the H1N1 in pigs prior to the human outbreak.

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jinxjar t1_jdk7b1k wrote

it's like that time when i did the math problem wrongly but got the correct result.

i failed that test, but H1N1 passes.

no fair

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phred14 t1_jdirlwl wrote

I was under the impression that Omicron and later were better at evading immunity and that nothing worked in a lasting fashion against them - everything wanes fairly quickly.

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PHealthy t1_jdiztvk wrote

Omicron isn't a single serotype (immune recognition), it's actually a ton:

https://covid.cdc.gov/covid-data-tracker/#variant-proportions

So this isn't waning immunity, it's serotype emergence that escapes immunity.

ELI5: we get a great pitcher versus the first batter but they keep changing batters as we strike them out until eventually our pitcher is terrible. Then we bring in a new pitcher to match against the best batter we've seen so far and it starts all over again.

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phred14 t1_jdj1pe4 wrote

Thank you for that perspective, it makes me feel much better about things. Not enough better to quit being careful, but still better than I had been.

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chimpfunkz t1_jdj2jfy wrote

The other half of it is, Even though the batters started hitting instead of striking out, they're mostly hitting singles or doubles instead of home runs. So it's easier to prevent runs from being scored (in this analogy, runs are deaths)

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mikmckn t1_jdje2qd wrote

And as time progresses, the batters learn to go for base hits instead of home runs because it maximizes their time on base instead of killing the host.

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northatlanticdivide t1_jdjwo1o wrote

I’ve followed mutations on nextstrain for a while and those of you who are more visual learners like me may find it interesting. It was particularly fascinating watching the rise of delta and it’s being overtaken by omicron. You can also track flu, Ebola, measles, etc.

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kurai_tori t1_jdjboh1 wrote

This is why the latest booster is based on the mRNA of two variants. Both to increase your immunity to an increased number of variants (there is some cross protection from related variants, depends on how similar the spike protein/antigen is to the original that the antibodies previously produced (e.g. via vaccination).) as well as to increase your "standing army" of antibodies (specific antibodies levels drop after a while, leaving memory cells that will "activate" when reexposed to the Covid antigen (variant-specfic spike protein). Problem is the memory cell response might be too slow, hence the need for boosters of the same variant.

Flu shots are a good example of this and we will likely be moving to a similar approach with COVID.

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fakeittil_youmakeit t1_jdjbodw wrote

Question for you - I couldn't get the most recent booster due to some health issues at the time. I'm doing much better now and could probably be in a good enough place to do it in the next couple of months or so, at that point, is it even worth it or will the serotypes have changed so much it's not effective anymore? If that's the case are there going to be annual boosters and should I just wait for the next one in October or something? TIA!

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Tephnos t1_jdk617u wrote

You should still get the bivalent booster now if you can. In the US, it is based off of BA.5, which isn't too far removed from the current circulating XBB 1.5 and BQ1.1 strains.

It is likely that later this year we'll get an updated booster again, possibly targeting XBB if it still sticks around.

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KruppeTheWise t1_jdk9j3q wrote

Is the fact we vaccinated during the pandemic likely to have put evolutionary pressure on selecting serotypes that can defeat vaccine protection?

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Psyc3 t1_jdj1meq wrote

You have to take into account what evading immunity can mean. It means it can infect people and they can spread it, it however doesn't mean they have a serious disease or need hospitalisation.

The issue with COVID-19 was lack of any immunity at all, while early variants infected the lungs, later, more infectious variants started to infect the upper airway more seriously, but the reality is while this allows more effective spread, the upper airway is largely irrelevant, it isn't what absorbs your Oxygen supply, it is just causes a really bad cough instead.

Then you have to take into account this issue isn't a disease existing, it is everyone getting it at the same time, and then a significant percentage needing hospitalisation at the same time. Imagine everyone broken their arm at the same time, A+E would collapse, orthopaedics would collapse, any requirement for surgery would be overwhelmed (it is needed in 2 weeks), there would be no ability to get people effective rehabilitation, and people would start dying from complications of broken arms.

That is essentially what happened in COVID, with "a broken arm" being an unknown disease with an unknown treatment pathway, which once again is a massive problem. It is fine if you can treat 95% of your patients with X known treatment, it is another thing when you are trying to work out what treatment is needed, then when you do, don't have the equipment to implement it, or the specialists to manage it.

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NutDraw t1_jdjtgv0 wrote

>Imagine everyone broken their arm at the same time, A+E would collapse, orthopaedics would collapse, any requirement for surgery would be overwhelmed (it is needed in 2 weeks), there would be no ability to get people effective rehabilitation, and people would start dying from complications of broken arms.

Excellent example. The biggest risk with something like COVID are the huge waves of cases that overwhelm response systems. Sure, the vast majority of hospitalized people will survive with some supplemental oxygen, but if you only have enough tanks and masks for half of them the death rate skyrockets.

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kurai_tori t1_jdjcc0h wrote

This is why I've been sure to get the lastest booster and am still relatively careful. I don't want to be a cog in the damn viruses' mechanisms. I want my immune system to be able to say "this isn't free real estate".

Cause if you get infected, even if it's asymptomatic, you are a carrier/vector at that point. And you give the virus a chance to thrive, and mutate, and possible mutate to a worse form (viruses can be fatal as long as that still allows them to thrive, and direction of mutation is not always to safer, less fatal forms. Really it's whatever features allow them to outcompete their competitors).

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mikmckn t1_jdjh59d wrote

If more people took that approach it might have helped early on but eventually it was going to come down to a couple different end games.

  1. We eradicate COVID-19 (sars-cov_2). The fact that there are many different coronaviruses out there would indicate this isn't likely to work. The willingness of this thing to mutate would also seem to be a big speedbump in this road. It's not smallpox.

  2. We beat it back so it's uncommon in this country, like polio or mumps. We'd measure outbreaks in the hundreds and it makes the occasional news report instead of being among the leading causes of death. This MIGHT have been possible with an earlier response that was more restrictive and heavier vaccine use. However, other nations did this and still didn't manage to beat it back before it moved into the 3rd option. China is still trying for zero COVID-19.

  3. Endemic. COVID-19 is here for the long haul. It's in the population. Mothers are going to pass their immunity onto new children. Survivors built antibodies. Vaccinated people built antibodies. Less deadly variants managed to sneak under the radar. We'll be stuck with this long term and probably forever. Coronaviruses are adaptable little jerks. Some just cause cold symptoms. Others cause SARS. Like it or not, we are here.

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fang_xianfu t1_jdj48aq wrote

"Omicron and later" has huge variation. The variants people are getting now are as different to Omicron as the initial variant was from Omicron. They get named based on how concerning they are - they're Variants of Concern - not how different they are. So when they say "nothing works in a lasting fashion against them" it's because there are many of them.

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WaitForItTheMongols t1_jdiz0hx wrote

It's important what "immunity" you're referring to.

At this point with the number of variants, it's more helpful to think of COVID as a family of illnesses, rather than an illness. Immunity to other variants won't work against Omicron very well. But if you have immunity to Omicron, it works against Omicron.

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Nicolay77 t1_jdjaxs7 wrote

I was under the impression Omicron was so contagious and so not-deadly that getting it actually was like getting vaccinated against most variants of Covid.

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Bone-Wizard t1_jdke1nv wrote

That’s the sub where I first read about Covid in mid-December 2019… back when it was a case series of 20ish people with pneumonia in Wuhan. Great sub.

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[deleted] t1_jdiy83h wrote

[removed]

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dannymurz t1_jdj0pjq wrote

Transmission wasn't halted because the vaccine doesn't produce great mucosal immunity since so the virus easily and quickly replicates and is able to be spread, vaccine does great against more moderate and severe disease, which takes days and weeks to develop.

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StickySnacks t1_jdjb3s6 wrote

What are the chances the vaccine is actually ineffective?

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Alwayssunnyinarizona t1_jdiozcj wrote

It's a bit like asking if the wooly mammoth could come back.

Delta has for practical purposes "gone extinct", out competed by other, more successful variants.

At this point, it may only exist in a lab setting, where it could in theory be resurrected. It's only chance to persist really is with a little human help because more competitive strains are still out there on the landscape.

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porkypuha t1_jdirgk3 wrote

Are the current strains way less contagious? I lead a life that should make it really easy for me to contract the virus but I still haven’t caught it. I test myself whenever I slightly suspect I may be infected.

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Alwayssunnyinarizona t1_jditzmk wrote

The most common strain in the US currently, omicron xbb 1.5, transmits better than previous strains - the virus would die out if it didn't. There's the pressure exerted by herd immunity, but if the viruses didn't transmit more efficiently, they'd die out.

I also lead a life that should make it really easy to get infected, but the vaccines continue to work. There's a high chance you've been exposed and the infection was so mild you didn't even notice - either because you were vaccinated or immunologically lucky.

I'm also a bit surprised, as when something has been in the news - RSV or norovirus, for example, we've already had it a week prior (kids in daycare/school), so we're certainly at high risk of exposure for something like covid. All I can say is that the vaccines seem to be working.

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Matrix17 t1_jdj5svb wrote

What's the current guidance on how often you should get boosted?

Girlfriend and I did in the fall, then at Christmas we both got sick but only she tested positive. So I dont know if I should be waiting a certain time after that

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Alwayssunnyinarizona t1_jdjaqo7 wrote

There's no real specific guidance, but it's starting to turn into more flu-like guidance - vaccines recommended every year around the same time you'd be getting an annual flu vaccine, regardless of whether you were infected in the last 6-12 months or not. Expect there to be additional combo vaccines this fall (flu/covid), and that may persist for years until/unless covid starts to fall below background common cold status.

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Matrix17 t1_jdjfkq1 wrote

Yeah I hope it becomes a combo vaccine. Since the uptake now is low, it might boost the numbers a bit. But the same people who won't take a covid vaccine are probably the same that won't take a flu vaccine. And it's not like flu vaccine numbers are high to begin with

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SwimmingWonderful755 t1_jdjqc1q wrote

(New Zealand) I was recently part of a medical trial relating to getting a covid vaccine at the same time as, or 6 weeks after a flu jab. Pfizer funded, double blind, decent sized pool, one of many countries participating, tra la. Results aren’t available publicly yet, but work is being done on the viability of piggybacking them, at the very least.

Anecdotally, I had covid and flu jabs at the same time (soreness at the site etc (and later confirmed when unblinded) and placebo at 6 weeks, no reaction more than swelling at the injection site. Chatting with others in the waiting room, sounded like it was similar in our cohort, at least.

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MidnightAdventurer t1_jdkcgs1 wrote

The latest booking system on the NZ MOH website gives you the option to have both at the same time.

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SaltConfiscation t1_jdkbsti wrote

So it would behoove one to wait until the fall at this point? I was meaning to get boosted last fall but wound up missing it, but I'm unsure what to do. Official guidance always says to get it of course, but is that really worth it?

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Alwayssunnyinarizona t1_jdkebp9 wrote

That'd probably fall under the category of giving medical advice. There may be an updated vaccine in the fall, I'm not really sure how that will play out.

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drunkenknight9 t1_jdje7kd wrote

It's not about the number of cases out there but rather the severity. If everyone is getting covid but no one is getting sick enough to die or need intensive care, there won't be a need anymore for a vaccine. The natural life cycle of any virus is for it to become more infectious and less dangerous to the hosts since that's the best way for the virus to survive. The multitude of viruses that cause the common cold have already undergone that evolution. Influenza is a very unique case because of the structure of the virus that allows recombination among and between strains from different species means novel flu strains can happen any time without much warning and our immunity can be very variable. There are other outliers like HIV but most viruses that have ever infected humans have become relatively inert. A great example of the most extreme form of becoming inert is JC virus which is entirely asymptomatic and inconsequential unless someone is prescribed certain immunosuppressive medications. If you do get put on one of those medications you have to be tested for it otherwise it can reactivate and cause progressive multifocal leukoencephalopathy which is almost universally fatal.

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Matrix17 t1_jdjfvml wrote

The only issue with that approach is long covid is still a thing even in mild cases, and we still don't know enough about how it's caused or the best way to treat it

You can end up with similar issues with any respiratory virus, but covid is unique in that it happens more frequently, is more severe, and covid itself spreads more than the cold, flu, or other common respiratory viruses

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Alwayssunnyinarizona t1_jdjnje1 wrote

>The natural life cycle of any virus is for it to become more infectious and less dangerous to the hosts since that's the best way for the virus to survive.

That's not really true.

>As evidence mounts that the omicron variant is less deadly than prior COVID-19 strains, one oft-cited explanation is that viruses always evolve to become less virulent over time.
>
>The problem, experts say, is that this theory has been soundly debunked.

​

And in my comment, I did not distinguish case numbers vs. case severity. I said "until/unless covid starts to fall below background common cold status." I'm sorry that you read it that way.

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sciguy52 t1_jdk5p46 wrote

> The natural life cycle of any virus is for it to become more infectious and less dangerous to the hosts since that's the best way for the virus to survive.

This is a myth that gets repeated too often. Viruses sometimes become less deadly, sometimes more deadly. And many remained as lethal as always.

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Corvus-Nox t1_jdjpav6 wrote

In Canada, I believe the guideline is 6 months between boosters or after an infection.

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MaybeTheDoctor t1_jdjm4vv wrote

This is probably not a question you should ask strangers on the internet. But my belief is that I have gotten my last booster, and same is true for most people, unless they have some other medical reasons, and unless something else changes this is now just over.

We are down to a rate of 10 cases per 100000 people, so it will just slowly die out from here on, or worst case just linger on forever as a mild illness you can risk to get together with a million other mild illnesses we never cared to do much about.

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Matrix17 t1_jdk669w wrote

The numbers aren't representative though because very few are testing now and being logged

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QualityKoalaTeacher t1_jdivdcb wrote

Current dominant strains are purported to be more contagious. Like someone else said you may have caught it but just never showed symptoms (asymptomatic) which does happen in many cases.

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underbrownmaleroad t1_jdiz9i4 wrote

What an incredible mutation for a virus to attain. That has to help spread it so much

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RyanW1019 t1_jdj280w wrote

Whenever a virus replicates, there is a chance for the new virus particles to develop mutations. If these mutations make them less contagious, they will quickly get outcompeted by the old lineage and die out. If the mutations make them more contagious, they will outcompete the other strains until they become the new dominant version that new mutations develop from.

The only upside is that viruses don't usually benefit from becoming more deadly; if anything, that makes them less able to multiply if they kill their hosts. (Exception: if the host becomes very contagious before dying to the virus, more lethal strains could still develop as long as they are able to successfully leap from person to person before their victims die.) So in the long run, many viruses tend to get more infectious but less lethal, since the mechanism that makes a virus lethal is usually complicated and most random changes to it from mutations tend to reduce severity, not increase it.

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underbrownmaleroad t1_jdj3fal wrote

Very cool write up, especially learning how viruses tend to become less lethal and more contagious. It’s like the use us humans as the method for their life and once they reach their max potential it’s like oops yeah I didn’t mean to kill every one on the way

Is there any evidence that colds use to be more deadly and now they’ve reached a point that they’re largely contagious and less deadly?

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Matrix17 t1_jdj64rx wrote

> viruses tend to become less lethal and more contagious

This is not always true. Remember, there has to be some sort of evolutionary selection for it. As an example, the reason delta even became a thing, which was more deadly than the original strain, is because covid was spreading before people had symptoms. So it didn't matter if it killed the host or not, because they likely spread it before they even knew they had it. So there was no selective pressure for it to become less deadly. If covid had only spread after someone was symptomatic, it may not have turned into a pandemic at all

We just got lucky that the omicron mutation happened. If delta was still circulating, we would be in a very bad spot

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Tephnos t1_jdk6rpz wrote

> Very cool write up, especially learning how viruses tend to become less lethal and more contagious.

They don't. It's a myth that continues to be propagated because it sounds logical to the layman. It is our immunity that makes them less lethal (when we survive).

If viruses behaved this way as a given, we wouldn't have been getting killed by smallpox and many other viruses for millennia.

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yukon-flower t1_jdity8h wrote

Are you vaccinated or have you caught it previously (or both)? It’s entirely possible you’ve been exposed but your body fought it off before you could harbor enough to test positive.

We had a houseguest test positive (after previously daily testing negative ☹️), and I was definitely exposed. I felt under the weather for a few days but never actually tested positive. According to what I read in the NYT this means I successfully fought it off. I’m fully vaxxed/boosted.

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Naxela t1_jdj11hi wrote

A common rule of virus evolution is that viruses tend to evolve to be more contagious and less deadly. The rationale here is that a dead host is not a viable vector for contagion, and if your strain kills the host, then the strain dies along with the host body.

As a result, strains that keep people in contact with each other rather than isolated at home or in a hospital are going to be way more successful and will outcompete each other, and it goes without saying that of course the more contagious the virus is generally, the more successful it is as well.

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joshuas193 t1_jdivqzo wrote

As far as I'm aware the current virus is more contagious but less severe.

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Tephnos t1_jdk75gb wrote

Yes, and no.

It is less severe because everyone has some kind of immunity to it. The virus inherently is probably still as virulent as the original type to someone with zero immunity.

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azahel452 t1_jdjsqtu wrote

That's how it usually goes with virus, it's their version of natural selection. If they're too strong, they kill the host and that's not good for the perpetuation of the species, so those variations die out. The weaker but more contagious versions are the ones that have more success in reproducing. It's quite fascinating to think about.

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Tephnos t1_jdk72mf wrote

Wrong.

It doesn't matter if the host dies or not, all that matters is that it can spread before the host dies. COVID was perfectly capable of doing this via asymptomatic spread. (see: Delta).

Omicron outcompeted Delta because it had mutated so wildly that it could bypass all the antibodies the vaccines had generated up to that point, plus it drastically reduced the incubation time, meaning more spread potential. That's it. It could've been as lethal as Delta and would've still been successful.

Omicron is likely as severe as the original strain, the difference is now everyone has some kind of immunity to it, so it wasn't killing people nearly as much on a per-person basis.

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Harsimaja t1_jdkhqqm wrote

They outcompeted it by being more contagious. They are, however, less virulent (ie, less nasty should you get it). There may be a trend where these two correlate but it’s very far from a rule.

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Tackit286 t1_jdkabzy wrote

Typically viruses evolve to be more contagious, but less deadly.

Chances are you’ve either had it without realising, or still carrying some immunity from your last infection and/or vaccination.

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Demiansky t1_jdjcjzn wrote

Good analogy, but I'd compare it more to something like "could Homo Erectus come back???" The answer is "not really" because it already exists in us, today. Its like asking whether your great, great grandfather can come back.

Older versions of the virus can't come back because they've already evolved into the more modern version of the virus we see today.

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Booty_Bumping t1_jdjo2k0 wrote

Delta is not the ancestor of Omicron. Delta did not "evolve into" Omicron — it doesn't even have alpha variant in its lineage.

Another way this analogy breaks down is that humans have sexual reproduction whereas viruses are almost entirely asexual (with rare gene transfer exceptions). Neanderthal genes can enter humans because they are sexually compatible, but viruses have to rely on convergent evolution.

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Demiansky t1_jdkfryf wrote

Well, no, not every strain of the virus was on some kind of conveyor belt of evolution anymore than the hominid family tree. But all of the earlier, less virulent variants are the direct ancestors of modern variants.

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Alwayssunnyinarizona t1_jdjownw wrote

I thought about an Australopithecus analogy, but thought readers might grasp the idea of bringing back the wooly mammoth as it's currently in the news (along with the dodo). Apart from that, I've lost track of whether omicron is a straight derivative of delta, or if they have a shared common ancestor - which would make it more like the mammoth analogy ;)

Actually, according to this article in Science, it looks more like they shared a common ancestor....so, mammoth rather than Homo erectus.

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number1dork OP t1_jdit9md wrote

That's one aspect I was curious about... if the variants have to compete with each other in the same ecological niche. I would think there's enough unvaccinated people in the world that there would still be room for a new Delta infection. But does the presence of the newer, more contagious variants prevent it?

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Alwayssunnyinarizona t1_jdivhuu wrote

The viruses are racing to find people who are susceptible enough to infect. It would be like Jesse Owens trying to keep up with Usain Bolt. Jesse was fast for his time, but Usain is going to beat him to the finish line e: 99.9999% of the time - enough that if you weren't paying very very close attention, you'd never see that one time Jesse beat him. .

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florinandrei t1_jdix80n wrote

Yes. The newer variants have won the Darwinian struggle against the old variants. The old variants have been outcompeted.

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Large_Ad_3095 t1_jdk4jzs wrote

They also continue to exist in chronically infected people, mutating over the course of infections that could last years(or decades?)

These are 3 Delta variants detected this January, one of which was up to 90 mutations(and probably still mutating):
https://twitter.com/LongDesertTrain/status/1624464486596849670

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Alwayssunnyinarizona t1_jdk59ar wrote

Similar thing happens in cats with FIP, another coronavirus.

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Large_Ad_3095 t1_jdk6rj3 wrote

I never knew that! I just read that it can turn fatal due to a mutation, but do these spread in cats like COVID variants? Omicron and Delta already demonstrated that outcompeted variants can come back far worse.

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Alwayssunnyinarizona t1_jdk7931 wrote

They're typically mild infections, but some cats can be chronically infected. In those cats, a mutation in part of a specific gene can cause FIP.

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Large_Ad_3095 t1_jdk80dc wrote

Sorry, what I meant to ask is if such a mutation could go beyond the chronically infected cat and replace other FIP viruses.

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Alwayssunnyinarizona t1_jdkb53l wrote

Ah, I see. I need to read up more on feline coronaviruses, but my understanding is that the disease itself (FIP) is not transmissible per se. One cat with FIP won't give FIP to another cat, for example - it's a syndrome that is as much cat-dependent as it is virus dependent.

The coronaviruses themselves (there are various strains) are transmissible, but you need a specific mutation in a chronically infected cat to cause FIP. Once that virus has mutated, it may infect other cats, but won't cause FIP. I am not aware of any particular strain that is guaranteed to mutate and produce FIP in every (or even most) cats.

Does that make sense?

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pfmiller0 t1_jdixvik wrote

Can we say for sure that Delta doesn't exist in animal reservoirs somewhere?

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Alwayssunnyinarizona t1_jdj082m wrote

Some derivative of it likely does, but it's been eons (in viral time) since delta was first identified, so almost without a doubt it has continued to evolve in those reservoirs - much like mammoths have gone extinct but we still see their close relatives in elephants. For the time being, anyway.

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aggasalk t1_jdjqoc4 wrote

similar viruses don't really compete. you can be infected with multiple COVIDs at the same time. the older variants disappear because of mass immunity, not because of competition.

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Alwayssunnyinarizona t1_jdjvznu wrote

They are competing for resources in terms of susceptible individuals. If virus A is more transmissible, replicates in cells more quickly, or bypasses immunity that would otherwise prevent infection with virus B, then virus A has outcompeted virus B.

With evolution, everything is competition.

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Dinierto t1_jdk2fzq wrote

So what we need is a new strain of covid that can squeeze out the others but which we can easily cure, that's what you're saying

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nomnomnomnomRABIES t1_jdj2yka wrote

However the original spike is included in the bivalent vaccines. What is the scientific justification for including the spike for extinct variants?

Edit: re: u/Tephnos why are extinct strains of flu not included in the flu vaccine then?

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Alwayssunnyinarizona t1_jdj5d3u wrote

The answer is part scientific, part administrative, and part practical.

Scientifically, the spike protein is made up of many different epitopes (smaller parts of the protein that are recognized by antibodies or T cells). Some of those epitopes still convey protection for current variants.

Administratively, Covid vaccines still have to go through hoops that eg influenza vaccines currently don't, so it's easier to just use what's already gone through trials and approval processes. Soonish, the vaccines can bypass those regs and update as fast as flu vaccines do. Whether that is helpful or not is up for debate, as we've seen that flu vaccines are often outdated by the time they're released.

Practically, if the vaccines are still effective, there's not a lot of pressure on eg Moderna or Pfizer to "retool" the production lines to make an updated vaccine.

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Tephnos t1_jdk7nvx wrote

To prevent the original strains from coming back when immunity to those (eventually) wanes.

We don't want to start going backwards. Plus, there's cross-reactive immunity so that similar mutations can be recognised by the immune system without ever seeing that particular one before.

Keeping a wide breadth of spike mutations allows that to work more effectively.

Edit: u/nomnomnomnomRABIES, the reason is that Flu is an entirely different beast to COVID. Despite all the mutations COVID has gone through, it is not all that different to the original strain (which is a good reason why our immunity still holds so well). Coronaviruses do not mutate all that much, as they have the largest genome of all RNA viruses. COVID is just mutating a bunch, relatively, because of how widespread it is.

Flu, on the other hand, drifts massively, and constantly. There's no point including older strains because it doesn't help you fend off next year's Flu. Maybe once or twice in your life you'll come across a strain that is similar to one you were previously vaccinated against, which is nice, but no point wasting time cramming a Flu vaccine with all these historical Flu strains.

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IseereydarReturns t1_jdizuf1 wrote

The old variants would have continued to mutate as they spread, they won't resemble them much. But, we still have a bit of a COVID problem.

The hospitalization rate for COVID may be in a valley right now, but look at that 'valley' in some countries. In Australia, it is just a bit below the Delta waves PEAK. We still have concerns about T cell damage and illnesses in general taking longer to get over due to this damage... I would keep up on epidemiologists sharing data online, and monitor their findings for anything alarming.

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LaconicLacedaemonian t1_jdjgswl wrote

But if something is alarming, what is there to be done at this point?

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psychoticdream t1_jdjoxrn wrote

Mitigation.

One of the biggest concerns is that the tcell damage makes it susceptible or oncogenic. Which might (note, "might") explain some cancer cases around the world.

So mitigation is important.

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SoHiHello t1_jdjhdxp wrote

Didn't Australia have very low peaks or am I thinking New Zealand?

Low peaks are easy to hit again without it being too problematic.

If India was hitting previous peaks I'd think we have a massive problem.

Can you give some context for Australia?

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Whimsical_manatee t1_jdjoy9m wrote

Australia had very aggressive lock downs to manage Delta, since most Australians still weren't vaccinated in the second half of 2021 and some states were entirely COVID free and wanted to stay that way.

The hard lockdowns significantly slowed the spread of Delta but weren't able to drop the numbers. In NZ they were able to reduce number of Delta cases but their lock downs were in even stricter (take-away food was closed for five weeks I recall) and ultimately they decided to relent a little, there was a hard boundary around Auckland and changed lockdown levels from 5 to 4 I believe.

I can't remember the Australian hospitalisations numbers from that time but you might be able to find them online somewhere, try ABC or Chris Billington.

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Call_of_Tculhu t1_jdjljvu wrote

Variants are the evolutionary response to immunity, once people's immune system is exposed to it, it's very unlikely it comes back, as the strains that mutate are the ones that manage to spread.

This is why the flu will never go away, there's no winning against evolution, only playing catchup.

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sf_sf_sf t1_jdix8sr wrote

There are definitely animal reservoirs of older variants. Whitetail deer, rats, and other animal species have their own Covid epidemic of older variants. I wouldn’t be surprised to see a spill over event from one of those sometime in the future.

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Matrix17 t1_jdj72qw wrote

Difference being that the population at large might have some immunity to a variant like that this time

Unless it's wildly different

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[deleted] t1_jdjklmb wrote

[removed]

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sf_sf_sf t1_jdjstg7 wrote

There were a couple: Dec 2021 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8702434/

but also a counterpoint https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9111207/

a run down of 3 theories (un detected evolution and transmission, long infection of an AIDS patient, or animal spillover) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8757324/

A good web search is "omicron mouse origin" and you'll see a bunch of papers and articles that are interesting

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NotAnotherEmpire t1_jdj0c30 wrote

There's a significant concern that Alpha or Delta could be hiding out in an animal reservoir, for example white tail deer.

https://www.pnas.org/doi/10.1073/pnas.2215067120

Anything that emerged would be quite distant from the earlier variants, having evolved in animals for years. But if it still has a human compatible spike protein, that would be bad. Omicron's spike changed drastically in isolated evolution; it wasn't competing against other circulating viruses. Omicron proved very fit.

The primarily barrier to zoonotic disease is that they aren't efficient at going after human receptors. Something that was adapted to humans first is potentially dangerous.

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Large_Ad_3095 t1_jdk42tb wrote

Non-Omicron variants like Delta are only extinct in the sense that they are no longer widespread in the general population. Even so, they continue to mutate in chronically infected people for years, resulting in variants that make even Omicron look "pedestrian." https://www.nature.com/articles/d41586-022-02996-y

Here are three Delta variants detected this January, one of which got up to over 90 mutations: https://twitter.com/LongDesertTrain/status/1624464486596849670

This might be how Omicron started and how the next big variant emerges.

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PopularStaff7146 t1_jdjaz48 wrote

Variants kind of fade out. From an evolutionary perspective, a virus’s entire purpose is to live and replicate within it’s hosts. That’s why we’ve generally observed later variants of some viruses to be less fatal. It doesn’t do a virus much good to kill its host.

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Booty_Bumping t1_jdjpvzt wrote

> That’s why we’ve generally observed later variants of some viruses to be less fatal. It doesn’t do a virus much good to kill its host.

While this is somewhat true, there are important limitations to this model. If a virus has already done enough spreading, from an evolutionary perspective it doesn't matter much if the patient dies later. Another factor, observed in Delta variant, is that having a respiratory virus that is more contagious might also mean it is more deadly, because it is disrupting more cells to produce more viruses.

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melanthius t1_jdjfjti wrote

Wouldn’t a virus do just fine if it re-infects a few people on average before the host dies?

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barchueetadonai t1_jdjg7dd wrote

Yes, but it’s very difficult to be infected with two very similar virus stains at the same time, so a more infectious variant (like Omicron) would get to most hosts first, so the other strains would keep hitting hosts that are already infected with the more infectious strain.

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valryuu t1_jdjie0x wrote

So does the more infectious strain just basically outcompete the less infectious ones, and prevent the latter from even actually infecting the person?

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Adorable_Librarian57 t1_jdjprqv wrote

From what I remember in virology. A lot of what everyone is saying is true. Considering that an infected host results in some 8 trillion replicated virus’s, any variants that help it replicate and survive more effectively will be come an additional strain. The general trend of the virus should be similar to that off parasites. ‘A good parasite doesn’t kill its host’. That is to say it should just jack you up and not kill. Unlike Ebola, which burns through those close to each patient zero. I will say that each virus is unique and the above are only generalizations.

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deltadoodle747 t1_jdjncqr wrote

Its still out there but changed into a new strain or outcompeted by others. In those that caught it, much like most harmful bacteria it may live in or on them and could make them sick of they get seriously injured in another way and their immune system is unable to fight enough of the various invaders

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provocative_bear t1_jdjm7gz wrote

Delta waned because it got outcompeted by Omicron. Omicron is way more infectious, better at evading immunity/vaccines, and since it’s less harmful and deadly, societies don’t tend to lock down as much during waves of it. Natural selection has spoken, unless something drastic like an Omicron-specific vaccine drastically changes the equation before Delta goes extinct.

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