The origins of Covid

Wuhan Institute of Virology, image Wikimedia Commons.

 

This post was originally published in French here.

On June 3^rd, an opinion piece was published in the New York Times with the title: “Why the Pandemic Probably Started in a Lab, in 5 Key Points”. The author of the article, Alina Chan, is a postdoctoral researcher at MIT and Harvard. She also co-signed in 2021, with journalist Matt Ridley, a book promoting the thesis that the coronavirus pandemic resulted from an accident, a laboratory leak at the Wuhan Institute of Virology, in China (lab leak theory). This opinion piece received a lot of attention, and praise as well as condemnation.

The team of This Week in Virology (TWiV) has notably returned to this question in a special program dissecting the evidence and discussing the state of knowledge. Let's say it without nuance, the TWiV team gives no credit to Chan's theses.

Remember that there are essentially two theories to explain the origins of the pandemic: on the one hand, a zoonosis (the passage of the virus from an animal host to a human host), with a bat as the original animal host, taking place in the Huanan Seafood Wholesale Market, which also sold live wild animals. On the other hand, accidental contamination of researchers by the virus during their work, within the Wuhan Institute of Virology (WIV), contamination which would not have been contained and would have spread throughout the population. Let's put the cards on the table right away. At this time, the exact origin of the pandemic is not known, and it may never be known. Nevertheless, there is a preponderance of scientific evidence pointing to zoonosis, and so we must treat this as the most likely hypothesis, with the caveat that new information could change the situation.

Many articles (scientific or otherwise) have been published on this subject. I have found particularly useful, honest, and well-considered the summary of evidence written by American researchers James Alwine, Lynn Enquist, and three editors of scientific journals published by the American Microbiological Society: Arturo Casadevall (mBio), Felicia Goodrum (Journal of Virology) and Michael Imperiale (mSphere). This article, published at the end of March 2023, immediately warns us that a definitive determination of the origins of covid may remain impossible. One reason is that all the evidence is circumstantial (I provide a partial inventory a little further down).

Alwine et al. (2023): "The best existing scientific evidence supports a direct zoonotic origin. As new evidence continues to emerge from scientific studies or other investigations, our understanding of the origin of SARS-CoV-2 will continue to evolve. Nevertheless, it is possible that its origin may never be known with certainty."

But what could be the definitive evidence in favor of one or the other hypothesis? For the zoonotic origin, this would involve, for example, identifying an animal sold on the Huanan market that carries SARS-CoV-2. (After all, this was the case for the first SARS epidemic, in 2002-2003.) It is almost mission impossible, since the Huanan market was closed and the animals were exterminated (cremated or otherwise), shortly after the start of the epidemic, for obvious public health reasons. Concerning the laboratory leak, it would be a question of determining that the Wuhan Institute of Virology was studying SARS-CoV-2 before the pandemic, and that some of its researchers were the first people contaminated by covid. But as Alwine et al. explain, for this we would need proof from the archives of the institute of virology, but none exists, and the Chinese government has denied this possibility. Unfortunately, Chinese transparency has not been exemplary here, fueling doubts.

So, we will have to do with indirect evidence. Concerning the lab leak theory, there are in fact several sub-theories, some suggesting that SARS-CoV-2 was modified in the laboratory by genetic engineering, or even created from scratch. But as Alwine et al. note, there is no evidence to support this sub-theory, which is not even considered credible by U.S. intelligence. Genetic engineering leaves recognizable signatures in DNA, but no signatures are visible in the genome of SARS-CoV-2. Jointly, or shortly after the publication of the article by Alwine et al. in 2023, new elements have come to redistribute some cards.

The first element is the discovery in March 2023 of DNA sequences in samples from the Huanan market, sequences which support the origin by zoonosis. We owe this discovery to Florence Débarre, research director at CNRS, who came across the sequences by chance while browsing a virology database for her research. Until this date, in samples taken from the Huanan market no one had identified any co-occurrence of SARS-CoV-2 with non-human animal DNA. Thanks to Débarre's discovery, there is now evidence of the co-occurrence of covid with raccoon dogs and civets, animals sold on the market. Note that this is not definitive proof that these animals were infected with covid, but it is still a big step in that direction.

Strangely, immediately after this discovery, the Chinese researchers who had posted the sequences in the database requested their removal. It's not entirely clear why, but it doesn't help a tarnished image when it comes to transparent data sharing... But soon after, in early April 2023, Chinese researchers published the results including these new animal data. This publication was welcomed, but still left open questions regarding the analysis of this data. However, the existence of these sequences contributes to further weakening the lab leak thesis, in particular by showing that samples collected in areas of the market housing live animals had a greater chance of testing positive for the coronavirus.

The second element is the publication in June 2023 of an article published on their Substack ‘Public’ site by journalists Michael Schellenberger, Matt Taibbi and Alex Gutentag. The article claimed that sources within the US government had confirmed that the first Covid patients were researchers at the Wuhan Institute of Virology (if proven, this would, as explained above, be definitive evidence in favor of the laboratory leak). But the government sources cited remain anonymous... It must be said that these revelations do not seem so extravagant, when we know that certain official American bodies, such as a Senate committee or the Department of Energy, have publicly qualified the lab leak hypothesis as more likely than that of zoonosis, although with a low level of certainty.

The authors of the Public article had suggested that infections within the WIV would be confirmed in previously classified documents that were to be made public in June 2023 by US intelligence services. To the dismay of the journalists, the declassified documents do not confirm that, or even say the opposite: if certain WIV researchers were indeed ill at the end of 2019, covid was not diagnosed, and some of the symptoms listed are not compatible with covid.

Evidence in favor of zoonosis and against the laboratory leak, ranked in order of importance according to my own assessment:

1. All the historical examples of pandemics and epidemics that we know of have originated from a zoonosis, none from a laboratory leak. This is the case for SARS-CoV (the first), MERS, Ebola, coronaviruses causing colds, HIV, and many others.

2. Sequencing analysis of the first cases of covid in Wuhan showed that two genetically distinct lineages of SARS were involved very early in the pandemic. The existence of two distinct lineages is consistent with zoonosis but unlikely in a laboratory leak.

3. Analysis of the SARS-CoV-2 genome reveals no signature of laboratory passage or modifications by genetic engineering. The experience amassed by covid researchers shows that the virus, once cultivated in the laboratory, systematically undergoes characteristic changes. These changes are not present in SARS-CoV-2.

4. Epidemiological data showed that among the first documented cases of infection, half were associated with the Huanan market, supporting the idea that the market is the hotbed of the pandemic.

5. Covid DNA was identified in samples from the Huanan market which also contained DNA from non-human animals (raccoon dogs).

6. In the databases of the Wuhan Institute of Virology, no sequences corresponding to SARS-CoV-2 have been identified to date. Certainly the sequences could have been deliberately hidden, but it is difficult to imagine that no trace remained somewhere.

The facts therefore clearly speak in favor of zoonosis. And yet, I must admit, a slight doubt remains in my head. The reason ? The coincidence that the pandemic began in Wuhan, the city which is home to the virology institute known worldwide for its studies of coronaviruses. I have not yet heard this coincidence explained in a completely satisfactory manner, and unfortunately the article by Alwine et al. don't mention it. It was this extraordinary coincidence that for example journalist and talk show host Jon Stewart noted, which led to him being scolded. It is regrettable that the mere mention of the possibility of a laboratory leak arouses such outcry, because a priori it is not entirely far-fetched.

But perhaps this coincidence is less surprising if we take a closer look at it? This is what Brianne Barker does in the TWiV episode already mentioned (the discussion of the coincidence begins at 14'). Barker notes that it is not at all surprising that the pandemic emerged in a large city like Wuhan (7th largest city in the country with more than ten million inhabitants), because the first detections of a virus require good medical infrastructure and experts capable of realizing that this respiratory disease is not common and that it must be sequenced. Some commentators have also pointed out that the majority of major Chinese cities have a laboratory working on coronaviruses. These points are valid: Wuhan is a large city with the infrastructure necessary to detect a new viral outbreak. However, we risk overlooking the fact that there are many large cities in China (the twenty-three largest cities have at least five million inhabitants), and especially the fact that the WIV is not just one lab among many, but THE internationally recognized laboratory for the study of coronaviruses in China. The coincidence is therefore possible, and perhaps less surprising than it seems, but it remains, at least for me, a thorn in the side.

 

The quiet revolution of Oswald Avery

 

Avery in his lab, 1948. Source: Rockefeller Archive

Imagine a world where we build skyscrapers more than 300 meters high, where we know of nuclear fission, where the first digital computers have been designed, where the first color television has been produced, but a world where we do not even know what stuff genes are made of! [1] This is the world of the early 1940s, before Oswald Avery achieved his ‘quiet revolution’ – to borrow an expression from the biologist and author Matthew Cobb  on the subject.

I knew of Avery and his experiments – as do all microbiologists – from the textbooks and microbiology class: working on pneumococci, Avery showed in 1944 that the active compound in bacterial transformation was DNA. In that he was providing an explanation to the illustrious findings of Griffith in the late 1920s, who demonstrated that, in infected mice, avirulent mutants of Streptococcus pneumoniae could be effectively transformed into the deadly kind via an unknown process involving contact with heat-killed virulent cells (again, textbook knowledge).

Alas, textbooks usually fail to convey much excitement about such groundbreaking episodes of human inquiry. To be fair, this is of course not the textbooks’ mission. This said, I can’t remember that my microbiology class fared much better in that task – often the amount of material to be covered in class does not allow for much dwelling into the historical context.

So I was thrilled to (re)discover the story of Avery in Cobb’s excellent book, Life's Greatest Secret: The Race to Crack the Genetic Code (2015), which explores in depth the work that led to the resolution of the DNA structure and later to the deciphering of the genetic code. Cobb spends a whole chapter on Avery’s work and life, and brings to light many fascinating aspects.

The career of Oswald T. Avery (1877-1955) centered in the study of pneumonia bacteria and the immunological response they elicit. We have to remember that, before antibiotics became widespread, pneumonia was among the deadliest infectious diseases in the world [sadly we should also stress that millions of people still die of pneumonia every year, although this number is decreasing]. Avery had joined the Rockefeller Institute Hospital in New York in 1913 in order to pursue this research, with the goal of developing therapies against pneumococcus. He stayed at Rockefeller thirty years, until his retirement in 1943.

Avery was interested in why certain pneumococci are more virulent than others. In the 1920s, he found that virulent strains typically embed themselves within a large polysaccharidic capsule that protects them from the human body’s defenses. In 1928, in London, Fred Griffith found that pneumonia bacteria devoid of capsule could be transformed into virulent ones producing capsules, simply by putting them into contact with dead capsule-producing bacteria. But what was the process? Griffith thought incorrectly that the avirulent bacteria were using the capsules of the dead virulent bacteria as a template to make new ones.

From the early 1930s, Avery worked to isolate what they called ‘the transforming principle’ from cultures of pneumococci, and to identify its chemical nature, with the help of the Canadian scientist Colin MacLeod. They managed this feat by using a messy, dangerous procedure with a commercial kitchen cream separator that leaked and produced tons of aerosols – I kid you not. They also found that calcium chloride precipitated nucleic acids into a white, gooey substance (if you have done DNA extraction you know how that looks like). The white precipitate, which contained nucleic acids and polysaccharides, was very potent in transforming bacteria, as demonstrated by MacLeod, who had to leave the lab in 1941.

 

Avery lab around 1920. Source: Rockefeller Archive

At that time another young researcher joined the Avery lab. His name was Maclyn McCarthy, and he made a decisive contribution by showing that the polysaccharides could be enzymatically digested in the precipitate without it losing its transforming ability. It became increasingly clear that most of the transforming precipitate was made of DNA. What is more, some enzymes active on DNA were able to block transformation.

This should have been the nail in the coffin of that story, however, resistance to grant DNA that extraordinary role was strong: DNA shows no variation whatsoever, how could it be the transforming principle? Proteins are varied and very low amounts show activity – surely they are the stuff responsible for transformation. And you can never be sure that your precipitate is totally protein-free!

So while all the evidence pointed at DNA as the agent of transformation, many were still convinced that it could not be – a powerful expectation bias that complicated the acceptance of Avery’s work. He and his team continued to work tirelessly to strengthen the case for DNA. Avery noted, in a letter to his brother:

‘We have isolated highly purified substance of which as little as 0.02 of a microgram is active in inducing transformation… this represents a dilution of 1 part in a hundred million – potent stuff that – and highly specific. This does not leave much room for impurities – but the evidence is not good enough yet.’

In 1943, Avery proposed the connection between DNA and genes. He had not solved the problem of protein impurities – after all, you cannot prove a negative – but at that time the attitude towards DNA was changing, weakening the opposition to its role. Avery started to write down all their results, a pile of evidence from different types of experiments. He wrote in that paper:

‘The inducing substance has been likened to a gene, and the capsular antigen which is produced in response to it has been regarded as a gene product.’

The paper, authored by Avery, McLoed and McCarthy, was published in February 1944 in the Journal of Experimental Medicine. Its initial reception by the scientific community was good and, in the next couple of years, Avery and McCarthy continued to publish, adding more evidence to their case. Avery received the Gold Medal of the New York Academy of Medicine. Erwin Chargaff, inspired by Avery, started to study DNA composition. In 1945, André Boivin at the Institut Pasteur demonstrated transformation in E. coli, supporting Avery’s findings on the importance of DNA.

After 30 years of hard work, the quiet revolution was very much underway. Avery received many awards for his work on pneumococcus, albeit never the Nobel Prize... 

Reference: Cobb, Matthew. (2015) Life's Greatest Secret: The Race to Crack the Genetic Code.   Basic Books, 464 pages.

 [1] In 1933, Thomas Hunt Morgan noted, during his Nobel Prize acceptance lecture: ‘There is no consensus of opinion amongst geneticists as to what the genes are – whether they are real or purely fictitious.’