Coronavirus news & views

Part 3: Gain-Of-Function Research At The Wuhan Lab—Are The Chinese Hiding Something About The Lab?

This is a re-post of a blog, but with additional material. I added new information about the Chinese government response to the first SARS epidemic. You can find that section two-thirds of the way through the post under the headline in bold "The Chinese have done this before:"

“In a time of deceit telling the truth is a revolutionary act.”
― George Orwell

Yeah, I know, I said this would be a two-blog series about the research at the Wuhan Labs. But a comment a reader made on my second blog post made me think that I should make a third post to briefly address the apparent secrecy and lack of cooperation from the Chinese government regarding the research at the Wuhan Institute of Virology (WIV).

The Chinese have failed to cooperate to help us find the origin of the SARS-CoV-2 virus that caused COVID. They have denied access to WIV lab records or research personnel beyond what was posted on their coronavirus database as I mentioned in my prior blog post. This secrecy and lack of cooperation began in early January 2020 immediately after Chinese officials realized that they had a coronavirus superspreader event at the Wuhan wet market as I described almost three years ago in these pages.

This apparent secrecy on the part of the Chinese has led many people to jump to the conclusion that the Chinese are hiding something sinister—sinister like they secretly created SARS-CoV-2 and accidentally released it and don’t want the world to find out. But, as I have posted several times in these pages, most recently here, there is precious little evidence that supports the notion that the virus came out of a lab. On the other hand, there are several pieces of consistent, but still circumstantial evidence for its natural origin. However, that conclusion is not definitive and could change with new evidence. Hence, we cannot say with certainty that we know where the virus came from. But, remember, it took 14 years and a LOT of work to learn the origin of the virus that caused the first SARS outbreak; it took much longer to discover the source of HIV, and we still do not know where the Ebola virus came from. These things are very hard to learn and take time to figure out.

However, I don’t believe that the best explanation for the Chinese lack of cooperation is that they are hiding something sinister from the world because it seems very unlikely that the virus was man-made. After all, we have several examples of novel coronaviruses popping up in animals and humans, and all have had natural origins. And as I described in my prior post in this series, it is next to impossible that the virus was accidentally released from the Wuhan labs since they really did not work live viruses at all. I think one of two other explanations for Chinese intransigence is more plausible.

The least likely alternative explanation is that WIV lab safety protocols for handling dangerous pathogens were substandard and for the Chinese to allow access to lab records would reveal to the world how careless they were. Perhaps they were concerned about their world image and did not want to be embarrassed. It could deleteriously affect their R&D collaborations with other countries. But, we already had an idea that their safety protocols were not up to Western standards so this would not have been a terribly shocking revelation. That is why I don’t think this is the most likely explanation for the lack of cooperation and transparency.

More likely, however, I think the lack of cooperation probably reflects the general and significant deterioration in science and technology collaboration between China and the US that has been going on for five years. This was the topic of a long article in the Wall Street Journal just a few days ago. In fact, US-China science and tech cooperation has gotten so bad in recent years that US lawmakers are pushing to let a long-standing agreement between the two counties to cooperate broadly on science and technology lapse. It was originally signed in 1979 and renewed every five years since, but will expire this month if not renewed as several lawmakers are pushing.

A once highly productive cooperative science and technology agreement between the US and China seems to have begun falling apart in 2018, before COVID, according to the WSJ article. That is when the US DoJ launched its China Initiative to ferret out Chinese economic espionage. Over time the program increasingly focused on interactions between US universities and Chinese institutions. NIH also launched hundreds of investigations into ties between US science and China. While all these investigations largely failed to turn up criminal conduct, they understandably put a major damper on further cooperation between China and the US. They also led to an exodus of Chinese scientists from American labs. Given all that, it is not surprising that Chinese officials are not opening the doors and books of the Wuhan labs to us.

Thus, this lack of cooperation regarding access to the Wuhan labs is happening as cooperation is seriously deteriorating across the scientific spectrum, not just at the Wuhan labs.

The Chinese have done this before: The Communist Chinese government also has a long history of invoking repressive secrecy in order to prevent itself from looking bad. For example, they also clammed up during the first SARS outbreak back in November 2002 and it threw the country into its worst political crisis since the 1989 Tienanmen Square uprising. The government’s first response to the emerging epidemic was to hide the outbreak from its people, and even from its own public health officers. Despite the cloak of a news blackout, SARS spread throughout the country, reaching Beijing that March (viruses don’t read the newspapers!). But doctors do, and the cloak worked on them. Because of all the secrecy, they were caught by surprise by the sudden and prolific appearance of a new disease, and only learned what was going on via surreptitious text messaging.

In April, WHO officials finally were allowed into the country to inspect Beijing hospitals in order to assess what was going on, but sick patients were shuttled out of the hospitals in ambulances to different hospitals or checked into hotels to hide them from inspectors. Because Beijing tried to hide all this from the world, the epidemic, which might have been limited to that city, found its way into 32 countries around the world (viruses are very slippery). Fortunately, those other countries were not as furtive and were able to nip their infections in the bud with public health measures such as quarantines, contact tracings and isolation, and public closings.

SARS allowed the world to see and compare how repressive and self-sensitive China vs other world countries handle a deadly contagion. China was afraid of losing face and tried to hide its problem from public exposure. However, this backfired and showed China to be a repressive country that was willing to risk the safety of its people and the world in order to avoid accountability for the first SARS outbreak.

Therefore, it is not terribly surprising that the Chinese government again is using repressive means to avoid being put into a position of accountability for the second SARS outbreak.

The bottom line is that to think the Chinese are hiding something nefarious and conspiratorial at the WIV is pure speculation and is backed by no evidence at all. So far. There are alternative explanations for the lack of cooperation by the Chinese that are more feasible and reasonable to believe at this point. New information could change this assessment of course, but evidence that the Chinese are hiding something is lacking. Too bad they won't let us confirm that.

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Part 2: Gain-Of-Function Research At The Wuhan Lab—What Exactly Was The Wuhan Lab Doing With Coronaviruses?

“I’m just a soul whose intentions are good; Oh Lord, please don’t let me be misunderstood.”  —The Animals

In the first part of this two-part blog series, I described what gain-of-function research entails in order to set the stage for this blog post which describes the coronavirus research that went on in the Wuhan labs. So, was it dangerous and risky? Did it likely lead to the release of SARS-CoV-2 that caused COVID? Let me try to clarify all that now.

Coronavirus research at the Wuhan lab: After the first SARS epidemic in China in 2002, the Wuhan Institute of Virology (WIV) had established itself as a world class coronavirus research lab. It was from their diligent work that the world learned that the first SARS virus came from a horseshoe bat via other animals such as civets and raccoon dogs. That was the result of years of arduous research trudging through bat guano muck in hundreds of caves throughout China to collect samples from thousands of bats. They reported their finding 14 years after SARS appeared and shortly after another strange, lethal flu popped up in the Middle East that was soon attributed to yet another bat-borne coronavirus that came via camel intermediate hosts—MERS.

Before these two coronaviruses that jumped from animals to cause significant disease in humans, the viruses were only known to cause mild human maladies; basically, the common cold. Therefore, when it was learned that the deadly SARS and MERS diseases were caused by coronaviruses, it rattled the cages of health experts around the world. This was brand new!

Hence, even before COVID struck, bat-born coronaviruses were hot on the radars of infectious disease nerds and public health worrywarts. The WIV, as one of the world’s preeminent labs for identifying novel coronaviruses was given international funds to continue their efforts to identify and catalog bat coronaviruses. As they did years earlier when they identified the origin of the SARS virus in horseshoe bats, WIV scientists traveled to far-flung Chinese caves to collect bat guano and biological samples (blood, saliva, fecal) from captured bats. The samples were brought back to the lab in Wuhan for analysis.

Since it is exceedingly difficult and potentially very dangerous to grow wild viruses from such samples (failure is the norm even when many viruses are present in the samples) the lab resorted to their previous tried and true methods of searching the samples for viral genome sequences. They found a LOT of new ones!

Their first and primary order of business in this research was the very mundane task to sequence and catalog all the different coronaviruses they found. They then colligated these genomes into trees of different virus families and posted all the data in a vast database for world scientists to use. They were coronavirus genealogists.

The database is an enormously useful research tool for scientists around the world studying the origins and evolution of coronaviruses in animals and humans. (Coronaviruses also cause significant animal disease, so they also are of great agricultural interest around the world.)

The Wuhan lab also was charged with predicting which of the new virus sequences they found might pose future health threats to humans.

This is where all the controversy begins.

Remember that the Wuhan scientists actually did not have these viruses on hand, just their genome sequences. So, without the actual virus, how could they evaluate the ability of new coronaviruses to infect humans? To do this WIV scientist, Zhengli Shi, used a genetic engineering technique first published in 2015 by Univ. of North Carolina Scientist Ralph Baric to study coronaviruses from their genome sequences (she was a collaborator on Baric’s 2015 paper, so was quite familiar with the approach). It was a technique that also was in use at the time by several labs around the world. It is notable that NIH funded this coronavirus research conducted by Baric at UNC well before COVID appeared and didn’t consider it to be GoF research then.

Using Baric’s genetic engineering technique, Shi’s lab at the WIV used as a tool, a benign coronavirus that they could grow in the lab that was only distantly related to the first SARS virus, but was not known to cause human disease. Its genome sequence was not at all related to SARS-CoV-2 that caused COVID, and which had not yet appeared.

Shi’s lab removed the spike protein gene sequence from the genome of this benign lab virus tool and methodically replaced it with spike protein sequences from each new virus they sequenced. They then grew the lab virus tool carrying the new spike protein and tested its ability to infect human cells in tissue culture.

It is the spike protein that determines whether a coronavirus can infect human cells. Therefore, if the chimeric lab virus carrying the new spike gene infected human cells, it would indicate that the virus the spike protein sequence came from was a likely human pathogen and that virus sequence was then listed on the database as a potential human risk. However, if the chimeric test virus failed to infect the human tissue culture cells, that meant that the spike protein from the new virus genome would not support infection of human cells and the new virus sequence was not categorized as a concern for human infection.

This is how newly identified coronavirus sequences were categorized as potential human health threats without ever having to grow or isolate each virus itself.

In other words, this test simply expressed the spike protein of each novel coronavirus on the backbone of the safe lab virus genome in order to see if it could infect human cells. This completely negated the need to grow and handle the potentially much more dangerous wild-type virus.

It is important to notice that this strategy eliminated all risk of a lab leak of any dangerous virus since it was not necessary to grow or handle potentially dangerous wild-type viruses using this technique.

Is this gain-of-function-research? Strictly speaking, no. Remember, this sort of coronavirus engineering research had been done years earlier in Baric’s UNC lab, and was being done in other labs around the world, and it was never regarded as GoF research then by NIH.

NIH considers GoF research on pathogens to be research that either: 1) increases the pathogenicity of a microbe (that is, makes its disease worse), 2) improves its transmissibility or its ability to infect hosts, or 3) alters the host range of a pathogen. Therefore, in the WIV experiments to assess the ability of novel virus genome sequences to infect human cells, the chimeric test viruses that simply expressed new spike proteins on a laboratory virus backbone either retained the ability of the original lab virus to infect human cells, or they lost the ability to infect human cells.

Therefore, the chimeric viruses gained no new function that was tested. They either retained or lost the ability to infect human cells. The experiments were not at all designed to give the test virus any new functions. Furthermore, these experiments could not have led to the development of SARS-CoV-2 that caused the COVID pandemic, even by accident, since the laboratory test virus used to create the chimeric viruses in the experiments was not at all related to the SARS-CoV-2 virus.

There is a devil in the details: But. Notice that one of the the NIH definitions of GoF research is research that alters a pathogen’s host range. For example, take a flu virus that only passes between birds; avian flu. If you make changes in its genome so that the birds can also pass it to humans that mutation alters its host range and is a GoF change.

In the WIV lab, viruses with new spike protein gene sequences were only tested for their ability to infect human cells in a petri dish. The ability of these chimeric viruses with new spike proteins to also infect other animals was not tested. Theoretically, the chimeric test viruses could feasibly also infect, say a water buffalo, or a wart hog, or some other animal that the original lab virus might not have been able to. That would be a technical gain-of-function. But, that begs the question; in such an experiment, how would you know whether or not the host range of the chimeric virus had changed until you possibly had tested its ability to infect every known animal? A logistical impossibility.

Therefore, based on this theoretical point, it cannot be definitely stated that the experiments were not GoF experiments. In fact, chances are pretty good that some of the novel spike protein sequences attached to the lab test virus in fact altered its host range and, thus, the experiments would technically be GoF research.

Bottom line: Technically speaking, therefore, these experiments carried out at the WIV probably could be called GoF experiments. By a lawyer. Not by a scientist. That picks the proverbial nit and splits a very fine frog hair, to mix metaphors. The same research had been done ten years earlier in Ralph Baric’s UNC lab and was not considered GoF then. What is important is that the research at the UNC or the WIV never set out to create viruses with enhanced virulence, transmissibility, or altered host range. That was never the intent. The aim of the WIV research was solely to predict the human risk posed by novel coronaviruses without actually having to directly work with the potentially dangerous pathogens. Actually working with the dangerous viruses would have posed a very real risk.

Bottom, bottom line: The research conducted at the WIV was the most safe and responsible way to identify new coronaviruses that could potentially pose future human health risks. It is to the detriment of human health that this research has come under heavy criticism and that such future research has been hampered by criticism from people who fail to understand what the research is about and have, therefore, demonized it and want to prevent it.

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Gain-Of-Function Research At The Wuhan Lab: Part 1

“Mater artium necessitas"

 A lot of news print, band width, and fevered comment has been bandied about regarding “Gain-of-Function” (GoF) coronavirus research at the Wuhan Institute of Virology (WIV). It usually has been done so with an unspoken insinuation that something was very wrong or careless with that research. People are left with visions that GoF research involves mad scientists creating Franken-viruses and that that perhaps caused the pandemic. Certainly when scientists begin fiddling around with the genomes of nasty pathogens bad things can possibly happen. In fact, bad things can occur simply by growing and culturing dangerous microbes—accidents can happen.

Did we in fact get the SARS-CoV-2 virus, which caused COVID, from scientists in Wuhan playing Russian (or Chinese) roulette with coronaviruses and their genes? Did irresponsible or careless research lead to an intentional, or, more likely, an accidental event that unleashed a virus that devastated the world for two-plus years?

These questions and rumors have floated around long enough that people now believe the premise--say it often enough and people will believe. But, hardly anyone knows what research was being done in the WIV labs. Few people even know what GoF research entails because no one has taken the time to describe it.

Let me give a shot at clarifying all this. I will do this in a two-part blog. The first blog post, which you are now reading, will explain what gain-of-function research is. It will surprise readers to learn that humans have been doing it for thousands of years and that it is going on all around us all the time. In the second blog that I will post in a few days, I will delve into what exactly was going on in the Wuhan labs and try to explain the research so non-scientists can grasp what they were doing.

My aim in these two blog posts is to give readers the ability to parse through the rhetoric and understand the reality. Here we go.

GoF research backstory: Basically, gain-of-function simply is when a mutation in an organism--animal, plant, or microbe--changes some function in it. That is what drives evolution, That is how bacteria acquire resistance to antibiotics, as an example. Microbes and cells do it all on their own via happenstance mutation followed by natural selection in an environment that favors the mutation.

Humans have been purposefully doing GoF research ever since we began farming and raising animals. We just never called it gain-of-function research. The minute we began selectively breeding animals and crops to produce better products, we were doing GoF research. Selective breeding first identifies animals or crops with desired traits that arose by chance genetic mutation and then selectively chooses the animals with those traits to breed. That fixes the genetic mutation and its desired trait into the genome of the plant or animal. Gain-of-function.

Then came recombinant DNA technology in the 1970s. We began cloning and mutating genes in the lab, and  inserting the lab-altered genes into animals and plants, thereby speeding up the long, arduous process of selective breeding. We do this all the time now in making genetically engineered crops and animals. It also is how we are now beginning to genetically treat certain diseases in plants, animals and humans. This is all gain-of-function technology. It is happening all around us all the time.

GoF technology also is a very common research tool used in almost every cell biology and microbiology lab in the world. For example, at one point in my own research lab, we studied how a change in a normal human gene might cause what was an untreatable leukemia. We took a cloned version of the normal human gene, mutated it, then put it in a virus to shuttle the mutated gene into bone marrow cells growing in tissue culture. The gene we altered caused normal bone marrow cells to become leukemia. That is how we proved the alteration in the normal human gene was sufficient to cause leukemia. From all the research that followed in many labs using that GoF leukemia model, the leukemia is now mostly curable. That illustrates the value of GoF lab research. It is done all the time in countless labs around the world to understand how genes and cells work.

What about GoF research on dangerous pathogens? Just like in the cell biology experiments above, GoF experiments on pathogens can tell us how certain viruses and bacteria become dangerous. As just one example, in the early 2000s, flu researchers at the University of Wisconsin did experiments to learn what made the 1918 Spanish flu so much more devastating than other seasonal flus. They systematically replaced genes from a mundane cloned laboratory flu strain with genes from the 1918 strain that had been cloned from stored patient samples dating from 1918. The goal was to learn which of the 1918 flu genes increased the transmission and/or virulence of the lab strain. Gain-of-function.

Bottom line: Similar GoF studies are undertaken all the time in many labs around the world that work with many other dangerous pathogens. Information from such studies has been enormously valuable for understanding how dangerous pathogens become dangerous and cause disease, and how to protect us from them. These studies have been conducted without causing major problems for the world.

Sure, GoF research can be used for nefarious purposes. A malevolent actor can use it to make terrible pathogens like anthrax resistant to all antibiotics and turn it into a weapon. It would be simple to do; a college microbiology student in a college lab could do it if he got his hands on the bacteria (which can be easily grown from soil). Ebola is a terribly lethal virus, but it is very difficult to transfer between people,  which has limited it to controllable regional epidemics. If a mad scientist manipulated its genome to turn it into an airborne pathogen, it could wreak world-wide havoc, probably worse than COVID or the Spanish flu. And so on.

Therefore GoF research on pathogens can be both beneficial and dangerous. This is called “dual purpose research.” Scientists and government officials are very aware of this dual threat from such research and sometimes science publications purposefully withhold critical data that a bad actor could misuse.

Needless to say, this is a very controversial tightrope science walks when dealing with dual purpose science, such as GoF research on dangerous pathogens. Science is entirely based on disclosing what it discovers, but it can sometimes discover things that, while enormously useful for humans and the world, can also be enormously destructive. What do you do then?

Have you seen the movie, Oppenheimer?

Now that we have established grounding in what gain-of-function research entails, the next blog post, will describe the coronavirus research that went on in the Wuhan Institute of Virology. Hopefully, these blogs will give you a clearer understanding of whether or not the lab was responsible for the virus that caused the COVID pandemic.