How the novel coronavirus has evolved • Hacker News Board

Re: How the novel coronavirus has evolved

#71

Post by rossdavidh » Sat, Dec 12, 2020, 2:04 PM UTC

someotherperson wrote: post #35

Since this will continue to be misunderstood, it's important to emphasise that the article explicitly mentions that there is 1. No evidence to support the idea of strains that have any impact on infection 2. No evidence to support the idea that the strains will resist the vaccines or weaken vaccine efficacy. This is not a "strain" in the sense of the flu, COVID-19 hasn't fundamentally changed in any meaningful way th…

Well, that's _mostly_ true, but the very fact that one virus variant displaces another over the course of a month or two, while by no means definitive proof of anything, is at the very least suggestive that for one reason or another it is better able to spread.

It _could_ be a neutral mutation that just spread due to a "founder affect" or something, but it would not be in any way surprising if a virus which is brand new in humans, evolved in the direction of adapting better to that new environment. What spreads better in bats, may not be the same as what spreads better in humans, and there is no particular reason to expect that this virus wouldn't be mutating in the direction that allows it to adapt to its new host.

Now, that could even be a good thing, if it was adapting in the direction of not triggering the host's immune system as strongly, since it is largely an immune system overreaction that kills the host. But, while by no means definitive, I don't think we can say that there is _no_ evidence to support the idea that strains have any impact on infection. the very fact that the initial strain has been largely displaced by others, suggests at least the possibility that it has.

Re: How the novel coronavirus has evolved

#72

Post by rossdavidh » Sat, Dec 12, 2020, 2:07 PM UTC

yumraj wrote: post #17

So which strain are the various vaccines targeting? Or are they multi strain vaccines like the flu vaccine?

There was a suggestion that one of the variants seen in Denmark's mink infection, might make at least some of the vaccines slightly less effective. But even in that case the effect was not large, and in any event the variant in question hasn't been seen since September.

Re: How the novel coronavirus has evolved

#73

Post by Throwaway1771 » Sat, Dec 12, 2020, 2:32 PM UTC

twic wrote: post #41

brian_cloutier wrote: post #37

Earlier quoted context omitted.

Nature has a decent article on this: https://www.nature.com/articles/d41586-020-02544-6 Apparently we have little idea whether D614G is more infectious but that is hard to believe given that it has so thoroughly outcompeted other strains.

Hard to believe, but true - because it didn't outcompete other alleles, it was just in the right place at the right time, as has been carefully documented: https://twitter.com/ballouxfrancois/status/13316691180015370... Still, assuming that massive success is due to competitive advantage rather than random chance is extremely on-brand for HN.

Totally uncalled for, and hilarious, knifejab by a man in black pajamas.

Re: How the novel coronavirus has evolved

#74

Post by bonzini » Sat, Dec 12, 2020, 3:05 PM UTC

Scarblac wrote: post #61

herendin2 wrote: post #54

Earlier quoted context omitted.

It's important because focussing on that 20% might be far more efficient and effective

I don't think anybody knows who are going to be part of that 20% in advance though.

Maybe not who they are, but what they do.

Re: How the novel coronavirus has evolved

#75

Post by alistairSH » Sat, Dec 12, 2020, 3:18 PM UTC

melling wrote: post #9

“If the virus changes substantially, particularly the spike proteins, then it might escape a vaccine. We want to slow transmission globally to slow the clock,” Is this why some are saying we might need a booster shot in a few years?

As noted in sibling, the booster shots are to "remind" your immune system that an infectious bug is out there.

If COVID begins to mutate in ways that make the vaccine (and anti-bodies it causes) less effective, we would be in a situation like the flu - annual vaccines based on that year's strain (which takes some guesswork). The disease is then called endemic.

But, there is currently no indication COVID will become endemic. It might. It might not. We don't know, but current knowledge tends to indicate it won't.

Re: How the novel coronavirus has evolved

#76

Post by soulofmischief » Sat, Dec 12, 2020, 3:27 PM UTC

randomsearch wrote: post #62

sillysaurusx wrote: post #38

What does everyone think of the idea that there is an 80/20 rule in play for Coronavirus? Specifically, 80% of the infections come from 20% of the infected. I’ve heard some hearsay about it, but nothing conclusive; I was hoping someone knew either way.

Did anyone else think that 80/20 sounds too neat, especially when you consider that the definition of superspreaders is subjective? It suggests confirmation bias and reminds me of when biologists etc assume normal distributions but when you did into the detail you find normal is actually not normal.

Power laws aren't rigid, domain-specific variables create local fluctuations even in models like population or wealth distribution. It's just a general baseline which we can use to model certain characteristics of a system.

Re: How the novel coronavirus has evolved

#77

Post by learnstats2 » Sat, Dec 12, 2020, 3:28 PM UTC

herendin2 wrote: post #54

graderjs wrote: post #46

Earlier quoted context omitted.

I don't know either way about your question, but aren't these sort of power law dynamics common in everything? I don't think it would be surprising if that was the case with this "pandemic" nor would it make this virus special. Just like 90% of the content is created by 10% of the people in social media, or something like that.

It's important because focussing on that 20% might be far more efficient and effective

I think we have already somewhat focussed on that 20%, by asking people not to hang out in big groups.

Churches and meat-packing plants are still a concern.

Re: How the novel coronavirus has evolved

#78

Post by throwaway2245 » Sat, Dec 12, 2020, 3:40 PM UTC

neogodless wrote: post #68

blackrock wrote: post #44

Earlier quoted context omitted.

Interesting premise. But why doesn’t anyone look at the bigger elephant in the room? Sometime in April 2019, reports of a mysterious illness started surfacing. They thought it was related to vaping products. [1] Then in July 2019, a respiratory illness hit a retirement home in Virginia, and killed a bunch of old people. [2] Then the Wuhan military games was in mid October 2019. Then China reported of an unknown pneum…

Looks like the CDC investigated the outbreak - if there was a virus responsible, wouldn't it have been found then? If it was related, it doesn't make sense that it would not have easily begun to spread at that time. http://www.fairfaxtimes.com/articles/three-dead-amid-respira... Trying to connect dots makes for adventurous brainstorming, but it doesn't manifest reality. > The whole origin of this virus was always ver…

> if there was a virus responsible, wouldn't it have been found then?

Viruses are hard to identify, but the CDC here suggests it was a rhinovirus (not related to coronavirus): https://www.fairfaxcounty.gov/health/outbreak-investigation-...

If it was SARS-CoV-2, the CDC could confirm that now retroactively with stored blood samples. I suggest it was probably not.

However, then, it does point to proto-pandemics happening as a regular occurrence. A fatal viral outbreak is contained within a care home rather than spreading - either by being slightly sub-exponential in the general population (R<=1), or perhaps just by pure luck.

Re: How the novel coronavirus has evolved

#79

Post by jl2718 » Sat, Dec 12, 2020, 3:40 PM UTC

Antibodies mostly target the attachment heads of RNA viruses, which mutate very quickly to evade them. But that mutation also applies to its own reproductive mechanisms, like RNA polymerase, which degrades in the presence of evolutionary pressure from the immune system against the attachment proteins, so the latter strains become dormant because they lose reproductive integrity. It then takes conditions lacking an immune response to evolve back to a working polymerase and attachment head.

I think it is interesting to note that the immune system itself is largely responsible for spreading most RNA viruses: inflammation, coughing, sneezing etc. Is this us evolving population-level (probably more like Dunbar number than 8B) defense in response to the general threat of viruses, or is it a weakness that each individual virus evolves to exploit. It seems to me that this involuntary spreading behavior is much more pronounced in humans than other mammals.

https://scopeblog.stanford.edu/2020/04/03/how-coronaviruses-...

https://mbio.asm.org/content/2/5/e00150-11

Re: How the novel coronavirus has evolved

#80

Post by therealx » Sat, Dec 12, 2020, 3:48 PM UTC

rswail wrote: post #65

blackrock wrote: post #44

Earlier quoted context omitted.

Interesting premise. But why doesn’t anyone look at the bigger elephant in the room? Sometime in April 2019, reports of a mysterious illness started surfacing. They thought it was related to vaping products. [1] Then in July 2019, a respiratory illness hit a retirement home in Virginia, and killed a bunch of old people. [2] Then the Wuhan military games was in mid October 2019. Then China reported of an unknown pneum…

The vaping issue was related to Vitamin E in THC vaping and was not related to vaping in general. The Vitamin E was being vaporized and inhaled directly into the lungs, which caused the problems. Inhalation of Vitamin E into the lungs is a known cause of lung disease symptoms. See https://www.cdc.gov/tobacco/basic_information/e-cigarettes/s... There's no evidence that EVALI is related to COVID-19 or SARS-cov-2. The v…

I know vitamine E acetate is a scourage in the vaping community, but I was under the impression that outbreak was a distincly different thing, at a different time.

Although the uninteresting answer is often true, I do dislike that people refuse to entertain anything remotely fringe. Some of the declassified CIA documents stated that they intentionally furthered this attitude as much as they could, as it allowed them to make many of thier projects dissappear.

What is the most promising theory of origin? A 5-10min search didn't help.

The lab theory is of course the most fun, but not the most probable. The fact that they were working on similar diseases, the lab was newish, and the country itself isn't exactly well known for IP security make me not discredit it as fast as I normally would.

The animal->human route via food (or less likely, bites/other contamination) seems to be most likely. It's happened plenty of times in the past, and given the SES level of the area and cultural norms, it could have definitely happened.

The rest of the ideas seem like a long tail where all of them have fairly obvious "gotchas" that make typing them out a waste, but I'd love to hear what other people think.