Evidence for a mouse origin of the SARS-CoV-2 Omicron variant
ncbi.nlm.nih.gov
ncbi.nlm.nih.gov
> We found that mutations accumulated in ORF S at a rate of ∼0.45 mutations per month on average. In sharp contrast, 27 mutations accumulated in ORF S in Branch O during the 18 months spanning May 2020–November 2021, equivalent to ∼1.5 mutations per month, or ∼3.3 times faster than the average rate of other variants
> We found that the Omicron spike protein sequence was subjected to stronger positive selection than that of any reported SARS-CoV-2 variants known to evolve persistently in human hosts, suggesting a possibility of host-jumping
Although host jumping is undoubtedly occurring (eg infection has been serologically observed in white-tailed deer and other animals), I’m skeptical that it is the primary factor as this paper suggests.
Another possibility is that viral mutation rates are underestimated, and/or infections are systematically underestimated. There is evidence of both in the literature.
Combined with enhanced selective pressure on the spike protein RBD due to mass vaccination campaigns, these are scientifically supported alternative explanations for the observations in OP.
Depends on the campaign. The major Chinese vaccines are “inactivated” and might pressure things differently than our spike-protein focussed viruses in the west.
1) Certain types of mutations are favored by different host biologies. In other words, in humans, you would tend to see one type of coding substitution, in mice, pigs, bats, etc. you'd see another type of coding substitution. The paper gives specific mechanisms that underly this biases; I'm not an expert in these, so I can't say for sure if they are correct, but it the mechanisms as proposed make sense on a first read-through.
2) The early omicron variants have a set of mutations that would be consistent with evolution in a non-human host, overlapping most strongly with mice biology.
3) Perhaps even more significantly, _later_ omicron variants that have spread through human populations have picked up mutations that are once again more consistent with human biology. So the paper manages to show both positive and negative data toward their hypothesis, which makes it stronger.
For the TL;DR crowd, figure 3 summarizes this pretty well.
To analogize this in computer terms, it's as if someone was tracing the evolution of memes by observing the types of compression artifacts introduced in various re-compressions of the meme. For example, JPEG might introduce artifacts related to DCT math, whereas JPEG-2000 would introduce artifacts related to wavelet math. The analysis shows that the artifacts of this new Omicron meme has compression artifacts consistent with, say, Wavelet compression up until it jumped to being shared by JPEG-users, at which point newer modifications to the Omicron 'meme' show JPEG-consistent artifacts.
That's basically the scientific core of the paper. So, to contest the validity of the paper, I think it would be helpful to find citations that dispute the observation that mutations accumulate with a certain bias based on the host biology, rather than whattaboutism pointing to other hypotheses and leaving it at "there are other alternative explanations" therefore this paper is not interesting.
So, while I don't dispute your statement that there are other alternative explanations, what I would really like to see are comments addressing the core scientific thesis of the paper, which is that certain mutations appear more frequently in other host biologies; and that the first omicron cases showed a preponderance of these differently-biased mutations; and that since it has been circulating in humans, the later mutations are once again consistent with a human host.
At the very least, I thought it was a very interesting analysis, as I had never seen the molecular bias of mutations used as a proxy for host biology before. If this is true, then viruses that can spread through alternate host biologies would gain a diversity of mutations that would be less available co-evolving with a single host, which could lead to evolutionary advantages over viruses that are unable to hop between hosts.
If SARS-COV-2 jumps this easily, well, we'll have serious problems predicting the mutations, a challenge for vaccine and drug design.
Now, the origin in a different country does suggest a human host somewhere but it is not strictly necessary.
To be clear that is not being disputed. IMO the central thesis of the paper is:
> the progenitor of Omicron jumped from humans to mice, rapidly accumulated mutations conducive to infecting that host, then jumped back into humans
That hypothesis is primarily supported by statistical evidence related to the frequency of certain amino acid mutations in the viral genome. For example:
> Considering that these two amino acid mutations are uncommon in human patients infected by non-Omicron SARS-CoV-2 variants (0.005% and 0.002%, respectively) we proposed the hypothesis that the progenitor of Omicron evolved in mice.
> searching against the GISAID database using Omicron’s backbone sequence. The top hits were again from the B.1.1 lineage, which differed from Omicron by 31 mutations, indicating that human SARS-CoV-2 variants reported to date could not provide a backbone for Omicron
While the paper certainly presents intriguing preliminary evidence, critically there was no analysis performed which accounted for variation or underestimates in viral mutation rates, number of infected hosts, or gaps in genomic DBs, etc. As such, there are certain hidden assumptions that were not explicitly addressed or conclusively proven.
Moreover, the "pleiotropic effect" is a significant confounding factor:
> predictions showed that the adaptation of Omicron to mice also promoted its adaptation to other species, such as humans, camels, and goats, via stronger RBD-ACE2 interaction (Fig. 6). Such a “pleiotropic effect” of mutations was likely caused by structural similarity of ACE2 across species
Finally, given that selective pressure due to mass distribution of S protein targeted vaccines was also not considered, I think it's fair to say that the evidence pointing to mice is fairly tenuous at this point. But the paper is still valid & interesting (I did not intend to suggest otherwise).
I guess part of the problem is that I don't know how to do the statistics on this sort of a problem, unless say I were to actually model the drift events on a computer and "manually" calculate probabilities given a certain set of assumptions. Do i trust biostatisticians to get this right? No. (Yes, I've worked with them)
https://visualcapitalist.com/visualizing-relative-size-of-pa...
Hypothesis 1: UV-C light at 300 nm can make the COVID dance itself to pieces.
Hypothesis 2: UV-A or UV-B light at different wavelengths can cause mutations.
Assumption 2: masks are COVID concentrators. They catch the droplets and virus particles so our lungs don't get it.
Hypothesis 3: putting masks in environment leads to increased risk of mutations. Flies lick masks, bats eat flies, bats give us COVID again.
Conclusion: pick up the COVID concentrators (masks) and put then in a biohazard bin. All people are responsible for all litter seen. We're only responsible for what we see, but we are personally responsible for everything we see.
No, that's not going to happen. Biohazard disposal is expensive even for hospitals, and applying that to everyone... ruinous.
Half kidding.
Will it be perfect? Of course not perfect. But better than nothing. Reduce the entropy a little, and then it'll be easier to handle.
Handle them specially? I handled 122 masks in the car parks of Botany Town Centre, east Auckland, with bare hands yesterday, gathering them into a rubbish bag.
Today I saw 180 COVID concentrator masks, and was able to pick up 136 of them (for the other 44 masks, I was on a bus or in a car and couldn't stop to get down)
Putting masks into regular bins (e.g. landfill) will delay the feedback loop by 100 years. That's good enough for now, so that's my recommendation for those who don't have access to mask recycling.
However, I do have access to mask recycling.
My usual work is automated software testing and language translations for embedded systems, specifically the Fisher & Paykel Healthcare Airvo device. I've come to believe that we need to run an anti-virus algorithm on the world, and it's more efficient with a real-time distributed model, where we all love our neighbour by cleaning up what we see.
https://en.wikipedia.org/wiki/Antivirus_software#Real-time_p...
Also, I'm triple-vaccinated (2x Pfizer + booster), am a young man with no family and a psychological martyrdom complex. I'll take the risk. And wash my hands thoroughly for 20 seconds afterwards. And shower when I get home.
Be a tidy Kiwi.
Clean as you go.
Always leave the code (and world) better than you found it. (Robert C. Martin (Uncle Bob))
I don't want to do it though. Cause I don't want to touch a used mask with bare hands (I got gloves with me, but these are against cold weather specifically). However, with a grapple device and bag (the bag being the easy part) it could be reasonably easy and clean to take care of them. I got one, but I'm not carrying it around to e.g. work or family (that's when I usually see a mask). When I go with my child to the playground, and I'd see one, I could go home to get the grapple. However, I don't remember that occurring. There's quite some firework plastic still lingering around, so I could clean that up before I go with my child to the playground (mainly, to clean the playground).
Btw, I want to comment on the amount you found. 122, 180. That's a lot. How much time did it take you? Cause I only see a mask occasionally (but it annoys me).
I haven't yet logged detailed times (only started counting yesterday, before that was just picking these up as regular litter on my commute). But here's a few from today's log.
32 total between Gossamer Dr and Pakuranga bus stop ~11:45 - 12:40, of which 9 on road (usually a 15 minute bike ride, was more like 25 minutes that time due to stopping regularly, then a walk through the car park)
16 masks Shore Care/Smales Farm has infectious substances bin from 18:45 to 19:30
4 masks Pakuranga plaza (1 countdown, 3 warehouse) 20:40-21:05
Heading rows:
Mask count, Centre GPS coordinates, Radius (km), Start date and time, End date and time, Comments
https://docs.google.com/spreadsheets/d/1ap2lpLXWzK1WcdsasP8c...
Apologies if there's less data tomorrow, I'm not sure what time I'll wake up. But I really wish I could get to Sylvia Park and some other malls and gather some more data points.
Please can an expert in data visualisation draw a heatmap?
I agree that in direct sunlight, some types of pathogens can be broken down. However, the 2 hypotheses are that there is a risk.
Also, I guess that flies are attracted to licking moisture before it evaporates. Therefore the flies are likely to be looking to lick masks if they think they can get an easy drink.
Hypothesis 1: UV-C light at 300 nm (resonant size of particle) can make the COVID dance itself to pieces.
> Issue: UV-C light causes sunburn and is blocked by the ozone layer.
>> Solution: in Shanghai, the public bus service uses UV-C light to disinfect each bus at the end of the day.
https://www.scmp.com/video/china/3075171/shanghai-introduces...
Hypothesis 2: UV-A or UV-B light at different wavelengths can cause mutations.
> https://en.wikipedia.org/w/index.php?title=Mutation_(genetic...
> {Bit string mutation, Flip Bit, Boundary, Non-Uniform, Uniform, Gaussian}
>> Translated to computer programming: off-by-one errors.
Yes, this is fairly well studied, see: https://www.csiro.au/en/research/health-medical/diseases/cov... and https://www.dhs.gov/science-and-technology/sars-calculator
> Also, I guess that flies are attracted to licking moisture before it evaporates. Therefore the flies are likely to be looking to lick masks if they think they can get an easy drink.
Various insects including flies can mechanically carry SARS-CoV-2 around, but they can't be infected. There are no documented cases of insect-borne COVID-19 (doesn't mean it's never happened but we can infer it's a "rare" event).
UV does induce mutations but not sure that masks make much difference here since that effect will be much the same on virus floating in the air (aka primary transmission mechanism) in any case.
Finally, the virus that causes COVID-19 can't actually infect bats, this would require a reverse zoonosis event.
Picking up masks is great though. Personally I would recommend PPE for this (gloves / grabber & mask) if you are going to do it a lot, because COVID is not the worst thing that could be on the masks. You could get really unlucky and handle a mask with TB or something else nasty. It's low likelihood but the risk is worth thinking about if you plan to handle thousands of masks.
Has it been studied?
> "virus floating in the air"
Air with humans is an I/O. There is a minor risk of COVID on cigarette butts, because they made contact with peoples' lips, but that is basically inhalation. I'll make another Assumption: more COVID comes from exhalation.
How do we stop exhalation? Masks with 0.1 µm between each fibre (that's an N95). The common surgical masks are less efficient, but because we breathe several times, the lower efficiencies are increased. Breathe in, breathe out. Breathe in, breathe out. Breathe in, breathe out. The efficiencies add up closer to 100%. But the wind blows! Which is why we also need 2m distancing.
Yes, there's a risk in handling PPE without extra PPE. But having thought about this, if I do that, then people will think I'm professional. So they'll think that I'm going to be there to do it tomorrow. The reality is, the Bus factor on this process is distressingly low.
I'm not planning to handle thousands of masks! I'm planning to dispose of every mask I see. Unfortunately, a large portion of the rest of the population decided that they don't care enough to help, which means there are thousands out there.
This is a call to help, and arguing on the Internet about whether it is or isn't beneficial to the world in the precise way that I imagine it works is just causing division between people, which isn't desirable. Rather, let's find someone else who is a better communicator to rewrite this as an academic paper in order to persuade you that there's an environmental feedback loop, and we should love our neighbour.
"The best way to get the right answer on the Internet is not to ask a question, it's to post the wrong answer."
https://github.com/dwmkerr/hacker-laws#cunninghams-law
If that is so, then is it possible to generate UV-C light with a wavelength of 100 nm?
I'm just asking for a standard deviation on "so low".
What is especially underestimated is viral mutation in HIV-positive and other immunodeficient people. It is suspected [1] that Omicron may have been "bred" aka accumulated its mutations in the body of such a person in South Africa... and once again, the failure of the Western nations to provide access to medical service and at least basic wealth in Africa for decades - and that in general, not just in HIV treatment and prevention - bites us in the behinds here. As long as large swaths of the continent live in utter poverty and war, it will be a giant petri dish for all kinds of pathogens.
[1]: https://www.npr.org/sections/goatsandsoda/2021/12/01/1055803...
First, it’s not certain that Omicron emerged in South Africa, but in another nearby sub-Saharan African country without the same resources. All of South Africa’s neighbours with the exception of Botswana (which Moderna was making pay an eye-watering $30 per shot) are reliant on external aid for vaccination.
So South Africa’s relative wealth is probably irrelevant here, and the argument about how insane the rich world’s refusal to help mass vaccinate the rest of the world is still applies.
Second, South Africa only hit uptake constraints in the past month or so, until then it was affected by serious supply constraints like those other developing countries experienced, with the rich world getting production priority. Price, too, was a factor with pharmaceutical companies refusing to provide doses at anywhere close to their estimated actual cost. As a result money that the South African government could have spent on more vaccination outreach and infrastructure, especially in more rural and poor areas, was instead spent on buying doses.
The long-standing supply constraints also meant that during a crucial time when public sentiment was more in favour of vaccination South Africa could not get enough doses to meet the demand and the delay allowed misinformation campaigns to wreak havoc. Had it been able to source enough supply in those crucial months, South Africa might have overcome a substantial portion of that hesitancy as people saw their friends, families, and colleagues get safely vaccinated.
Third, there’s also a point to be made about the effect of predominantly American anti-vaccine misinformation on social networks, especially Facebook and YouTube, that has had a massive impact on South African society and the willingness of people to get vaccinated. Researchers have seen the same in other African countries. Not sure how that in particular can be solved or dealt with, but it needs to be taken into account when trying to understand global vaccine hesitancy.
South Africa has about 20% of their population infected with HIV [1], given a total population of 60M people that's 12M people! We can argue about Western responsibility all day, but at the end of the day the facts are clear: large parts of not-the-Western-countries have issues with getting vaccines and/or with antivaxxers, there is no way that all these 12M people are on proper antiviral treatment, large parts of the population have already experienced COVID [2] (which is likely why the Omicron variant didn't hit South Africa hard with deaths despite the variant being discovered there), and we're sitting by doing nothing while the combination of insufficiently treated HIV positive people contributes to whatever comes after Omicron. And for what it's worth, it's not just South Africa that's a problem in that regard - poor living conditions in slums will also be a problem for the future. India was the likely origin of the Delta variant, and Brazil is suspected to be the breeding ground of P1/P2 (that were IIRC out-competed by Delta).
If humanity wants to prevent yet another deadly round of an immuno-evasive SARS-CoV-2 variant, we all have to contribute to eliminate poverty and inequality regarding access to vaccinations and medical care. Worldwide.
[1]: https://databank.worldbank.org/reports.aspx?source=2&series=...
[2]: https://www.theguardian.com/world/2021/dec/17/south-africa-s...
Gotta be careful saying stuff like that in places other than HN ;-) People freak out at the notion of vaccines driving the evolution of new strains.
This paper finds very strong evidence that omicron jumped to infecting mice in May 2020, then jumped back to humans again in Nov 2021.
* Mutations in the spike protein, which are likely to depend on which animal is best infected, were a far closer match in mice than any of 20 other species tested (P<1.6x10^-11 )
* The types of genetic changes (ie. transitions from one base to another) were not those expected to be found in human cells, but were those expected to be found in mouse cells (P<0.008)
* Omicron binds far better to mouse cells receptors than any other animal or human tested (P<1x10^-5 )
* The genetic changes seen happened at a rate far 3.3x faster than expected in humans.
(my summarization here has traded scientific accuracy for simplicity)
Any of those fist 3 bullet points I would consider pretty decisive evidence. To have found all three is amazing.
Each is calculated in a different way, using mostly-non-overlapping evidence, so it's almost legitimate to multiply them together to get P<1.3x10^-18... Not that there's any need - each alone is very convincing.
The whole lot really should have been written as three separate papers, with better written abstracts, and a metapaper, written by different authors, combining the evidence and comparing to the evidence for other hypothesis.
Yes. Most of the extremely low p-values come from binomial tests with a very low binomial probability p_bin relative to the fraction of positive outcomes. For example,
> We identified 45 point mutations that were introduced in Branch O (hereafter referred to as “pre-outbreak mutations.”) We observed that the pre-outbreak mutations were over-represented in ORF S (P = 1.2 × 10−13, binomial test with the expected probability equal to the length of ORF S relative to the SARS-CoV-2 genome).
So p_bin = len(ORF S)/len(genome). The spike protein sequence (ORF S) is roughly 1300 bases and the entire SARS-CoV-2 genome is roughly 30 kilobases long, yielding p_bin ≈ 0.04. If there are 45 total pre-outbreak mutations, and assuming they ought to be uniformly distributed across the genome (big assumption, BTW!), then seeing 17 of them occur in the spike protein sequence would yield a binomial p-value (one-sided test) on the order of 1e-13.
The other low p-values either also come from binomial tests with similarly low binomial probabilities relative to positive outcomes, or from Fisher exact tests with gross imbalances between categories (and high counts to back those up).
Despite that, I still believe the overall conclusion of this paper is backed up by very strong evidence.
I don't think this is entirely implausible because current research is doing things along those lines: There is an established "mouse" model now and people are actively working on chimeric vaccines, engineering virus variants with different spike proteins (for chimeric vaccines see e.g. https://www.science.org/doi/10.1126/science.abi4506). They engineered several COVID variants in that paper, some which antagonise the innate immune response.
> To confirm that scrambled coronavirus spikes are biologically functional, we also designed and recovered several high-titer recombinant live viruses of RsSHC014/SARS-CoV-2 NTD, RBD, and S2 domain chimeras that included deletions in nonessential, accessory open reading frame 7 (ORF7) and ORF8 that encoded nanoluciferase (fig. S1C). SARS-CoV-2 ORF7 and -8 antagonize innate immune signaling pathways (25, 26), and deletions in these ORFs are associated with attenuated disease in humans (27, 28).
and made sure that the "single" spike vaccine was ineffective vs. the chimeric vaccines, which gave broad protection.
Given we know that lab leaks happen continually we should all perhaps be campaigning vigorously for an end to wet markets, protection for cave habitats, better controls in labs in general and a complete moratorium with gain of function research.
We don’t know where this pandemic came from but we know enough to say that it’s likely all those things could be sources in the future. So perhaps leave the debate alone and focus on stopping the next pandemic.
Perhaps you mean campaigning against eating exotic animals?
Extended, concentrated exposure to animals has always been a breeding ground for new plagues.
Even a perfectly hygienic butcher shop and wet market can transmit a new disease. Keeping it clean is good to reduce the transmission of common illnesses - but the genesis of a new disease can easily be passed in a clean market.
Gain of function research is a vital tool in preventing pandemics. Moratoriums are pretty much universally opposed by virologists and are already regulated under DURC/DUCG (which both require unaffiliated oversight from the public). Influenza for example is able to be researched without having to infect human subjects because we used GoF to make lab strains infect rabbits.
I'm not saying it's definitely a lab-leak, but it strikes me as ridiculous to confidently claim it wasn't given the information currently available.
Source? AFAIK those bats coronaviruses were only found in caves in Yunnan, which is ~1300 km from Wuhan.
According to the previous link, HIV may have been spreading on the US since the 60s.
It's really not much of a coincidence.
If you can explain how SARS-1 happened without a lab -- and you MUST be able to do this at the end of the day, because it really did happen -- then you can explain how SARS-2 happened and the lab was just a coincidence.
since then, Biden's own security advisor has briefed him on the relevant proof (which has remained the same), but it was not broadly covered by the media
furthermore, the wet-market hypothesis was debunked in peer-reviewed science (and never had reasonable support from the start)
at this point there is literally no credible support for the idea that the lab leak data is incorrect
Nonsense. There is media outside the US, and no one really cared about that.
The problem has been that literally no one in charge had any interest to investigate. Obviously not China, but the US was involved in the gain of function research in Wuhan too; France/EU knew about the problems there.
And rightfully so, the first few weeks of media coverage were focused on other things than pointing fingers. Trump talking about blame, was seen as a distraction from the catastrophic handling of the pandemic by the administration - and there was clear evidence for that.
I think we will never know the origin of this virus, but we can prevent a possible lab leak in the future, outlaw gain of function research and internationally enforce lab safety standards on the highest political level.
Regardless of causation/correlation, that lab in Wuhan could have been the source of this pandemic, which killed 5.5 million so far and crippled the world economy for 2 years and counting: The french withdrew collaboration, because the lab wasn't meeting standards for the proposed risky research, and the exact gain of function seen in SARS2 was proposed to be researched there.
The possibility of a lab leak should not have existed in the first place. We can prevent a next pandemic of lab origin, now.
The question is only: Could it have happened this way? Is it plausible? If so, then we need to increase our security measures.
I think it is very plausible. There have been SARS lab leaks before, there were local attempts at cover up, and so on. There is no evidence for a lab leak, but it could have happened, and that is enough.
How do we tighten the security measures? One way would be to ban gain of function research. I'm not an expert, so if you say we need this research, we have to find a way to do it more safely. Maybe we can perform the research with 100% transparency. Complete surveillance of the lab, only joint multi-national labs allowed, frequent external audits, intense medical observation of the researchers, .... I'm sure experts can come up with useful precautions. The thing is there are likely precautions that were possible but considered too cumbersome or expensive. But in the light of a global pandemic and the plausibility that it may have been a lab leak, it is time to reevaluate the cost-benefit analysis.
(And of course, the zoonosis hypothesis is also plausible, and we have to do something about it... and think about deforestation, urban growth, wet markets, and so on.)
Maybe because there was a virology lab they identified the disease there first?
It's always a "kill the messenger" attitude. South Africa and the UK got punished with demonization and travel bans for doing the correct thing and sequencing a lot of positive samples to identify variants. China was also punished in a similar way, but at least there a bit of that punishment is warranted given how utterly intransparent China was and still is and how local cadres tried to hide the outbreak in the first place.
Once the pandemic is under control, humanity as a whole will have to establish a framework on pandemics that prevents "perverse incentives" aka hiding suspicious events, manipulating data, threatening researchers or not sequencing variants.
This is not a correlation/causation fallacy at all. It is a simple application of occam's razor. The "wet market" hypothesis has only ever been a convenient distraction.
Coronaviruses are one of the most common types of viruses in nature.
“Let’s weld a horn on a horse and make unicorns. No, too dangerous.” Two years later we see unicorns running around the same lab that proposed it.
It happened to be 600 to 1000 miles from where the bats carrying such viruses are found. The closest bat virus to Sars Cov 2 was found in Laos 1000 or so miles away and samples were shipped to the Wuhan lab.
So if nation develops biological weapons by creating viruses in a lab, we just ignore it?
This sure seems like a fun spot for an Iraq WMD joke.
Perhaps the virus was not a deliberate weaponization but some research for a weapon when things went wrong and it got out of the lab.
Even the worst judical systems still require at least a pretense of probable cause.
How can you say its baseless when there is no evidence of Covid jumping from animals to humans?
China could have given access to outside investigators but they chose not to, that is your probable cause.
And also, yes, swatting is a really big issue. Maybe the police should not show up in military gear and itchy trigger fingers to every unsubstantiated anonymously called in. Not saying that they shouldn't do nothing.
> I'm saying that you can not base probable cause on such flimsy evidence.
Which is why China should be open and transparent to outside investigators because clearly they could not handle the situation.
- China's economy grows 18.3% in post-Covid comeback [0]
- New cases January 1st, all of China: 191 [1]
Whether or not Sars-CoV2 came from animal transmission or a lab leak has zero bearing on where Omicron came from.
Where are all of these talking points in the thread coming from?
Did they change the source article?
Right now we have the same option to get the origin of SARS-CoV2 completely wrong and waste a lot of money and effort while also hurting people. Wouldn't it make more sense to be cautious about the research based on previous experience instead of charging forward based on the idea that narrative fit is more important than science?
The correct response would be to start shutting it all down. All farms with crowded animals are bioreactors which create "serial passage" experiments which can be utilized by viruses for natural gain of function.
That will sure as hell not happen, not in my lifetime anyway.
And we'd have to admit that the vegans were right all along for a start.
I have this funny mental image in my head of all the people who like their BBQ and smoked meats an bacon one day waking up in the morning and realizing that the pandemic was due to meat farming and everyone shuffling off to apologize to the local vegan community one by one like they're repenting their sins. The way that feels so absurd and the contrast with all the common vegan jokes and acceptance that to be part of our culture that you have to eat meat shows how that just isn't going to happen.
So we're probably going to be back here in another 5, 10, 20 years or so...
(And I'm not vegan at all -- but the pandemic and things like the New Brunswick disease have me thinking of at least shooting more for a flexitarian diet)
Oh although the original transmission from bats to humans may have been due to bat guano farming, which is used to fertilize crops, so not even the vegans may be untainted.
For the former, essentially you're dealing with multiplying lower chance of death with much higher infection rate, resulting in bigger count of deaths (and other events like hospitalisations, isolation, etc., which increase economic disruption).
Once you jump it back to humans it's a new roll of the dice on whether it's more or less deadly and infectious.
We're going to deal with long history of disablement caused by how COVID attacks neural tissue, for example, something I think might be more disastrous long term (1918 flu was similar, with some historic effects like Aktion T-4)
But, also this: https://twitter.com/andrew_croxford/status/14762098046666014...
Ah, and I see the tweet is trying to dispel fear that was worked up around this. Got it.
Reasonable starting point for looking further:
A better argument against it would be that there is a huge unknown, and the very uncertainty about something which cannot be undone, is a reason not to do it.
Besides the "short term overload" aspect, this doesn't have much weight if both viruses ultimately end up infecting the majority of the population.
Yes, that is technically possible. Mice and humans also come into contact fairly often, so natural transmission from humans to mice (and back) wouldn't be that rare an event.
> and spread it later to human to counter more agressive variant
I think you might be giving too much credit to virologists - I don't think anybody could know from observing a virus in mice if it was going to be more or less aggressive in humans.
> and help that way bring up natural immunity?
Natural immunity doesn't seem to be very useful against covid. Or, at least, not more useful than the vaccines we already have. Stories of people getting covid twice, even three times, are getting more and more common. This doesn't seem to be a "get it once and you're set for life" virus.
Do you have any evidence for that? The question has obviously become politicised. Experts figure out what information they think might make people more relaxed or careless about covid, and heavily push the reverse line. It's no wonder people's trust in experts is failing.
https://www.theguardian.com/commentisfree/2021/oct/24/which-...
https://www.medrxiv.org/content/10.1101/2021.08.24.21262415v...
It’s been a couple weeks so maybe there is better, less preliminary analysis available now
On hospitalization risk in the UK: https://www.imperial.ac.uk/mrc-global-infectious-disease-ana...
On reinfection/breakthrough risk: https://www.medrxiv.org/content/10.1101/2021.12.27.21268278v...
If such an exercise could save TRILLIONS of dollars in the short to mid term, do you still stand by your statement?
This is not even a novel idea. The idea of finding and spreading the least harmful variants was proposed very early in the pandemic (circa June 2020) in an article I read here. Of course that’s slightly different than what GP proposed.
However, I would’ve never thought that mRNA vaccines could be produced so quickly. Given the incentives at play, I bet a surprising amount is possible.
Absolutely I do. You can test for binding affinity to receptors, and make a guess - but you can’t know, and releasing a modified virus without knowing would be reckless beyond comprehension. It’s a good idea, for sure, and one day we may be able to do things like this intentionally, but I’m pretty confidant we’re not there today.
Omicron is more transmissible. Less pathogenic. It evades immune responses from vaccines, and previous delta infections. But: it creates an immune response that seems to protect against delta, and possibly future variants.
Looks like the spec sheet of a miracle ... and now we find it was optimized through (accelerated?) selection in mice?
I still haven’t seen any study on naive omicron infected cross reactivity to other variants, specially over the RBD.
Apparently not so much with this one.
- severely reduce severity
- replace previous variant
- more transmittable
I'm just wondering. Since even Lions in the zoo in Belgium had COVID.
Evidences require at least an reproducible experiment.
Nothing based on estimated probabilities and correlations is an evidence by definition.
Again, this is nothing but hypothetical speculations with too many assumptions.
COVID-19 isn't that drastically different from SARS, MERS, etc. The main difference is transmissibility of asymptomatic carriers that allowed it to leave Asia undetected. So while the rest of these viruses had been handled in a mature and efficient fashion by the countries affected the very idea of a modern viral pandemic was new to the Western world and it showed, boy did it show.
Instead of just focussing on the issue at hand it was immediately the "Chinese virus" and the American political machine was in full swing to capitalise on the situation. Most of the Western world followed suit with political lines being drawn around responses (or lack there of) and assignment of "blame". In the UK and USA this resulted in probably hundreds of thousands of needless deaths off the back of delayed and then ham-fisted action by Boris Johnson and Donald Trump's administrations.
Meanwhile in Asia it remained apolitical for the most part (I say most part because aspects of pandemic control did become quite political of late). I was in Thailand for the entire duration of the pandemic and despite having access to less resources, late access to the vaccine and being one of the first nations to be exposed outside of China Thailand actually performed very well. Lots of insinuations were made this was due to climate and other factors, anything that shifted the blame away from politicisation of the pandemic as the root cause of performance differences. However as time has wore on and countries with more facts based approaches have continued to out-perform it's obvious - politics is the only real difference among the developed nations, hell it's so strong that it overcomes better access to vaccines and higher ICU bed/capita which should both dominate.
The accessory to all of this was the vaccine/lab origin censorship by big tech, who are kind of seen as over-woke liberal bastions.
To lockdown or not lockdown, to mask or not mask, to vaxx or not vaxx, to Ivermectin or not Ivermectin, lab leak or no lab leak … why so binary? Ah, because we went political with this a long time ago.
If there was one person we needed to literally not say anything about this, it was Trump. But alas, he was the fucking president and we also needed him to say something.
The Pandemic histrionics are an age old Shakespearean play. A tragedy.
History is something else when you have the primary sources right before you. I would never need to read a book on all the nuances of everything that happened. Makes you wonder how easily historians can spin history in all those books, when in reality those events could have been as simple and silly as this one.
This is incredibly dangerous and at this point I don't know what it takes to diffuse it. I thought Biden winning the US election would help and admittedly it has but by much less than I envisioned.
Unfortunately US politics spill over into the rest of the world through media syndication, doesn't help Murdoch owning almost all conservative media in US/UK/Australia... This means this extreme politicisation while birthed in America is spreading around the world.
I strongly believe this is the real threat. The pandemic just showed us how dangerous it can be.
Decent summary, you can find him discussing it on YouTube:
https://medium.com/@dina.osman/what-is-mass-formation-d2ac63...
The gist of it is what I’ve mostly concluded over the last few years. There’s a pathological level of frustration/anxiety/apathy that is leading to all of this at a mass scale (which makes sense considering we are virtualizing lives at scale, and I use the word virtual in it’s most abstract sense, not necessarily digital). We all have a very abstract identity that is unfulfilling because at the levels of abstraction we are at virtually is not relatable or realistic. I know, it’s a serious hot-take, but this is roughly where my line of thinking is at now days. The outcome of all of this is, well, people now bask in the cacophony of whatever life even is at this point (especially because there’s not a chance in hell any of us will be able de-scale the world (tech/vanity/capitalism/etc)).
Quoting the most important part:
… if ANY narrative is distributed through the mass media identifying an Object of the anxiety and providing a strategy to deal with that Object, mass formation can thrive. Since it provides the masses a sudden connection to a heroic struggle allowing them to meet their needs and provides them with a release — giving them a new social bond and meaning that has been lacking.
There you have it, people are literally bonding via this constant hysterical back and forth.
There are more powerful factors at work here. Some combination of exploitation of mass hysteria by politics, some amplification of that by modern technology/social media and some slow degradation of respect for custom and tradition that prevented such behaviour by politicians in the past.
The culmination of this is modern politics in US/UK/Australia, all of which are frankly embarrassing for intellectual citizens of all three but somehow staggeringly effective in elections.
The system does help intent to be shown by the first vote, but also shows that it does not lead to power.
This is why all discussions about STV, instant runoff, multiple rounds are essentially irrelevant. They may help show intent, but does not change the status quo.
At the most recent House election, 12 electorates were won by the candidate that was in second-place based on the first preferences (ie, the result differed from that under FPTP). Interestingly the Greens' seat was not one of these - Bandt lead on the first preferences and would have won under FPTP.
Single Member Electorates will often lead to overall non-proportional outcomes.
I think that is revisionist. Trump surely didn't help, but Hydroxychloroquine treatment was only ever promoted in special circles, while COVID-19 ravaged communities that would never even consider voting for Trump or consuming horse dewormer.
The actual failure is the CDC denying that transmission was mainly airborne and even later refusing to eat humble pie and publicly recant. WHO is even worse. (Google "situationally airborne" to read some of the mental gymnastics that they used to insinuate that they were right all along) Many regions to this day treat it as droplet based infectious disease, because there was never a clear and loud change of direction, it was mostly silent.
If CDC had taken measures against airborne diseases like mask mandates which helped Asia early on, there would have been a much different pandemic in the US.
Edit as this is being downvoted: the WHO's and national health bodies' resistance against labeling COVID-19 airborne is well documented. https://wellcomeopenresearch.org/articles/6-126
Only in May 2021, the CDC updated their guidance to state that there is airborne transmission (but without using the word "airborne", go figure).
I can't comment on the UK's history, but I can tell you that you are 100% wrong with respect to what you think the response was in the US. This isn't a matter of opinion on my part. This is a matter of documented fact. The timeline lives on the internet if one bothers to do the research.
The basic timeline goes something like this (again, google is your friend as far as stringing this together):
On January 31st. 2020, Trump announces travel restrictions from China. On February 2nd (and for about a month after that) various officials from New York as well as Nancy Pelosi are on video telling the public that there is nothing to this virus, that they should continue life as normal, get on the subway, buses, trains, go to work, restaurants, festivals and entertainment venues. You can find the governor, mayor and director of health of New York making these statements as well as saying and implying that Trump was something between crazy, racist and hateful for sounding the alarm.
If you look at how the infection spread in the US, you'll quickly discover that it absolutely exploded in New York and quickly launched everywhere. I am sure the data exists to trace with more detail. People were leaving the New York area like rats on a sinking ship. The infection quickly spread to adjoining states. And, from there, to the rest of the nation.
In effect, what happened, is that, in particular, New York officials, due to a combination of ignorance and absolute politically motivated hatred for Trump, caused the direct infection of tens of thousands of people and a chain reaction that likely infected beyond hundreds of thousands as secondary and tertiary layers of the chain reaction. I find it very interesting to see how the media narrative has the world believing Trump did not act, when, in reality, he acted early and it was New York officials who caused the massive early spread of the virus because of their political bullshit.
When I heard that Trump imposed travel restrictions on January 31st. I immediately checked our supplies, placed orders for six months worth of food and critical items and warned friends and family members. By the time the pandemic was in full force I, and those who listened to me, were ready to lock down and navigate the storm. And all of it was because of a simple observation: Regardless of what I thought of Trump, imposing a travel restriction on China was a serious enough move that there had to be far more under the surface than what the vast majority of the media narrative contained (he is a racist, etc.). It is quite possible that, by ignoring politics and taking action based on the meaning of the moment, I saved lives within our family and circle of friends.
One name stands in my mind, I remember because it is unusual: Dr. Oxiris Barbot, New York Health Commissioner. Look up what she said to the public on February 2nd., 2020, just a couple of days after the travel restrictions were announced, and tell me that had no consequences. Then trace every NY official through video on a daily basis in February and March. No, that was criminal. Trump was trying to lock things down, these people fought him every day, the media fought him every day and effectively told everyone to go get infected during February and March, if not longer. Facts matter.
In the US the president and federal government do not have the authority to do as you suggest. That's part of the problem. When the other side chooses to wage war against him, despite the fact that we were at the doorstep of a disaster, well, the rest is history.
Please note that I did not disagree with you about the negative effects of playing politics with a pandemic. You are absolutely correct. What I wanted to note is that the Trump administration did take seriously bold measures very early on. The only reason the entire nation didn't take this seriously is because media is overwhelmingly dominated by Democrats in the US and they were so blinded by wanting to destroy Trump that they actually caused death through COVID across the nation.
Nobody likes to talk about this because people just can't escape their ideological bias and look at reality in an objective fashion. As the pandemic started nearly our entire media machinery as well as the Democratic party were in full-out, take-no-prisoners war against Trump at every level. When the pandemic starts, that train had so much inertia that it was literally impossible for media giants like CNN and MSNBC to halt their war and do a 180. They were making money with the hate Trump narrative. Imagine turning around to say he was right and that we all had to support him. Impossible. And so, people died.
I hope history looks at this objectively because there's an important lesson here that we must learn and there's a real risk of not learning it. Most historians are Democrats and it is probably fair to say most of them are part of the Trump hatred machinery. And so, nobody will be held accountable for what pain and loss they caused, not only in this nation but likely elsewhere.
Every time I heard Trump speak on TV I wanted to vomit. The guy had the social skills of a brick. However, I think it is fair to say that nearly every single program he initiated and measure he took was right on point, including how the pandemic was handled. The entire world owes the very vaccines we are using to save countless lives to the effort his administration organized and ran to develop multiple vaccines faster than ever in history. The current president and vice president were actively maligning the vaccines and promoting all kinds of doubt upon them until they got elected. And then, all of a sudden, they wanted everyone to get vaccinated. The game they and their party played was nothing less than disgusting, if not criminal. It wasn't until a few weeks ago that Biden actually publicly recognized that the Trump administration got us the vaccines in record time. Unbelievable.
While I would never denigrate scientific fundting, there's stretching the truth and there's propaganda. We do not "owe" the development of vaccines from the US funding program.
And while the ModeRNA and AstraZeneca vaccine took US funding, BioNTech did not. As vaccines for "the world" goes, a lot of it was Sinovac and Sputnik.
https://www.cnn.com/factsfirst/politics/factcheck_565aa63a-4...
As the other commenter pointed out, the executive branch of government lacks authority to do so. Courts have decided over and over again (like with the eviction moratorium, worker vaccine mandate, etc.) that Congress needs to authorize this.
So it is very much a failure of Congress to act. And since no action was taken, neither before nor after changing majorities in Congress, all parties failed.
Facts matter indeed! Please do a google search as it sounds like you were completely checked out from news in the USA during February 2020 and have got your impression from politicized propaganda later on.
Trump downplayed the coronavirus that entire month and the democrats, while mildly sounding the alarm, followed his lead and repeated his theories that people shouldn’t take action.
https://www.cbsnews.com/news/timeline-president-donald-trump...
* Trump Jan 30, 2020 “ "We think we have it very well under control. We have very little problem in this country at this moment — five — and those people are all recuperating successfully. But we're working very closely with China and other countries, and we think it's going to have a very good ending for us … that I can assure you,"
* Trump February 10 “ I had a long talk with President Xi — for the people in this room — two nights ago, and he feels very confident. He feels very confident. And he feels that, again, as I mentioned, by April or during the month of April, the heat, generally speaking, kills this kind of virus,"
* February 24 “ The Coronavirus is very much under control in the USA. We are in contact with everyone and all relevant countries. CDC & World Health have been working hard and very smart. Stock Market starting to look very good to me!"
* February 26 “ And again, when you have 15 people, and the 15 within a couple of days is going to be down to close to zero, that's a pretty good job we've done,"
The Nancy pelosi in Chinatown comment you reference took place on February 24, the same day Trump said there was nothing to worry about and Covid was completely under control. They were actually in sync! https://www.nbcbayarea.com/news/local/nancy-pelosi-visits-sa...
For me, at least, when the travel restrictions went up on January 31st, this represented a very serious indicator that something was seriously wrong. This was a move three standard deviations away from the mean, if not more. As I said in a prior comment, the very next day I checked our supplies and placed online order for a six month lockdown, including N95 masks. I also told friends and family. Everyone who paid attention to my warning did very well and navigated 2020 with very little to worry about other than staying safe.
My point is that politicians have a back channel for communications that they should use during these kinds of events. If I had been in politics at the time this started to develop I would ask myself a very serious question: Why did the US president just shut down travel from China?
I would not have pulled the answer out of CNN. I would have reached out to the administration and had a serious conversation, regardless of being a member of the opposing political party. I certainly wouldn't have gone on TV to tell people to get on the subway, buses, trains and go to festivals without first understanding something three standard deviations away from the historical mean.
Trump was an idiot in public. Not so behind closed doors. The travel restrictions imposed on China on January 31st. carried gravity lots of people, news outlets and politicians chose to ignore, and this cost lives.
To beat this one to death: No, the US president --no politician really-- could not go out there and say "we are all going to die". The masses can't handle stuff like that. What the masses want to hear is "we are going to be OK". However, the masses also need to be told how not to kill themselves.
We likely would have saved tens if not hundreds of thousands of lives had we come out with a unified message asking people to not participate in high density activities (subway, etc.) because this new virus spread quickly. It would have been just fine to come out and say "we need a few weeks to asses the situation, until then, we ask that you do these five things...". Instead they came out and effectively said "Trump is racist. Ignore him.". And the rest is history.
Ironic, when you consider that their "racist" likely saved their lives and that of hundreds of millions by mounting and effectively executing the fastest and most effective vaccine development program in human history. Go figure.
It's OK to be politically partisan, but sometimes one has to also be willing to be honest. The man inspired projectile vomiting every time he spoke, and yet the things he did were pretty much always on point. Today we are seeing almost exactly the opposite: Someone who speaks well and is a complete disaster at almost every level. I can't even imagine what reality would look like today if Trump hadn't gotten vaccines done by November of his last year. It's probably fair so say millions would have died in the US. Biden/Harris would have been running around like chickens with their heads cut off.
This is not at all what Trump was trying to do behind closed doors. He’s on tape speaking to Bob Woodward at the time about his strategy. “Play it down” was what he wanted to do.
When the Democrats made even small suggestions about needing to make stronger action, he sent his chief of staff out to accuse them of wanting to shut down the country to destroy the economy and ruin his re-election.
This is all on tape.
Yes, Trump approved the relatively weak travel ban proposed by his staff like Fauci. He then spent a month saying everything was fine and attacking anyone who warned of danger.
When a CDC official went off message on Feb 24 to suggest that disruption to public life might happen, they were immediately removed from public communication by Trump who was still in denial. https://www.businessinsider.com/cdc-official-warned-us-coron...
There's even a really obvious reason why New York and London were hit first that has nothing to do with Trump or Boris - look at when Milan Fashion Week happened and what else was going in that region of Italy, then at the other major fashion centers of the world that'd have lots of travel to Milan that week. It's right slap bang next to the epicenter of Italy's big outbreak which had somehow gone basically undetected, with Italy consistently reporting zero cases a day or two beforehand. Like, the reason populist politicans seem to have played such a disproportionate role in making Covid so bad is because the media ignores any screw-ups that happen in countries run by the kind of boring techocrat they like - I personally have no doubt Italy would've been blamed for dooming the world if Berlusconi or someone like him was in charge.
Until there is new data, it's just a lot of noise and no signal.
Indeed, seeing the lab leak hypothesis mentioned in every comment was very confusing. There is some decent discussion of the paper, but it certainly took some scrolling.
edit: I take it back, there is incredibly little decent relavant discussion here. Should probably just flag the post.
That's why I've started aggressively downvoting and sometimes flagging posts making claims against the common expert opinion as long as they are presented with unreasonable certainty. Presenting an unusual position is fine as long as it is accompanied by an adequate amount of self-doubt or clearly expressed as speculation.
I think the second half of this applies to the first. How can you be confident of your own judgment of "most experts" positions without being something of an expert yourself? I often see people claiming that something is "what most doctors/scientists/people/experts/etc say", and I'm always skeptical of how a non expert confidently comes to that belief.
In reality, I tend to assume that these positions are in fact what the most resources were spent on telling people, in other words the ideas that had the largest marketing budgets behind them (or whatever is viral at the moment).
When I see a random person on the internet claiming to echo what most experts believe, I assume that its really what their twitter feed believes, which I don't know how to value, so I don't value it very highly.
I very much agree on the arguing ferociously part though. I think a lot more humility is called for all around.
As a layperson the technical meat of the research is harder to assess, but there are lit reviews and editorials that you can read, in addition to reading blog posts and such by people in the field
This is basically how I've formed my own opinions, so I hope that its close to whatever consensus is (if there even is one yet, I assume real stable consensus takes time).
But I temper my certainty a bit and limit myself to saying things like "there is evidence that [xyz]", because I know that's a true statement that I can back up. I can't speak much to the quality of the evidence, but I can be aware that it exists and I can also try to find supporting/countering evidence, or a lack thereof. I don't know that I can get all the way to judging what the consensus is though.
Once I get to secondary sources, I feel like I'm on much shakier ground. There are just too many forces at play: social/political pressures, monetary incentives (bloggers have to give their base what they want if they want to thrive), the difficulty of understanding something novel, and a rapidly changing world on top of it all.
So when I see people pulling out the "most experts" card (consensus in other words), I can't help but discount it heavily. They could be friends with the actual only researchers publishing on a topic, or they could have gotten it from their uncle on Facebook, or anywhere in between.
What do you know that the U.S. president and U.S. intelligence doesn't?
https://www.washingtonpost.com/national-security/wuhan-coron...
> The two main hypotheses — that the virus jumped from animals to humans in a natural process, or that it escaped from a research laboratory in China — remain on the table, ODNI said. Both theories are plausible, the agencies concluded.
Fact check: false. The early cases in Wuhan almost all cluster near the wet market, not the virology lab, which is on the outskirts of town on the other side of the river some ~30km from the market. (And to the extent they don't cluster near that market, they do favor quite strongly the market's side of the river, not the virology lab's side of the river.)
> Biden called for U.S. intelligence to figure out if the original virus came from a lab
Because a government has never, ever called for an investigation or an action to be taken because of political pressure despite its internal knowledge bases saying there is no need to investigate it.
Crucially, however, the now famous “earliest” COVID-19 case (1), a 41-year-old male accountant, who lived 30 km south of Huanan Market and had no connection to it—illness onset reported as 8 December—may have become ill with COVID-19 considerably later. . . . This suggests that he may have been infected through community transmission after the virus had begun spreading from Huanan Market.
[C]onclusive evidence of a Huanan Market origin from infected wildlife may nonetheless be obtainable through analysis of spatial patterns of early cases and from additional genomic data, including SARS-CoV-2–positive samples from Huanan Market, as well as through integration of additional epidemiologic data. Preventing future pandemics depends on this effort.
To be considered:
> the Wuhan CDC ‘hosted animals in laboratories for research purpose, one of which was specialized in pathogens collection and identification’. Moreover, the Xiaos described how a lead researcher at this laboratory who collected bats had featured in articles and at least one broadcast video revealing that ‘he was once attacked by bats and the blood of a bat shot on his skin. He knew the extreme danger of the infection so he quarantined himself for 14 days. In another accident, he quarantined himself again because bats peed on him.’ Given that ‘surgery was performed on the caged animals and the tissue samples were collected for DNA and RNA extraction and sequencing’, relatively close to the Huanan seafood market where clusters of Covid-19 cases had been detected, it was reasonable to ask whether an accident had occurred, the two scientists argued.
If a case like this was hypothetically true, it would sit on a line between zoonotic origin and lab leak. Remember that lab leak doesn't imply bioengineering.
> the virology lab, which is [...] some ~30km from the market.
Independently of lab leak or not, this is wrong. You can check on google maps that by car (and even more in a straight line), is less than 15 km.
[EDIT:] But you're right about the "deliberate inaction". The obvious way to fight pandemics (as opposed to less contagious health threats) is to make sure everyone in society has access to relevant health care and other vital resources. This came naturally to many societies that earned much lower covid death rates than USA earned.
This is gross oversimplification. The fact that some scientists may know doesn't imply that the only possibility is deliberate action.
Since there have been a lot of money poured on Coronaviruses research in the last decade, it's reasonable that, (important!) even not assuming a lab leak (/important!), scientists working on it, don't want to disclose it.
Even those who didn't work on it are disincentived to talk about it, as their reputation is on the line (in particular, because of the misguided opinion that lab leak equals bioengineerd virus). A few co-subscribers of the Lancet letter changed their mind on the topic. It doesn't surprise me that they did it only recently - precisely because their position is now less endangered.
> This pandemic was predicted for many years by scientist
It's hard to extract any value from this, especially without a very serious analysis, because at any point in time, there will be people predicting that events of any kind will happen.
14^2 * pi * 59 = 36,329 km2
36,329 / 148,326,000 = 0.000245
> "About 90% of the earth’s people live on only 10% of the land."
And let's assume that all of those 59 labs are in that 10% as well.
I'm sure it's actually smaller than that - since not all of that 10% of the land has enough density to be the epicenter of an outbreak, but... let's roll with that 10%
That'd put you off by a factor of 10.
14^2 * pi * 59 = 36,329 km2 148,326,000 * 10% = 14,832,600
36,329 / 14,832,600 = 0.00245 aka 0.2%
On top of that there have been multiple tries at this - in recent memory we've seen SARS classic, Covid-19, MERS-CoV, and Swine Flu. That's four chances at a target at least as big as 0.2%.
My probabilities are rusty, but I believe that's 99.8% * 99.8% * 99.8% * 99.8% = 99.2% chance of none of those appearing near a lab or an 0.8% chance it was near a lab. If we take that into account, it starts to seem a bit more likely that we'd see something like this...
And let's not even touch the > 1300 BLS3 labs that are out there.
Do you not find it absurd in the extreme that the novel Coronavirus lab a few km from the outbreak of a novel coronavirus was barred from investigation?
Is it not a giant raging blinking neon clue that when Australia wanted an investigation China threatened them with economic apocalypse?
And in this context, you think a .8% chance that it would appear near a lab is high enough to discount the possibility??? My head is exploding.
I wasn’t trying to prove a point, I was trying to dis-prove a point: that you can’t prove the lab leaks based on geography alone. 0.02% chance is VERY unlikely - it’s not proof but it sure does suggest. A 0.2% chance or a 0.8% chance is… well it’s still rare, but not shockingly rare. Again I suspect the geographic odds are even higher, if you properly correlate outbreak-size population density and labs. Bsl3 labs brings the odds closer to 5% (or 19% if you count the four other novel disease incidents and I’m doing my probability math right).
Again, none of this disproves a lab leak. But it sure does tell us that we can’t prove it with geography, as the post I was responding to suggested.
No to mention that the outbreak is the first known one, not the origin which - if not spread from a lab - is likely somewhere considerably more rural and less likely to attract attention. Took 15 years to trace the probable natural origin of SARS in China (1000km away from the first city outbreak, 1km from a neighbouring village) which wasn't as highly politicised. The subsequent lab-originated local SARS outbreaks were traced to people associated with the labs more easily (though again, they weren't as highly politicised).
Epidemiologists conducted an extensive investigation to trace the origin. The probability of detection is not higher in the city. So I'm afraid that's incorrect. You're not making any sense here. You're disputing both the lab leak theory and the wet market theory? You're just shifting the goalposts to fit your argument.
Of course a novel coronavirus - especially one that does not produce severe or unusual symptoms in most infected people - is more likely to be identified when it becomes established in a city where it spreads quickly to many people with access to good healthcare, not a rural area where there are fewer people and more basic healthcare which infected people are less likely to use. This is why the outbreak of the original SARS novel coronavirus was identified in an urban area 1000 miles from the suspected zoonotic source of the virus, not in the neighbouring village whose unidentified inhabitants (or animal produce) most likely transmitted it to the city. It is not me "shifting the goalposts" that you continue to pretend I didn't point that out in my first post.
The closest related natural viruses to SARS-CoV2 were not found in Wuhan. They were found in caves in Yunnan, and possibly Laos.
> The same caves three of that lab's researchers went into before becoming hospitalized with a flu-like illness in December of 2019
Again, Yunnan, not Wuhan. The researchers worked at the Wuhan Institute of Virology.
Noted, about "nearby", edited.
ETA: parent comment (to their credit!) edited the above to remove the world "nearby" either while I was replying or right after. Still leaving this comment up because it's worth pointing out just how far those caves are from Wuhan.
"(4) (FALSE) Wuhan is a place where SARS transmits from animals into humans frequently. That's why the Wuhan Institute of Virology was built there.
Actually, Wuhan is ~1000km away from SARS spillover zones. Its human population was even used as a negative (no SARS) control group."
1. Wuhan is not known for spillover.
2. Cave visits did happen but this has never been connected to the 3 "sick researchers" reported by US intel.
3. Sure, lab origin, zoonosis, engineering or not, all still on the table, just factually what OP wrote was inaccurate or misleading.
Also, I believe that the first recorded outbreak of SARS was in Guangdong while the origin of the virus was eventually found to be in Yunnan, 1000+km away.
- an infected animal at the market transmitted the virus to humans
- an infected human at the market transmitted the virus to humans
> This China-WHO report revealed a different picture from that given by media reports. The market was called a seafood market for a reason: most of the stalls were selling seafood and freshwater aquatic products. Crocodiles were being sold alive. Snakes and salamanders were being slaughtered on the spot for sale. From sales records in December 2019, just ten stalls were selling meat or products from birds and mammals, including chickens, ducks, geese, pheasants and doves; and deer, badgers, rabbits, bamboo rats, porcupines and hedgehogs. According to the market authorities, all of these animals were from licensed farms and no illegal trade in wildlife was detected.
> The authorities tested 457 samples from 188 animals spanning 18 species. They all proved negative for SARS-CoV-2 genetic material. This included 27 stray cats (a species that is susceptible to the virus), which were presumably living free in or around the market, as well as 52 rabbits and hares, 16 hedgehogs, ten mice, seven dogs, six muntjac deer, six badgers, six bamboo rats, a number of pigs, five chickens, three giant salamanders, two wild boar, two crocodiles, two soft-shelled turtles, two fish, one sheep and one weasel. They tested 616 animals of ten species from the suppliers to the market and found no sign of SARS-CoV-2 genetic material.
Note that this doesn't imply the lab-leak hypothesis, as the human in the second case may have contracted the virus from an animal elsewhere.
It is not just a coincidence, but a plausible hypothesis, just like the hypothesis that it is a zoonosis from an exotic animal market.
I think we have to take all possible causes seriously. Act as if it was a zoonosis and act as if it was a lab leak, in order to prevent another pandemic.
(Actually, I think the lab leak is both the more scary and the easier to prevent cause, so no matter what actually happened we should try to shut down this possibility as much as possible in the future.)
Again, if it's zoonotic it's surprising that it would emerge in a city with much less animal trade than somewhere like Guangdong, and in the slow months of that trade.
My point here is assuming zoonotic origin, it isn't a one in a trillion coincidence that Wuhan has a coronavirus lab. It has a coronavirus lab for the same reasons a zoonotic origin appears likely - it is within trading/sampling expedition distance to bat caves and is an urban hub. Perhaps Guangdong still was the more likely candidate for a pandemic emergence, but based on what we know today Wuhan appears to be 1-in-100 betting favourite, plus or minus an order of magnitude.
Authorities seem to stand behind the Wuhan "wet market" theory but there's really no evidence of that, specifically if it came from an animal population, how come 2+ years later we haven't found that animal population? Also the bat coronavirus population is hundreds of miles away so how did this end up in Wuhan?
This brings us to the "lab leak" theory. There are lots of possibilities here. If this is true (and that's a mighty big IF) then my suspicion is that this was an accident and the CCP doesn't necessarily know what happened but there's absolutely incentivized not to find out. I find claims that this was a deliberate release to be unconvincing.
The key factors supporting this theory, or at least are open questions requiring further investigation are:
1. There's really no compelling alternative theory supported by substantial evidence;
2. The WHO has really lost a lot of credibility here. In early 2020, the WHO was bending over backwards not to upset China and not much has changed. In 2021 there was a joint investigation with the Chinese but the scope was pretty limited;
3. There used to be a database of coronaviruses that China had. In late 2019 this was taken offline. To date AFAIK this has never been examined by WHO investigators or any independent authority. Now this doesn't prove anything by itself but you'd think a thorough investigation would include examining it in its scope.
4. A long time (over a year) passed between the start of the outbreak and the investigation. This is a long time for evidence to go cold or "missing".
To compare, the origins of two previous coronavirus outbreaks (ie SARS and MERS) were relatively quickly identified.
No lab worker or official wants to be responsible for a leak (if there was one). No one wants to find out they were responsible. The CCP also doesn't want to set the precedent they're answerable or accountable to international authorities. This is what I mean when I say I suspect the CCP doesn't know and doesn't want to know.
What definitive evidence can we provide of an animal host now? What definitive evidence can we provide of a lab leak? Of a deliberate release?
I don't think we can provide definitive evidence for any of the options, that proponents of another theory, even the reasonable ones, will accept, so ... I believe it is exactly 3 angels.
Secondly you discuss the lab leak theory at length and construct the state of being that because not A it must be B but there is no dichotomy here, there are many choices, including the fantastical which break Occam's razor but alas may turn out to be true. Simply because we have not found a wild host does not make lableak "true" or even more likely.
I have no idea what the origin is. I'm not in the field, I'm not competent to judge. What I read suggests most people who are competent to judge want more evidence.
If your point is that the CCPs exclusion of external verification of theories is proof, I'm sorry but it's just not proof: there are many reasons why the Chinese government does this, guilt is not a given although fear of guilt is plausible. Shaming the state is not easy or wise for people in this political system and "Strong China" Plays inside the government and the party (they are different things btw) as well as differences between ministries, departments, provinces, external parties make this a very complex problem.
Power struggles often have nothing to do with the ostensible reasons they are fought over.
I also judge most people's opinions are being formed from at best secondary and probably tertiary sources.
I personally think your clarion call isn't helping.
The fact that a lab leak was even possible but it took over a year to get any researchers into the lab is a serious issue for data collection, not to mention the fact that the CCP got to pick those researchers and didn't share any lab records.
Its important that we learn from how this played out, but seems very unrealistic to think we could pinpoint the initial transmission event now.
In a field like mathematics it's obvious that we don't have the necessary tools to evaluate expert evidence, but the same is true in most complex fields, of which epidemiology is certainly one. The experts of course won't always be right, and their best guesses will evolve as more evidence is gathered, as they should. But asking people without specific domain knowledge, even intelligent generalists, to independently weight expert evidence without resorting to trust of experts is likely to result in less informed decision making, not more.
We can't let the sheep make up their own minds, we have to make up their minds for them; for they are only sheep of course, and we are the pigs.
I mean, what would happen in one of those stupid sheep had a thought to themselves? They might think
Hey isn't that a coronavirus reasearch lab right down the street? Maybe
they know something about this new coronavirus?
....
Human beings are built to defer to *legitamite* authority, its a principle of how we organize ourselves. Doesn't matter if its mathematics or goverment. But that legitamacy must be demonstrated. If a mathematician fails to answer basic mathematical questions, then his authority on the subject comes into question. When the authorities fail to answer basic questions (like where did this virus come from? Why aren't we investigating the wuhan lab? Why was Fauci funding it? Why was the man in charge of the WHO investigation the man who was in charge of funding it?), they are failing to demonstrate *legitamite* authority. In a functioning democracy, that failure would be met with replacement.
Does it? It's brought up in nearly every covid related thread both here and on Reddit. I couldn't avoid talking about it or reading about it even if I tried.
https://www.researchgate.net/publication/352536433_Prometheu...
His research is ongoing: https://prometheusshrugged.substack.com/
Covid is here and we have to cope with it. It's just our stupid monkey brains that thrive on x did y to z narratives that are demanding answers, as if they were in any way relevant.
If it was a lab accident that's extremely important to know as we could easily mitigate (or eliminate) that risk. If it was zoological, there may be changes that could make that less likely. If it was a third cause that no one is even thinking about, that's even more important because it somehow was missed by everyone looking for the most likely cause.
China has closed the book on this discussion. There's no further steps to take on the matter, even if you had unassailable proof, unless you wish to go to war.
Nobody wants to go to war (like that, anyway - the CIA may well wish to step up the trade war, based on how much anti-China sentiment is being stoked in the US population over the last dozen years).
Wonder if insurance companies would generally have the same opinion.
If there was an actually provable origin, do you reckon insurance companies _wouldn't_ give them the bill? ;)
Is this the endgame for all social nets?
I understand where you are coming from, but the ultimate goal is to stop COVID, not get everyone a jab in the arm. If the jabs (legitimately) stop working we should stop the jabs. Compliance with COVID rules isn't a goal unto itself.
Vacccinating mice is a fun idea to think about, but you'd have to develop vaccines for squirrels, raccoons, and pigeons shortly after the mouse one. Also think about all the unintended consequences (your food vaccine getting into waterways, for example). So yeah, this is the kind of idea that makes antivaxxers look sane.
https://en.wikipedia.org/wiki/Marek%27s_disease
"The evolution of Marek's disease due to vaccination has had a profound effect on the poultry industry. All chickens across the globe are now vaccinated against Marek's disease (birds hatched in private flocks for laying or exhibition are rarely vaccinated). Highly virulent strains have been selected to the point that any chicken that is unvaccinated will die if infected.[14] Other leaky vaccines are commonly used in agriculture. One vaccine in particular is the vaccine for avian influenza. Leaky vaccine use for avian influenza can select for virulent strains.[15]"
Isn't this exactly what we are doing with the current COVID vaccines? How does one explore this question without being labeled a crazy antivaxxer?
> Chickens become infected with MDV by inhalation of dust contaminated with virus shed from the feather follicles of infected birds. In a contaminated poultry house, chicks are infected soon after hatching and remain infectious for life
A "leaky" vaccine isn't a problem in itself if it helps clear the infection faster, because in fact that means there will be fewer chances for mutations. Now in a massified poultry industry, that vaccine only helped chickens not die while remaining infectious, and that's obviously turning farms into mutation making machines.
The Marek scenario applies to very few diseases.
Money quote from your cited paper: "Our data show that anti-disease vaccines that do not prevent transmission can create conditions that promote the emergence of pathogen strains that cause more severe disease in unvaccinated hosts."
However, despite the small odds of a population bottleneck, mutations naturally happen and with "[...] more than a million new infections occurring every day and billions of people still unvaccinated, susceptible hosts are rarely in short supply. So, natural selection will favor mutations that can exploit all these unvaccinated people and make the coronavirus more transmissible." [0].
This [1] nature article from 2020 has a different view on the relation of leaky vaccines, spread control and disease severity; money quote: "Bailey et al. performed transmission experiments using Marek disease virus in chickens and found that the herpesvirus of turkeys vaccine significantly reduced feather viral load in both vaccinated birds and unvaccinated contact individuals. The authors found that contact birds were less likely to develop disease and die, and that they displayed milder symptoms and shed less virus, when infected by vaccinated birds, potentially because of a lower infectious dose"
The article based on current research [2] _also_ examining Marek disease.
So there you are: one probem, multiple views by experts and a bunch of hackernews readers, unable to evaluate the papers.
[0] https://scitechdaily.com/what-is-causing-all-these-new-coron...
[1] https://www.nature.com/articles/s41579-020-0358-3
[2] https://journals.plos.org/plosbiology/article?id=10.1371/jou...
If you're gonna use the ever-classic Marek scenario to push against vaccination, at least use it against the vaccination of a disease that shares some basic characteristics with MD.
Sorry if it came off as aggressive, but Marek disease situation is well-loved and ill-interpreted by the antivax crowd, and often brought up even though the similarities between the diseases and their clinical courses alone make them completely incomparable from an epidemiological perspective.
Amusingly enough, he also worked on actual mRNA therapeutics for quite some time, in addition to viral delivery vectors in cancer therapeutics. Has a PhD, his h-index is ~15, I think. Triple vaxxed, if you must know his medical status. You should be able to google him rather easily, only 20-40 people in the country that do this.
Looking forward to hear about your credentials.
Remember: science has always been about questioning the dogma. Not the other way around. Criticism and open dissent must be the norm, not something to be scorned and ostracized.
can't believe I'm actually writing this on a technology forum.
Since you popped an argumentum ab auctoritate (without even giving a name?), I'd drop that he obviously also has a PhD, and an h-index of 88 which is actually remarkable.
[0]https://journals.plos.org/plosbiology/article?id=10.1371/jou...
[1]https://theconversation.com/vaccines-could-affect-how-the-co...
For your information, this kind of planned massive change in the environment always ends in disaster, and is a hallmark of totalitarian thinking, e.g. Mao's Four Pests campaign.
It is being hosted on the NIH’s mirror of an Elsevier journal. Specifically, the URL decodes as:
* PMC: PubMed Central, an information portal hosted by
* NCBI: The National Centre for Biotechnology Information, part of
* NLM: The National Library of Medicine, brought to you by the letters
* NIH: The United States National Institutes (more than 1!) for or-is-it-of Health. (The hyphenated part is silent.)
As for the paper itself, it’s just too bad that their Data Availability Statement is basically “yes” without linking to it. Googling the file names in their R scripts found them easily enough.
But, with respect to the original authors, it’s more like “Mice did this!” alongside “www3.docs.nih.gov/~jeff45/theories/drafts/mice.htm?”
I have no idea if the particular Elsevier journal (in the banner at top of the page) is reputable, but the science here seems at least robust.
If I wanted to discredit this paper, I would point out the authors developed an analysis technique they want to apply to other diseases/models. COVID is a nail and they have a specific hammer, no matter if it’s the right kind of hammer.