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Viruses! In the time of COVID-19, we are all talking about viruses all of the time, but our understanding is very surface level. What is this mysterious beast that has beset all of our lives? How can we understand it, and what hope is there?

I find comfort in understanding, and so in this time of quarantine, I have decided to spend some time studying viruses. Not exclusively SARS-CoV-2, the COVID-19 culprit, but that one will likely make appearances. I learn by writing, so I will write as I read, and perhaps you will learn alongside me. Virology is a deep field, and one could spend years and still only be a novice, but we will start at the top and see how far we get. This first post is a high-level introduction, full of gross generalizations, but I will explore these topics in greater detail in future posts. So, to begin--

What is a virus, anyway?

A virus is an intracellular parasite that relies on a host cell to replicate. Put another way, viruses are entities too small to be seen by an ordinary light microscope that do not eat, reproduce, or intend in the way that we normally think of living things doing, but instead must invade host cells to replicate themselves. (Of course, "invade" here implies intent, and it is likely as I write this that I will use many anthropomorphic terms to describe viruses. But that has more to do with the way I think as a human than any actual intent on the side of the virus; as far as we can tell, it does not want to replicate. It just de facto does.)

That is a functional definition of a virus, based on what the virus does. We might also use a descriptive definition: a virus is a container made of proteins and sometimes lipids that contains a payload of nucleotides. The nucleotides can be DNA or RNA, and collectively are called the viral genome. Viruses do not contain enough cellular machinery to reproduce or replace their components, and they therefore rely on the cellular machinery of host cells to read their genome to make new proteins and viruses. In other words, viruses are assembled from pre-existing components, and do not grow in the sense that animals, bacteria, and other traditionally living things do.

Do all viruses have capsids and genomes?

Nature being nature, there are all sorts of exceptions that live at the edge of our definition of virus. For example,

• Viroids are virus-like in that they are intracellular parasites that need host machinery to replicate, but they don't have capsids; they are short, circular RNA molecules, naked without containers, known for infecting plants. 
• Virusoids are similar to viroids, but they ride along with larger viruses, protecting themselves within the larger virus's capsid. 
• Prions, the devils behind mad cow disease, are submicroscopic infectious agents, but they have no genome and don't seem to derive any benefit from the host (e.g., replication). They are mis-folded proteins, and they induce host proteins to misfold or distort. 

Are any of these viruses? Not exactly, but that's more of a semantic distinction that humans make than a hard biological line. In any case, the molecular functioning of viroids, virusoids, and prions is different from what is described above for viruses, so we'll take them off the table for now.

Defining a virus is the first step, and in the next installments, we will learn more about each of these different components, starting with the nucleotide payload, or genome. See you next time!

Sources

• Image: https://commons.wikimedia.org/wiki/File:CMVschema.svg
• https://en.wikipedia.org/wiki/Viroid
• https://en.wikipedia.org/wiki/Virusoid
• https://www.scientificamerican.com/article/what-is-a-prion-specifica/
• Cann, Alan J. Principles of Molecular Virology (Sixth Edition). Academic Press, 2016. Chapter 1. https://doi.org/10.1016/B978-0-12-801946-7.00010-9.