With a name that could have been straight out of a comic book, it is no surprise people are feeling apprehensive about the new Omicron variant. And with a whopping 30 mutations in the spike protein, there may be cause for concern.
Omicron has recently been added to the phylogenetic tree of SARS-CoV-2, which uses DNA sequences to show how closely related the variants are. Instead of evolving from the delta variant as you might expect, Omicron is out on its own branch and appears to have evolved separately, leaving very few clues as to where it came from. Current theories of Omicrons’ origin include the jump of a different coronavirus from an animal to a human, a new strain that has evolved within a patient with a chronic coronavirus infection or a new strain that has evolved in an area with low rates of sequencing where it wasn’t detected until it spread to South Africa.
Sequencing data has revealed 30 amino acid substitution mutations within the spike protein of Omicron, which is found on the surface of the virus. This occurs when a mutation in the DNA sequence changes an amino acid, which affects the protein that the amino acids make up. This is like changing a step in a recipe, which means a different ingredient is added and results in the food you have made tasting different. We don’t know yet what the impact of these differences will be. There are also 3 deletion mutations and an insertion mutation in the spike protein of Omicron.
The location of 15 mutations in the Receptor Binding Domain (RBD) is alarming to some scientists, as this is the region that enables coronaviruses to bind to receptors on human cells and gain entry into the body. The vaccines used to protect against COVID-19 were developed based on the spike proteins of the alpha variant, so if the spike protein of the Omicron variant is very different, the vaccines may not provide as much immunity. The variant also poses a problem with PCR detection, causing what is called S gene dropout, affecting the detection of one of the genes used to identify coronavirus.
Here is a breakdown of the current mutations that have been identified in Omicron. Two mutations (H655Y and N679K) are located near the furin cleavage site, which plays a role in the entry of the virus into human cells. There is another mutation called P681H and it has been found in the Alpha variant as well. The final key mutation identified so far is N501Y, which affects how the virus binds with the ACE2 receptor on epithelial cells (outer layer of cells that line parts of the body) and this could increase transmission of the new variant.
The decision on whether to go into a lockdown or not balances on a range of different factors, and the lack of data available about the new variant poses a challenge for making this decision. Although the emergence of a new variant is worrying, the UK is pushing the population to get boosters to increase immunity and currently 68.34% of the population have a double dose of the vaccine. We are therefore in a very different situation to last Christmas. With so many dimensions of research needed to fully understand the new variant, it may be some time before the answer is uncovered. Only time will tell what Omicron will bring this Christmas.