Did SARS-CoV-2 Originate in the Wild?

It's Unlikely

The SARS-CoV-2 virus was the pathogen behind the COVID-19 pandemic, which is estimated to have killed 25 million people around the world. An understanding the origin of SARS-CoV-2 is of critical importance because it will help us predict, plan for, and prevent future epidemics and pandemics.

Until recently, laboratory manipulation wasn’t possible and all viruses originated in the wild. The virus existed in an animal population, was transmitted from animals to humans, and then was eventually transmitted from humans to humans. Because close contact between humans is far more common than close contact between wild animals and humans, for a pandemic to commence, this last step of effective transmission between humans is essential.

Given that the great majority of viruses originated in the wild—called zoonotic origin—it is reasonable to consider the case that the SARS-CoV-2 (often shortened to SARS2) virus originated in the wild.

How are animal viruses transmitted to humans?

For wild animal viruses to be transmitted to humans, the virus needs a natural reservoir, which means a population of animals in which the virus is endemic. This population of animals could be rats, birds, bats, or anything else. Let’s focus on bats to explain how this might work.

Imagine a cave with a large population of bats. Within this bat population, a particular virus circulates. This virus has, over time, been optimized, via mutation and natural selection, to enable both transmission among these bats and infection of the bats. A virus must be able to do both things. A virus that infects but can’t transmit will die out. A virus that transmits but can’t infect will die out.

A virus is considered transmissible when it can move from one individual to another. Transmission can happen via bodily fluids, water, soil, aerosols, etc. A virus is infectious when it can enter the cells of its host and hijack the cell’s mechanisms to create more copies of itself. These viral copies then leave the cells and enable transmission.

Consider the scenario where a person explores a bat-infested cave and some bat saliva gets into the mouth, nose, or eyes of the human. That virus, which has proven successful in infecting bats, must now “try” to infect the human. Normally, the original virus won’t be very good at this because bats and humans, while both mammals, have important differences. It may take many, many attempts (bat saliva getting onto humans repeatedly) to have a successful infection. Even if the virus can successfully infect the human, it may not be optimized for humans and the virus, through mutation and natural selection, will take some time to become better at infecting humans.

The human victim may die, presenting an evolutionary dead end for the virus. The human victim may clear the virus via an immune response, presenting an evolutionary dead end for the virus. The only way for the virus to survive is to become infectious and transmissible in humans. Once a virus can be transmitted from person to person, it can engulf an entire population if the route of transmission is effective enough. Some routes of transmission are better than others. A virus that requires sexual contact, such as HIV, will be transmitted slowly and the ultimate extent of the spread is limited because careful people can avoid having sex with infected people. A virus that can be spread through aerosol particles, on the other hand, can spread rapidly and allow one infected individual to infect many others in a short period of time, perhaps at a public event.

Once a virus has infected many humans, scientists will characteristically investigate its origins. Therefore, we can evaluate the strength of the evidence favoring the zoonotic theory and the forensic evidence left behind by the virus:

(1)      The original viral reservoir should still exist. It is highly unlikely that a virus that was endemic in a bat population will die out at the exact moment it spreads to humans. Even though the bat version of the virus won’t be identical to the human version of the virus, the two will be closely related because mutations, which are random genetic “errors,” happen at a measured and often predictable rate. It may be difficult to uncover the endemic bat virus if that virus is seasonal or if it that epidemic waned. However,  bats in that population will usually have biological evidence of being infected, for example blood-borne antibodies.

(2)     There will usually be evidence of some early human victims becoming sick and/or dying from a mysterious disease. This typically shows up in medical records and oral histories, and frequently in blood databases where evidence of an ancestral version of the virus is available for examination long afterwards. The genealogical record of the virus can often be mapped as it mutates to optimize itself for human infection and transmission.

(3)     The geographic record of the virus can be understood and mapped. The first human exposures to the virus will likely occur close to the caves that house the bat population. For example, it would be unlikely for the first human victims of a new virus that originated in Arizona to show up in New York City. It might seem that a person could become infected at a bat cave in Arizona and then take a flight to New York. And yet the person infected from the bat in Arizona is unlikely to become infected with a version of the virus that has evolved enough to become transmissible among humans. More frequently, that person traveling to New York would simply get sick and either die or clear the virus via an immune response. Usually, the virus would need multiple bat-human infections near the bat caves and enough time for it to evolve sufficiently within that human population before a person could fly to New York with a more optimized version of the virus and infect others there or on the way. The virus could also travel from Arizona to New York City over time by sequentially infecting individuals a little closer to New York until it ultimately reaches NYC. Of course, this approach depends on a distribution of susceptible individuals to allow a chain of infection between Arizona and NYC.

(4)     Sometimes an intermediate species is involved. For example, perhaps bats infected mice and then the mice infected humans. While the difference between the original bat virus and the eventual human virus will be greater, due to an additional evolutionary step in the middle, everything that has been described above will still apply.

Let’s consider the strength of the evidence for a zoonotic origin of SARS2, looking at each aspect of the evidence that might be able to illuminate the linkages described above.

Natural reservoirs of SARS2

                  Past forensic successes

·      Viruses that come from the wild often leave ample evidence. “The intermediary host species of SARS1 was identified within four months of the epidemic’s outbreak, and the host of MERS within nine months.”

                  Past forensic failures

·      The original SARS virus [SARS1] has not been found in bats. “Believe it or not, although we all believe SARS in 2003 was caused by a bat virus, we still cannot find SARS-CoV in bats in the last 17 years.” However, as described above, the intermediary species has been found.

·      “To date, a complete Ebola virus has never been isolated from an animal in the region where the world’s largest outbreak occurred between 2013 and 2016.”

                  Current forensic evidence

·      SARS2 shares some similarities to coronaviruses found in pangolins and bats.

·      No natural reservoirs of SARS2 have been found.

·      The Chinese government tested 80,000 animals (from 209 species, including wild, domesticated, and market animals) and didn’t find a single animal infected with SARS2, or even an animal infected with a close relative of SARS2.

·      Many still claim that the SARS2 virus came from the Wuhan “wet market,” even though there’s not a single piece of evidence for this theory and the Chinese government has long ago conceded that the market was not involved.

Evidence of prior infection by SARS2

·      According to an article in Science, “It is highly probable that SARS-CoV-2 was circulating in Hubei province at low levels in early-November 2019 and possibly as early as October 2019, but not earlier.”

·      There is no evidence of infection from earlier versions of SARS2. SARS2 appears to have appeared on the planet in one sudden event and it came optimally designed to be infectious to and transmissible among humans. There are no early samples of SARS2-like viruses in blood banks or blood databases, as explained below.

·      According to Richard Muller and Steven Quay, “[b]ased on experience with SARS-1 in 2003 and MERS in 2012, we know that many people are infected by a host animal long before a coronavirus mutates to the point where it can jump from human to human. An extensive data set from late 2019—more than 9,000 hospital samples—is available of people exhibiting flulike (thus Covid-like) symptoms in China’s Hubei and Shaanxi provinces before the epidemic started. Based on SARS-1 and MERS, the natural zoonotic theory predicts 100 to 400 Covid infections would be found in those samples. The lab-leak hypothesis, of course, predicts zero. If the novel coronavirus were engineered by scientists pursuing gain-of-function research, there would be no instances of community infection until it escaped from the laboratory. The World Health Organization investigation analyzed those stored samples and found zero pre-pandemic infections. This is powerful evidence favoring the lab-leak theory.”

Geographical evidence of SARS2

·      The earliest surge in hospital activity related to COVID-19 happened at the hospitals closest to the Wuhan Institute of Virology (WIV).

·      China’s two most advanced biological research laboratories, both in Wuhan, the Wuhan Institute of Virology and the Wuhan Center for Disease Control and Prevention, were involved with collecting live bats from caves across China to study viruses. This can explain how the virus could have traveled 1,000 miles from a cave in southern China to Wuhan.

·      The closest viruses identified, in the bats in southern China, are not geographically close to Wuhan. Not only are the caves in question far from Wuhan, but also the topology, flora, fauna, and weather are very different between the two places. It would have been unlikely that the bats themselves traveled from the southern caves to Wuhan.

·      Spillovers of diseases from bats to humans are rare.

·      If the virus infected a researcher at the caves in southern China and then that researcher traveled back to Wuhan, why is there no record of anyone becoming sick during the trip back?

Evidence of an intermediate species

·      If SARS2 had jumped directly from bats to humans, without an intermediary species, then SARS2, which hasn’t changed much since it first appeared, should still be able to infect bars. It isn’t. “Tested bat species are poorly infected by SARS2 and they are therefore unlikely to be the direct source for human infection,” according to one group of scientists.

·      Early in the pandemic, a so-called “wet market,” where different animals were sold, was implicated in transmitting the virus from animals to humans. Some researchers found that “more than 47,000 wild [live] animals had been sold in Wuhan in the two and a half years before the first confirmed cluster of Covid-19 cases.” However, the two species that are most likely to transmit SARS2 to humans, bats and pangolins, were not sold at the Wuhan wet market: “Notably, no pangolin or bat species were among these animals for sale.” Chinese researchers have since reported that the first cases had no contact with the market. The Chinese government has acknowledged this fact.

Genealogy of SARS2

·      SARS2’s closest relatives are bat and pangolin coronaviruses.

·      The closest viruses identified, in bats in China, are not very close genetically. No known natural coronaviruses have the key “furin cleavage site” that SARS2 uses so effectively to attack human lung cells.

·      Viruses can recombine and share genetic material. However, only viruses that are from the same general family can do this. A “National Institutes of Health database shows no FCS [furin cleavage site] in more than 1,200 viruses that can exchange with SARS-CoV-2.”

·      The furin cleavage site on SARS2 makes it especially able to infect humans. “[O]f all known SARS-related beta-coronaviruses, only SARS2 possesses a furin cleavage site.”

The evolutionary optimization of SARS2

·      SARS1 and MERS, which both emerged from the wild, showed a history of optimization in which they got better at infecting humans. SARS2 showed no such history; SARS2 didn’t change much “until a minor variation occurred many months later in England.” The original SARS2 virus was determined to be “99.5% optimized for human infection.”

·      According to Claudia Hoyen, at University Hospitals and Cleveland Clinic, “Omicron is the second most contagious virus on the planet,” after measles.

·      The Wuhan Institute of Virology had a bat coronavirus, RaTG13, that was found in a cave that was 96% the same as SARS2. While that encouraged some scientists looking for a zoonotic source, 96% isn’t very close. It is estimated that, if RaTG13 and SARS2 are indeed relatives, their evolutionary path diverged about 40 years ago.

·      According to Robert Redfield, former director for the Centers for Disease Control and Prevention, “I do not believe this [SARS-CoV-2] somehow came from a bat to a human. And at that moment in time, the virus came to the human, became one of the most infectious viruses that we know in humanity for human to human transmission. Normally, when a pathogen goes from a zoonotic to human, it takes a while for it to figure out how to become more and more efficient." Redfield was arguing that a virus in a wild animal may infect a human, but for that virus to be able to jump from human to human, that virus needs other features that often take some time to develop. SARS2 came “out of the box” with the ability to jump from human to human. This ability to be superbly good at transmission is exceptionally unlikely to be present in a virus that, up to that point, jumped from animal to animal and had had no human contact.

·      “By the time SARS-CoV-2 was first detected in late 2019, it was already pre-adapted to human transmission to an extent similar to late epidemic SARS-CoV [SARS-CoV-1].” This was highly unusual. Normally viruses that leap from wild animals into humans need time to adapt to their new hosts. For SARS1, this process of adaptation to humans is well documented and each step has been studied.

·      “SARS-CoV-2 emerged in Wuhan with a furin cleavage site never before seen in a sarbecovirus. It needs to be emphasized that, to the best of our global knowledge, “sarbecovirus with furin cleavage site” did not exist in nature before 2020, but it did exist in a grant proposal to make something not found in nature, and that biological novelty was proposed to be made in Wuhan.”

The assessments of experts

·      “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, They continued by saying, “scientists ‘overwhelmingly conclude that this coronavirus originated in wildlife.’” We have since learned that this paper was initiated and organized by Peter Daszak, president of the EcoHealth Alliance, whose organization funded coronavirus research at WIV. Even with such an egregious conflict of interest, the authors concluded, “We declare no competing interests.” Further, at least five of the authors have since distanced themselves from the Lancet letter. One later said, “I’m convinced that what happened is that the virus was brought to a lab, they started to work with it, and some sloppy individual brought it out.” Another said, there is too much coincidence and “it is more likely that it came out of that lab.”

·      Another group of scientists, led by Kristian G. Andersen of the Scripps Research Institute, claimed, “Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.” Apparently, they based this claim on the abilities of older gene manipulation techniques. However, newer techniques don’t leave the telltale signs Andersen et al. were referring to.

·      According to science writer Nicholas Wade, “[p]roponents of natural emergence have a rather harder story to tell... No one has found the bat population that was the source of SARS-CoV-2, if indeed it ever infected bats. No intermediate host has presented itself, despite an intensive search by Chinese authorities that included the testing of 80,000 animals. There is no evidence of the virus making multiple independent jumps from its intermediate host to people, as both the SARS1 and MERS viruses did. There is no evidence from hospital surveillance records of the epidemic gathering strength in the population as the virus evolved. There is no explanation of why a natural epidemic should break out in Wuhan and nowhere else. There is no good explanation of how the virus acquired its furin cleavage site, which no other SARS-related beta-coronavirus possesses, nor why the site is composed of human-preferred codons [genetic structures]. The natural emergence theory battles a bristling array of implausibilities.”

·      Viruses that come from the wild leave ample evidence. “The intermediary host species of SARS1 was identified within four months of the epidemic’s outbreak, and the host of MERS within nine months.” After intensive search, neither an original animal population nor an intermediary host for SARS2 have been found. Further, there’s no evidence that SARS2 was circulating in Wuhan prior to the first cases being identified. “Natural emergence remained a conjecture which, however plausible to begin with, had gained not a shred of supporting evidence in over a year [now 4.5 years].”

·      “What virus comes out of a bat cave and infects humans by the millions? It’s not biologically plausible,” said Robert Redfield and Marc Siegel.

·      Some U.S. government agencies, such as the CIA, have concluded that the COVID-19 pandemic most likely arose from a zoonotic origin. However, a whistleblower has claimed that of the seven-member CIA team, only the senior member believed the zoonotic explanation. “The whistleblower further contends that to come to the eventual public determination of uncertainty, the other six members were given a significant monetary incentive to change their positions.”

·      The U.S. Energy Department and FBI have concluded that the COVID-19 pandemic most likely arose from a lab leak.

·      “The odds of the alignment between a grant in 2018 [the EcoHealth Alliance DEFUSE grant] and the unnatural, unprecedented genome of a virus in 2019 are nearly zero under a natural origin.”

·      According to ecologist and evolutionary biologist Alex Washburne, “Papers claiming a zoonotic origin have all been debunked.”