In the millions of articles, opinion pieces, and news stories written about Covid there is one topic that is more important than all the others. It’s more important than masks, vaccines, or lockdown measures. The origin of the virus is critical because no matter how many people die from covid, or how many businesses are wiped out, it’s critical that IF the next virus can be stopped, it mu st be.
A science writer named Nicholas Wade has written the most thorough study on the origins of Covid to be released to the public. Wade has worked with Nature, Science, and the New York Times, but this article was released on the public platform Medium. In this article Wade goes through three possible scenarios and then draws the most likely conclusion. This is a long read, but it might be the most important article yet written during this pandemic.
Here is the beginning of this extensive article from Medium. Click here to read the full article on Medium.
Origin of Covid — Following the Clues
Did people or nature open Pandora’s box at Wuhan?
The Covid-19 pandemic has disrupted lives the world over for more than a year. Its death toll will soon reach three million people. Yet the origin of pandemic remains uncertain: the political agendas of governments and scientists have generated thick clouds of obfuscation, which the mainstream press seems helpless to dispel.
In what follows I will sort through the available scientific facts, which hold many clues as to what happened, and provide readers with the evidence to make their own judgments. I will then try to assess the complex issue of blame, which starts with, but extends far beyond, the government of China.
By the end of this article, you may have learned a lot about the molecular biology of viruses. I will try to keep this process as painless as possible. But the science cannot be avoided because for now, and probably for a long time hence, it offers the only sure thread through the maze.
The virus that caused the pandemic is known officially as SARS-CoV-2, but can be called SARS2 for short. As many people know, there are two main theories about its origin. One is that it jumped naturally from wildlife to people. The other is that the virus was under study in a lab, from which it escaped. It matters a great deal which is the case if we hope to prevent a second such occurrence.
I’ll describe the two theories, explain why each is plausible, and then ask which provides the better explanation of the available facts. It’s important to note that so far there is no direct evidence for either theory. Each depends on a set of reasonable conjectures but so far lacks proof. So I have only clues, not conclusions, to offer. But those clues point in a specific direction. And having inferred that direction, I’m going to delineate some of the strands in this tangled skein of disaster.
A Tale of Two Theories
After the pandemic first broke out in December 2019, Chinese authorities reported that many cases had occurred in the wet market — a place selling wild animals for meat — in Wuhan. This reminded experts of the SARS1 epidemic of 2002 in which a bat virus had spread first to civets, an animal sold in wet markets, and from civets to people. A similar bat virus caused a second epidemic, known as MERS, in 2012. This time the intermediary host animal was camels.
The decoding of the virus’s genome showed it belonged to a viral family known as beta-coronaviruses, to which the SARS1 and MERS viruses also belong. The relationship supported the idea that, like them, it was a natural virus that had managed to jump from bats, via another animal host, to people. The wet market connection, the only other point of similarity with the SARS1 and MERS epidemics, was soon broken: Chinese researchers found earlier cases in Wuhan with no link to the wet market. But that seemed not to matter when so much further evidence in support of natural emergence was expected shortly.
Wuhan, however, is home of the Wuhan Institute of Virology, a leading world center for research on coronaviruses. So the possibility that the SARS2 virus had escaped from the lab could not be ruled out. Two reasonable scenarios of origin were on the table.
From early on, public and media perceptions were shaped in favor of the natural emergence scenario by strong statements from two scientific groups. These statements were not at first examined as critically as they should have been.
“We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin,” a group of virologists and others wrote in the Lancet on February 19, 2020, when it was really far too soon for anyone to be sure what had happened. Scientists “overwhelmingly conclude that this coronavirus originated in wildlife,” they said, with a stirring rallying call for readers to stand with Chinese colleagues on the frontline of fighting the disease.
Contrary to the letter writers’ assertion, the idea that the virus might have escaped from a lab invoked accident, not conspiracy. It surely needed to be explored, not rejected out of hand. A defining mark of good scientists is that they go to great pains to distinguish between what they know and what they don’t know. By this criterion, the signatories of the Lancet letter were behaving as poor scientists: they were assuring the public of facts they could not know for sure were true.
It later turned out that the Lancet letter had been organized and drafted by Peter Daszak, president of the EcoHealth Alliance of New York. Dr. Daszak’s organization funded coronavirus research at the Wuhan Institute of Virology. If the SARS2 virus had indeed escaped from research he funded, Dr. Daszak would be potentially culpable. This acute conflict of interest was not declared to the Lancet’s readers. To the contrary, the letter concluded, “We declare no competing interests.”
Virologists like Dr. Daszak had much at stake in the assigning of blame for the pandemic. For 20 years, mostly beneath the public’s attention, they had been playing a dangerous game. In their laboratories they routinely created viruses more dangerous than those that exist in nature. They argued they could do so safely, and that by getting ahead of nature they could predict and prevent natural “spillovers,” the cross-over of viruses from an animal host to people. If SARS2 had indeed escaped from such a laboratory experiment, a savage blowback could be expected, and the storm of public indignation would affect virologists everywhere, not just in China. “It would shatter the scientific edifice top to bottom,” an MIT Technology Review editor, Antonio Regalado, said in March 2020.
A second statement which had enormous influence in shaping public attitudes was a letter (in other words an opinion piece, not a scientific article) published on 17 March 2020 in the journal Nature Medicine. Its authors were a group of virologists led by Kristian G. Andersen of the Scripps Research Institute. “Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus,” the five virologists declared in the second paragraph of their letter.
Unfortunately this was another case of poor science, in the sense defined above. True, some older methods of cutting and pasting viral genomes retain tell-tale signs of manipulation. But newer methods, called “no-see-um” or “seamless” approaches, leave no defining marks. Nor do other methods for manipulating viruses such as serial passage, the repeated transfer of viruses from one culture of cells to another. If a virus has been manipulated, whether with a seamless method or by serial passage, there is no way of knowing that this is the case. Dr. Andersen and his colleagues were assuring their readers of something they could not know.
The discussion part their letter begins, “It is improbable that SARS-CoV-2 emerged through laboratory manipulation of a related SARS-CoV-like coronavirus”. But wait, didn’t the lead say the virus had clearly not been manipulated? The authors’ degree of certainty seemed to slip several notches when it came to laying out their reasoning.
The reason for the slippage is clear once the technical language has been penetrated. The two reasons the authors give for supposing manipulation to be improbable are decidedly inconclusive.
First, they say that the spike protein of SARS2 binds very well to its target, the human ACE2 receptor, but does so in a different way from that which physical calculations suggest would be the best fit. Therefore the virus must have arisen by natural selection, not manipulation.
If this argument seems hard to grasp, it’s because it’s so strained. The authors’ basic assumption, not spelt out, is that anyone trying to make a bat virus bind to human cells could do so in only one way. First they would calculate the strongest possible fit between the human ACE2 receptor and the spike protein with which the virus latches onto it. They would then design the spike protein accordingly (by selecting the right string of amino acid units that compose it). But since the SARS2 spike protein is not of this calculated best design, the Andersen paper says, therefore it can’t have been manipulated.
But this ignores the way that virologists do in fact get spike proteins to bind to chosen targets, which is not by calculation but by splicing in spike protein genes from other viruses or by serial passage. With serial passage, each time the virus’s progeny are transferred to new cell cultures or animals, the more successful are selected until one emerges that makes a really tight bind to human cells. Natural selection has done all the heavy lifting. The Andersen paper’s speculation about designing a viral spike protein through calculation has no bearing on whether or not the virus was manipulated by one of the other two methods.
The authors’ second argument against manipulation is even more contrived. Although most living things use DNA as their hereditary material, a number of viruses use RNA, DNA’s close chemical cousin. But RNA is difficult to manipulate, so researchers working on coronaviruses, which are RNA-based, will first convert the RNA genome to DNA. They manipulate the DNA version, whether by adding or altering genes, and then arrange for the manipulated DNA genome to be converted back into infectious RNA.
Only a certain number of these DNA backbones have been described in the scientific literature. Anyone manipulating the SARS2 virus “would probably” have used one of these known backbones, the Andersen group writes, and since SARS2 is not derived from any of them, therefore it was not manipulated. But the argument is conspicuously inconclusive. DNA backbones are quite easy to make, so it’s obviously possible that SARS2 was manipulated using an unpublished DNA backbone.
And that’s it. These are the two arguments made by the Andersen group in support of their declaration that the SARS2 virus was clearly not manipulated. And this conclusion, grounded in nothing but two inconclusive speculations, convinced the world’s press that SARS2 could not have escaped from a lab. A technical critique of the Andersen letter takes it down in harsher words.
Science is supposedly a self-correcting community of experts who constantly check each other’s work. So why didn’t other virologists point out that the Andersen group’s argument was full of absurdly large holes? Perhaps because in today’s universities speech can be very costly. Careers can be destroyed for stepping out of line. Any virologist who challenges the community’s declared view risks having his next grant application turned down by the panel of fellow virologists that advises the government grant distribution agency.
The Daszak and Andersen letters were really political, not scientific statements, yet were amazingly effective. Articles in the mainstream press repeatedly stated that a consensus of experts had ruled lab escape out of the question or extremely unlikely. Their authors relied for the most part on the Daszak and Andersen letters, failing to understand the yawning gaps in their arguments. Mainstream newspapers all have science journalists on their staff, as do the major networks, and these specialist reporters are supposed to be able to question scientists and check their assertions. But the Daszak and Andersen assertions went largely unchallenged.
Doubts about natural emergence
Natural emergence was the media’s preferred theory until around February 2021 and the visit by a World Health Organization commission to China. The commission’s composition and access were heavily controlled by the Chinese authorities. Its members, who included the ubiquitous Dr. Daszak, kept asserting before, during and after their visit that lab escape was extremely unlikely. But this was not quite the propaganda victory the Chinese authorities may have been hoping for. What became clear was that the Chinese had no evidence to offer the commission in support of the natural emergence theory.
This was surprising because both the SARS1 and MERS viruses had left copious traces in the environment. The intermediary host species of SARS1 was identified within four months of the epidemic’s outbreak, and the host of MERS within nine months. Yet some 15 months after the SARS2 pandemic began, and a presumably intensive search, Chinese researchers had failed to find either the original bat population, or the intermediate species to which SARS2 might have jumped, or any serological evidence that any Chinese population, including that of Wuhan, had ever been exposed to the virus prior to December 2019. Natural emergence remained a conjecture which, however plausible to begin with, had gained not a shred of supporting evidence in over a year.
And as long as that remains the case, it’s logical to pay serious attention to the alternative conjecture, that SARS2 escaped from a lab.
Why would anyone want to create a novel virus capable of causing a pandemic?
I’m a science writer and have worked on the staff of Nature, Science and, for many years, on the New York Times. [email protected]
By the way.. Medium is a fascinating place. If you haven’t checked it out yet here’s a link to medium.com.
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Most unused COVID-19 vaccines will expire at the end of the year: auditor general
By Laura Osman in Ottawa
Tens of millions of doses of COVID-19 vaccines are likely about to expire and go to waste because of a failure to manage an oversupply, Canada’s auditor general reported Tuesday — a failure with an estimated price tag of about $1 billion.
Karen Hogan has released the results of her office’s investigation into the government’s efforts to get ahold of COVID-19 vaccine doses in the early days of the pandemic, and track how many people got them.
The auditor gave the Public Health Agency of Canada and the Procurement Department a thumbs up when it came to quickly getting enough doses into the country to meet vaccination goals, but said the government did a much poorer job of managing all that supply.
“We found that the Public Health Agency of Canada was unsuccessful in its efforts to minimize vaccine wastage,” Hogan wrote in the report.
The government knew that by signing advanced purchase agreements with a number of pharmaceutical companies there was a risk of buying up more COVID-19 vaccines than Canadians needed.
PHAC and the federal government signed deals with seven companies that were developing vaccines in 2020 and 2021, in case only a few them were approved by Health Canada.
So far six of those have been authorized by the drug review agency.
“In my view, it was a prudent approach given all the uncertainty back in 2020,” she said at a press conference Tuesday.
The auditor found that about half of the 169 million doses the government paid for have made it into the arms of Canadians between December 2020 and May 2022.
The federal government announced plans to donate some 50 million surplus doses to other countries, but as of May 31 only about 15 million had been given away and another 13.6 million expired before they could be donated.
Canada has offered the remaining 21.7 million doses to other countries but so many countries are now offering donations that the market is saturated, Hogan said, and those vaccines will be wasted if they are not distributed soon.
There were also 32.5 million doses in federal and provincial inventories by the end of the audit period in May, worth about $1 billion, based on the auditor’s estimate.
Hogan said in her report that the majority of those doses will expire by the end of 2022.
Hogan said the public health agency informed her that another 10 million have expired since the end of the audit and another 11 million were donated.
Part of the problem, she said, was that provinces and territories did not communicate and share data with PHAC.
“Although some provinces and territories consistently reported to the agency, the agency was unable to obtain complete data from most. This meant that the status of these doses was unknown and reduced the agency’s ability to predict supply needs and plan for donations,” the report said.
The auditor general’s office and the public health agency itself warned for a decade before the COVID-19 pandemic that there were serious gaps in the federal and provincial health data sharing plans.
In January 2021, Deloitte Inc. was awarded a $59.1 million contract to come up with a national vaccine management system called VaccineConnect to share timely information about vaccine distribution, coverage and safety.
Some elements of that program were up and running on time, but others were delayed and the auditor found that PHAC was instead using spreadsheets to manually track expiration dates and waste as of June 2021.
The information silos made it difficult for vaccine companies to monitor national safety indicators of their products, as they’ve been ordered to by Health Canada.
“Companies cannot entirely fulfil this requirement when they do not have access to the necessary data on adverse events,” the report said.
Hogan found two incidents in 2021 where companies learned of adverse effects to their vaccines from the media and urgently requested the data from the government, but couldn’t get access to it for three months.
Canada is also the only G7 country that does not follow World Health Organization guidance to share case-level information about patients who have adverse effects after immunization, and instead sends only summary data.
This report by The Canadian Press was first published Dec. 6, 2022.
Military was told to prepare to intervene in ‘Freedom Convoy’ protests: official
OTTAWA — The Defence Department’s top official says he directed the military to prepare to intervene in the “Freedom Convoy” protests earlier this year, but the resulting plans were never seriously considered — in part due to concerns about another Oka Crisis.
Deputy minister Bill Matthews and another top defence official also said the Canadian Armed Forces was prepared to fly police officers to demonstration sites across the country, but that its tow trucks were too big — and too old — to help with the protests.
Matthews and Defence Department associate deputy minister Stefanie Beck made the comments in an August interview with lawyers for the public inquiry looking into the Liberal government’s decision to use the Emergencies Act to end the protests.
A summary of that interview is among thousands of documents released by the Public Order Emergency Commission, which will ultimately determine whether the government was justified in invoking the act in February.
Neither was called to publicly testify before the commission.
The Liberals faced public calls in January and February to deploy the military as thousands of protesters opposed to vaccine mandates and pandemic restrictions gridlocked Ottawa and border crossings with the United States for three weeks.
The inquiry was also shown text messages in recent weeks in which federal Justice Minister David Lametti and then-Alberta premier Jason Kenney raised the prospect of using the military alongside police to clear protesters.
In one text exchange, Lametti and Public Safety Minister Marco Mendicino raised the idea of using a tank to end the protests. Lametti told the commission last week that the exchange was a joke.
Lametti and Defence Minister Anita Anand instead told the commission that the military was always considered a last resort — a position that Matthews and Beck echoed in their interview with commission lawyers.
Both defence officials “strongly emphasized that CAF members are not police officers,” the summary reads.
“They are trained to use lethal force, not do crowd control. Indeed, the domestic use of military force is, and in their view should always be, seen as a last resort.”
Matthews did say he asked defence officials to prepare “for the possibility that the CAF might be called out to intervene in the protests,” with a number of scenarios and internal plans subsequently drawn up.
“These plans considered the use of military equipment, infrastructure and deployment of CAF members.”
Yet Matthews and Beck said it was clear throughout the planning process that the government and the minister did not want to use the military due to fears “deploying the military in any way would inflame tensions with the protesters.”
The two officials “noted that the shadow of the Oka Crisis still looms large,” reads the summary.
On July 11, 1990, Quebec provincial police moved in on a barricade near the small town, which is about 50 kilometres northwest of Montreal. The barricade was erected by Indigenous activists to protest the planned expansion of a golf course and development on ancestral land.
After a police officer was killed, the situation escalated into a tense, 78-day standoff between Mohawk and thousands of Canadian soldiers that captured the country’s attention and raised enduring concerns about using the military in protests.
Matthews and Beck told the commission lawyers that they shared their concerns about a possible repeat of the crisis with senior officials in other departments, but that the military’s actual plans were not shared with them or with Anand.
“It was a necessary planning exercise, but the option of deploying the CAF was never seriously considered.”
The military did end up providing limited support to law enforcement efforts, with Ottawa police using the Cartier Drill Hall in downtown Ottawa as a staging area. It also provided 1,200 ration packs to the Parliamentary Protective Service.
The Defence Department and Armed Forces expected and considered requests for military planes to fly police to various parts of the country, but Matthews and Beck said domestic flights ended up being adequate.
Officials also considered whether the military could be used to clear protesters’ trucks from downtown Ottawa, the border crossing in Coutts, Alta., and other places where local officials were having trouble getting local tow companies to help.
However, Matthews and Beck said that ultimately wasn’t an option as the military’s own tow trucks weren’t designed for the types of vehicles involved in the protests, and using them would damage not only those vehicles but also any roads driven upon.
There were also concerns that moving the military’s tow trucks would represent a “significant logistical effort” and could have “drawn significant attention to themselves and the CAF members operating them.”
“Third, the trucks are quite old and require frequent maintenance,” the interview summary adds. “DND has plans to replace these trucks.”
This report by The Canadian Press was first published Dec. 1, 2022.
Lee Berthiaume, The Canadian Press
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