Andersen KG et al. The proximal origin of SARS-CoV-2. Nature Medicine, March 2020.

Cases of Covid-19 first emerged in December 2019, when a mysterious illness was reported in in the city of Wuhan, China. The cause of the disease was soon confirmed as a new kind of coronavirus, and the infection has since caused a large-scale epidemic and spread to more than 70 other countries. Coronaviruses are a large family of viruses that are related to a broad spectrum of illnesses, the first of which was the 2003 Severe Acute Respiratory Syndrome (SARS) epidemic in China. A second outbreak of severe illnesses began in 2012 in Saudi Arabia with the Middle East Respiratory Syndrome (MERS). On December 31 of 2019, Chinese authorities alerted the World Health Organization of an outbreak of a novel strain of coronavirus named SARS-CoV-2 causing severe illness. As of February 20, 2020, nearly 167,500 Covid-19 cases have been reported, though many milder cases have likely gone undiagnosed. More than 6,600 people have already died as a result of contracting this virus – and the numbers will be much higher when you will be reading this article. Chinese scientists sequenced the genome of SARS-CoV-2 very shortly after the epidemic began and made the data available worldwide. The analyses of genomic sequence data have shown that Chinese authorities rapidly detected the epidemic and that the number of Covid-19 cases have been increasing because of human to human transmission after a single introduction into the human population.

Recently, a group of scientists used this sequencing data to explore the origins of SARS-CoV-2 and how it has become the version that it is now. The scientists specifically focused on the genetic codes for spike proteins, the mechanical framework on the outside of the virus that it uses to grab and penetrate the outer walls of human and animal cells. There are 2 major parts of the spike proteins: the receptor-binding domain (RBD), a molecular hook that grips onto host cells, and the cleavage site, a molecular can opener that allows the virus to crack open and enter host cells. The scientists found that the RBD portion of the SARS-CoV-2 spike proteins mutated to effectively target a molecular feature on the outside of human cells called ACE2, a receptor normally involved in regulating blood pressure. The SARS-CoV-2 spike protein was exceptionally effective at binding to human cells, and the scientists concluded this could only be a product after a natural selection process and not the product of human-designed genetic engineering. This evidence was further strengthened by data on SARS-CoV-2’s backbone molecular structure. If someone were to engineer a new coronavirus as a pathogen, they would have constructed it from the backbone of a virus known to cause illness. But the scientists found that the SARS-CoV-2 backbone differed substantially from those of already known coronaviruses and mostly resembled related viruses found in bats and pangolins. These two features of the virus, the mutations in the RBD portion of the spike protein and its distinct backbone, basically ruled out laboratory manipulation as a potential origin for SARS-CoV-2. Based on their genomic sequencing analysis, scientists came up with two possible scenarios as the most likely origins for SARS-CoV-2.

In the first scenario, the current pathogenic state of SARS-CoV-2 has emerged naturally in non-human hosts such as bats or pangolins and then jumped to humans. Coronaviruses are well known to undergo genetic recombination. In fact, this is exactly how previous coronavirus outbreaks have emerged, with humans contracting the virus after direct exposure to civets (SARS) and camels (MERS). The researchers proposed horseshoe bats as the most likely reservoir for SARS-CoV-2 as it is very similar to a bat coronavirus. There are no documented cases of direct bat-human transmission so far, suggesting that an intermediate host was likely involved between bats and humans.

In this particular scenario, both of the distinctive features of SARS-CoV-2’s spike protein and the cleavage site would have mutated to their current pathogenic state prior to entering humans. In this case, the current epidemic would probably have emerged rapidly as soon as humans were infected, as the virus would have already equipped with the features that make it pathogenic and able to spread between people.

In the second proposed scenario, a non-pathogenic version of the virus jumped from an animal host into humans and after a mutation process it has acquired its current pathogenic state within the human population. For instance, some coronaviruses from pangolins, armadillo-like mammals found in Asia and Africa, have a spike protein very similar to that of SARS-CoV-2. A coronavirus from a pangolin could possibly have been transmitted to a human, either directly or through an intermediary host such as civets or ferrets.

In this scenario, only the cleavage site could have mutated within a human host, possibly via limited undetected circulation in the human population for months or maybe years prior to the beginning of the epidemic. The researchers found that the SARS-CoV-2 cleavage sites have similarities that resemble strains of bird flu that can transmit easily between people. In the case of SARS-CoV-2, such a virulent cleavage site could have been formed in human cells and soon the current epidemic got initiated, as the coronavirus would possibly have become far more capable of spreading between people.

At this point, it is almost impossible to know for sure which of the scenarios is most likely. If the SARS-CoV-2 entered humans in its current pathogenic form from an animal source, it raises the probability of future outbreaks, as the illness-causing strain of the virus could still be circulating in those animal populations and might come back to humans again. It is still noteworthy that a non-pathogenic coronavirus entering the human population and then acquiring properties similar to SARS-CoV-2, the second scenario, is less likely than the first scenario.

In conclusion, this study brings an evidence-based view to the baseless rumors and conspiracy theories that the SARS-CoV-2 was deliberately manufactured in a lab and concludes that the virus has emerged after a natural process that took place in multiple hosts over time. These genetic findings are also consistent with how SARS-CoV2 is currently behaving. The virus has a low fatality rate (1% to 3.4%) and does not seem to act like a bioweapon compared to pathogens such as anthrax or Ebola. Given the previous coronavirus epidemics and the persistence of the culture of eating exotic mammals in China and other parts of the world, the current COVID19 epidemic is unfortunately not a big surprise for scientists and experts. We have to take necessary measures to be more prepared for such outbreaks that may take place in future.

The genera Escherichia is thought to have emerged around 102 million years ago and is known as a gram-negative pathogenic bacteria mostly found in the intestines of warm blooded animals [1]. German pediatrician and bacteriologist Theodor Escherich discovered E. coli in 1885, and for many years the bacterium was simply considered to be a commensal organism of the large intestine. It was not until 1935 that a strain of E. coli was shown to be the cause of an outbreak of diarrhea among infants [2]. The reason its pathogenic properties were discovered so late is that many of its strains are harmless. However, virulent strains of E. coli can cause various diseases in humans and in domestic animals, and are also sometimes responsible for product recalls due to contamination. Gastroenteritis, urinary tract infections, and neonatal meningitis are the most commonly observed diseases in humans, and in rare cases virulent strains are also responsible for haemolytic-uremic syndrome, peritonitis, mastitis, septicaemia and Gram-negative pneumonia [2]. Various outbreaks all around the world have been caused by E. coli, causing millions of deaths and sick people and billions of dollars have been spent fighting it. Even though death rates have decreased with the evolution of modern medicine and the discovery of antibiotics, the outbreaks are still a major concern for all countries, such as the recent outbreak in Germany in 2011 affecting 3,950 people and killing 53 [3].

Its reputation has not been one of great dignity, and it has ruined the reputation of many. You may recall in 1993, the fast food chain restaurant “Jack in the Box” suffered a major corporate crisis involving E. coli O157:H7 bacteria. Four children died of hemolytic uremic syndrome and 600 others were reported sick after eating undercooked patties contaminated with fecal material containing the bacteria at locations in Seattle and the Pacific Northwest, USA. The chain was faced with several lawsuits, each of which was quickly settled but left the chain nearly bankrupt and losing customers.

But don’t these creatures have any properties to be appreciated, I wonder…

Compared to eukaryotic cells, bacteria have a pretty basic mechanism of functioning. They don’t have sophisticated organelles, and they do not have a cell nucleus where their DNA is stored. Everything is floating along all together in the cell cytoplasm (which shocks me when I reflect upon how such a small and simple organism can cause such severe pain on “highly evolved modern humanity”). It has the basic metabolic tools for survival. And even though, at first sight, it is tempting to look down on its simplicity, today we know that it is this simplicity that gives us space for making many modifications and experiments on it, whereas in more complicated cells, like animal cells, the moment a modification is made, the entire system reacts to that and causes much trouble in the process.

The turning point of E.coli making a huge impact on our lives was in 1973, when Stanley Cohen and Herbert Boyer discovered the “Recombinant DNA Technology.” This technology allowed specific genes to be isolated from one organism and cloned to another organism by the help of bacterial plasmids. The first commercial product to be synthesized by this technology was human insulin, which is used for the treatment of diabetes [4]. This brought an amazing amount of recognition and appreciation for the technology, as the practical aspect of the technology was now proven to be commercially profitable. For the insulin to be produced, the DNA sequence that encodes human insulin was synthesized and transplanted into a plasmid that could be maintained in a non-pathogenic strain of E.coli [4]. Now the bacterial host cells acted as biological factories for the production of the two peptide chains of human insulin, which, after being combined, could be purified and used to treat diabetics who were allergic to the commercially available porcine (pig) insulin, or for diabetics from certain religious groups who abstain from pork products such as Muslims, Jews, some Christian groups, and many more who have similar concerns.

This was only the start of an incredible new technology which used bacteria to produce different proteins or enzymes to cure human diseases. Today more than 200 new drugs have been produced by recombinant DNA technology and have been used to treat over 300 million people for diseases such as cancer, multiple sclerosis, cystic fibrosis, and stroke, and to provide protection from other infectious diseases. Over 400 new drugs are in the process of being tested in human trials to treat such diseases as Alzheimer disease and heart disease (to name only two) [4].

Today E.coli is frequently used as a model organism for all kinds of microbiological experiments. In the lab, E. Coli. is one of the first micro-organisms that is thought of for testing a biological experiment. The reason is that E.coli cells are cheap to purchase and to sustain. They grow easily and rapidly in lab conditions and have non-pathogenic strains, so they are not dangerous for the researches doing the experiment. Whereas purchasing more complicated cells such as cancer cells or stem cells may be very costly, and moreover, may need special lab conditions to be sustained; so before more complicated cells are purchased, the experiments are usually tried out with E.coli or some other kind of model organism. More importantly, E. coli was one of the first organisms to have its genome sequenced; the complete genome of E. coli K12 was published by Science in 1997 [5]. Other areas in which modified E.coli has helped humanity are vaccine development, bioremediation (fighting pollution), and production of immobilised enzymes [6].

One specific example of the benefit of recombinant DNA technology for the environment is its use in the paper industry. Before the 1970’s, when there wasn’t much environmental awareness in the paper producing industry, poisonous chlorine compounds were conventionally used to achieve pulp brightness of a high order in the manufacture of high-quality paper products [7]. This chemical bleaching technique precipitated a tremendous environmental concern considering the magnitude of the industry. Plants treated with elemental chlorine produced significant amounts of dioxins. Dioxins are highly toxic, and their health effects on humans include reproductive, developmental, immune and hormonal problems. They are also known to be carcinogenic. Over 90% of human exposure is through food, primarily meat, dairy, fish and shellfish, as dioxins accumulate in the food chain in the fatty tissue of animals [7]. One alternative for these chemical bleaching processes is the use of the enzyme “xylanase,” which degrades the linear polysaccharide beta-1,4-xylan into xylose, thus breaking down hemicellulose, one of the major components of plant cell walls. Even though the use of xylanases in this industry has increased significantly with the discovery of Viikarri et al. (1986), the enzyme needs further improvements for it to be commercially acceptable [6]. To ensure the commercial utilization of hemicellulosic residues in the pulp and paper industries, the production of higher xylanase yields at low capital cost is required [6]. Such studies are ongoing with the purpose of partially mutating the amino acid sequence for the purpose of especially increasing the thermal stability of the enzyme and also increasing its metabolic activity. The gene mutation and gene expressions are generally done in either E.coli or yeast cells. Davoodi et al. has mutated the enzyme up to the point where the transition temperature increased 12 0C by introducing disulfate bonds in the enzyme [8]. The wonders this enzyme can do for the health of the environment is breathtaking, and is an area which should be further studied until finding the commercially viable kind that will eliminate chemicals from the paper industry during bleaching.

Even though some controversy remains on gene transferring, its tremendous positive impact on humanity cannot be denied. I personally think that it does need constraints and strict regulations, but this technique is one of the most remarkable techniques discovered in modern times, and E.coli has no doubt played a great role in the availability of this technology.

Even though condemning E.coli and stating its “evilness” seems like the most obvious path, we all ought to appreciate the variety and uniqueness of these creatures which also allow us to produce such large varieties of drugs. We ought to appreciate its simplicity, which allows it to have a chance of producing such sophistication. We ought to reflect upon the fact that something can be classified as “good” or “bad” only by the means in which we perceive it, and the reality of it may be completely opposite of what we had thought initially.

McPen is a freelance writer in natural sciences, Montana, US.

References

1. Battistuzzi FU, Feijao A, Hedges SB. 2004. “A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land”. BMC Evol. Biol.
2. Todar, K. “Pathogenic E. coli”. Online Textbook of Bacteriology. University of Wisconsin–Madison Department of Bacteriology.
3. “German-grown food named likely culprit in deadly outbreak”. CNN. (5 June 2010).
4. Glick, Bernard, Jack Pasternak, and Cheryl Patten. 2010. “MOLECULAR BIOTECHNOLOGY Principles and Applications of Recombinant DNA . 4th Edition.” Washington,DC: ASM Press, pp. 3-13.
5. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (September 1997). “The complete genome sequence of Escherichia coli K-12”. Science 277 (5331): 1453–62.
6. Cornelis P. 2000. “Expressing genes in different Escherichia coli compartments”. Curr. Opin. Biotechnol. 11 (5): 450–454.
7. Beg, Q.K., M. Kapoor, L. Mahajan, and G.S. Hoondal. 2001. “Microbial xylanases and their industrial applications: a review.” Springer.
8. Davoodi J., Wakarchuk W.W., Carey P.R., Surewicz W.K. 2007. “Mechanism of stabilization of Bacillus circulans xylanase upon the introduction of disulfide bonds.” Biophysical Chemistry, 125 (2-3) , pp. 453-461.