SARS-CoV-2 was probably not released from a research lab
I’m a molecular biologist who also has an undergrad degree in microbiology. Those facts and the additional facts that (a) I was in the Moderna phase III trial and (b) my medical school is one of ten NIH designated vaccine testing and evaluation units made me an avid student of the unfolding COVID-19 story.
Given everything we know over centuries of experience, the null hypothesis is that any pandemic has a natural origin. But since the COVID-19 pandemic originated in China and the US president at the time saw a political opportunity, the GOP null hypothesis became that the pandemic originated in a Chinese lab.
Critical thinking wasn’t helped when some prominent scientists (David Baltimore, Richard Ebright) weighed in with arguments based more on authority than evidence in favor of the lab leak hypothesis. The mountain of data that has accumulated since then points heavily in favor of natural origins. Baltimore has stated publicly that he regrets his earlier assertions.
Kevin Drum, who is not a molecular biologist or a virologist nevertheless has a nifty summary of the current state of scientific evidence, which still points to natural origins. Does this prove that COVID-19 wasn’t engineered or the result of a lab leak? No. It is impossible to prove a negative, and anyway, science doesn’t deal in proofs, it deals in the weight of evidence.
Read the rest here: Origins of SARS-CoV-2
Perfectly presented; really nicely done.
ltr:
It is possible for you to do this yourself as I described it. I think I posted the model in a comment to you one time before. If you look in edit for your comment, you can see how it was done. No need to do this portion rel=”nofollow ugc” as the system add it.
I do appreciate the help. Thank you, still again.
doesn’t matter, but i think i heard evidence (rumors?) of usa dabbling in weaponizing disease agents, so i wouldn’t be surprised that another country might be doing the same thing. perhaps they are less careful. more likely pure random chance practically guarantees there is going to be a leak somewhere sometime.
as for those centuries of experience and the null hypothesis, well, who knew there were bioweapon labs centuries ago.
meanwhile i got confused by all the arguments from authority.
Joel,
I am dismayed the link was not something you wrote as a microbiologist……
the furin cleavage so adept at acting in humans needs to be anteceded in nature, it seems to be a too long “evolutionary” jump.
and 40 odd months since lockdowns and no accepted natural animals source.
question abound about the links between “variants” as well
@paddy,
I’m not a microbiologist, nor have I claimed to be one. But this thread isn’t about me, it’s about SARS-CoV-2.
Which SARS-CoV-2 variants do you believe can’t be explained by natural processes? Since the beginning of the pandemic, there have been cladograms mapping the appearance of all the variants, as far as I know. According to this paper, “genetic diversity of virions in an infected host covers all possible single nucleotide substitutions”:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8237675/
There are certainly natural mechanisms by which the furin cleavage site could have arisen in SARS-CoV-2. A detailed discussion can be found here:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8689951/
There are certainly candidate animal sources and mechanisms. The fact that there’s no consensus probably reflects the challenges of that kind of research including undersampling, not some nefarious conspiracy. Here’s a discussion of the most likely animal source(s):
https://www.science.org/doi/pdf/10.1126/science.abh0117
Hope that helps.
The Ongoing Mystery of Covid’s Origin
NYT magazine – July 25
Where did it come from? More than three years into the pandemic and untold millions of people dead, that question about the Covid-19 coronavirus remains controversial and fraught, with facts sparkling amid a tangle of analyses and hypotheticals like Christmas lights strung on a dark, thorny tree. One school of thought holds that the virus, known to science as SARS-CoV-2, spilled into humans from a nonhuman animal, probably in the Huanan Seafood Wholesale Market, a messy emporium in Wuhan, China, brimming with fish, meats and wildlife on sale as food. Another school argues that the virus was laboratory-engineered to infect humans and cause them harm — a bioweapon — and was possibly devised in a “shadow project” sponsored by the People’s Liberation Army of China. A third school, more moderate than the second but also implicating laboratory work, suggests that the virus got into its first human victim by way of an accident at the Wuhan Institute of Virology (W.I.V.), a research complex on the eastern side of the city, maybe after well-meaning but reckless genetic manipulation that made it more dangerous to people. …
If you feel confused by these possibilities, undecided, suspicious of overconfident assertions — or just tired of the whole subject of the pandemic and whatever little bug has caused it — be assured that you aren’t the only one.
Some contrarians say that it doesn’t matter, the source of the virus. What matters, they say, is how we cope with the catastrophe it has brought, the illness and death it continues to cause. Those contrarians are wrong. It does matter. Research priorities, pandemic preparedness around the world, health policies and public opinion toward science itself will be lastingly affected by the answer to the origin question — if we ever get a definitive answer.
But much of the evidence that might provide that answer has either been lost or is still unavailable — lost because of failures to gather relevant material promptly; unavailable because of intransigence and concealment, particularly on the part of Chinese officialdom at several levels.
Take the natural-spillover hypothesis, for instance, and assume that the virus passed to humans from a wild animal — maybe a raccoon dog (a foxlike canine) or a Malayan porcupine — somewhere in the Huanan market. To test that hypothesis, you would want samples of blood, feces or mucus taken from the raccoon dogs, porcupines and other wildlife that languished, caged and doomed, in the market. You would screen those samples for signs of the virus. If you found the virus itself, or at least sizable bits of its genome, you would then make a comparative analysis of genomes, including some from the earliest human cases, to deduce whether people got the virus from the wildlife or vice versa. …
But you can’t do that, because whatever raccoon dogs or porcupines or other wild animals were on sale in the market during December 2019 had vanished by Jan. 1, 2020. On that date, the market was closed by order of Chinese authorities, with no (reported) effort to sample the most suspect forms of wildlife.
Or take the lab-leak scenario, some versions of which point accusingly at a nonprofit organization in New York, EcoHealth Alliance, and its collaborative relationship with Dr. Zhengli Shi, a senior researcher at the W.I.V. Shi and her team study coronaviruses, especially those carried by bats, extracting fragments of viral RNA (the molecule in which coronavirus genomes are written) and occasionally live virus, from samples of guano and other bodily material, and assembling whole genome sequences, like jigsaw puzzles, from the fragments. They perform experiments, sometimes combining an element of one virus with the backbone of another, to learn how that element might function in the wild; and they publish scientific papers, warning which bat viruses could pose a threat to humans. What if a researcher or technician under Shi’s leadership, handling a virus very much like SARS-CoV-2, became infected by accident and then spread the infection to others? That question became, from the early months of the pandemic, a suspicion and then a hypothesis and then an accusation. …
(Really long article continues at the link.)
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Joel,
I misremembered your profession in the time it took to be frustrated by the link.
I will read the link on furin cleav. ‘Could’ is an untested hypothesis. My regard for nih is small.
I will also dig around about the skepticism that there is an evolution of the variants from the so called wuhan virus.
I have a fair exposure to hypothesis testing, design of test, etc. and have little regard for a lot of “knowledge”.
Joel,
Regarding ‘furin sequence recognition’: from your link:
Jack Nunberg, whose group first inserted an S1/S2 FCS into the spike of SARS-CoV, said: “there is no way to know whether humans or nature inserted the site” in SARS-CoV-2 (Cyranoski 2020). In 2006, Nunberg’s group had investigated whether the fusion activity of SARS-CoV could benefit from proteolytic cleavage, similar to other CoVs that had been characterized at the time. They inserted a synthetic furin recognition sequence at the putative R667 S1/S2 cleavage site, and demonstrated that an FCS insertion (as compared with a substitution) upstream of R667 markedly increased the ability of the spike to induce cell–cell fusion (Follis et al. 2006).
The possibility this furin sequence unique to humans could have happened in nature without finding evidence is very small.
On topic about links between variants and wuhan:
(1) Ethical Skeptic ☀ on Twitter: “@leoniedelt @WarrenFahy @AlexisKat6 @TracyBethHoeg @DrJBhattacharya @WSJ Omicron’s genetic diversity even within 2 months of its discovery, based upon the slow/steady rate of SARS-CoV-2 mutation, easily places its cryptic origin to 2017. This is the only way to explain what we saw. https://t.co/v1D2ZdZGKg” / X
This tweeter’s point is sar-cov-2 has been around since 2017 in China, the variants suggesting that, and:
China’s CCP Concealed SARS-CoV-2 Presence in China as Far Back as March 2018 | The Ethical Skeptic
Another suggests that a spike in pneumonia deaths in USA in 2018-19 may (a hypothesis) have been sars cov x.
You can review these, this analyst is quite thorough in his critical thinking and applying questioning including of his own hypotheses.
My position on lab leak is I cannot reject the statement that the “wuhan strain entered humanity via a lack accident”.
@paddy,
“Jack Nunberg, whose group first inserted an S1/S2 FCS into the spike of SARS-CoV, said: “there is no way to know whether humans or nature inserted the site” in SARS-CoV-2 (Cyranoski 2020).”
Thanks. That makes my point. The presence of a FCS in SARS-CoV-2 is not dispositive for a lab origin.
“My position on lab leak is I cannot reject the statement that the “wuhan strain entered humanity via a [lab] accident”.
Nor can I. Nor can any serious scientist. And nothing I’ve posted here says otherwise.
Dobbs
I would hate to be called a contrarian because i said it didn’t matter. i meant it didn’t matter for purposes of fixing the blame on someone. of course it matters if honest research into the question leads to new knowledge…about virus transmission.
i did not see anything in the post that suggested a research design that might do that. You and Paddy have enlightened me a bit.
a contrarian is someone who takes a contrary position for the fun of it, or because he believes the mob is always wrong. me i only take contrary positions against positions i disagree with, either because I know someting or because i think the proponent doesn’t know something.
Believe me, I go out of my way to agree with you and he who cannot be named whenever i can.
Dobbs
looking back, I see that my “doesn’t matter” was followed by “but i think…”
and remember that what i was feeling at the time was that “it doesn’t matter what i think”
so, unless i am misreading your “contrarians say..” we maybe both need to be a little careful how we read what other people say. sometimes it is not what we think.
The null result in the before times was hindsight is 20/20
We were tested, and found wanting. Other than as prolog, the past is pointless. I’ve been harping on viruses thawing out of the thawing tundra that haven’t seen a human since before we were human for … a long time, hard to keep track. Where it came from is actually moot, the evidence points to a natural jump from raw bat to undercooked dog to unhealthy human though not all wacko conspiracy theories are wack
It has been my position from the start (of sars-covid) has been this isn’t the one that kills us all … but the next one may be. We were presented with a global pandemic and we failed
All else is moot
Tangent, but as secrecy regarding UAPs unwinds at an increasing pace, are we soon going to understand that the on-going secrecy is mostly to protect the prior 70+ years of secrecy, specifically the activities involved to hold on to the secrecy? The craft debris and crew remains are less important now than the disclosure of an accurate account of how the secrecy was maintained. Important US officials, who were in positions to know much, much more about this virus than any of our elected officials, were moving with speed and energy in early 2020 to combat a lab leak hypothesis. This was no careful sifting of evidence – which China (+ others) was strongly obstructing gathering – but a program to get people to believe lab leak wasn’t possible. Why was that so important to these officials? So decades later “ You know those ‘UFO whack jobs’ actually were right about these crafts and things, but they were completely wrong about us intimidating or even harming folks to keep it secret.” Right.
@Eric,
Here we are in the middle of 2023, and (a) there’s no compelling evidence for a lab leak of COVID-19 and (b) all the available evidence is compatible with the most parsimonious hypothesis, natural origin.
“Important US officials, who were in positions to know much, much more about this virus than any of our elected officials, were moving with speed and energy in early 2020 to combat a lab leak hypothesis. This was no careful sifting of evidence – which China (+ others) was strongly obstructing gathering – but a program to get people to believe lab leak wasn’t possible.”
Link, please.
well, still relying on argument by authority . first, i will stipulate that he whom i cannot name knows more than i do about the “proof” or “evidence” that Covid was not caused by a lab leak.
the proof would most likely depend on the science of viral evolution which i don’t know enough about to have an opinion.
but not even a hint of that science is offered here.
what has been offered is a string of “arguments by authority.” I know I would be very hard put to find links to what i have heard about, say, china shutting down the Wuhan laboratory.. which, if true, would constitute “evidence” of guilt… (if they had no reason to suspect a lab leak, they would have kept their lab open to investigate the virus…and its possible origins. i have heard of no “evidence” that a likely precursor of the pandemic virus is present in animal populations. it is easy for me to imagine a laboratory genetic manipulation disrupting the “normal” chain of genetic innovation (mutation?)…but obviously my imagination is not evidence.
which is meant to say that evidence presented here, and lack of links to contrary evidence,,,does not constitute “evidence” for any theory of Covid (shorthand for pandemic) origins. so my opinion “doesn’t matter.” and it was he who i cannot name who madde himself the subject of his own post by beginning with his “qualifications” which he claims were not meant to be claims of authority but merely a kind of biographical “why i became interested.” of course this is possible, but it also looks like the kind of disingenuous explanation we get from politicians who slip in a misleading phrase and then explain it away when some someone calls attention to it.
so: i am not being a contrarian here, i am just pointing out that i am dissatisfied with the evidence not presented, the “hundred years of experience” and whatever the “null hypothesis” was supposed to mean without any experimental design to even suggest a hope of rejecting or failing to reject that “null hypothesis”.
this is not meant to be personal. it just happens…that my own intellectual history has made me sensitive to questions of adequacy of arguments. [disclaimer: note this is not a claim of expertise, just a bographical note of how i got this way.] i have been trying to cure myself of commenting on such, seeing that it does absolutely no good in the “blog” environment.
i have noted, i think, that the post has led to some comments that point the way to further understanding, and that is a good thing for the post to have accomplished.
“This was no careful sifting of evidence – which China (+ others) was strongly obstructing gathering…”
“I would be very hard put to find links to what i have heard about, say, china shutting down the Wuhan laboratory…”
Both these assertions are completely incorrect.
ltr
and yours is without content. “i would be hard put..” is a statement about me. the other statement was from someone else. calling either statement “incorrect” does not show that they were incorrect.
i think you would be hard put to show that my statement about myself was incorrect.
if you think the other statement was incorrect, you need show at least arguable evidence that it was.
‘I would be very hard put to find links to what i have heard about, say, china shutting down the Wuhan laboratory.. which, if true, would constitute “evidence” of guilt…’
This is nonsense and offensive, but typical when having decided to demean the Chinese. Do try to avoid being prejudiced.
ltr
worser and worser. you failed to notice the “if true.” i was and am more interested in intelligent argument than in demeaning the chinese, which you have accused me of as a knee jerk response to everything i say that you do not understand. how’s that for offensive?
i have absolutely no knowledge of what the Chinese are up to, or what the Americans are up to for that matter. all i know about is what people say right here, and that is what i react to.
i should tell you that i utterly failed to teach undergraduates to think clearly about simple math.
at first, i blamed myself.
Great powers (and their military folks) are going to be ‘investigating’ bioweapons in these times, certainly to understand what ‘others’ might be doing at least. And this is inevitably dangerous to the world at large. Sort of like nuclear weapons. And the secreats assoicated with them, which may end up lying around yer locker rooms & the like.
Dobbs
yes. that is what i was trying to say in the first place.
@Fred,
You mean like when Colin Powell lied about anthrax in Iraq? That wasn’t science, that was pure politics. Just like yellow rain and the lab leak hypothesis for COVID-19.
Those were the days…
Bush Jr had a huge grudge against Iraq, as we know. Lying was rampant about ‘weapons of mass destruction’. The Defense Department regards all chemical, biological and nuclear weapons as ‘WMDs’. We knew that Iraq had aluminum tubes that could be used to make the centrifuges used to concentrate atomic bomb making materials because we sold them the tubes. (They were not quite the right kind of tubes for this, but there were tubes.) So, we lied. It was in a good cause. They tried to kill his dad!
Sadam Hussein was afraid/unwilling to admit that he did not have such programs. Well, he did have programs for making nerve gas apparently, maybe anthrax also. Evidently he used them on his in-country enemies.
But this was in the aftermath of 9/11. The worse thing to happen to us since Pearl Harbor, sleeping-giant wise.
Y’know, Colin Powell also misspoke about the Pottery Barn Rule.
Wikipedia: Pottery Barn Rule
There is (was?) no such rule in the Pottery Barn shops.
“In reality, Pottery Barn—a chain of upscale home furnishing stores in the United States—does not have a “you break it, you bought it” policy, but instead writes off broken merchandise as a loss, as do most large American retailers.”
But this rule was posted in Bennington Potters. Both shops existed in the MA/VT area that Colin Powell visited with his wife from time to time. So have Mrs Fred and I. Never ran into the Powells there however, I’m pretty sure.
“Powell denie(d) using the term “pottery barn rule”, but stated:
i think it is safer for me to leave it for others to figure out which is a non sequiter to which.