How the novel coronavirus has evolved
graphics.reuters.com
graphics.reuters.com
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-...
(Anecdotal) This may be why I laugh so hard each time the dog sneezes. It doesn’t happen often, and it’s hilarious when it does.
https://blogs.sciencemag.org/pipeline/archives/2020/12/10/th...
Back in February-ish (I forget exactly when), we had confirmed community spread in Washington (West-coast state in the US), with the belief that it had been spreading for weeks and no one noticed, because of how few cases there were, and no bump in hospitalizations. This was likely the Wuhan strain, which likewise had been spreading in Wuhan for at least a month and a half before it was detected.
On the flipside, when it reached Italy, it hit that country hard. It wasn't clear why, but I remember a report sometime during the summer that the most prevalent version of the virus in Italy was distinct from the Wuhan one, and could possibly be labeled a different strain because of its increased infectiousness, that mutation apparently occurring somewhere in Europe and spreading out from there (France was also hit hard at the same time IIRC, but Germany for example was not).
Not long after that I remember a cross-country comparison that said the primary version of the virus in New York (US East coast, also hit hard) matched the one in Italy, but not the Wuhan one, and that what we had in Chicago was a mix of the different strains with (at the time) no one winning out over the others.
Nice to finally see confirmation about there actually being different strains that are shifting over time, but unfortunately the timing makes it look like lockdowns may have selected for the more virulent version and caused the pandemic to be worse than it otherwise would have been (see the graphs in the "G strains take over" section, where the cases spike only after, well, the "G" strains take over and the Wuhan "L" strain has been pushed out).
The only thing known is that we can decode the genome across the world and that the virus, as it spreads, slowly gets some small changes which could be followed.
There's no sign that anything people did (especially "lockdowns") up to now had any evolutionary effect on the virus. Coronaviruses mutate much slower than a lot of viruses. The majority of experts believe that what we observe (these still minimal changes) could be attributed to the "founder effect."
Putting it in concrete terms, if you have two versions of the virus, X which for each infected person tends to infect 1.8 others, and Y which tends to infect 2.8 others, then after ten days there might be more people infected with Y than X, but X would still be around.
Now if everyone takes precautions, maybe those rates are cut in half. Now X only infects 0.9 people per infected person, and thus dies out, while Y is still infecting 1.4 people per infected person, and thus is still spreading, just slower.
This is actually an observed effect in many transmittable illnesses; over time, they become more transmittable, and less deadly. Extremely deadly forms kill their hosts, ending the ability to reproduce via transmission, and the more transmittable strains reproduce effectively. This type of optimization leads to things like the common cold and flu. The scary thing about COVID19 is that it has a very long lead time between infection and symptoms, if they develop at all, meaning it can circumvent some of those "normal" optimization peaks; it can be both very deadly, and very transmittable, because of the latency in the signal.
Actually I think I should have said "infective" rather than "virulent" there; basically lockdowns select for versions of the virus that can spread despite the lockdowns. It only looks more virulent because of the larger number of total infections.
Later strains may indeed turn out to be more infectious, but I don't think we have the evidence for that yet.
a lockdown would select for a more communicable strain, not a more virulent strain. the big problem is this virus has morbidity latent to infection incubation and transmission.
these conditions mean that the virus can be 100% lethal and not succuum to the usual dynamics
The original strain would effectively be a vaccine. The lockdown would be the equivalent of the anti-vaxxers.
There’s no evidence the mortality rate has actually increased; this was just a thought experiment.
In prior pandemics (1918 flu), future strains were more deadly than earlier strains.
The nightmare scenario now is that a COVID-20 emerges with a 5% mortality rate instead of 0.5%. If catching COVID-19 gives you immunity to COVID-20 (and all the vaccines fail), then the lockdown would increase the death toll by 10x.
These are all hypotheticals that looked somewhat plausible in April, and implausible today.
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.
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.
You have assumed I'm ignorant when you could have attempted to understand why I believe the things I do which seems at least as big a mistake as the one you accused me of making.
this modifies what was a specific key into a lockpick. this allows the virus to bind to a number of allelic versions of ACE2 rather than one or few specifics. thus promiscuous binding.
In general, Italians have issues with high blood pressure. High blood pressure seems to be a factor in the severity of the illness.
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 pneumonia in early December. They thought it came from a seafood market, which was proven incorrect.
The western world harassed them and accused them of eating bats, and transmitting the disease, which is also proven to be incorrect.
China then back-traced the earliest case to mid November. Which happens to coincide a few weeks after the Wuhan military games. Just the right amount of time for the virus to incubate and wreck havoc.
New evidence is suggesting that the virus was in Italy before it was in China. [3]
But the interesting thing, is that when they took MRI scans of the vaping outbreak patients, they saw white orbs in the picture in their lungs. Coincidentally, Covid-19 victims also had these white orbs in their lungs.
The whole origin of this virus was always very mysterious. Something just never seemed right about it.
The vaping thing just came and disappeared. Nobody really knows what caused it, just a few random theories about contaminated cartridges. But here’s the strange thing. Those vaping pens, are all made in China. And are sold all over the world. People in China uses those vaping pens everywhere, but there were no reports of a mysterious illness from it in China. Only in the United States and a few in Canada. Not even Europe reported any issues.
Why was it reported only in the United States? Then soon after, all the other pieces began to fall into place, one after the other.
To get down to the true origin of this virus, then they need to check those vaping people. Check them for the Covid-19 antibodies.
Then check the nursing home people from Virginia, for those that survived, for Covid-19 antibodies.
Then check the people that went to the Wuhan military games for Covid-19 antibodies.
Or not. And just conveniently blame China for being the origin of the virus, just because they were the first ones to detect it, and report it.
[1] https://en.wikipedia.org/wiki/2019%E2%80%932020_vaping_lung_...
[2] https://www.cnn.com/2019/07/11/us/virginia-retirement-commun...
[3] https://www.reuters.com/article/health-coronavirus-italy-tim...
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 vaping "thing" hasn't just come and disappeared. The CDC has stopped reporting on it.
See https://www.thelancet.com/journals/lanres/article/PIIS2213-2...
So that correlation is not causation, EVALI is not COVID-19.
EVALI is not related to the vaping pens or where they originated.
The disease was reported where people were using THC cartridges that were diluted with Vitamin E, which is primarily the US.
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.
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 very mysterious. Something just never seemed right about it.
This is exactly the kind of language utilized to create a sense of mystery and intrigue, but is not based on any facts.
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.
Only for the record/FYI, there is growing evidence that the virus (cannot say which strain) was present in Italy months before, possibly since September 2019.
https://www.reuters.com/article/health-coronavirus-italy-tim...
Churches and meat-packing plants are still a concern.
Like health workers who visit lots of houses, gets tested often.
https://en.wikipedia.org/wiki/Superspreading_event
> Some cases of superspreading conform to the 80/20 rule, where approximately 20% of infected individuals are responsible for 80% of transmissions, although superspreading can still be said to occur when superspreaders account for a higher or lower percentage of transmissions.
> "Coronavirus does not spread evenly. Most people who get the virus won’t pass it on to anyone at all. But a small number of people will spread it widely. Scientists estimate as few as 10% of infected people are responsible for 80% of infections."
Based on this, they go on to explain why, if it's true, it becomes worthwhile to do backward contact tracing to reduce R.
https://www.sfgate.com/bayarea/article/Santa-Clara-County-do...
Split by race, it’s not 80/20. Splitting by occupation or socioeconomic status would certainly reveal a stronger divide than splitting by race.
>This Overlooked Variable Is the Key to the Pandemic It’s not R. https://www.theatlantic.com/health/archive/2020/09/k-overloo...
about the number k which is a more mathematically sophisticated take along those lines. Obviously reality is a bit more complicated than 80 20.
If you have a limited number of vaccines, you can vaccinate the propagators first and have 80% of the benefit of full population vaccination for 20% of the cost.
A good heuristic for knowing which model to apply is tantamount in absence of a testable environment.
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 that lets us do anything other than track the pandemic's spread.
Toyoshima, Y., Nemoto, K., Matsumoto, S. et al. SARS-CoV-2 genomic variations associated with mortality rate of COVID-19. J Hum Genet 65, 1075–1082 (2020). https://doi.org/10.1038/s10038-020-0808-9
The measured variation between the now extinct L strain and the new current G strain is the G strain was about 2% higher correlation between strain and fatality rate. The actual fatality rate was not 2% higher which would be huge, but the % of L in a population vs population fatality rate correlated 2% higher based on euro country data in the spring.
Certainly there's only two real impacts on fatality rate right now, both incredibly politically incorrect to discuss, there's an enormous staggering stunning huge disparity in fatality rate by age, and a merely giant disparity in fatality rate by comorbidity rate. The medical science seems clear, but the political impact makes it impossible to discuss quarantine policies that would minimize total death rates. Hundreds of thousands of lives could be saved by locking up everyone over 60 and everyone over 300 pounds and a couple other pre-existing conditions, but AARP is one of the strongest PACs out there and even if it saves her life, grandma will vote out anyone who "locks her up for a year for her own good".
Personally I'm old enough that I'm working very hard to max out my cardio health for when I inevitably get it.
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.
This is especially baffling considering how much more prepared we are (or should be?) and how much more we (should) know about the virus now vs. before.
It seems like one or more of the following is happening:
- Actually fewer people are wearing masks, or are wearing them less vs. previously
- Even though lockdown mandates/recommendations are increasing, they’re not being followed/enforced as much
- Masks aren’t as effective as we think
- It’s spreading in other ways that we’re unaware of
I’d love an ELI5 of why we’re continuing to see record numbers of positive test rates + deaths + hospitalizations, in spite of (again, supposedly) more diligence with masks and lockdowns.
To be clear, I’m a strong believer in wearing masks and staying home (I almost never leave my house, and when I do, I’m wearing a mask), but it’s baffling and a bit frustrating to see the numbers continue to rise without anyone seeming to have answers as to why.
I think hospitalizations are still a somewhat consistent percentage of cases, and will increase as the number of cases go up.
Anthony Fauci summed this up pretty well a few days ago in a press release. He basically said that the USA is really bad at following rules, which we are, and that with the recent holidays (Halloween, Thanksgiving) and because of the cold weather (people stay indoors more, share the same air, air being recycled and heated in HVAC systems to reduce energy consumption), that numbers would rise. And so they are. I think these human explanations are the main source of the rise in numbers.
Another interesting one was in a WHO release a few weeks ago, that people seem to be experiencing "mask fatigue", or what is more generally known as "caution fatigue", where people, after having to be cautious for a long time, and not experiencing the source of that caution personally, just lose their ability to pay attention to the problem. It's the same reason the TSA inserts fake firearm pictures into the x-rays of luggage, and the same reason the military regularly inspects guard posts in key locations.
This was one of the running theories back in the spring, but it was hard to tell for sure until seeing it spike back up this fall exactly as one would expect if this were the case.
> - Masks aren’t as effective as we think
Also this, I think - masks are good at catching droplets from talking or coughing, but sometime between summer and now it's suddenly become commonly known that this virus can hang in the air for an extended period indoors when there isn't good ventilation - being truly airborne like that means it can just slip around the edges of the mask as you breathe. Even disregarding that it was known back in March that fabric masks only reduced the amount of virus that could get through the mask, it didn't actually completely stop the virus as people nowadays seem to want to believe.
What you see practiced in hospital and intensive care units is what works.
The rest have spotty evidence at best. Hopefully something good will come out of this and we will see more research on public health. Look at the recent Danish on general public face mask use as a good example.
I've been to about 20 states during this pandemic and I have never seen lock-downs strictly enforced... and I don't blame them.
> Since then, there have been documented reports of individuals being reinfected with different versions of the virus.
Yes, reinfections have been extremely rare so far. But if the immunity really is strain-specific, the warnings about Covid becoming endemic in the global population should now carry a lot more weight. The virus will mutate. In a likely scenario, previous immunisations are likely to be less useful, and we all need annual shots against the newly emerging strains.
On the upside, if Covid strains become just another aspect of the flu jab, then we at least already have an existing infrastructure to manage it in the future. Production capacity of vaccines will take some time to ramp up, though. Maybe now would be a good time to invest in drug manufacturing and logistics?
Planet Money did an episode on Covid vaccine logistics and one data point stuck with me. The global production of vaccines is between 3.5B and 5B doses a year. That's for ALL vaccines, across the entire spectrum of diseases and treatments. Adding another 12B to 16B doses on top of that is going to require a lot of new infrastructure, from production facilities to all the materials needed in the logistics chain.
> [...] But if the immunity really is strain-specific
Reinfections have been recorded from different strains because it's much easier to demonstrate that someone has been reinfected with a new strain. If someone has been reinfected with the same strain then it is hard to distinguish that from an infection that wasn't fully cleared originally. It doesn't necessarily mean that immunity is strain-specific.
(I don't know why you were downvoted; your comment seems reasonable to me!)
Meanwhile, I am baffled we didn't prioritize n95(or kn95) masks. Well... It's government, I'm not that baffled
A significantly more rational policy would have been to prioritize masks with filters and for the less than 1/12 of elderly people who live with younger generations, move them into a hotel room and pay for food delivery and care services.
All of this is cheaper and healthier than what was done.
2. Some people don't even know they are at risk especially when they are young.
3. You can't fully isolate old people anyway. That's why we continue to see infections in hospitals, nursing homes, etc.
4. Even if you managed to isolate all risk groups, the spread of covid19 without any restrictive measures would be extremely rapid. While only a small fraction of the rest of the population would become severely ill, a tiny fraction of a large population can still be huge and might be enough to overwhelm hospitals.
If it were as easy as you suggested, surely it would have been tried - at least somewhere on the planet.
They did. Production is up 5x. But factories take time to build.
Entire new types of filters have actually been invented this year, going forward humanity is going to have a lot more choices when it comes to high quality filtering masks.
That "spike" in the graph comes from sequences in the nucleotides coding the spike on the virus, which is somewhat expected given it's repeated on the surface of the virus membrane.
Apparently most of the spike encoding is from a South Asian fish. Reference in the repo.
As in, that's where the virus evolved/stole it from?
EDIT- Be careful reading too far into statements like “XYZ mutation makes it easier to bond to ACE2 therefore it’s more contagious” Infection is more than just binding to a receptor, even if lower quality preprints jump the gun in their conclusions
Is this why some are saying we might need a booster shot in a few years?
There is little selection pressure on the virus for the spike proteins to evolve and change. SARS-CoV-2 infects human cells just fine using its current spike protein. [1]
We’ll have to watch for signs of selection pressure as more and more of us get vaccinated to recognize the spike protein. Hopefully SARS-CoV2 mutates too slowly to escape the vaccines, or can only escape with sharply reduced infectivity and virulence.
> Studies of common-cold coronaviruses, sampled across multiple seasons, have identified some signs of evolution in response to immunity. But the pace of change is slow, says Volker Thiel, an RNA virologist at the Institute of Virology and Immunology in Bern. “These strains remain constant, more or less.”
So there seems to be a pretty good chance that this won’t really be an issue.
Anyhow, if the spike proteins vary too much, then we'll need a new vaccine all together, not just a booster for the current one
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.
Besides, we already know there are a lot of ridiculous anti-vaxxers out there who will refuse the vaccine regardless. And a lot of those people are elderly or at risk!
The longer this situation goes on, the less palatable shutting down huge chunks of society seems to me to be. If this is going to be endemic, which a lot of signs and common sense reasoning points to, then the management of the disease needs to change.
You're asking why a virus would mutate more slowly than a virus that mutates extraordinarily fast.