The role of each individual mutation is still unclear, but a particular mutation in the spike protein called N501Y is noteworthy because all three variants have it. The spike protein is how the coronavirus enters cells, and N501Y is in an especially important region called the receptor-binding domain, which latches on to the cell. An N501Y mutation may make the spike protein stickier, allowing it to bind to and enter cells more readily. Such a virus could become more transmissible. On the plus side, however, the mutation doesn’t seem to affect immunity from vaccines.
Here’s how to read the names of the mutations, by the way: Proteins are made up of building blocks called amino acids. N501Y means that the 501st amino acid was originally an N, which stands for the amino acid asparagine, but has been changed to a Y, which stands for tyrosine.
N501Y is not unique to these three variants, though; it’s been found in a number of sequences around the world. What is unusual about these three variants is that they also have an additional constellation of other mutations in other parts of the virus. A change in a variant’s behavior, such as increased transmissibility, is probably “due to not just one mutation, but multiple mutations,” says Emma Hodcroft, a molecular epidemiologist at the University of Bern. The U.K. variant has more than a dozen other mutations, which have not been scrutinized as much as N501Y. But the variant’s increased transmissibility is looking more certain: It’s growing more prevalent not just in the U.K., but also in Ireland and Denmark, two other countries that regularly sequence large numbers of samples. The CDC recently warned that it’s likely to become the dominant variant in the United States by March.
(Scientists have given all three variants more specific names, but they have not, alas, standardized them yet. The U.K. variant is also known as B.1.1.7, and 20I/501Y.V1, and VOC 202012/01. The South Africa variant is sometimes called B.1.351 or 20C/501Y.V2. The Brazil variant is known as P.1 and 20J/501Y.V3.)
The South Africa and Brazil variants also have a second and third mutation in common in the spike’s receptor-binding domain: E484K and K417. Scientists know a little bit more about the E484K mutation. It switches a negatively charged amino acid for a positively charged one; it’s like flipping a magnet. This likely changes the spike protein’s shape as it is binding to a cell, but this change seems to work in synergy with the N501Y mutation, Andersen said. These mutations, possibly along with others, may make the virus better at binding to cells.
But the South Africa and Brazil variants might have an additional advantage. A recent study suggests that viruses with the E484K mutation might be better at evading antibodies from the blood plasma of recovered COVID-19 patients. Some viruses with this mutation could become a little better at reinfecting people or even infecting vaccinated people.