Looking for science behind “the new mutant strain”​ headline?
By: Think Bold Horizons
Tags: Mutation, Science, Immune System, Antibody, Covid 19

Here are key points about what is known and what scientists are working hard to find out.

Events are rapidly changing. This article was written on December 19th, 2020 and is a personal synthesis of the available evidence.

It is hard to know how a new variation could affect how quickly SARS-CoV-2 spreads or how serious the resulting disease will be.

Without getting into all the science, the best precaution is to avoid getting any of the variants. Protect yourself and your loved ones. This is a top priority. Wear a mask. Keep socially distant. Get vaccinated when you can.

Variations occur, a lot.

Variations in viruses like SARS-CoV-2 are a common occurrence. Most of the time it makes no difference to the protein that is formed.

There are also variations that cause a difference in the protein — these are called non-synonymous mutations. A lot of these variations have already happened. Scientists studied 126,219 viral genomes and found 1,777 different non-synonymous mutations in spike glycoprotein’s gene S.

We care about those variations, because the spike protein is the key that fits the ACE2 protein ‘lock’ in our bodies. Think about how hard it can be to get a regular house key copied accurately: when there is enough of a variation, the key no longer works. The good news is many of these viral variations will have no effect, or could even make it harder for the virus to enter our cells.

Thinking about the key-lock analogy, there is ‘drift’ of the virus. When you make a copy of a copy of a key, it gets a little bit further removed from the original template. This is also what is happening in the virus. Monitoring the natural ‘genetic drift’ helps scientists track how the virus is spreading.

What is happening in South England?

In December 2020, the number of people with the SARS-CoV-2 variant in the UK called VUI-202012/01 (VUI variant under investigation) was concerning enough to cause a heightened lockdown. This variant has accumulated 17 changes.

A key change is N501Y mutation in the spike protein. The location of this is in the figure below.

Location of variations in the spike protein

The spike protein is a chain of 1287 building blocks called amino acids.

A change in one of those 1287 amino acids has an exact location. So N501Y is a variation at amino acid 501. It is easy when you know!

The figure shows a representation of the spike protein with red to show where variations tend to occur.

Key Questions

Q: Will these variations cause a difference in transmission?

The question of cause versus correlation comes up here. How can we tell which is the case? This is a tough question to answer definitively. There are many types of expertise and data that are needed.

If the spike protein variation causes a better fit to the ACE2 protein ‘lock’ then that can lead to increased entry. Experiments to model the viral structure using computer algorithms, experiments in the laboratory with real cells, and tracking the spread of the virus will give scientists better information to answer this accurately.

The COVID-19 Genomics UK Consortium (COG-UK) is tracking N501Y because it shows increased binding affinity to human ACE2 receptor. This means the viral key better binds to the human lock than before.

“There is currently no evidence that this strain causes more severe illness"

One practical step to take is: assume that others are carrying the virus and take precautions to avoid the spread.

Q: Will this variation affect the new vaccines?

Here’s what we know.