Flu season is upon us and the movie Contagion about a global epidemic is out in the theaters. So clearly it is time for a three-part Common Science series on viruses, the immune system, and influenza. 

Viruses are frightening, but they are also fascinating. At the top of the page are illustrations of the HIV (top left) and influenza (top right) viruses. The graphic of influenza provides a good guideline for a typical virus. At the heart of a virus is a nucleic acid, either DNA or RNA, which contains the genetic instructions that the virus will give to the cell it infects. The nucleic acid is encased in a protective protein coating called a capsid. In many viruses like influenza, the capsid layer is further covered with a layer of lipids (fats) as additional protection. (As a quick aside, the lipid layer is something viruses steal from the cells they infect, pernicious buggers that they are.) On the outside of the virus are protein spikes or tails which often have long, hard-to-pronounce names. For the rest of this blog I will just refer to them as protein spikes. 
Now that we know the structure of a virus let’s get back to the fascinating part. Consider the parts of the virus, a nucleic acid with some protective coating(s), and some protein spikes. A virus is not really life. Dictionary.com defines life as follows:
1.       The condition that distinguishes organisms from inorganic objects and dead organisms, being manifested by growth through metabolism, reproduction, and the power of adaptation to environment through changes originating internally.
2.       The sum of the distinguishing phenomena of organisms, especially metabolism, growth, reproduction, and adaptation to environment.
Being alive requires having a metabolism. Viruses do not eat, or grow, or have respiration. They are just a collection of molecules which, when not infecting a cell, do nothing. As such, they are not alive. This makes for a clear contrast with the other germs which typically make us ill, bacteria. Bacteria are organisms with cells walls, nuclei, metabolisms, and reproductive processes. Bacteria are alive, so we can kill them. As we will explore in this series, the fact that viruses are not alive is part of what makes them so challenging to fend off and eliminate.
Despite all of our advances in medical science, the origin of viruses remains an open question. There are two primary theories on the origin of viruses:
1.       That viruses began their evolution as small cells and over time ceased to reproduce their entire organism, evolving into the parasitic particles which they are now.  There are in fact some small cells that invade and infect other larger cells, giving credence to the idea that viruses once had this form. The theory is that over time the viruses developed a strategy to move from host cell to host cell without needing to maintain their own cell during the journey. Personally, I don’t find this theory to be very compelling.
2.       That viruses co-evolved with life starting from the primordial ooze where the first organic molecules began to assemble. The self-assembly of organic molecules can be explained by basic thermodynamics. If you take atoms of carbon, hydrogen, oxygen, and nitrogen, put them in water and add energy, some of the atoms will assemble into amino acids and other organic molecules which make up living organisms. Through some unknown process these simple organic molecules organized into life, which has complex cells, DNA, and metabolic processes. If you consider a virus, it’s somewhere in the middle on the complexity scale between a molecule and a cell, like a stage you have to pass through on the way.  In this theory viruses were formed during the very beginning of life they have been infecting us ever since. This theory is more compelling to me.
So if viruses are not alive, what do they do and how do they do it? A virus, as long as it is not subjected to harsh conditions, is fairly stable. As it moves through the world, in saliva, on a counter top, or in a sneeze-induced projectile, it is waiting for its protein spikes to find the right cell. Once the virus finds a cell to which protein spikes can attach, it then migrates into the interior and takes over operations. Since a protein spike-cell wall match is necessary for the virus to enter, certain viruses can only infect certain cells. Once inside, the nucleic acid in the virus starts giving instructions to the cell, instructions which override those coming from the DNA in the nucleus of the cell. The virus then forces the cell to make copies of the virus, lots and lots of copies. After enough copies have been made, the virus moves on to other cells either by killing the host cell or diffusing back out through the cell wall.
While the virus is inside the cell some interesting things can happen.   The virus can make a mistake in creating a copy of its DNA or RNA. Some viruses can swap DNA with the nucleus of the host cell. The most interesting, and frightening, possibility can occur when a cell which is already infected is invaded by a second type of virus. Now the two viruses can swap DNA. All of these DNA swaps and mistakes are called mutations, most of which create DNA which is not viable and cannot perpetuate itself. But when the DNA is viable, a new strain of the virus is created. When the new strain comes from a swap between two different types of viruses a pandemic, akin to that portrayed in Contagion, can occur. I’ll review pandemics in part 2 of this series.
[Quick Fact Check on Contagion: Generally I thought the science treatment in the movie was OK. However,  at one point the movie implies that the flu virus which is killing everyone has mutated by swapping DNA with HIV in a “cluster in Durbin, South Africa.” Since the protein spikes on influenza only allow it to infect epithelial cells in the respiratory tract and the spikes on HIV only allow it to infect T-cells in the immune system, they have no opportunity to swap DNA and create a mutated strain.]
Viruses can also leave the DNA of the cells they have infected cells permanently altered, either by donating some of their DNA or damaging the original DNA in the cell. The damage left by viruses can be quite serious. For example, women who get human papilloma virus (HPV) are far more susceptible to cervical cancer. Merck Corporation has developed a vaccine for HPV called Gardasil which is being given to teenage girls all across the county which will help protect them from being infected with this virus and, thereby, dramatically lower their chances of getting cervical cancer. Lately, HPV vaccination has become an issue in the campaign to become the Republican Party’s presidential nominee. I’ll try to refrain from political commentary this week, but you have to admit that they are provoking me.
Once you are infected with a virus, your immune system mounts an impressive, multi-pronged defense which slows or prevents the virus’ ability to replicate or enter new cells. The battle between your immune system and the virus is also a fascinating topic and will be the subject of part two this series.

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