Let’s take a step back and look at how organisms use genetic codes to produce the building blocks of life, the proteins.
How do organisms reproduce genetic material?
Most organisms have DNA as their genetic code. DNA in organisms is the code that dictates what proteins the organism can produce. DNA is made up of a sequence of 4 different molecules called nucleotides arranged in a sequence. There are two strands of DNA in most organisms (some viruses actually only have 1 strand) and these strands are identical in sequence and joined together to form a helix. The helix coils up very tightly to form the chromosome of the organism. Ta dah!
In order to reproduce, a cell has to uncoil its DNA, split its double stranded DNA sequence into two single strands, and then copy each single strand back into a double strand. This is done by an enzyme called DNA polymerase. This video shows how this happens (it’s a bit dull, but good). DNA polymerase has lots of ways of detecting and correcting errors in the new code of DNA that allow it to produce a faithful reproduction of the original strand of DNA. This process means that mutations in DNA are very uncommon.
Strands of RNA can be produced in a similar way by an enzyme called RNA polymerase. Unfortunately, RNA polymerase isn’t very good at detecting errors and correcting them, and so mutations in RNA do occur and are actually pretty common, “hello Omicron!”
But what do we need DNA or RNA for?
DNA to RNA to protein
Most of life is controlled by the production of proteins which carry out various body functions. We are essentially made of different proteins which all have specialist jobs, e.g. haemoglobin is a protein that helps us transport oxygen from the lungs around our bodies, insulin is a protein involved in the use of sugars, amylase is a protein in the gut which helps us breakdown starch into sugar. We are our proteins; but how are they produced?
In most organisms, in order to produce a protein from individual amino acids the DNA code has to be “read” to see what sequence of amino acids is needed to be included and in what order. To do this the DNA is converted into messenger RNA (mRNA), by an enzyme called RNA polymerase, which is then released from the chromosome and sent out into the cell to the ribosome where protein production happens. The mRNA binds to shorter sequences of RNA called transfer RNA (tRNA) which picks up the specific amino acids and presents them to the ribosome which then combines the amino acids into a protein chain. Each specific group of 3 nucleotides in the tRNA (and hence in the original DNA) represents a specific amino acid. It sounds pretty complicated, but I found this video that also helps explain what is going, I think it’s pretty good…. But ECIC thinks it’s even duller than the last one!!! She thinks this one is better although not so microbiology related!!! unless you read this blog!
Anyhow back to proteins…It may seem like a convoluted way to produce proteins but the reason this method has evolved for most organisms is that DNA is much more stable and has a better checking mechanism than RNA; therefore it is much less prone to mutations which might actually be harmful to the cell and the organism.
Viruses can take a short cut to proteins
RNA viruses, like SARS CoV2, take a short cut to protein production. Remember that viruses aren’t alive, they cannot reproduce themselves. Instead, they hijack the host cells reproductive mechanism in order to produce proteins and more RNA.
RNA viruses don’t need DNA, when released into the host cell the RNA sequence of the virus is automatically used by the host cell ribosome as mRNA, attracting tRNA and therefore causing proteins to be reproduced. It’s quick, simple and efficient.
But remember RNA is unstable and so it is common to get errors in the sequence of RNA and this leads to different sequences of proteins being produced. Mutants!!
Organisms with different changes to their genetic codes, and hence changes to their proteins, are what we often refer to as mutants, or in the context of viruses, variants.
So, when the news tells us about a new variant of SARS CoV2 e.g. Alpha, Delta or Omicron, then what they are talking about is SARS CoV2 which has changed its RNA sequence and is therefore able to produce different proteins.
But why does this matter?
Immunity is based on proteins
Our immune system has evolved to recognise foreign proteins, known as antigens, and then get rid of them. The system is carefully controlled so that the immune system ONLY targets the specific foreign protein; if the immune system targeted one of our own proteins, we would get what is known as an autoimmune disease. Once our immune system easily recognises the foreign protein as abnormal, we become immune to the disease.
Vaccines are used to expose the immune system to specific proteins which then help the immune system recognise potential pathogens without actually having to have the infection first. It is usually a safer process than getting sick in order to become immune. In the context of SARS CoV2 the vaccines are triggering an immune response against a viral surface protein called the spike protein.
However, because the immune system is very specific (it has to be to prevent autoimmune diseases) small changes in the foreign protein (e.g. the spike protein) can lead to the immune system no longer recognising the antigen and we become no longer immune to the disease and can get it again.
THIS is the worry with all variants of SARS CoV2. We are worried that mutations in SARS CoV2 will result in variants that have spike proteins that are no longer recognised by the immune systems of people who have either been vaccinated or had Covid-19 before, and who could become infected again. We all have been “told” by the news that this would essentially return us to the “beginning” of the pandemic with everyone being at risk of infection again and many thousands of people getting severe Covid-19 and dying. Clearly, no one wants that to happen! But not all mutations in viruses are bad! This is where I may get a little controversial…
Are all mutant viruses bad?
The simple answer is in fact no, not all mutant viruses are bad. Most mutations in viruses are actually detrimental to the virus. Most of the time that the genetic code is changed, the protein that is produced no longer has the correct sequence of amino acids, and hence it won’t be able to perform the function it was supposed to do. If the virus is not able to produce all its proteins it will no longer be able to reproduce and will not infect other cells or other people. So a mutation in the spike protein may be detrimental to the virus, or it might not!
It is also possible for a virus to mutate so that it still produces functional proteins, but that these new proteins result in a virus that is less capable of causing disease so that people get infected but don’t really get sick. Mutations don’t automatically make the virus “more transmissible”, “more virulent” or “more deadly”… that’s just what we are “told on the news”. In fact, over time becoming “less capable of causing disease” is probably the most likely way a virus would evolve. Honestly!
Think about it. What is better for a virus? Make your host really sick so that they either die or self-isolate, so they don’t infect other people. The result is that the virus doesn’t spread, doesn’t reproduce, and therefore the virus eventually dies out. Can this happen naturally? Sure, it’s what we think happened to the original SARS CoV back in 2003; the virus was so aggressive to humans that it burned itself out. The virus evolved in such a way that it’s fitness to reproduce and spread was compromised and hence selective pressure caused it to disappear. On the other hand, if SARS CoV had evolved to be less aggressive it would have had much greater opportunity to spread and could even have caused a global pandemic back in the early 2000s!
So, what would happen if SARS CoV2 mutated to produce a variant that could still spread but which didn’t make people that sick; maybe they just got a bit of a cold or lost their smell? In this case we would have a virus capable of naturally inducing immunity without anyone being sick. Would this be a bad thing? Is this a virus we would want to stop spreading? Hmmmmm… it’s an interesting thought.
If SARS CoV2 had spilled over in 2019 and caused millions of people to get a bit of a cold would anyone have even noticed? Probably not. We would have all said, “it’s a bit of bad year for colds” and carried on regardless.
In fact, we use mutant viruses all the time to vaccinate against infections; we just call then “live attenuated vaccines” to make them sound better than “genetically mutated viruses”, but that is what they are. The viruses in these vaccines have been modified to make them good at getting the immune system to recognise the more aggressive naturally occurring viruses without the person getting sick e.g. mumps, measles, rubella (MMR), chicken pox, Rotavirus and yellow fever.
So, if you’re watching the news and wondering why SOME scientists are advocating more measured responses to variants (or mutants) of SARS CoV2 then remember that not all mutants are bad, and that as long as these mutant variants are not making people sick then we don’t need to panic and start locking the country down again. In fact, if a variant causes much less severe infections then we are probably better off letting it spread to become the dominant strain in the population. That way it might actually protect us from more severe infections in the future. At the moment we aren’t being told anything about the Omicron variant to suggest it is more severe even if it may be spreading faster than the Delta variant… just because it spreads faster doesn’t make it more severe… let’s wait and see.