COVID ORIGINSCoronavirus Origins: The Debate Flares Up, but the Evidence Remains Weak

By Francois Balloux

Published 29 October 2022

A recent, not-yet-peer-reviewed, study claims to have identified possibly unusual sequence patterns in the SARS-CoV-2 genome which may indicate that the virus was genetically modified in a lab. The study has been poorly received by most experts in the field. The evidence reported in the study is neither conclusive nor final, and the findings may turn out to be a fluke, or generated by a flaw in the method, as the study’s authors concede. This study and its reception remind us that it would be unwise to suppress a discussion of the lab leak theory by arguing that such a discussion has fueled conspiracy theories. A confirmation of an accidental lab leak – if such a leak has indeed occurred – would be less damaging than a confirmation of a lab leak whose evidence has been aggressively suppressed.

Nearly three years since SARS-CoV-2 first emerged, we’re still not certain where the virus behind COVID-19 came from.

The location of the initial outbreak close to the Wuhan Institute of Virology drew suspicion that it may have been a lab leak. But scientists largely came out in favor of a natural spillover from bats to humans, through an intermediate animal host, at the Huanan seafood market located a few kilometers away. To date, though, no immediate ancestor of SARS-CoV-2 has been found in bats nor in any other animal that was on sale at the market.

A recent preprint (a study yet to be peer-reviewed) claims to have identified possibly unusual sequence patterns in the SARS-CoV-2 genome. These patterns may indicate the virus was genetically modified in a lab.

It should be emphasized that any realistic lab origin scenario would point to an accidental escape, and not to any nefarious intent. Viruses have no application as bioweapons in the modern world. They’re difficult to produce in large quantities and to deploy. They take days to be effective, and if capable of human-to-human transmission, they’re likely to spread to unintended populations, including friendly forces.

The preprint has been poorly received by most experts in the field, with many reacting to it on social media.

This mixed reception is largely unsurprising. Scientists and members of the wider public often hold strong opinions about the origin of SARS-CoV-2, despite all the available evidence remaining weak and circumstantial. In the absence of strong facts, opinions are bound to be largely based on emotions and group affiliation, particularly when the stakes are considered to be so high.

More About the Science
The genomes of all organisms, including SARS-CoV-2, are formed of long stretches of four different nucleotides (A, T, G and C). These are the building blocks of RNA and DNA.

Large viral genomes, such as those of coronaviruses, can be cut into smaller pieces, or fragments, that can be mixed and matched to study the effect of different genes and mutations. Scientists might do this, for example, to understand which genes or mutations could increase the risk of a virus spilling over to humans.

The standard way to cut viral genomes into smaller pieces is with restriction enzymes, sometimes called molecular scissors. Restriction enzymes recognize and cut specific sequences of nucleotides (for example, GAATTC). Out of around 3,000 different restriction enzymes, only a fairly small number are commonly used to manipulate viral genomes. Among these are type IIS enzymes.