A new variant of SARS-CoV-2, named Omicron, dominated the news this week. Detected in South Africa, it is reported to be highly transmissible and have many mutations in the spike protein, making it unlikely that current vaccines will be effective against it. But how true is this and what can we expect in the coming months?
It seems just as we are recovering from one lockdown, another is set to begin. With less than a month until Christmas, the news of the omicron strain is a blow, however as a virologist this new strain was somewhat expected. Any virus, particularly one made of RNA like coronavirus, mutates as it spreads through a population. These mutations can be thought of as mistakes or accidents that happen when the virus is copying itself and many are bad for the virus (see post on Molnapurivir), however some mutations can lead to a virus that is even better adapted. Helpful mutations (for the virus) can increase transmissibility, environmental survival or evasion of the immune system. Mutations that lead to evasion of the immune system are particularly useful, because they provide the virus with some reprieve from our defence systems, including antibodies.
For a well-known example, consider influenza virus. A relatively harmless virus to most people, this virus mutates so rapidly that new vaccines are needed each year to keep up with the new strains (yearly flu-shots). Someone who is unvaccinated could potentially get infected with influenza viruses multiple times a year, each time with a different strain. Importantly, even someone who is vaccinated can get infected if the virus has mutated enough to become different from the vaccine strain.
Image: Yearly flu shots are required to combat the rapid mutation rate of influenza virus. Photo credit CDC on Unsplash.
We have been living with COVID now for almost two years, so it is unsurprising that so many strains have arisen. However, there is a difference between a new SARS-CoV-2 variant and a variant of concern. For the past year and a half, variants have been denoted using a Pangolin lineage: a numbering system aimed to track the evolution of strains. For example, a B.1.23 and B.1.5 strain both evolved from the parent B.1 strain, which evolved from the B strain. However, this rapidly became too complex for mainstream media, and in 2021 the World Health Organisation decided to introduce the variant of concern labelling, denoted by Greek letters. The original SARS-CoV-2 strain was designated Alpha, the main strain circulating in 2020 was Beta, and many others have followed. It is important to note that not every new strain is given a Greek name, but only the concerning ones.
So what makes a variant concerning? Variants of concern tend to have accumulated enough mutations over time to be quite different from previous variants, or have major mutations in important regions of the genome. Probably the most important region of the genome is the Spike (surface glycoprotein). This protein protrudes from the outside of the virus and is the first thing that contacts our cells and immune system. It is also the first thing recognised by antibodies trying to fight it. If this protein mutates too much, it can become unrecognisable to our immune system and therefore run rampant and unchecked. This means that infection with a previous strain e.g. Alpha is unlikely to protect you from reinfection with a new variant of concern e.g. Omicron.
Image: a model of SARS-CoV-2, the viral cause of COVID19. The surface glycoproteins (spike) are shown in red and are the target of the immune system and vaccine-induced antibodies. Image credit CDC on Unsplash.
Unfortunately for us, the current COVID vaccines use the older variants to teach our body how to fight the virus by producing antibodies that can recognise the spike protein. If new variants arise with mutated spike proteins, our vaccine-induced antibodies may not be able to recognise them. This seems to be the pressing issue with Omicron – it contains more than 30 mutations in the spike protein, making the efficacy of previous vaccination questionable. Scientists are currently testing just how effective vaccination is against this new variant and studying its transmissibility. It is too early to tell just how dangerous this new variant is, and the next few weeks will be crucial, with reports that infected travellers have reached NSW.
So what will the next few months look like? If Omicron is successful at evading vaccine antibodies and/or more transmissible, it is likely that it will spread rapidly. Strict hygiene practices including wearing a mask in public, regularly sanitising and social distancing in crowded places will go a long way to reduce the severity and spread of outbreaks. The best thing, in my opinion, would be to rapidly develop a booster shot for Omicron. We have sequenced the genome of the Omicron variant and know exactly how it differs from previous ones. With this knowledge we can tailor design a new vaccine which can augment previous ones to teach our body how to recognise the Omicron variant – exactly like the yearly flu shots. Unfortunately mutation and variation is in the nature of viruses, especially ones as widespread as SARS-CoV-2. This is not the first mutation and it will not be the last, however we are much more prepared than we were this time two years ago. We have base vaccines, the technology and the infrastructure to develop more. Booster shots may be a part of the next few years for continual protection and antiviral development for treatment is progressing rapidly. But until that is an accessible reality, masks and distancing are best strategy to minimise your risk this holiday period.
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