This article was reviewed by one of our subject matter experts, Dr. Sebastian Lequime of the University of Groningen.
(The paper we’re demystifying can be found here, if you want to follow along)
You’ve probably heard the conspiracy theories- that nCoV-19 (AKA SARS-CoV-2), the virus that causes COVID19, is an escaped bioweapon, that it was made in a lab, that this is all an elaborate attack on [insert group here] by [insert another group here].
A group of scientists from Scripps Research Institute, The University of Edinburgh, Columbia University, the University of Sydney, Tulane University and Zalgen labs recently published a correspondence in Nature Medicine highlighting the work that they’ve done and it’s clear, extremely important conclusion:
“Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus”
-Andersen, Rambaut, Lipkin, Holmes, Garry. Nature Medicine (2020)
Beyond this very important point (read it again, if you want), this publication shows something else that’s very important about the COVID-19 research happening every single day: it’s worldwide, and it’s collaborative. That means that experts, the best of the best, are joining together from around the world. This is a team effort, and they’re making enormous strides.
Now on to the paper.
This paper opens with a brief introduction to the virus, and puts the research into context: SARS-CoV-2 is a coronavirus and is the seventh known coronavirus that can infect humans. Of these seven there are four- HKU1, NL63, OC43 and 229E- that cause relatively mild symptoms. The remaining three are SARS-CoV (also known just as SARS, the virus that caused the outbreak in 2003), MERS-CoV and our current pandemic causer- SARS-CoV-2, also known as nCoV-19. These three are all known to cause more severe disease.
(At this point it’s important to note that SARS-CoV-2 and nCoV-19 refer to the virus itself. COVID-19 is the name of the disease. Put another way, COVID-19 is the name for the symptoms, while SARS-CoV-2 and nCoV-19 are names for the cause. This is just like how HIV is the virus that causes AIDS).
The authors state that they have conducted comparative analysis of genomic data. What this means is that they’ve looked at the genetic code of SARS-CoV-2 and have compared it to the genetic code of other similar viruses. By doing this, they can tease apart where the virus came from and how it got to the point it’s at today. It’s like a jigsaw puzzle, or a scene in CSI. Simply put, the scientists have used genome sequencing to give themselves a bunch of clues and then they worked to crack the case.
(This paper talks a lot about mutation, which means this post is going to talk a lot about mutation. If you want to know more about mutation, how it works and what it means, check out this sidebar!)
From this genetic sleuthing, the research team found a lot of cool stuff. They begin by highlighting two interesting things about the SARS-CoV-2 (the virus that causes COVID19) genome:
- Mutations in the receptor-binding domain
Now. What on earth does that mean? The receptor binding domain (RBD) of a virus is the skeleton key the virus uses to get into a cell. You can think of a virus as a secret agent and a cell as a top-secret compound. Cells are very picky about what gets in and out. There are guarded gates, bodyguards and all sorts of barriers. Viruses get in by tricking the system. They use their RBD like a skeleton key- attaching it to a protein on the cell’s surface and using that attachment to pull themselves into the cell. The RBD of SARS-CoV-2 sticks to ACE2, a protein on the lining of the cells in the alveoli within the lungs. Because the RBD of this virus binds to ACE2, the virus targets lung cells. In this way the RBD acts both as a skeletal key and also as a guidance system.
The RBD of SARS-CoV like viruses have six amino acids that are like the teeth of the key- these amino acids are critical for the proper binding that allows the virus to infect the cell. The researchers found that the RBD of SARS-CoV-2 has mutations that change 5 of these 6 amino acids to different amino acids. This change made the SARS-CoV-2 RBD bind very strongly to ACE2 receptors in humans (as well as ferrets and cats). So whatever caused those 5 mutations, it worked out well for the virus… and badly for humans.
One thing that this discovery told the scientists is that those mutations were NOT caused by human intervention. They know this because humans wouldn’t have even known that these mutations would’ve made the virus bind human cells more strongly. Scientists have a lot of really cool computer software that can look at particular mutations and tell them how those mutations would change the way a protein or virus would behave. When you feed these five mutations into that computer software, the computer predicts that the mutations are not ideal for binding human cells. If a computer was asked to predict what mutations to make to get the same outcome, it would’ve suggested completely different ones. From this the scientists concluded that the strong binding of the SARS-CoV-2 RBD to human ACE2 is the outcome of natural selection, not a scientist in a lab.
- Polybasic furin cleavage site and O-linked glycans
Real mouthful there. Breaking it down, scientists found a stretch of amino acids that have a basic pH (pH>7) that allows a molecular scissors called furin to cut the spike protein. In other viruses, this usually determined how infective the virus was and how many different species it could infect. In other viruses, adding this sort of a cutting site tended to make the virus more pathogenic (disease causing), and in other cases this sort of a cut allowed MERS-like coronaviruses to jump from infecting bat cells to infecting human cells.
The researchers also found a particular amino acid called proline at the start of this basic sequence. Proline has the effect of making the protein twist in a way that would favour the addition of sugars to the oxygen molecules of other nearby amino acids. The exact function of this isn’t really clear yet, but a lot of viruses tend to use this technique to try and avoid the immune system. This is another piece of evidence that suggests that the virus was not lab made. In order for it to evolve a method to avoid an immune system, it has to have been in something that has an immune system. Cell cultures, which are used in labs, do not have immune systems.
The researchers then noted one of the most important pieces of evidence against the ‘lab made virus’ theory. No matter the field, you can’t make something out of nothing, and science is no different. Coronaviruses are very difficult to genetically manipulate because of their really big genome and how unstable their RNA is in the systems normally used for genetic engineering. Because of this, when scientists want to genetically engineer a coronavirus, they have to use one of several established reverse-genetic methods specific to coronaviruses. These methods allow manipulation of the virus genome but all the methods leave their little fingerprints. There are reverse-genetic systems available out there for beta-coronaviruses, but SARS-CoV-2 does not have fingerprints of any available system.
On top of this if the virus was made in a lab, they would have built it using an existing disease-causing virus as a scaffold. However, the genetic backbone of SARS-CoV-2 is very different from already-known coronaviruses. From this, the researchers concluded that SARS-CoV-2 is not made from any previously used viral backbone.
From these discoveries, the researchers have suggested three theories on how SARS-CoV-2 might have originated. Let’s go through them now.
- It evolved via natural selection in an animal host, then jumped to humans
SARS-CoV-2 is very similar to bat SARS-CoV-like coronaviruses. RaTG13, a coronavirus from a species of bat, is 96% similar in genetic code to SARS-CoV-2. However, it does not have the same mutations in the RBD, suggesting that the bat virus would not be able to infect human cells as efficiently.
Malaysian pangolins also have coronaviruses and some of their coronaviruses have RBDs very, very similar to SARS-CoV-2. In some cases, the RBD has the same six key residues. This shows that the SARS-CoV-2 RBD is likely a product of natural selection, because it already evolved in nature once in the case of the pangolin coronaviruses.
This theory suggests that the precursor virus to SARS-CoV-2 evolved in an animal host with a high population density (because otherwise the virus would not be spreading and duplicating enough for natural selection to occur efficiently) and an ACE2 gene that is very similar to the human gene. Although this animal and the potential precursor virus haven’t been found yet, that doesn’t mean they don’t exist. The many different coronaviruses in bats and all the other species haven’t been fully sampled and it’s entirely possible that the precursor virus the researchers are theorizing might be out there- just waiting to be discovered.
- It jumped to humans from animals, then underwent natural selection
In this theory, a great-grandpa of SARS-CoV-2 jumped into humans first, then went through the mutations to produce the new RBD and the polybasic cleavage site through adaptation and natural selection that happened over many rounds of undetected human-human transmission. Until the new, stronger binding RBD and the polybasic cleavage site were evolved it’s entirely possible that the virus was just too weak to make any sort of a detectable impact. Once they evolved and the virus adapted to the human cell it would begin to cause more cases and would then be detected.
All of the SARS-CoV-2 genomes that have been sequenced up until now have the same common genetic features, which means that all of the viruses came from one common ancestor that had them too (them being the new RBD and the polybasic cleavage site). Because the RBD of the pangolin virus is very similar to the RBD of SARS-CoV-2, it’s possible that this different RBD was already in the virus before it jumped to humans. That means that in this theory the polybasic cleavage site had to have evolved during human-human transmission.
The virus emerged in late November 2019 to early December 2019. If this theory is correct it would imply that there was a period of undetected transmission in humans before this point of detection. If the virus jumped from animal to human, spread from human-human for a short time and then jumped back to animals, the virus could’ve evolved this polybasic cleavage site during the brief human-human transmission periods without being detected.
- Selection during passage
A lot of research goes on around the world that focuses on bat SARS-CoV-like viruses. Knowing this, it’s only fair that the researchers investigate the possibility of a virus escaping from a lab.
They acknowledge that it is theoretically possible that SARS-CoV-2 picked up the mutations in the RBD while it was being passaged (grown and proliferated) in lab grown cells. However, the researchers believe that the presence of a near-identical RBD in pangolin viruses gives a stronger explanation of how SARS-CoV-2 got these mutations through recombination (swapping around its genome) or mutation.
The researchers also say that the polybasic cleavage site AND the O-linked glycans argue against the lab jailbreak theory. Generating SARS-CoV-2 in a lab would have required the isolation of a parent virus that was highly genetically similar, which has not been described anywhere in the literature. Accidentally generating the polybasic cleavage site after that would have required that the virus be grown in cells or animals with ACE2 receptors very similar to humans, which also hasn’t been described. More importantly (as stated above), the O-linked glycosylation implies that the mutations occurred in the presence of an immune system and lab cell cultures do not have immune systems.
Based on the evidence above, the research group has concluded that SARS-CoV-2 is not a purposefully manipulated virus. All the notable features of the virus, including the strongly binding RBD and the polybasic cleavage site, were observed in nature and the residues making up the optimized RBD would never have been predicted by laboratory computer programs. More importantly, no fingerprints of any currently available reverse-genetic systems for betacoronaviruses were found in the SARS-CoV-2 genetic code, indicating that there was no human genetic manipulation in the history of this virus.
All in all, these researchers have done an incredible job and this is a very important piece of research. This correspondence was published online on March 17, 2020 and no doubt put a lot of people’s fears to rest.
Just another example of how scientists are fighting for you, every single day.