A coronavirus epidemic hit 20k years ago, new study finds

People keep posting archive links to "non-paywalled" copies, but the study itself has freely available full-text not behind a paywall. No need to read the NY Times at all. Just go straight to the source: https://www.cell.com/current-biology/fulltext/S0960-9822(21)...

sinsterizme• 5 years ago

I’d personally rather read the NYT article because it’s much easier to understand as a layman

acituan2• 5 years ago

I prefer just the opposite, even if the jargon is harder to consume at a glance, the extra layer of editorializing can obfuscate central facts or salience peripheral details based on whatever their target demographic wants to hear (nothing exclusive to NYT).

kragen• 5 years ago

That's not helpful if what the NYT article says is wrong, which it probably is. As a general rule, any popular-press story about a scientific paper is wrong, usually dramatically, spectacularly wrong. I'm invariably better off just reading the paper's abstract.

neals• 5 years ago

Even better: The data is readily available in the world! All you need to do is a bit of research and travelling and you could come to a similar conclusion!

breck• 5 years ago

Here is the source code, AFAICT: https://github.com/DavidPierreEnard/Gene_Set_Enrichment_Pipe...

I've been involved in GWAS before, so have an inkling of what's going on. I love the creativity in this paper.

The stuff is super fascinating, but the pipelines are still very primitive—so I encourage programmers to get involved in bioinformatics if you like this stuff! In the future I expect we see work like this accompanied by not only source code but Spore like simulations that let you explore the ideas like a video game.

UncleOxidant3• 5 years ago

It's written in Perl.

mynegation• 5 years ago

Could you please give some guidance on the topic of “what programmers could do for bioscience”? Or point to any resources doing so? Absolutely serious question.

HarryHirsch2• 5 years ago

So - how did this virus spread through the population? 20 kyrs ago people didn't live in cities but in small bands of a few dozen people. It's easy to see how an epidemic might spread through a village but how would it move between isolated groups?

CyberRabbi• 5 years ago

I’m not an expert but scientists have found that coronaviruses are aerosolized. So i think the process of aerosolization probably played a part.

Source for reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293495/

kadoban• 5 years ago

I don't think aerosolization matters when you're not in the same building and you're any reasonable distance away (certainly when you're miles away from the closest infected, you're safe, right?)

colechristensen2• 5 years ago

Groups interacted with each other. A large reason that humans are found more or less everywhere on the planet was pressure from interacting with other humans.

HarryHirsch2• 5 years ago

They absolutely did but how frequently? The first villages in China are attested 7500 BCE, that's 10 kyr later, if the dating is correct.

bigpumpkin2• 5 years ago

Maybe the virus was not a pandemic 20k years ago. Small tribes that carried genes that are resistant to the coronaviruses spread later on as they established larger communities/cities.

autokad• 5 years ago

Human civilization was probably much more developed back then than 'experts' believe. Look at a satellite map, most of that light blue you see was land during that time. The East China sea was mostly land. You think people, like the majority of people, weren't living there?

Just look at the gobekli tepe story.

Florin_Andrei2• 5 years ago

They were less "isolated" than you imagine. They traded with each other, intermarried, fought wars. You can see that in populations having a similar life style nowadays (there's very few of them now).

f6v7• 5 years ago

The same way the infectious face cancer spreads among the Tasmanian devils.

bigpumpkin2• 5 years ago

Look at the infection/death rate in Southeast Asia. It strongly suggests past community transmissions of past coronaviruses.

TX0098812• 5 years ago

Aren't coronaviruses pretty common...?

colechristensen2• 5 years ago

Yes, people seem to miss this. There are several mild endemic coronavirus diseases in humans, usually called "common cold" along with many others.

shoto_io• 5 years ago

Yes. But then again they didn’t start out as endemic virus but as a pandemic one. They probably wrecked a lot of havoc before becoming just a cold. Mayas and Aztecs can tell.

Fomite• 5 years ago

Yes. They've also caused three major epidemics in the past two decades - there's no reason they shouldn't have emerged historically from time to time.

Florin_Andrei2• 5 years ago

So, a likely scenario is: a new virus appeared, it swept through the population, caused serious disease, a bunch of people died, the survivors had better resistance to it, it settled as a mostly innocuous thing (such as the common cold) or disappeared completely, and the next generations remembered it as "the plague of emperor Fancy Pants" or something.

binarymax• 5 years ago

“It should make us worry,” said David Enard, an evolutionary biologist at the University of Arizona who led the study, which was published on Thursday in the journal Current Biology. “What is going on right now might be going on for generations and generations.”

Should it though? Seems like we've survived this many times as a species, and now have the technology to combat it! I'm more optimistic with this information, and hopefully we can eradicate coronavirus forever with mRNA and next-gen vaccinations.

_jal• 5 years ago

Seems like we've survived this many times as a species

I'm reasonably sure the species will survive climate change. Some nation states, civilizations and cultures' odds look more iffy.

I think your bar for worry may be a bit higher than mine.

e40• 5 years ago

And specifically about a pandemic, even if 50% of humans died in it the species would continue, but that would very much be something to worry about. Even at much lower percentages it would be worrying. Or the fact that it could continue for generations.

zamalek• 5 years ago

Yeah, it's like surviving falling from an airplane. You technically survive, but life will be extremely different.

cosmie• 5 years ago

It's not the climate change that'll get us, but each other.

Left to nature alone, we'd likely evolve and adapt and survive in some form or fashion. But the advancement of humanity has led to all kinds of ways we could do ourselves in if we put our minds to it.

And those nation states and civilizations facing iffy odds aren't likely to go down quietly. In the throws of desperation, all bets are off (why care about stuff like MAD[1] when you're already facing imminent destruction by nature).

[1] https://en.wikipedia.org/wiki/Mutual_assured_destruction

subsubzero• 5 years ago

I think whats going on here are people are fatigued with covid related news and in the news in general. News publications are terrified and putting out these scaremongering stories to get people hooked again.

Just like the 1917/1918 swine flu didn't last for "generations"(meaning the potency of the virus was extremely deadly) this covid virus will do the same. It will def. be around but not in the same potency as when it entered the world stage late 2019.

f6v7• 5 years ago

The last thing we should do is to be laid back about this or next viruses. If we don’t use the momentum to reduce vaccine rollout times among other things - we failed.

chiefalchemist2• 5 years ago

To your point: "...who led the study and is now seeking notoriety and additional funding..."

While I hate to sound like a cynic, this is the human side of science time and again. The fact that too many "journalists" don't recognize the context only makes matters worse.

To that I'll editorialize and add, key word "might." Such unsubstantiated hyperbol only makes the source even more suspect.

lamontcg4• 5 years ago

Should it though?

Fuck no. I'm really tired of these stories.

(this is all directed at the author that put that "it should make us worry" quote in the NYT piece, not at any HN poster, but I really need to vent)

The 1918 pandemic turned into seasonal influenza one we had enough herd immunity, enough people had T-cells that recognized H1N1 and the virus was forced into making sacrificial choices in order to spread.

This virus will not achieve an escape mutation that puts us back to square one with vaccinated or recovered people at the same risk everyone was at in 2019.

If you look at what happened in 2009 the H1 envelope protein of that virus traces its lineage back to the 1918 pandemic, it spent 50 years mutating in pigs before it jumped back to humans (that is a LOT of generations of fucking "variants") and people who were born and exposed to pre-1957 H1N1 when it was endemic to the human race had cross reactive T-cells which protected them. They still got infected, but the disease burden was vastly lower so that pandemic fizzled:

https://pubmed.ncbi.nlm.nih.gov/21653752/

The human immune system isn't a binary on/off switch, and while circulating neutralizing antibodies are the gold standard of immunity they are far from the entire story.

If you want to read an article supporting the idea that the coronavirus will transition to milder endemicity without all the irritated swearing read this:

https://science.sciencemag.org/content/371/6530/741

And everyone can fuck off in advance about the idea that ADE will happen. If it was going to happen it would have already happened and this isn't Dengue:

https://blogs.sciencemag.org/pipeline/archives/2021/02/12/an...

All the fucking headlines about how 99% of the people who are dying now are unvaccinated are screaming out that there's no fucking ADE anywhere to be found. People still talking about ADE need to see a psychiatrist to deal with their addiction to doom and gloom.

This pandemic is ending. I'm 2 months post vaccination and everyone I'm in close contact with is vaccinated, so its pretty much entirely over for me.

Now I need a fucking snickers bar.

noduerme3• 5 years ago

"If you look at what happened in 2019 the H1 envelope protein..." was that date a typo?

LocalPCGuy3• 5 years ago

I generally agree with you (minus the rage) and agree re: being vaccinated at this point means it's pretty much over for individuals and their associates who are also vaccinated.

The only quibble I take is that, while it's likely you (and by proxy, the experts you cite) are correct that we won't go back to square one, it is still a (low) possibility. Probably low enough that it isn't worth concerning yourself with, except to be aware that the possibility is there. And probably slightly higher than the normal chance of a random breakout until we get closer to vaccinated herd immunity worldwide. But I'm not suggesting it should necessarily change any significant behavior of those vaccinated, just something to pay a bit more attention to than normal and be ready to take action if needed (i.e. don't throw away all the masks just yet).

And that said, I really appreciate you including sources and I'm sorry I don't have any handy to back up my statement, but it does come from reading and listening to experts. That said, it's my recollection and summary of that so I'd encourage anyone to take it with that grain of salt.

UncleOxidant3• 5 years ago

Yeah, I didn't quite understand why it should make us worry. We do have a lot more tools at our disposal than people had 20,000 years ago - vaccines, antivirals (in a few years), knowing to social distance, etc.

jacquesm3• 5 years ago

Population density, commercial air travel.

Social distancing is something that people even now are loathe to engage in, fortunately more and more people 'get it' but there are still plenty that do not. Arguably that's Darwin at work, but still.

WalterBright• 5 years ago

Other things we have today that mitigate spread:

1. sanitation

2. hand washing

3. understanding of how the disease spreads (not swamp gas)

4. knowing that throwing virgins into volcanoes does not work

5. clean water

peter303• 5 years ago

People lived in small groups most of the time. Harder to spread.

99_00• 5 years ago

Should it though?

Yes of course it will. The mainstream narrative is that the virus came from a wet market. Wet markets are still open and there is no discussion about what to do about it. The most basic lessons and precautions are forbidden topics.

jeremyjh• 5 years ago

Should it though? Seems like we've survived

Someone survived - but for the mutations to have a selection benefit strong enough to dominate that gene pool there would have to be more people who didn’t survive than did.

nradov3• 5 years ago

Not necessarily. Even a virus with a low infection fatality rate could have caused significant evolutionary changes if it was endemic across many generations.

robocat• 5 years ago

but for the mutations to have a selection benefit strong enough to dominate that gene pool there would have to be more people who didn’t survive than did.

To be pedantic: the gene pool is mostly influenced by anything that prevents reproduction, i.e. if you have your kids, and then die that doesn't affect the gene pool to a first approximation (there are selection pressures of becoming an orphan, but they are likely usually very weak. If being an orphan makes it more likely one will have kids or more likely to have more kids than one would have otherwise, then the selection pressure will select for death, which is inverted from what is naively thought! Edit: And if you are older and have never had kids and die, there is very little chance for selection pressure.).

LatteLazy• 5 years ago

If 99.99% of people die, the species lives on, but everyone reading this is gone and so is civilisation.

MikusR• 5 years ago

So China has discovered time travel?

trasz• 5 years ago

Nah, must have stolen it from the US.

viach• 5 years ago

Is it a best practice nowadays to use word "coronavirus" for all the viruses with the particular molecular structure pattern instead of word "flu"?

zeven7• 5 years ago

Well, it's not influenza...

Majromax• 5 years ago

It's best practice to use "coronavirus" for coronaviruses, and "flu" for influenza.

While they can cause similar symptoms, they are very different diseases, caused by viruses that have no particular genetic link.

8note• 5 years ago

Flu viruses are usually described more specifically too: H1N5 and the like

newacct5835• 5 years ago

It's absolutely not appropriate to call these "flu". That is a contraction of "influenza", which is an entirely different family of viruses.

And yes, the family is named "coronavirus". The one we're dealing with now is a strain properly calls SARS-Cov-2, which causes a disease officially termed COVID-19.

rsynnott3• 5 years ago

Where do people get this? Covid is nothing to do with influenza. Some of the viruses which cause the ‘common cold’ are coronaviruses, but flu is unrelated.

imvetri• 5 years ago

Interesting. Ice age ended 10k years back.

hatware5• 5 years ago

I'd love to never hear about another coronavirus again.

We went too far prescribing a certain agenda in the last year, and it's time to reflect on that.

In my opinion studies and articles like this are doing more to fuel the fear porn than they are at teaching anything substantial.

f6v7• 5 years ago

I'd love to never hear about another coronavirus again.

We should definitely hear about coronavirus again and again until everyone learns that millions of people might die unless we completely master immunology. Public awareness, safety measures, and vaccine development should get as much attention as possible until we have a pipeline that allows to develop and distribute vaccines in a matter of months. We never know what next pandemic might strike.

hatware5• 5 years ago

until everyone learns

See, that's the problem. You can't force anything, but you present it as a "must be done at all costs" proposition. That's very disingenuous.

Regardless, I think you missed my point. Some of us are just sick and tired of every crusade that dominates the news cycle with severe lack of pragmatism. There are plenty of more important issues than coronavirus and it sounds like you're suffering from a lack of perspective.

rsynnott3• 5 years ago

Well, good luck with that. There have been three coronavirus epidemics in the last 20 years. And probably hundreds at least more throughout human history. And the current one won’t be entirely gone anytime soon.

hatware5• 5 years ago

Epidemics don't need marketing departments, something that is very obviously part of the equation with "the current one."

ArkanExplorer• 5 years ago

For COVID to have an impact on the gene pool, it would have to be killing people within reproductive age.

As of February 2021, only 11,000 people in the USA under 45 died of COVID - and most would have been very sick with existing health conditions and unable to reproduce anyway.

There are 193,000,000 people in the USA in this age range, so the death risk from COVID is 0.006%

COVID is of no threat to young and healthy people so there will be no impact visible genetically.

uncoder0• 5 years ago

Hmmm, wonder why this fact based comment is being down-voted.

Throwawayaerlei2• 5 years ago

Raw data is here, is current as of May 10th: https://data.cdc.gov/NCHS/AH-Provisional-COVID-19-Death-Coun...

I haven't looked at it since February, the numbers then were around what ArkanExplorer is saying.

usefulcat• 5 years ago

"Studies on each of these coronaviruses indicate that they jumped into our species from bats or other mammals."

Has this been proven for covid 19? I thought it was still a theory at best.

nradov3• 5 years ago

The genome for SARS-CoV-2 shows strong evidence of passing through both bats and pangolins. But how it made the jump to humans is still unclear.

justinator• 5 years ago

You eat them

https://www.youtube.com/watch?v=BZY7x1166EQ

newacct5835• 5 years ago

It remains a "theory" in all cases, except ones where we've managed to actually observe the jump.

But yes: consensus among experts remains that this is a natural virus, precisely because (as per e.g. the linked article!) such pandemics are literally as old as life. We knew a big human pandemic was going to show up sooner or later, because it happens to some species or another every year or two.

It's true we can't rule out the lab theory as much as we'd like to. There was a good WSJ article a few weeks back claiming that western intelligence sources knew about a disease cluster among staff at the lab which would be consistent with the start of the pandemic. That at least is something to hang the more conspiratorial hats on.

But really, no one serious was "surprised" by covid in any meaningful way. It was going to happen.

eplanit2• 5 years ago

"It's true we can't rule out the lab theory as much as we'd like to."

Why is it desirable to rule it out? It's not only plausible, but the evidence seems to be accumulating, not diminishing. Thorough investigations seem very much warranted[1]. Let's not ignore the possibility because we wish such things can't/don't happen.

[1] https://www.nytimes.com/2021/06/23/science/coronavirus-seque...

INGSOCIALITE• 5 years ago

Did it originate in China?

kazinator• 5 years ago

What is going on right now might be going on for generations and generations.

Because, why? The vaccines hand sanitizer, soap, masks and social distancing didn't work 20K years ago, so why would they now?

Can someone please write something this topic without the fear mongering?

But whatever happened in East Asia seemed to have been limited to that region.

Because the WHO recognized the problem sooner, and countries shut down international air travel sooner than we did this time around.

A coronavirus epidemic hit 20k years ago, new study finds

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