It is the middle of April 2020, and we find ourselves at a unique intersection of scientific discovery and breaking news. Information is being released, updated, and refuted at an alarming rate. New scientific information is easily published and disseminated by different types of media outlets, which do not necessarily offer critical and unbiased interpretations of emerging research. That said, it is easy to get caught up in this zeitgeist, especially at a time when most of us are a combination of frightened and bored while self isolating at home.
As a scientist, I've become the go to expert for many of my family and friends. I hope that this blog has helped with that mission. One such topic is the theory that SARS-CoV-2, the virus which causes COVID-19, was developed in a laboratory. The American Association of Public Opinion Research reported that 29% of Americans polled believed that SARS-CoV-2 was created in a lab. This theory has two variations: the virus was the engineered in the laboratory and through human error was accidentally released, or the virus is the product of bio-weapon research. The conflicting theory is that SARS-CoV-2 is the product of natural selection, in which a virus that infects, but does not cause a disease, in bats became highly infectious and pathogenic in humans.
There are plenty of sources that go down the rabbit hole of these theories, but I don't want to lend too much credence to conspiracy theories or unnecessarily tarnish the names of scientists that have been implicated in these theories. Instead I'd like to present a report written by group of scientists with expertise in virology, evolutionary biology, and pathology that was published in Nature Medicine which discusses and disputes these different theories.
The proximal origin of SARS-CoV-2. Nat Med. 2020 Mar 17 : 1–3.
Kristian G. Andersen, Andrew Rambaut, W. Ian Lipkin, Edward C. Holmes, and Robert F. Garry
While this report does not contain data to dispute the claims that SARS-CoV2 has a laboratory origin, it provides a series of research based arguments as to why they believe SARS-CoV-2 is the product of natural selection, passage through multiple species hosts, and adaptation to effectively spread from human to human. Since this report is meant for an audience of other scientists, I wanted to break down the major points to make it accessible to non-scientists.
The sequence of SARS-CoV-2 DNA is 96% identical to a virus found in bats, which is part of the same coronavirus family as SARS-CoV-2, SARS, and MERS. However, the differences from the original bat virus are very important.
One of the factors thought to increase the infectivity of SARS-CoV-2 in humans is the spike protein. The spike protein is expressed on the surface of SARS-CoV-2 and allows it to bind to host cells, so that the virus can gain entry into the cells.
Think of a key and lock. Many viruses use normal processes of the host as locks to gain entry into host cells. In this case, the spike protein is the key and the lock is human angiotensin converting enzyme 2 (ACE2). ACE2 is an enzyme that binds to the outside of host cells.
The bat spike protein does not bind strongly to ACE2. Instead the parts of the SARS-CoV-2 spike protein responsible for binding are nearly identical to that region on the spike protein of a different coronavirus. This second coronavirus normally infects an endangered ant-eater like animal called the pangolin. The pangolin is illegally hunted and sold for meat and its scales are thought to have medicinal value.
It is true that in biomedical research, viruses are often modified in the laboratory setting. By removing or changing sequences of DNA, we are able to determine the function and necessity of different parts of the virus. Conversely sequences of DNA can be added to change the function of parts of the virus. If changing the DNA makes the virus less infectious, it is considered a loss of function, and if it makes the virus more infectious, it is a gain of function. This is commonly done in research to better understand the viruses being studied, though in the United States, there are regulations prohibiting research which enhances the infectivity of highly pathogenic viruses such as influenza, SARS, and MERS.
Using the known sequence of the bat coronavirus, researchers are able to model and predict changes in the spike protein that would increase its binding to ACE2. According to the authors of this report, there are very logical changes which would increase the binding of the bat spike protein to ACE2. The substitution of the pangolin receptor binding domain is not a predicted change. The change in the spike protein of SARS-CoV-2 is most likely to have occurred through a transmission event from bats to pangolins. The presence of the sequences from both the bat and pangolin viruses highly suggests this scenario.
Binding to ACE2 by the spike protein is further enhanced in SARS-CoV-2 by the presence of a furin cleavage site and O-linked glycans near this cleavage site.
Stick with me, I'll try to make that last sentence less like the indecipherable dialogue of an adult in a Peanuts cartoon.
The spike protein has 2 subunits, S1 and S2. These two subunits are linked by a region, the cleavage site, that is recognized by an enzyme (in this case the enzyme is furin) which cuts the two subunits into two (cleavage in this sense is like a butcher cleaver and not revealed by a low cut top). O-linked glycans are carbohydrates which are attached by oxygen, and their presence further enhances binding of the SARS-CoV-2 spike protein to ACE2.
These O-linked glycans are not found in either the bat or pangolin coronaviruses. Rather, these are found exclusively in human coronaviruses. The authors suggest that this enhancement was gained when the virus made the jump from the animal hosts to humans, and permitted this virus to be spread from human to human.
Finally, laboratory experiments which study viruses often require another type of DNA to make enough virus to carry out experiments. This is a viral backbone, because it provides a structure in which the scientist can attach the DNA sequences they want to study. There are a number of known backbones, with known sequences, which help express the DNA the researcher wants to study.
There is no trace of this type of viral backbone in the sequences of
SARS-CoV-2 obtained from patients. This further convinced these authors that SARS-CoV-2
was not created in the lab.
The original bat virus was probably transmitted to the pangolin. The bat virus changed to infect the pangolin and acquired the changes in the spike protein of the pangolin virus. Most likely due to illegal hunting and trade of the endangered pangolin, the virus was transmitted to humans. The pangolin spike protein modifications allowed the virus to enter cells by binding to ACE2. Finally, the addition of the O-linked glycans around the spike protein cleavage site allowed the virus to not only infect humans, but to be transmitted from human to human.
The theory that SARS-CoV-2 arose from natural selection is supported by similar cross-species transmission events that have lead to the emergence of other novel viruses. Viruses can mutate rapidly, which is why there are many cases of viruses adapting to infect new host species. These transfers have involved bat viruses (Ebola, SARS, MERS), pig viruses (swine flu), and bird viruses (avian flu). The authors prove none of the theories with empirical data. Instead they compare the emerging data on SARS-CoV-2 with previous data on other coronaviruses and their own experience to critically consider the possibility that SARS-CoV-2 was engineered in a lab. It makes a compelling case that SARS-CoV-2 arose from a series of natural selection events, which could very likely occur again.
The final theory, that SARS-CoV-2 was created in a laboratory for use as a weapon is easy to get caught up in. It is easy to believe that a virus that has proven to be so deadly on a global scale could only be the product of a weaponized strategy. This theory is unfortunately possible, but hopefully not probable.
Sources cited:
The proximal origin of SARS-CoV-2. Nat Med. 2020 Mar 17 : 1–3.
Kristian G. Andersen, Andrew Rambaut, W. Ian Lipkin, Edward C. Holmes, and Robert F. Garry
Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus. Journal of Virology. April 2020 Volume 94 Issue 7. Yushun Wan,a Jian Shang,Rachel Graham, Ralph S. Baric, Fang Lia.
https://www.pewresearch.org/fact-tank/2020/04/08/nearly-three-in-ten-americans-believe-covid-19-was-made-in-a-lab/?fbclid=IwAR1OlziNS-1j7x5Pi6RQoW-rTiGzV19YKbgsO1Eni1gu6gOujODkmQ_OG-Q
Gain-of-Function Research: Ethical Analysis. Science and Engineering Ethics. 2016; 22(4): 923–964. Michael J. Selgelid
https://osp.od.nih.gov/biotechnology/gain-of-function-research/
Acknowledgements:
Special thanks to Dr.'s Emily Nelson and Henry Garcia for helpful discussions used to figure out the best ways to describe some of the more complicated ideas in the original report.
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