Is SARS-CoV-2 engineered in a lab?

Since the early days of the COVID-19 pandemic, suggestions have been made that the virus responsible for COVID-19, SARS-CoV-2, may have been engineered in a laboratory. The strongest, albeit very circumstantial, suggestion for this is the proximity of the institute for virology and the likely epicenter of the SARS-CoV-2 outbreak in Wuhan, China. 

A publication this week shows again that engineering is extremely unlikely.

Governmental and public suspicion of China´s more secretive behavior has certainly not helped the case. At this moment in time, there is no conclusive evidence of a lab-generated virus nor of a natural evolved virus. However, the latter is very, very, much more likely to have been the cause of the pandemic than the former. It also needs to be pointed out that an engineered virus needs to have come from a lab, a natural virus could still have escaped from a lab, although there is no direct evidence for this either.

Those of a lab-engineering predisposition were excitedly awaiting US governmental agency reports that were rumoured to include evidence of human intervention. However, the reports did not include this, and the reading strongly suggests a natural origin of SARS-CoV-2. The suspicion of engineering has been laid on a research project (Project DEFUSE) on bats in China and in the US, conducted by the NGO Ecohealth Alliance and funded by the NIH/NIAID, this even when as far as questions in the European parliament. 

But is it a plausible suspicion? Looking at science, the answer is that that is extremely unlikely. This is based on the absence of any data that the WIV had a coronavirus strain from which SARS-CoV-2 could have been made. This absence of evidence is even, and clearly, stated in the Office of the Director of National Intelligence (ODNI) report.

Research on coronavirus adaptation was proposed but was not funded. What was proposed is indeed inserting a Furin Cleavage Site (FCS) into Spike-coding viral material. However, and this is extremely important to understand, this work would take place using pseudo typed viruses, i.e. pseudo-viruses. This means that a coronavirus was never altered, and hence could not have given rise to SARS-CoV-2 nor could have escaped. What is used with this research is only the Spike coding part of a coronavirus, this part is expressed, with or without alterations, together with parts of other viruses to give virus-like particles. The original sequences to make these viral particles are expressed transiently in cell lines. Together they give viral particles that can infect another cell line, but only a single time. The reason is that critical genetic material needed to propagate a virus is not included in the produced particles. Hence, the name pseudo-virus. This is a very safe way, still biological safety level (BSL)-2 because of the potential to infect the experimenter, but not because of escape potential.
 
Now, this is science, and not as easy as often portrait in popular media, even if a coronavirus backbone were used, the likelihood this would have given rise to SARS-CoV-2 is extremely small. This is the reason the ODNI report speaks about the precursor virus needs to be at least 99% similar. Why is that?

We now know that inserting an FCS in a coronavirus does not make the virus a SARS-CoV-2. There are other parts of extreme importance, such as the loop surrounding the FCS, the part separating S1 from S2. This determines how accessible the FCS is to Furin or other proteases. This we did not know prior to 2019, but is extremely important, without an extension of the region (QTQTN), the FCS has no role.

This was just this week shown again, in coronaviruses found in bats in the UK, there are even putative FCSs found in these, and one virus can even bind human ACE2. Yet, mutating this putative motif to a full FCS did not enable spike cleavage! It did not enhance the virus. This shows that more adaptations are required than the insertion of an FCS before a coronavirus can infect humans. For those wondering, also in this research, pseudo-viruses were used.

To get this important message, prior to 2020, any scientist would have used standard FCS to assess its effect on coronaviruses. Now we know it takes more, an extended loop. In some viruses it will result in destabilization and the virions generated with loose the competition to the standard coronavirus. The reason for instability can be the very rapid cleavage of Spike into S1 and S2. Without S1, the virus cannot bind the host cell, and hence will not propagate and lose out on those virions that can.

This is a strong point against SARS-CoV-2 being engineered from a precursor in a lab: the original virus would not have been used, and even if used, the scientists would have encountered many problems that would not have allowed the generation of SARS-CoV-2.
 
Now, of course you can put it more extreme, and hence unlikely, what if there was a precursor that had all the perfect conditions and instead of a pseudo-virus, the virus was engineered with a at that moment known FCS? The well-known FCS sequence would be RRSRR, yet SARS-CoV-2 has PRRAR. Even then the resulting virus would be as “fit” as its precursor, and nothing seemed to have been gained. This would, prior to 2020, been a puzzle not solved by pre-existing data or knowledge.

Of course, a very persistent and determined scientist, and we are, could have continued and made all sorts of permutations, to subsequently assess these for enhanced cell entry. Supervisors, funding, and time would have had something to say about this endeavor but let´s imagine.

Well, there is the next hurdle. This is the cell entry itself. SARS-CoV-2 grows on VeroE6 cells, with added TMPRSS2. That would not have been used, it makes entry quite easy and does not leave room for accurate testing. Other cells would have been used (Calu-3, Hela, 293T). The essays would be difficult to establish an enhanced cell entry. If this would work, and if there would have been other constraints that would make this even possible are not known yet. Subsequently, the resulting virus would need testing in an animal model, Syrian hamsters as most likely candidate, but these are different from humans.

What makes this again very unlikely is that improving viral fitness with extending the S1/S2 loop of the FCS is not very conditional. If it were, there would be many insertions found in this area, and they are not. The opposite is true, deletions do happen frequently that affect the FCS itself (NSPRRAR) or the flanking sequence (QTQTN). The deletion of QTQTN seems to restrict late-phase viral replication, not cell entry. Yet, there seems to be some pressure that selects these deletion mutants, as well as a reasonable efficient way to delete this region. This is also seen in other coronaviruses. The removal of parts of the loop makes cleavage of S1/S2 easier.

Anyway, this would have been many years of work and generated so much new basic science data (for specialists), parts of it would have been written up in manuscripts and published. But, as we know, there is nothing. And please do not consider these experiments simple pasting in of new sequences, any wet-lab scientists can tell you they are not and are very time-consuming, especially without prior knowledge. In short, to have made SARS-CoV-2 in a lab, a feature that is easily lost, that not easily detectable to improve fitness and it only does that when several other features are just right, must have been generated without any of this being understood at the time, and still not being fully understood even now.
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Much is possible with hindsight, but that is not how biological sciences work. Much is found with lots of trial and error, frustration, technical errors, failed experiments, negative results, etc, and each new step takes much time, is documented, and published. This is the main reason that the likelihood that SARS-CoV-2 was engineered in a lab is nil.