Controversial New Study Suggests SARS-CoV-2 Shows Signs of Genetic Engineering

Two recent publications,wet marketThese markets sell live animals, often raised in poor conditions, and are known places where new pathogens jump from animals to humans. Early cases of covid-19 were concentrated in this market. Data on the first days of the epidemic are missing as this portrait may be inaccurate.

The opposite idea of ​​a leak from a laboratory is not implausible. Accidental spills of viruses from laboratories are more common than many realize. The 1977 flu epidemic is believed to have started this way. But an escaped virus does not mean an engineered virus. The virology lab is also full of raw varieties.

Research like the one done in Wuhan provides many ways the virus can leak out. Alternatively, someone may have been infected with a wild-harvested virus in the laboratory itself. However, some argue that sars-cov-2 may have been assembled in the lab from other viruses that were already on hand and then leaked.

Into this battle comes analysis from an unlikely source. Alex Washburn is a mathematical biologist who runs Selva, a small microbiome science startup based in New York. He is an outsider, but has worked in virological modeling in the past as a researcher at Montana State University. For this study, Dr. Washburn collaborated with two of his other scientists. One is Antonius VanDongen, associate professor of pharmacology at Duke University in North Carolina. The other, Valentin Bruttel, is a molecular immunologist at the University of Würzburg, Germany. Dr. Washburn and Dr. Vandongen have been active advocates of research into the Laboliek theory.

The trio base their claims on a new method of detecting plausibly lab-engineered viruses. Their analysis, published Oct. 20 on the preprint server bioRxiv, has several genomic features they say appear when the virus is spliced ​​together by some genetic engineering. By examining how many of these putative stitching sites there are in sars-cov-2 and how these fragments are relatively short, we can determine how similar the virus is to other viruses found in nature. is about to be evaluated.

They start with the assumption that creating a genome as long as sars-cov-2 would mean gluing together short fragments of pre-existing viruses. They say the ideal arrangement for coronavirus genome assembly is to use five to eight fragments, all less than 8,000 characters long. It will be created. These are molecular scissors that cut genomic material at specific sequences of genetic letters. If there is no such restriction site in the proper place in the genome, researchers usually create new restriction sites of their own.

They argue that the distribution of restriction sites for two common restriction enzymes, BsaI and BsmBI, is “abnormal” in the sars-cov-2 genome. And the length of the longest fragment is much shorter than expected. We took 70 different coronavirus genomes (not including sars-cov-2) and cut them into fragments with 214 commonly used restriction enzymes. We were able to calculate the expected length of the fragment if cut.

The paper, which has not been formally peer-reviewed as a preprint and has not been approved for publication in the journal, will be removed in the next few days. Because this is how science works. However, the initial reaction was largely divided. Francois Balloux, professor of computational systems biology at University College London, said the results were intriguing. “In contrast to many of my colleagues, I have not been able to identify a fatal flaw in reasoning and methodology. The distribution of BsaI/BsmBI restriction sites in sars-cov-2 is atypical,” Dr. Balloux said. However, Edward Holmes, an evolutionary biologist and virologist at the University of Sydney, said the features identified in the paper are natural and not found in other bat viruses. If someone were to design a virus, they would undoubtedly introduce some new virus.”There are various technical reasons why this is complete nonsense.”

Sylvestre Marillonnet, an expert in synthetic biology at the Leibniz Institute for Plant Biochemistry in Germany, notes that the number and distribution of these restriction sites does not appear to be completely random, and that the number of silent mutations found at these sites suggests that sars is – cov-2 may have been manipulated. (Silent mutations are the result of engineers wanting to make changes to the protein encoded in the sequence of genetic material without changing it.) But Marillonet said there are also counter-arguments to this hypothesis. One of them is a small length of one of the six pieces and “doesn’t seem logical to me”.

Another point Dr. Marillonnet points out is that the restriction sites do not have to be present in the final sequence. “Why would people introduce and leave sites in their genomes when they don’t need to?” he wondered. However, Professor Justin Kinney of the Cold Spring Harbor Laboratory in New York said that researchers had previously created coronaviruses and had such sites in their genomes. I left it… but warned that this paper needs rigorous peer review.

Erik van Nimwegen of the University of Basel says that the information is sparse and “it’s hard to draw anything definitive out of it”. He adds, “We can’t completely rule out what a set of sites like this can have.” It happened by chance ”. The authors of this paper acknowledge this to be the case. Christian Andersen, a professor of immunology and microbiology at the Scripps Research Institute in La Jolla, California, described the pattern on Twitter as “random noise.”

The conclusion that sars-cov-2 was designed will be hotly contested. China denies that the virus originated in a Chinese laboratory and has called for an investigation into whether it may have originated in the United States. Dr. Washburn and his colleagues say their predictions are testable. If the progenitor genome of sars-cov-2 is found in the wild with the same or intermediate restriction sites, it is more likely that this pattern evolved by chance.

The widely held conclusion that the virus was genetically engineered would have serious political and scientific repercussions. It sheds new light on the actions of the Chinese government in the early days of the epidemic, particularly its reluctance to share epidemiological data at the time. Questions also arise about what, when, and by whom was known about. As of now, this is the first draft of science and should be treated as such. But the inspector has already done his job.

Editor’s Note: A preprint by Bruttel, Washburne, and VanDongen, “Endonuclease Fingerprints Indicate Synthetic Origin of sars-cov-2,” can be found at the following URL: bioRxiv.