The Language of COVID: A Primer

Two years ago, many of you probably had never even heard of many of these terms. Now they're flying around left, right, and center, as are misstatements, misunderstandings, and misdeeds. For people without a solid scientific or medical background, it may sound like Greek. And, Greek letters are also flying around, both literally and figuratively, something I wrote about in July.

So, I thought that it might be helpful to put together "The Language of Covid" – a set of definitions that all of you non-scientists out there might find helpful. Maybe even a few scientists.

SARS-CoV-2

The virus that is now plaguing the world was briefly called the "Wuhan Virus." Later, in order to avoid stigmatizing Wuhan, the origin of the virus, it was referred to as the "novel coronavirus" – an ambiguous and rather stupid name. Neither term is used anymore. In February 2020 it was renamed SARS-CoV-2, which is an abbreviation for "severe acute respiratory syndrome coronavirus 2." 

Covid-19

Covid-19 is the disease caused by SARS-CoV-2. The 19 stands for the year 2019 when the infection first showed up in China.

RNA

Ribonucleic acid (RNA) is one of the two types of genetic material, the other being DNA (deoxyribose nucleic acid). All living organisms contain one or the other (1,2). The purpose of both molecules is to instruct cells on how to assemble amino acids into proteins. Think of RNA or DNA as instruction manuals. They provide information for how to make protein, but cannot do it on their own (See section on mRNA). One important difference between the two is that RNA is less stable than DNA, which is why RNA viruses, such as SARS-CoV-2 and influenza mutate more rapidly. This rapid mutation is the reason we're seeing different variants popping up all over the world. 

Messenger RNA (mRNA) 

Messenger RNAs are short strands of RNA that are made by RNA or DNA within the cell nucleus. The structure of a given mRNA molecule is dictated by the structure of the DNA or RNA that makes up the gene. The mRNA then floats out of the nucleus into the cytoplasm (the liquid outside of the nucleus that fills the cell) where protein-making machines called ribosomes are found. The ribosomes have one job – to make proteins based on the structure of the mRNA. So, mRNA really is a messenger. It takes information from the cell's nucleus and brings it to the place where protein is made. Once its job is done the mRNA breaks down to its original components. Think of mRNA as an instruction manual and ribosomes as the poor sucker who has to read the manual and assemble an IKEA bookshelf. 

Protein - Proteins are large polymers made up of 20 different amino acids. Proteins are responsible for the structure and function of all living organisms. The number and order of the amino acids determine the properties and function of a particular protein. This is controlled by the cell's genome (RNA or DNA). A single human cell contains 42 million protein molecules.

Spike proteins

Spikes are small proteins that protrude from the surface of viruses. They are not unique to SARS-CoV-2; these structures are found on the outside of all viruses, where they serve to attach the virus to the host cell and transport it into the cell. 

mRNA vaccine

The two approved mRNA COVID vaccines are very similar and work in the same way. About 4,000 nucleobases ("pieces") code for (another way of saying provide information to the ribosomes for protein synthesis) the spike protein chemistry. Once the sequence of an mRNA strand is known it is "easy" to synthesize it using well-established chemistry techniques. The synthesized mRNA is coated with a tiny oily glob called a lipid nanoparticle, which stabilizes the mRNA. ("Raw" mRNA injected into your body would not be stable enough.) A tiny amount of the encapsulated mRNA is injected into the arm. It then makes its way into your cells where it performs like any other strand of mRNA – "finding" a ribosome, which takes the information from the mRNA and turns it into many copies of the spike protein. (Ribosomes aren't that bright. They don't know or care what kind of mRNA they are fed. They just do what they're told.) The spike proteins are then released from the cell and are treated as a foreign pathogen; antibodies are formed to neutralize the spikes. When the virus tries to infect you the spike antibodies that were formed by the vaccine will "see" the spikes on the virus and act in the same way – attach to the viral spikes and prevent the virus from entering the cell.

Mutation

Mutation is the process that is responsible for evolution, whether in microbes or animals. It occurs when one of the gene's building blocks nucleobases (2), is mistakenly incorporated into a new, growing gene. For example, the infamous delta variant was formed by a single mutation out of the more than 4,000 nucleobases that carry the instruction to make the spike protein. In this case, the nucleobase guanine was mistakenly incorporated into the place in the gene where adenine should be. A mutation in a gene causes the "wrong" amino acid to be built into the protein. As a result, the amino acid #614 of the 1273 amino acids in the spike protein, "changed" from aspartic to glycine. (You may have seen the term D614G, which means that at position 614 of the spike protein aspartic acid (abbreviated D) was replaced by glycine (G).) This seemingly trivial change is anything but. The new protein had a better fit to the ACE-2 receptor – the place where the virus attaches. Hence, the delta variant.

Variant vs. strain

A variant is a different species that is formed by mutation. A strain implies a bigger difference, for example, MRSA (Methicillin-resistant Staphylococcus aureus) is a strain of Staphylococcus aureus that is resistant to a variety of antibiotics. Although the difference between the two terms is partly semantics it is safe to say that all strains are variants but all variants don't "qualify" as strains because they are too similar to the original organism.

Transmissibility, infectiousness, and virulence

Transmissibility is how easily a pathogen can spread between hosts. Infectiousness is subtly different; it is a measure of the ability of a pathogen to make you sick. Virulence is a measure of how sick the pathogen will make you. 

NOTES:

(1) Plants and animals also contain RNA. It works with DNA to enable protein synthesis but is not part of the genome. DNA is the boss.

(2) Although there is debate on whether viruses are living (I say no), they still require RNA or DNA to replicate. Since a virus has no nucleus their genetic material is stored in a protein core called a capsid. 

(3) The building blocks of RNA are guanine, uracil, adenine, and cytosine (abbreviated G, U, A, and C). DNA is also composed of G, A, and C, but uracil (U) is replaced by thymine (T).