EDITOR’S NOTE: This is the fifth article in our ‘Gain-of-Function Hall of Shame’ series profiling key players in gain-of-function research.

She’s known as China’s “Bat Woman.” Shi Zhengli is a virus hunter and microbiologist, and director of the Center for Emerging Infectious Diseases at the Chinese Academy of Sciences’ Wuhan Institute of Virology (WIV).

She also plays a central role in a whodunnit that may ultimately prove impossible to solve.

Shi’s work involves collecting bat viruses and using techniques of genetic engineering and synthetic biology to enable these viruses to infect human beings. 

Since the Biological Weapons Convention took effect, what scientists like Shi do has been called “gain-of-function” research or “dual-use research of concern” (DURC).

In other words, Shi, and other scientists like her, are in the business of weaponizing viruses by genetically engineering or otherwise altering them to make them more lethal, and more easily transmitted, to humans.

Did Shi have a hand in creating the SARS-CoV-2 virus causing the current COVID-19 pandemic?

The National Institutes of Health is investigating. 

On July 8, Michael Lauer, NIH deputy director for extramural research, sent a letter, later viewed by the Wall Street Journal and Science Magazine in which he asked:

• For an inspection of the WIV by an outside team that would examine the facility’s lab and records “with specific attention to addressing the question of whether WIV staff had SARS-CoV-2 in their possession prior to December 2019.”

• For a sample of the new coronavirus that Shi and her colleagues at WIV used to isolate its genetic sequence during the first week of January.

• Why WIV “failed to note that the RaTG13 virus, the bat-derived coronavirus in its collection with greatest similarity to SARS-CoV-2, was actually isolated from an abandoned mine where three men died in 2012 with an illness remarkably similar to Covid-19.”

• To “explain the apparent disappearance” of Huang Yanling, a scientist who worked in the Wuhan lab and who is suspected to be patient zero, the first to be diagnosed with the disease.

• To explain evidence indicating that WIV may have been shut down temporarily last fall, including “diminished cell-phone traffic in October 2019, and the evidence that there may have been roadblocks surrounding the facility from October 14-19, 2019.”

• To provide a response to the safety concerns described in a 2018 State Department cable. Between January and March 2018, U.S. science diplomats repeatedly met with Shi at WIV. The cable on the visits “warned about safety and management weaknesses at the WIV lab” and “also warns that the lab’s work on bat coronaviruses and their potential human transmission represented a risk of a new SARS-like pandemic.”

The letter with these demands didn’t go to Shi or WIV, it went to EcoHealth Alliance, a U.S.-based non-profit funded by the U.S. government, including the U.S. military, to support scientists working in 30 countries. EcoHealth Alliance is listed as a funding source on some of Shi’s most controversial papers. And EcoHealth Alliance scientists, including its president Peter Daszak, often co-author, with Shi, published papers.

Shi’s most infamous EcoHealth Alliance-funded paper is, “A SARS-Like Cluster of Circulating Bat Coronaviruses Shows Potential for Human Emergence.” In this controversial gain-of-function research collaboration with U.S. scientist Ralph Baric of the University of North Carolina at Chapel Hill, Shi and Baric used genetic engineering and synthetic biology to weaponize a bat coronavirus, maximizing its potential human infectivity.

Shi’s funding for this study came through a USAID Emerging Pandemic Threats-PREDICT grant to EcoHealth Alliance—but the record for this grant appears to have been scrubbed from the U.S. government’s database.

EcoHealth Alliance was a PREDICT partner during the 2009-2014 funding cycle, but there is no record of a USAID grant to EcoHealth Alliance for this time period among the $100.9 million in grants it has received from the U.S. government since 2003. 

Shi’s contribution to the work she did with Baric was the “RsSHC014-CoV Sequence That Was Isolated from Chinese Horseshoe Bats.”

Where did RsSHC014 come from?

Shi Zhengli and Peter Daszak announced their discovery of RsSHC014 in their 2013 paper, “Isolation and Characterization of a Bat SARS-Like Coronavirus that Uses the ACE2 Receptor,” and stated that it was found during “a 12-month longitudinal survey (April 2011–September 2012) of SL-CoVs in a colony of Rhinolophus sinicus at a single location in Kunming, Yunnan Province, China.”

What they don’t mention in their paper is that, in Kunming during this same period (April and May of 2012), six men were hospitalized after removing bat feces from a cave, and that the WIV  was involved in their treatment, testing the patients for Serum IgM, the first antibody the body makes when it fights a new infection.

These details come from the abstract of a master’s thesis that was arranged to be translated this year by scientists Jonathan Latham and Alison Wilson, “The Analysis of 6 Patients With Severe Pneumonia Caused by Unknown Viruses”: 

There were 6 patients with unknown pneumonia caused by unknown viruses sent to Dep. Emergency, the first affiliated hospital of Kunming medical university in April, May, 2012. They were all workers at the same mine where had a lot of bats and bats feces. After the treatment, 3 patients died and three patients survived.

According to the appraisal of the Kunming institute of zoology, Chinese academy of sciences, the type of the bat in mine where 6 patients worked is Rhinolophus sinicus, from which was extracted SARS-like-CoV when Scientists in China were in the process of looking for SARS pathogen.

Latham and Wilson have been investigating the origin of COVID-19 and have come to the conclusion that “a lab origin has at least as much circumstantial evidence to support it as does any natural zoonotic origin theory.” 

Summarizing the facts laid out in the master’s thesis, Latham and Wilson conclude that:

• Samples were taken from patients and sent to WIV.

• The thymus, an immune organ that could have contained large quantities of virus, was removed from one patient. 

• Any viruses recoverable from the miners would likely have been viewed by WIV  researchers as a unique natural experiment in human passaging offering unprecedented and otherwise-impossible-to-obtain insights into how bat coronaviruses can adapt to humans.

• The logical course of such research would be to sequence viral RNA extracted directly from unfrozen tissue or blood samples and/or to generate live infectious clones for which it would be useful (if not imperative) to amplify the virus by placing it in human cell culture. Either technique could have led to accidental infection of a lab researcher.

Latham and Wilson don’t connect the master’s thesis on the men who were hospitalized in Kunming with the paper Shi and Daszak published about the bat coronaviruses they collected in Kunming at the same time, but it seems obvious to do so.

Who sent the miners into the cave to collect guano? Could it have been Shi and Daszak? They were in Kunming collecting bat viruses at the time.

Shi Zhengli told her version of the story about the miners to Scientific American: 

“[In 2012] Shi’s team had been called in to investigate the virus profile of a mine shaft in Yunnan’s mountainous Mojiang County—famous for its fermented Pu’er tea—where six miners suffered from pneumonia like diseases and two died. After sampling the cave for a year, the researchers discovered a diverse group of coronaviruses in six bat species. “In many cases, multiple viral strains had infected a single animal, turning it into a flying factory for new viruses.

“‘The mine shaft stunk like hell,’ says Shi, who, like her colleagues, went in wearing a protective mask and clothing. ‘Bat guano, covered in fungus, littered the cave.’ Although the fungus turned out to be the pathogen that had sickened the miners, she says it would have been only a matter of time before they caught the coronaviruses if the mine had not been promptly shut.”

This inconsistency between Shi’s story and the master’s thesis is hard to reconcile. Considering WIV’s involvement in the treatment of the miners, how could Shi have not known that the miners died of a SARS-like virus, and not a fungal infection, as she told Scientific American? 

The virus Shi says she found in Mojiang was RaTG13. In a paper published on February 3, 2020, Shi announced that RaTG13 was 96 percent identical to the genomic sequence of the novel coronavirus, eventually named SARS-CoV-2. 

Here’s another troubling inconsistency: According to the Genome Sequence Archive, RaTG13 was “was extracted from bronchoalveolar lavage fluid,” which suggests that the virus was taken from a sick person, but RaTG13 is supposedly an RNA sequence taken from a bat fecal swab.

Daszak has his own version of the story of the discovery of RaTG13. Daszak claims they took the virus back to the Wuhan Institute of Virology and left it in a freezer for seven years untouched. But, as Boston Magazine reported, this claim was discovered to be untrue by “scientist turned detective” Alina Chan, who fact-checked him on Twitter:

Even though that virus had killed three miners, Daszak said it wasn’t considered a priority to study at the time. “We were looking for SARS-related viruses, and this one was 20 percent different. We thought it was interesting, but not high risk. So we didn’t do anything about it and put it in the freezer,” he told a reporter from Wired. It was only in 2020, he maintained, that they started looking into it once they realized its similarity to COVID-19. But Chan pointed to an online database showing that the WIV had been genetically sequencing the mine virus in 2017 and 2018, analyzing it in a way they had done in the past with other viruses in preparation for running experiments with them. Diplomatic yet deadpan, she wrote, “I think Daszak was misinformed.” 

Why the lies? Why won’t Shi and Daszak admit that WIV took samples from the hospitalized miners for diagnosis and study, knowing that the patients died from a SARS-like bat coronavirus? Why do they deny that the bat coronavirus most like SARS-CoV-2 was collected in the mine where the workers were exposed? Why don’t they acknowledge that this is a virus that was actively sequenced, analyzed and experimented on, not one that had been forgotten in a freezer for seven years?

Are they afraid to admit that the first SARS-like coronaviruses that use the ACE2 receptor was discovered in humans in a hospital, not bats in a cave?

Do they fear the public’s reaction to the idea of gain-of-function researchers taking advantage of the miners’ gruesome deaths to harvest a pathogen uniquely primed to infect human cells?

Shi and Daszak wouldn’t be the first bioweapons experts to do this. As the Washington Post reported:  

“The Soviets had a keen interest in the Marburg virus in the 1980s and managed to develop an especially lethal strain after an accident at the Vector Institute, their germ warfare center in Siberia. The chief scientist there, Nikolai Ustinov, accidentally injected his thumb with the virus, which was intended for a guinea pig he was holding.

“Ustinov suffered a devastating death, but the Soviets managed to profit from the mistake by harvesting Ustinov’s organs for fresh samples of the virus. These proved to be even more powerful than the original strain.”

The scientists of Japan’s secret Unit 731 biological weapons program used this technique deliberately, performing “passaging” experiments on Chinese subjects during World War II. According to Nicholson Baker’s book, “Baseless”: 

“Dr. Tabei Kanau said he injected a man with shigella dysentery. Three days later the man got diarrhea, and on the fourth day he hanged himself. Tabei also fed prisoners a solution of sugar water and paratyphoid. The disease was very contagious, he discovered when he placed one sick patient in a room with three uninfected ones. In an effort to find the most virulent strain of typhoid fever―V, VW, or W―Tabai fed thirty-six Manchurians tainted milk and sugar water. Tabei then heightened the virulence of the most lethal strain, VW, by passing it through three men in succession.”

Who funded the Kunming virus hunt?

In addition to funding from China and Australia, the Kunming virus hunt reported in “Isolation and Characterization of a Bat SARS-Like Coronavirus that Uses the ACE2 Receptor,” was supported by:

• National Institute of Allergy and Infectious Diseases (NIAID) award number R01AI079231, a $2.6-million grant to EcoHealth Alliance for “Risk of Viral Emergence from Bats,” (2008-2013).

• NIH and National Science Foundation (NSF) “Ecology and Evolution of Infectious Diseases” $3.7-million award from the NIH Fogarty International Center (R01TW005869) to EcoHealth Alliance for “The Ecology, Emergence and Pandemic Potential of Nipah Virus in Bangladesh,” (2002-2013).

• A $300,000 award from the NIH Fogarty International Center supported by International Influenza Funds from the Office of the Secretary of the Department of Health and Human Services (R56TW009502) to EcoHealth Alliance for “Comparative Spillover Dynamics of Avian Influenza in Endemic Countries,” (2012-2017).

• United States Agency for International Development (USAID) Emerging Pandemic Threats PREDICT, amount unknown. 

Who funded Shi’s virus hunting in Mojiang?

Shi’s paper, “Coexistence of Multiple Coronaviruses in Several Bat Colonies in an Abandoned Mineshaft,” was written by a team of scientists who were all Chinese nationals working at Chinese institutions. Nevertheless, in addition to funding from the Chinese government, the authors acknowledged support from the U.S. National Institute of Allergies and Infectious Disease (R01AI110964), a $3.7-million grant to EcoHealth Alliance for “Understanding the Risk of Bat Coronavirus Emergence,” (2014-2025).

Shi’s Pentagon funding

Shi Zhengli and her collaborators are also funded by the U.S. military. Peter Daszak’s EcoHealth Alliance currently receives more money from the Department of Defense’s Defense Threat Reduction Agency (DTRA) for Scientific Research Combatting Weapons of Mass Destruction than any other military contractor—$15 million (25.575 percent) of the $60.2 million dispersed in the last 6 months.

A Google Scholar search produced two papers Shi has published that lists DTRA as a funder.

To see how the first paper, “Comparative Analysis of Bat Genomes Provides Insight into the Evolution of Flight and Immunity,” is relevant to biological weaponry, it helps to understand the military’s interest in bat immunity. 

As Boston University microbiologist Thomas Kepler explained to the Washington Post in 2018, the bat’s unique approach to viral infection explains why viruses that transfer from bats to humans are so severe. 

This was the subject of a paper, “The Egyptian Rousette Genome Reveals Unexpected Features of Bat Antiviral Immunity,” that he published with military scientists and DTRA funding.

“A virus that has co-evolved with the bat’s antiviral system is completely out of its element in the human,” Kepler said. “That’s why it is so deadly — the human immune system is overwhelmed by the inflammatory response.”

The bat immune system responds very differently from ours to viral infection. Instead of attacking and killing an infected cell, which leads to a cascade of inflammatory responses, the bat immune system can starve the virus by turning down cellular metabolism.

The bat origin of SARS-CoV-2 may explain the cytokine storms that are hastening some COVID-19 deaths. According to WebMD:

“Certain kinds of cytokines trigger cell death. When you have many cells doing this at the same time, a lot of tissue can die. In COVID-19, that tissue is mostly in the lung. As the tissue breaks down, the walls of the lungs’ tiny air sacs become leaky and fill with fluid, causing pneumonia and starving the blood of oxygen.”

Kepler says the military is using its experiments on bat immunity to “develop drugs that dampen down inflammation and arrest the virus by depriving it of what it needs to grow rather than trying to kill it outright.” But, it clearly has another objective, as well: to make viruses more deadly by “passaging” them through bats. 

Without stricter enforcement of the Biological Weapons Convention, it is impossible to prevent so-called “defensive” programs from producing biological weapons, especially considering the stealth and plausible deniability with which biological weapons can be used, and how vulnerable labs are to accidents and “missing” agents.

The regulatory challenges associated with trying to prevent defensive biological weapons research from being used offensively were highlighted recently in India’s reaction to Shi’s other DTRA funded paper, “Filovirus-reactive antibodies in humans and bats in Northeast India imply zoonotic spillover,” published in 2019.

The study alarmed the public by finding “the presence of filovirus (e.g. ebolavirus, marburgvirus and dianlovirus) reactive antibodies in both human (e.g. bat hunters) and bat populations in Northeast India, a region with no historical record of Ebola virus disease.”

The Hindu reported that foreign entities operating the study should have been required to seek special permission to access live samples of bats and human bat hunters, but they did not do so. The Indian Council of Medical Research created a five-member committee to investigate.

In addition to military funding through DTRA, Shi’s paper was co-authored by two U.S. military scientists, Christopher C. Broder and Eric D. Laing of the Uniformed Services University of the Health Sciences, Department of Microbiology and Immunology.

China’s People’s Liberation Army controls the Wuhan Institute of Virology

The Wuhan Institute of Virology is China’s only biosafety level 4 lab. While it has always been under the control of the Chinese government, since January 26, 2020, it has been under the command of the People’s Liberation Army, specifically its top biological-weapons specialist, a major general named Chen Wei.

On FoxNews on September 15, 2020, Li-Meng Yan, a Chinese virologist who worked at the university of Hong Kong’s World Health Organization (WHO) reference lab, told Tucker Carlson that, based on the genetic fingerprint of SARS-CoV-2, she believed it was created―and intentionally released―by the Chinese government (you can watch the video and read a transcript of the interview here):

Tucker Carlson: “You’re saying that the Chinese government manufactured this virus, if I’m hearing you correctly. That’s what you’re saying?”

Li-Meng Yan: “Yes, exactly. Based on the virus genome, it’s basically like our fingerprint. So you can see the very unusual characters in their genome which clearly, based on the other evidence they left during the modification, we can see finally this is exactly the one [that] come from their own special bat coronavirus and it then targets humans.”

Tucker Carlson: “To make such statements, do you believe the Chinese government released this intentionally, on purpose. Did they do this?”

Li-Meng Yan: “Yes, of course it’s intentionally.”

Li-Meng Yan went beyond the available evidence when she claimed that the Chinese government released this virus intentionally. This threatens her credibility, as does her association with Steve Bannon. 

But even her detractors point to her “prolific and solid publication record on infectious diseases.”

Her paper on the lab origins of SARS-CoV-2, “Unusual Features of the SARS-CoV-2 Genome Suggesting Sophisticated Laboratory Modification Rather Than Natural Evolution and Delineation of Its Probable Synthetic Route,” is legitimate. 

However, it can only be seen as one of the many theories on the possible lab origins of SARS-CoV-2. (Mercola.com recently published a useful summary, “More Experts Point to SARS-CoV-2 Being Created in a Lab.”)

One thing every theory has in common, including Li-Meng Yan’s, is a reliance on Shi Zhengli’s work. That makes her claim that it was the Chinese government that released this virus problematic.

Shi Zhengli may work at a Chinese lab that is now controlled by the People’s Liberation Army, but throughout her career, her work has been funded by the U.S. government, including the U.S. military, with which she has actively collaborated.

China says the U.S. released the virus in October at the World Military Games in Wuhan. The U.S. is investigating whether WIV was the source of the virus.

Shi’s central role in this whodunnit makes it nearly impossible to figure out.

When you have a Chinese scientist weaponizing coronaviruses with Pentagon funding at a lab controlled by the People’s Liberation Army, and a virus escapes, which country is to blame?

Alexis Baden-Mayer is political director for the Organic Consumers Association (OCA). To keep up with OCA’s news and alerts, sign up here.