Influenza virus, TEM (colorized). Photo by C. Goldsmith, CDC, Wikimedia Commons
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A couple of months ago an old friend and former Penn State colleague sent me an email in which she wrote: “Just wondering if all viruses are bad and wreak havoc? Do some viruses do good things? What is the overall function of them? Just what is the purpose of a virus on this earth, and how did it help get us to where we are today? I’m just trying to look at the bigger picture of things.”
I promised that I would pull something together for her, and after mining through some of my old Cell and Molecular Biology lectures about viruses and several recent papers on them, here is what I hope to be the “bigger” picture about viruses.
There are two, typical starting points in any discussion about viruses. The first concerns how small and simple in structure they are, and the second is how abundant and diverse they are.
Size:
Most viruses range in size between 10 and 300 nano-meters. A nano-meter is one billionth (10-9) of a meter. For comparison,an average cell in your body is about 100 micrometers in diameter and an average bacterium is about 2 micrometers in diameter. A micrometer is one millionth (10-6) of a meter. So, without dwelling too much on the math, by volume an average cell in your body is a hundred million to a billion times bigger than a virus! Most viruses are so small that they cannot be seen with a light microscope, they can only be visualize with an electron microscope.
Simple diagram of a virus. Figure by domdomegg, Wikimedia Commons
Structure:
Viruses are extremely simple. They consist of a core of a nucleic acid (either DNA or RNA) surrounded by a “capsid” made up of proteins that is then, in some viruses, further surrounded by an “envelope” of lipids that is studded with glycoproteins. Viral nucleic acids typically encode the information for 30 or 40 genes, and these genes encode the information for the synthesis of a variety of molecules including the components of the viral capsid and most of the envelope. Viruses must utilize the metabolic machinery of a living cell to replicate themselves since they lack both energy generating systems for ATP and ribosomes for protein synthesis.
There, though, some “big” viruses out in nature. Recently, while exploring the waters of an artificial lake in Brazil, scientists found a virus that contains 74 genes! And, 68 of these genes have never been seen in a virus before!
Abundance:
How many virus “particles” exist on Earth? It is estimated that there are 1030 viruses in the Earth’s oceans and possibly an equal number on land and in the atmosphere. Sometimes it is hard to grasp the size of number expressed as exponents, but there are estimated to be “only” 1023 stars in the entire Universe! So, there are ten million times more viruses on Earth than there are stars in all the skies everywhere!
Another way to visualize this mind boggling abundance is to recognize that there are 50,000 viral particles in every drop of sea water, and, according to researchers at Virginia Tech (Environ Sci Letters, 2016) 10,000 viral particles in every millimeter of air. We are constantly introducing these viruses in to our lungs with each breath that we take!
We are absolutely surrounded by viruses!
Ebola virus (colorized SEM). U.S.Agency for International Development. Wikimedia Commons
Diversity:
Scientist have described and identified about 7000 species of viruses, but estimate that there may be millions or even trillions of actual species of viruses on Earth. Mathew Sullivan at Ohio State, for example, has thus far found (but not completely described or named) 200,000 different virus types in sea water!
If you consider all of the genetic information in the living systems on Earth, there is probably significantly more information contained in the summed set of the short, nucleic acid strands housed inside of viruses than in all of the information encoded in the long strands of DNA and RNA contained within every cellular, living organism (plant, animal, protist, fungi and bacteria). Viruses represent, then, not only a vast reservoir of genetic information and potential, but, and this may be the ultimate “function” of viruses in nature, viruses not only carry all of this genetic information, but they are also able to transfer this information between all types and all manners of cells. This ability to “horizontally” transfer genetic information between often totally unrelated species, may be a key factor in generating unique genetic combinations and driving the evolution of new species on Earth!
This is the “big picture!” This is what my friend was asking about! Viruses inject whole sets of genes into organisms and some of these genes work their way into the host’s cellular DNA. If the cells receiving these genes are reproductive cells (sperm or ova), then those genes will be passed along to the offspring of that individual. This is an incredibly more rapid mechanism for increasing genetic variability than simple nucleotide by nucleotide mutation of the host DNA!
Often these viral DNA inclusions are “silent” in the host cell, so no changes are seen in the organism. Sometimes, the impacts of these viral genes are disease and cell (or even organism) death. Sometimes, though, this additional genetic information conveys a fitness edge to the new organism, and via Natural Selection and evolution that more fit individual will predominate in its environment. A virus, then, can trigger a sudden and substantial change in an existing species!
It is possible to examine an organism’s DNA and pick out the viral sequences that has been added to it. In humans, for example, 8% of the 3 billion base pairs in the genome are from viruses. That means that there are 240 million viral nucleotide sequences in the average human genome! Some of these viral sequences do very important things. The genes that form the placenta, for example, are dominated by viral information! This suggests that the evolution of the placenta may have come about from a sequence of viral infections!
SARS-CoV2. Figure by Scientific Animations, Wikimedia Commons
Some recent published research about viral gene contributions include a study on sponges in which viruses contributed genetic information that enabled sponges to modulate their immune functions to better tolerate absolutely essential symbiotic bacteria (a 2019 paper in Cell Host Microbe). Also, a joint German and American research team studied heterotrophic zooplankta called “choanocytes” and found that they used viral DNA to established a rhodopsin based, non-chlorophyll photosynthetic energy system that augmented their typical heterotrophic life style! In Australia, an RNA virus that infects koala bears can cause leukemia and lymphoma and an increased susceptibility to chlamydia infections. This virus, though, has inserted itself into the koala’s DNA and become an inherited part of the koala genome. In some koala populations this viral sequence has mutated and may now be conveying some health benefits to the koalas! This report was published in the journal Cell last fall.
Of the 7000 or so species of viruses that have been described only 200 affect humans. Viruses have to enter cells in order for their genes to hijack the metabolic machinery of the cell to make more viruses. Entering a cell is not an easy thing even for something as small as a virus. On the cell membrane of a living cell are numerous proteins that act as enzymes or chemical receptor sites, or they allow and regulate the movement of many ions and molecules in and out of the cell. Often these membrane proteins are the doorways by which a virus enters a cell. The virus, though, has to fit very precisely into these channels in order to pass through them. Viruses that can pass through one species’ type of channel protein might not fit into a similar channel protein of a different species. So, many viruses can only infect certain species!
Life Cycle of SARS-CoV2. Figure by V. Asenio, Wikimedia Commons
The novel corona virus that cause COVID 19 is “SARS-CoV2.” I talked about this virus and what we initially knew about its disease in a special blog back in March 2020. SARS-CoV2 enters cells via the angiotensin converting enzyme 2 (ACE2) receptor that is located on the outer surface of the cell membrane. ACE2 normally functions to break down angiotensin II a protein that is part of a hormonal system that helps to control blood pressure. The studded, surface proteins of the corona virus (the physical feature that gives it its “crown-like” appearance on electron micrographs) match up to the ACE2 receptor and “open” the protein for the virus’s passage. Once inside the cell, the RNA contained in the corona virus takes over the cell’s metabolic machinery and begins to make huge numbers of new viruses. Eventually the infected cell ruptures and spills out the newly synthesized viruses which may then infect more cells in the host individual or be released in exhalations or coughs to potentially infect other people.
Variations in the molecular structure of ACE2 receptor (affected by genes or, possibly, by gender) may determine whether a particular individual “gets” COVID19 infections or it may affect how severe that infection might be.
So, we are all constantly bombarded by incredible numbers of an almost infinite variety of viruses. Most of these viruses cannot affect us since they are unable to cross though our cellular membranes. Viruses, though, are constantly changing and if a change involves its interaction with cellular proteins then that virus that once only affected, say, a chimpanzee or pangolin, may suddenly affect humans often with catastrophic consequences.
Viruses may represent the earliest life forms on Earth or they may have come about from the shed nucleic acids from the earliest cellular life forms. Either way, they represent a vast reservoir of genetic information that is flowing in between and constantly changing all of the other living species on Earth.