Coronavirus in rural areas
A Question for Readers About the Coronavirus Vaccine

Where Did This Coronavirus Come From?

Inquiring minds, of both honest and conspiratorial sets, have been pondering, speculating, and even authoritatively announcing the origin of the CoV-2 virus that is causing this pandemic. Some say it has a natural origin, others say it came from a lab, either accidentally or on purpose. Some say that the lab of origin is in Wuhan and others say it came from a US military lab and neither provide much evidence for their allegations. What do we believe?

At first, based on previous experience with SARS and MERS, people immediately pointed to bats with some animal intermediate as the source of the human infection. From that, the Wuhan wet market became immediately suspect for being ground zero. Then the silliness began. China shut down release of much information on its testing to find ground zero. Trump, Secretary of State Mike Pompeo and no shortage of shrill conspiracy fans pointed to the fact that Wuhan has an Institute for Virology where labs study coronaviruses; therefore, they announced it had to have come from that lab, either by design or by incompetence. The Chinese unhelpfully, and with just as little evidence and as much shrillness, countered that the virus was introduced to Wuhan by the US military. Other, more irrational tin-hatters claim that Bill Gates created this so he could develop a vaccine with which he can surreptitiously inject us with a microchip thereby turning us all into Stepford Wives or Manchurian Candidates. I even saw a video of an MD who claimed that there is no virus. Rather, he authoritatively asserted that the COVID-19 malaise comes from toxins excreted by our cells in response to 5G technology. It has all been great show, but I don’t know whether to laugh at or fear my fellow travelers who so willingly buy such bunk.

Maybe there are a few of us left who like to look at facts and evidence before reaching conclusions. This post is for you. All others can go back to their tinfoil hat channels.

Some backstory:

Early on, in January, as news about the virus began emerging, China began pointing to animals at the Wuhan market, probably a pangolin or scaly anteater (a delicacy in China) as the likely source of the virus. After a while that story began to break down as they found infected people in Wuhan who had no contact with the market and a large scale surveillance of coronaviruses in pangolins concluded that these animals are not the source of the human virus. Then the Chinese stopped releasing information to the world, while simultaneously totally isolating and Hubei province where Wuhan is found  from all outsiders. US reporters were kicked out of China. Meanwhile, the virus had already escaped and was rapidly racing around the world.

Recently the Wall Street Journal published an expose of what went on in Wuhan during the first few days of the outbreak. In the middle of the night on December 31st, before anyone outside China knew there was a coronavirus on the loose, Wuhan officials began disinfecting its wet market. Officials collected biological samples from the stalls, goods and animals. China’s CDC said that a team from Beijing arrived on Jan. 1 and collected 585 “environment” samples from a garbage truck, drains and sewers in the market. They reported that 33 of the environmental samples tested positive for the virus. 14 of the positive samples were from the area of the market where wildlife was traded.  

Four months later, however, China inexplicably has yet to release data on the animal samples they collected from the Wuhan market. Why? A UN body charged with coordinating research into the origins of the virus has been denied entry by China. The EcoHealth Alliance, a nonprofit organization based in New York, has studied coronaviruses in China for 15 years and helped establish that the SARS virus originated in bats then jumped to humans via an intermediate civet in a market in Southern China. But the Alliance’s partners in China also have been unable to investigate anything about this virus. Why?

Clearly, the virus passed through the market, but how did it get there? Its origin remains unknown and shrouded in mystery, which only fuels speculation.

The virus:

It is well known that bats are an important reservoir for coronaviruses. About 500 different coronaviruses have been isolated from bats around the world. Other animals also carry the virus. In fact there are about 7 (including SARS, MERS and CoV-2) that can be found in humans.

A virus isolated from a species of bat found in Southern China and not found in the Wuhan area has 96% genetic sequence identity to CoV-2. This suggests that this bat carried an ancestor of the Wuhan virus, but how did it make its way to Wuhan where that species of bat is not found? It is eminently plausible that an animal in Southern China picked up the virus, was trapped and shipped to Wuhan. It also is possible that this didn’t happen.

Did the virus come from a lab?

Scientists from around the world who have examined the sequence of CoV-2 are convinced that it has a natural origin. They say it lacks telltale signs that certain sequences were purposefully cut out of the RNA backbone and replaced with other engineered sequences. And as viruses replicate, they make random, infrequent errors in copying the millions of bases in their genomes and these mistakes are passed on to daughter viruses that go on to replicate. These small genome mistakes provide a sort of fingerprint from which forensic analyses can be done and the molecular sleuths all seem to agree that the fingerprints do not point to a guilty verdict. The scientific consensus is almost unanimous in rejecting that the virus was engineered by humans. In a letter to Nature in March, a team in California led by microbiology professor Kristian Andersen said “the genetic data irrefutably shows that [Covid-19] is not derived from any previously used virus backbone” – in other words spliced sections from another known virus.

However, a team of Australian scientists, led by Nikolai Petrovsky, very recently described evidence that the novel coronavirus has an unexpectedly high affinity for receptors on human cells. A virus from another animal would be expected to have primarily adapted to that species and not to have undergone changes that make it more infectious in a different species. From this they jumped to the conclusion that the virus could have been specifically designed by humans to penetrate human cells. This is not based on any experimental data, but on computer models that predict the virus’ ability to bind to receptors in humans and other animals. While this observation is not what one would expect for a naturally evolved virus, it remains eminently possible that the virus really did evolve this human preference by happenstance in other species. Most viruses do tend to prefer the species they are found in, but there are myriad molecular and biological reasons why they sometimes do jump across species. And this virus has shown an unusual propensity to move between species. The genetic sequence that encodes for the region of the viral spike protein that binds to cell receptors is also  known to be the most mutable part of the coronavirus genome, which makes it less surprising that it could spontaneously mutate in animals to a form that could more easily infect other species.

Therefore, in this blogger’s opinion, this computer simulation does little to answer the question regarding the origin of the virus. In the absence of more direct data proving it was engineered, and the reality that the molecular sequence shows no “fingerprint” of such engineering, it remains premature to claim that it was created in the lab.

In a recent interview, Francis Collins, Director of NIH, explained that If you wanted to design a virus weapon, you would not design this one because it looks like viruses we already know about. It is not very novel in its genome sequence. Genome analysis comparing this virus to all of the 500 or so known coronaviruses shows more compelling evidence that nature was the bioterrorist that created it and that its creation has been going on naturally for a long time.

Peter Forster, an archaeological research fellow at Cambridge University, co-invented phylogenetic algorithms that have, since the 1990s, become standard software for mining genetic data to reconstruct evolutionary trees, or networks. His team applied the software to genome samples of the earliest coronavirus sequences from China.  In the Proceedings of the National Academy of Sciences, Forster reported finding three main strains of the virus that he labeled A, B and C. His research determined that A was the founding variant because it was the version most similar to the ancestral Cov-2 found in bats from Southern China.  He also discovered that the A strain wasn't the predominant type in Wuhan. Of 23 Wuhan samples, only three were type A, the rest were type B, a version that was derived from A and that is identified by two point mutations that distinguish it from type A. In other parts of China type A was the predominant strain. In other words, it appears that the type A founding strain frequently appeared in other parts of China very early after it was first found in Wuhan in December. Forster’s research adds to the confusion of the virus origin since it seems possible that the virus could have been introduced into humans in a number of places in China, not necessarily Wuhan. This suggests, but does not prove, that the virus might not have even originated in Wuhan.

The Wuhan Institute of Virology:

The Wuhan Institute of Virology is a world class coronavirus research facility and many have speculated that the virus could have escaped the lab by accident. They point to a Washington Post article from 2018 that reported that US Embassy officials who visited the WIV had  concerns over the security of the lab. However, James Le Duc, the head of the Galveston National Laboratory in the US, the biggest active biocontainment facility on a US academic campus, poured cold water on that suggestion. He also visited and toured the lab and stated that it has safety and quality measures comparable to the best Western labs. Other Western scientists who have visited the lab also believe that an accidental release was “implausible” and highly rate the facility. One of the major responsibilities of the lab is to isolate coronaviruses from bats from all corners of China. They then sequence the viral genomes and post the sequences into a repository that is freely available to any researcher around the world. The genome sequence of the current virus does not match the sequence of coronaviruses posted in the library suggesting, but not proving, that they never worked on it.

Of course, it is possible that Wuhan lab researchers simply have not reported all of their research to the public, but until specific evidence of that omission is presented, that just remains an unproven possibility.

Bottom line:

It seems clear that the ancestral virus came from a bat, but there is little certainty about what happened after that. At this point, the only thing certain about the virus is its uncertainty.


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