Viruses: A Scourge or Gift to Mankind?

 

They are not evolving, but devolving

by Jerry Bergman, PhD

As of this writing, the coronavirus has dominated the news for over three weeks now. As people listen frantically to learn what they need to do to protect themselves, one question that comes up is: why did God create viruses? Do they ever do anything good? And are they evolving by mutations and natural selection? In short, viruses are well-designed for their various roles in life and are the most numerous and diverse genetic molecular assemblies on Earth today. And they are devolving, not evolving. In a perfect world, they would be gifts to help life, not afflict it.

What are Viruses?

I taught college-level microbiology for over a decade and developed the course I taught. In the course we called viruses gene machines because they, technically, are not living. To reproduce a virus must invade a living cell and take over its machinery to make copies of itself. Thousands of different kinds of viruses exist and the vast majority, like bacteria, are not harmful, but helpful. Most of the current microbiological and biochemical research is on viruses which researchers find very useful for medical research, such as the Lambda virus (or Lambda phage), which I worked with when I did research at the Medical University in Toledo, Ohio, first as a student, then as a research associate in the Department of Experimental Pathology.

The second type of viruses are those that cause disease, such as the influenza virus, which is of great interest to researchers for obvious medical reasons. The rest of the large virus family are usually of little interest.

Once a virus infects a susceptible cell, it can commandeer the cell machinery to produce more viruses.  Furthermore, many viruses produce proteins that modify the host-cell processes in order to maximize their viral replication rates well-beyond the level the cell uses for normal repair and growth. As a result, they can churn out thousands of new clonal viruses in a few hours.

Viruses are contained within a protein shell (or capsid) that is coated with markers used for identification, called spike proteins. Inside of the virus protein coat, a nucleic acid genetic code is contained that may be single- or double-stranded DNA (or RNA for retroviruses), together with some additional proteins. All viruses are designed to utilize the basic cellular ribosomes, tRNAs, and translation factors that all cells use to synthesis their own proteins. They are thus specifically made to do what they were designed to do.

The human immune system protects from virus invaders by producing antibodies that bond to certain parts of the protein covering of the virus, the spikes, preventing the virus from interacting with the host cells. All vaccines work by causing the body’s immune system to produce antibodies which result in innate resistance. Thus, when a pathogenic virus enters the body, the body is ready to aggressively attack it before it is able to infect many body cells.

Many viruses are very specific in what cells they are able to infect. The polio virus can infect only certain kinds of nerve cells, specifically motor neuron cells which control muscles for such things as swallowing, circulation, respiration, and movement of the trunk, arms, and legs.[1] Human nerve cells have a protruding protein structure on their surfaces that the virus must interact with in order to enter the cell. It acts much like a lock and key. When poliovirus encounters the nerve cells, the host protruding receptor spikes must attach to the virus particle, and it gains entry if the lock and key match. Once the virus is inside the cell, the virus hijacks the cell’s DNA-based protein assembly process, making thousands of copies in a few hours. Pathogenic viruses then may kill the cell and spread the clones throughout the body to infect other cells. Like a chain reaction, in a few hours thousands of cells are infected and millions of viral clones are now inside of the host.

Viruses are Workhorses of Molecular Biology

In contrast to polio viruses, many kinds of viruses can infect a large number of different cell types. For this reason, genetically-modified viruses can be used by scientists to carry foreign DNA into many different kinds of cells. This approach provides the basis for the now rapidly growing list of experimental gene therapy treatments. Because of the extensive use of viruses in cell biology research, and their potential as therapeutic agents, understanding viral structure and function is critically important.

A spherical influenza virion is designed very different than many viruses. It consists of a protein coat containing a hodgepodge of hundreds of proteins that originate from both the virus and its host.[2] In contrast, some viruses, such as the adenovirus, which is shaped like a perfect icosahedron, are made up of irregular influenza particles that are difficult to crystallize, making the study of its structure difficult as well.

The Many Roles of Viruses

One main role of viruses is to control the spread of bacteria, such as bacteriophages, or phages for short. Bacteriophages attack only their host bacteria, not human cells, so are good at keeping bacterial numbers in check without harming the host. Without this control, bacteria would soon take over a good portion of the world. Enterobacteria phage lambda is a bacteriophage that specifically infects the bacterial species Escherichia coli, known as E. coli for short—the bacterium that inhabits the human gut. Phages represent the most numerous and diverse replicating entities on Earth.[3]

Phages can reproduce via a lytic lifecycle, in which the phage makes proteins that produce holes in both the plasma membrane and outer cell wall. The holes allow water into the bacteria, causing the cell to expand and burst like an overfilled balloon, killing the bacterium and releasing the new phages. Some phages alternate between a lytic lifecycle and a lysogenic lifecycle, in which they don’t kill the host cell but make copies with the host’s DNA each time the cell divides. The fact is, “phages play key roles in the biology of microbes, which themselves impact environments at large.”[4] Now, with this brief background on viruses in general, I will detail some of the facts about the coronavirus.

The Coronavirus

The coronavirus identification protein, called the spike, is a multifunctional molecular machine that allows coronavirus entry into host cells. The spike protrudes from the virus surface, producing the appearance of a crown (corona is Latin for crown). It is a zoonotic virus, which means that it can jump from animals to humans. Other zoonotic viruses include SARS (which causes Severe Acute Respiratory Syndrome) or Ebola, caused by ebolaviruses that produce hemorrhagic fever in humans and other primates. In the coronavirus case, it may have come from a bat, a popular animal sold in the largely unregulated local animal markets of Asia.[5]

A research article published four years ago detailed how the coronavirus enters into cells. Notice the detailed level of knowledge of its molecular structure scientists had at that time:

It first binds to a receptor on the host cell surface through its S1 subunit and then fuses viral and host membranes through its S2 subunit. Two domains in S1 from different coronaviruses recognize a variety of host receptors, leading to viral attachment.[6]

The study then warned that

Coronaviruses pose serious health threats to humans and other animals. From 2002 to 2003, severe acute respiratory syndrome coronavirus (SARS-CoV) infected 8,000 people, with a fatality rate of ~10%. Since 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has infected more than 1,700 people, with a fatality rate of ~36%.[7]

The report then added,

In general, coronaviruses cause widespread respiratory, gastrointestinal, and central nervous system diseases in humans and other animals, threatening human health and causing economic loss. Coronaviruses are capable of adapting to new environments through mutation and recombination [causing changes in the spikes] with relative ease and hence are programmed to alter host range and tissue tropism efficiently. Therefore, health threats from coronaviruses are constant and long-term. Understanding the virology of coronaviruses and controlling their spread have important implications for global health and economic stability.[8]

This warning was ignored at our peril. The spikes of some viruses, such as those that cause colds and the respiratory flu, are engineered to change their spike epitope traits, i.e., their characteristic shapes, so we call them a new strain. When this happens, the immune system no longer recognizes it as a threat. Once we have been exposed to the new strain, and the immune system has built antibodies to it, we are no longer likely to become ill from that strain. When enough hosts become resistant, herd immunity usually prevents its rapid spread to those who are not resistant. The reason why we can come down with the flu each year is because a new flu strain arrives that we are not immune to unless we have had a flu shot. Designers of the annual flu vaccine have to predict which new strain will dominate during the next flu season. Microbiologists usually guess correctly the 3 or 4 most likely strains and prepare for them, but can and do miss the strain that dominates.

Many viruses, such as polioviruses, do not possess the system to alter their spikes, and once we have polio, or a polio shot, we are no longer susceptible to the disease. The reason a few viruses cause so much disease and death is because they, for various reasons, end up in the wrong host, causing a mismatch problem. Examples include Coronaviruses (SARS, MERS, COVID-19), HIV, Ebola and others which do not cause problems when living in their normal hosts, such as bets, but in the rare event they end up in the wrong host such as in humans, they can cause major problems. Another concern is the ability of a virus to mutate. This is similar to what occurs in bacteria when the well-known E. coli, a probiotic bacterium that normally lives in the intestines of humans and animals, mutated into the O157:H7 E. coli strain which can cause death in humans.

Summary

Virus-host relationships are enormously complex. The reason they cause such harm and death now is likely a result of the mutations in living things and viruses that have been steadily accumulating since the original perfect creation. For some viruses, the mutational load may cause burnout, leading to their inability to infect a potential host. This may be happening now with the coronavirus COVID-19. The health problems we experience from viruses are caused primarily by two factors: (1) entry into the wrong host (2) mutations that cause their normal and proper function to be perverted. These are examples of devolution, not evolution.

References

[1] “How the Poliovirus Works.” https://amhistory.si.edu/polio/virusvaccine/how.htm
[2] Sharlach, Molly. 2014. Anatomy of a Virus. The Scientist Magazine, September 16. https://www.the-scientist.com/daily-news/anatomy-of-a-virus-36843.
[3] Nabergoj, Dominik, et al. 2018. Effect of bacterial growth rate on bacteriophage population growth rate. Microbiology Open 7(2):e00558, October.
[4] Clokie, Martha R.J., et al. 2011. Phages in nature. Bacteriophage 1(1): 31–45, January-February
[5] Cyranosky, David. 2017 (with Editor’s note, January 2020). Inside the Chinese lab poised to study world’s most dangerous pathogens. Nature 542:399-400,February 22, p. 400.
[6] Li, Fang. 2016. Structure, Function, and Evolution of Coronavirus Spike Proteins. Annual Review of Virology  3(1): 237–261, September.
[7] Li, Fang. 2016. (Ref. 6)
[8] Li, Fang. 2016. (Ref. 6)

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Dr. Jerry Bergman has taught biology, genetics, chemistry, biochemistry, anthropology, geology, and microbiology for over 40 years at several colleges and universities including Bowling Green State University, Medical College of Ohio where he was a research associate in experimental pathology, and The University of Toledo. He is a graduate of the Medical College of Ohio, Wayne State University in Detroit, the University of Toledo, and Bowling Green State University. He has over 1,300 publications in 12 languages and 40 books and monographs. His books and textbooks that include chapters that he authored are in over 1,500 college libraries in 27 countries. So far over 80,000 copies of the 40 books and monographs that he has authored or co-authored are in print. For more articles by Dr Bergman, see his Author Profile.

 

Editor’s Note: It’s interesting to note how strictly that cleanliness was emphasized in the Law of Moses to avoid unclean animals (like bats) and quarantine the sick to prevent infectious disease. That’s good advice for us today. In the current coronavirus pandemic, individuals should take care to follow the guidelines set forth by the administration’s response team. The main thing is avoiding contact with the virus, which usually enters through facial orifices. Since individuals can be carriers without symptoms, self-quarantine is the best way for now to “bend the curve” down and prevent catastrophic mortality rates and infection levels that could overwhelm the nation’s healthcare resources.

We’re all in this together. For your part, practice social distancing, wash your hands frequently, and avoid touching the face. In addition, wash clothes and disinfect surfaces that may have been exposed. In time, herd immunity should kick in. When vaccines and medications become available, a recurrence will most likely be preventable. It remains to be seen how long immunity will last, and whether an individual can be re-infected.

Realize that the vast majority of viruses are beneficial. Viruses swarm around us all the time. There are far more of them in and on our bodies than our own cells. Bacteria outnumber our cells 10 to 1; viruses probably 100 or 1,000 to one! Only relatively few cause harm. So don’t fret viruses; people have lived with them since creation.

In the meantime, the springtime beauty of nature goes on! Get some sunshine and take walks in nature for prayer and refreshment. Use the occasion to minister remotely to others and build relationships with family and friends.