The first case of novel coronavirus disease (COVID-19) was reported in the city of Wuhan, China, in December 2019, and has since frantically spread across every continent except Antarctica. With number of affected patients and deaths continuing to spiral at a breakneck pace, the World Health Organization declared the outbreak a pandemic on 11th March, 2020.
Speculations regarding the COVID-19 as being engineered in a lab are running rampant in the scientific community, but the analyses of genome sequence data from SARS-CoV-2 and related viruses suggest evidence of natural origin.
Coronaviruses are a large family of virus that is common among many species of animals including humans. Until now, there had only been two other coronaviruses that had been known to be fatal to human: the Severe Acute Respiratory Syndrome (SARS) and the Middle East Respiratory Syndrome (MERS).
SARS, the first known fatal respiratory illness caused by a coronavirus, appeared in 2002 in China. It had an average fatality rate of around 10 percent with older people being the most vulnerable. MERS is also another severe respiratory illness caused by a coronavirus. Also known as the camel flu, the first case was reported in 2012 in Saudi Arabia. According to Centers for Disease Control and Prevention (CDC), 3 or 4 for every 10 patients diagnosed with the disease have died from it.
As soon as the Chinese officials notified the World Health Organization of an outbreak of a novel strain of coronavirus causing severe illness among humans, it was found to have proximal association to the SARS virus and was officially named SARS-CoV-2.
The fatality rate of the COVID-19 can’t be accurately determined as of yet, and we can’t even exactly picture the number of people who have contracted the virus. Also, many with few or mild symptoms may never make an appointment with a doctor, and even if they do, majority of the cases are likely to go undiagnosed. As of March 27, 2020, more than 500,000 cases have been confirmed with over 24,000 deaths.
Now going back to how the scientists figured out the virus was not made in a laboratory.
Shortly after Chinese scientists informed WHO of the epidemic, they began sequencing the genome of SARS-CoV-2 and made the data accessible for researchers to study. From the genomic data, Chinese authorities determined that the cases of COVID-19 have been increasing entirely as a result of human to human transmission through close contact after an initial introduction was made to the human population.
Then, Kristian Andersen, an associate professor at Scripps Research, and his team stepped in to reconnoiter this sequencing data to pin down how SARS-CoV-2 originated and evolved by studying its features.
A lot of the viruses that are dangerous to humans actually stem from animals. For example, HIV/AIDS originates in chimpanzees; and the deadly ebola virus likely comes from bats. And as for the coronavirus, researchers believe that it might have originated either in pangolins or bats, as SARS-CoV-2 bears striking genomic similarity with the coronaviruses found in both the animals.
The coronavirus has protruding spikes that look like crown or corona. These spikes are proteins or armatures that it uses to invade its host cells. So what the team did was they analyzed the genetic template for these proteins and drew on two of its important features, that is – the receptor-binding domain (RBD), a sort of hook that clasp onto host cells, and the cleavage site, a kind of a molecular tool that allows it to crack open and enter host cells.
To their surprise, they found clear signs of evolution in the RBD portion of the SARS-CoV-2 spike proteins which make it effectively bind a human cells called ACE2, an enzyme on the outer surface of cells in the lungs, arteries, heart, kidney, and intestines, and is known to lower blood pressure. So these spike proteins effectively targeting the human cells is a feat achievable only through the process of natural selection.
“By comparing the available genome sequence data for known coronavirus strains, we can firmly determine that SARS-CoV-2 originated through natural processes,” explained Kristian Andersen, an associate professor at Scripps Research Institute and author of the paper, the proximal origin of SARS-CoV-2, which is is available at the journal Nature Medicine.
Even the analysis of data on the virus overall molecular structure shows that SARS-COV-2 is the product of natural evolution, refuting the claim of laboratory as its potential origin.
If you were to create a deadly coronavirus, you would have to start it from the backbone of a virus known to cause illness. But comparing the SARS-CoV-2 backbone with those of already known coronaviruses yielded an entirely different molecular structure, yet looked so much similar to those found in bats and pangolins.
How COVID-19 evolved to its current pathogenic state and reached human population
Well, here are two takes on possible origins of SARS-CoV-2 which the researchers winded up with based on their genomic sequencing analysis.
First – Prior to making an entry to human population, the virus likely evolved to its current pathogenic state through natural selection in an animal. Previous coronavirus outbreaks such as SARS and MERS have emerged this way when humans contracted the virus after being exposed to civets and camels respectively.
The researchers are conjecturing bats to be the possible source of SARS-CoV-2 as it equals that of a bat coronavirus. There is no substantiated evidence of bat to human transmission but intermediary participant was likely involved between two species. So what happens here is that the RBD portion and the cleavage site would have acquired their pathogenicity before entering humans. And once a human were infected, the epidemic would have spread far and wide once as it would have already developed the ability to spread as well.
Second – In another take, a harmless version of the virus evolved its existing pathogenic state within the human population after being passed from a non-human host. The RBD of the coronaviruses from pangolins have a structure very similar to that of SARS-CoV-2, so it could have been transmitted to a human through an intermediary animal such as civets or ferrets. Then the cleavage site, too, could have mutated within a human host as it circulated under the radar in the human population before the epidemic had set off.
The strains of the cleavage sites of SARS-CoV-2 also look similar to those of bird flu. This explains why it has been transmitting easily between people. Also, by the time the SARS-Cov-2 invaded the human population, it could have mutated to develop such a destructive cleavage site and soon commenced the epidemic.
We can’t be certain which of these two cases is most probable, but given that the pangolin coronavirus has 99 percent genomic similarity with SARS-CoV-2 compared to 88 percent with that of the bat, the source of the disease is most likely pangolins.
Another thing we can all expect is that even if we slow and then stop the outbreak for now, there is high probability it will happen again in the future – if SARS-CoV-2 enters humans in its current pathogenic from an animal. Because the strain of the virus that’s fatal to human could still exist within the animal kingdom and might once again find its way to us. However, if a non-pathogenic coronavirus enters the human population and then evolve to develop a feature similar to SARS-CoV-2, the chances of future outbreaks are less.