A trio of scientists has come up with a controversial theory about the origins of the COVID-19 virus, suggesting it was genetically engineered – which if found to be true, would have profound ramifications, both political and scientific.
While there has been mixed reaction to their as yet not peer-reviewed pre-print (posted on bioRXiv), the idea is not implausible.
The Economist reports that a string of about 30 000 genetic letters was all that it took to start the nightmare of COVID-19, the death toll from which is likely to be more than 20m.
Exactly how this story began has been hotly contested. Many think its emergence was a zoonosis – a spillover, as so many new pathogens are, from wild animals, for it resembles a group of coronaviruses found in bats. Others have pointed to the enthusiastic coronavirus engineering happening in laboratories worldwide, particularly in Wuhan, where the virus was first identified.
In February 2021, scientists assembled by the World Health Organisation (WHO) to visit Wuhan said a laboratory leak was unlikely, a conclusion subsequently challenged by the WHO’s boss, who said eliminating this theory was premature.
Two recent publications have bolstered the case for a natural origin connected to a “wet market” in Wuhan, where live animals are sold, often housed in poor conditions, known to be sites where new pathogens jump from animal to human.
Early cases of COVID-19 clustered around this market. But critics say there are so many missing data about the epidemic’s initial days that this portrait may be inaccurate.
The opposing idea of a leak from a laboratory is not implausible. The accidental escape of viruses from labs is more common than realised. The flu epidemic of 1977 is thought to have started this way. But an escaped virus does not imply an engineered virus. Virology labs are also full of the un-engineered sort.
Research like that done in Wuhan offers numerous ways for a virus to leak out. A researcher on a field trip could have picked it up in the wild, returned to Wuhan, and spread it to others there. Or someone might have been infected with a wild-collected virus in the laboratory itself. But some argue that SARS-CoV-2 could have been assembled in a laboratory from other viruses already to hand, and then leaked out.
Into this fray comes an analysis from an unlikely source. Alex Washburne is a mathematical biologist who runs Selva, a small startup in microbiome science in New York. He is an outsider, although he has worked in the past on virological modelling as a researcher at Montana State University.
For this study, Washburne collaborated with two other scientists: Antonius VanDongen, an associate professor of pharmacology at Duke University, in North Carolina, and Valentin Bruttel, a molecular immunologist at the University of Würzburg, Germany. Washburne and VanDongen have been active proponents of an investigation into the lab-leak theory.
The trio base their claim on a novel method of detecting plausibly lab-engineered viruses. Their analysis, published on preprint server bioRxiv, suggests SARS-CoV-2 has some genomic features they say would appear if the virus had been stitched together by some form of genetic engineering. By examining how many of these putative stitching sites SARS-CoV-2 has, and how relatively short these pieces are, they attempt to assess how much the virus resembles others found in nature.
They start from the presumption that creating a genome as long as that of SARS-CoV-2 would mean combining shorter fragments of existing viruses together. For a coronavirus genome assembly they say an ideal arrangement would be to use between five and eight fragments, all under 8 000 letters long. Such fragments are created using restriction enzymes. These are molecular scissors that cut genomic material at particular sequences of genetic letters. If a genome does not have such restriction sites in opportune places, researchers typically create new ones of their own.
They argue that the distribution of restriction sites for two popular restriction enzymes – BsaI and BsmBI – are “anomalous” in the SARS-CoV-2 genome. And the length of the longest fragment is far shorter than would be expected. They determined this by taking 70 disparate coronavirus genomes (not including SARS-CoV-2) and cutting them into pieces with 214 commonly used restriction enzymes.
From the resulting collection, they were able to work out the expected lengths of fragments when coronaviruses are cut into varying numbers of pieces.
The paper, which as a preprint has received no formal peer review, and which has not been accepted for publication in a journal, will be dissected in the coming days, as it should be, for this is how science works. Early reactions, though, have been deeply divided.
Francois Balloux, a professor of computational systems biology at University College London, found the results intriguing. “Contrary to many of my colleagues, I couldn’t identify any fatal flaw in the reasoning and methodology. The distribution of BsaI/BsmBI restriction sites in SARS-CoV-2 is atypical.”
Balloux said these needed to be assessed in good faith.
But Edward Holmes, an evolutionary biologist and virologist at the University of Sydney, said every one of the features identified by the paper was natural and already found in other bat viruses. If someone were engineering a virus, they would undoubtedly introduce some new ones. He added: “There are a whole range of technical reasons why this is complete nonsense.”
Sylvestre Marillonnet, an expert in synthetic biology at the Leibniz Institute for Plant Biochemistry, in Germany, agreed that the number and distribution of these restriction sites did not look quite random, and that the number of silent mutations found in these sites did suggest that SARS-CoV-2 might have been engineered. (Silent mutations are a result of engineers wanting to make changes in a sequence of genetic material without making changes to the proteins encoded by that sequence.) But he also said there are arguments against this hypothesis. One is the tiny length of one of the six fragments, something that “does not seem logical to me”.
The other point Marillonnet makes is that it is not necessary for the restriction sites to have been present in the final sequence. “Why would people introduce and leave sites in the genome when it is not needed?” he wondered.
Previous arguments supporting the possibility of a lab leak have stressed that a manipulated virus would not need to have any such tell-tales.
However, Justin Kinney, a professor at Cold Spring Harbor Laboratory, in New York, said that researchers have created coronaviruses before and left such sites in the genome. He said the genetic signature indicates a virus ready for further experiments and that it needed to be taken seriously, but warned the paper needed rigorous peer review.
Erik van Nimwegen, from the University of Basel, says there are only small scraps of information and it is “hard to pull anything definitive out of that”. He adds: “One cannot really exclude at all that such a constellation of sites may have occurred by chance.” The authors of the paper concede this is the case.
Kristian Andersen, a professor of immunology and microbiology, at the Scripps Research Institute in La Jolla, California, described the pattern, on Twitter, as “random noise”.
Any conclusion that SARS-CoV-2 was engineered will be hotly contested. China denies the virus came from a Chinese lab, and has asked for investigations into whether it may have originated in America. Washburne and his colleagues say their predictions are testable. If a progenitor genome to SARS-CoV-2 is found in the wild with restriction sites that are the same, or intermediate, it would raise the chances that this pattern evolved by chance.
Any widely supported conclusion that the virus was genetically engineered would have profound ramifications, both political and scientific. It would put in a new light the behaviour of the Chinese Government in the early days of the outbreak, particularly its reluctance to share epidemiological data from those days. It would also raise questions about what was known, when, and by whom about the presumably accidental escape of an engineered virus.
For now, this is a first draft of science, and needs to be treated as such. But the scrutineers are already at work.
Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2
Valentin Bruttel, Alex Washburne, Antonius VanDongen.
Posted on bioRXiv on 20 October 2022
To prevent future pandemics, it is important that we understand whether SARS-CoV-2 spilled over directly from animals to people, or indirectly in a laboratory accident. The genome of SARS-COV-2 contains a peculiar pattern of unique restriction endonuclease recognition sites allowing efficient dis- and re-assembly of the viral genome characteristic of synthetic viruses. Here, we report the likelihood of observing such a pattern in coronaviruses with no history of bioengineering. We find that SARS-CoV-2 is an anomaly, more likely a product of synthetic genome assembly than natural evolution. The restriction map of SARS-CoV-2 is consistent with many previously reported synthetic coronavirus genomes, meets all the criteria required for an efficient reverse genetic system, differs from closest relatives by a significantly higher rate of synonymous mutations in these synthetic-looking recognitions sites, and has a synthetic fingerprint unlikely to have evolved from its close relatives. We report a high likelihood that SARS-CoV-2 may have originated as an infectious clone assembled in vitro.
To construct synthetic variants of natural coronaviruses in the lab, researchers often use a method called in vitro genome assembly. This method utilises special enzymes called restriction enzymes to generate DNA building blocks that then can be “stitched” together in the correct order of the viral genome. To make a virus in the lab, researchers usually engineer the viral genome to add and remove stitching sites, called restriction sites. The ways researchers modify these sites can serve as fingerprints of in vitro genome assembly.
We found that SARS-CoV has the restriction site fingerprint typical for synthetic viruses. The synthetic fingerprint of SARS-CoV-2 is anomalous in wild coronaviruses, and common in lab-assembled viruses. The types of mutations (synonymous or silent mutations) that differentiate the restriction sites in SARS-CoV-2 are characteristic of engineering, and the concentration of these silent mutations in the restriction sites is extremely unlikely to have arisen by random evolution. Both the restriction site fingerprint and the pattern of mutations generating them are extremely unlikely in wild coronaviruses and nearly universal in synthetic viruses. Our findings strongly suggest a synthetic origin of SARS-CoV2.
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