What’s up with the United Kingdom? Now a new SARS-CoV-2 strain?

First, Britain gives us the chimpanzee adenovirus and a clinical trial where they mistakenly under dose the subjects (and label it a “breakthrough”). Then, on the basis of two poorly characterized adverse reactions to the Pfizer vaccine, they suggest anyone who’s had a severe allergic reaction to anything avoid the vaccine.

Now, the United Kingdom has announced, with great fanfare, that they have a new ‘Strain” of the SARS-CoV-2 virus that causes COVID-19 that is “60% more transmissible” and is partly responsible for the current infection surge in the U.K. This claim was trumpeted in every newspaper from the London Star to the Wall Street Journal, as well as most media outlets. The British also used it as part of the justification for more aggressive public health measures to contain their fast-moving outbreak of COVID-19.

There have been many claims of new strains of the virus that causes COVID-19. Most of these strains are variants of the virus, differing by only a few amino acids and the genome that codes for several thousand amino acids and four major proteins. The claims usually focus on the spike protein, which is the viral protein than binds to human cells and is the target of all the vaccines. Given the notoriety of this new “London” strain and the fear it’s generated, I decided to look more carefully at what defines this virus.

First, there is no scientific report showing any unique characteristics of this virus isolate. All of the claims come from media reports that feature microbiologists who appear very anxious, but provide no data to support their concerns.

Fortunately, I was able to access data on the website GSAID, run by a non-profit organization. It provides a reliable source of information about viral sequences related to human disease outbreaks and has a very good discussion of this particular virus isolate.

It describes this isolate as a new variant (not a new strain), which has been named VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01) This variant is defined by multiple spike protein mutations (deletion 69-70, deletion 144-145, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H). These 14 alterations in amino acids are present in a protein with 1,255 amino acids, and therefore represent a 1.1% difference in the sequence of the protein.

Despite there being 14 differences, some of the amino acid changes don’t alter the protein much because the substituted amino acids are similar to the original ones. Also, many of these changes are in locations that do not directly impact the binding of spike protein to human cells. In this case, only one significant alteration is in the spike binding region: N501Y meaning an asparagine substituted by tyrosine at position 501.

As shown in the diagram below, only N501Y (orange in Figure) and the two deletions (cyan in Figure) are in positions contributing to potential spike surface variations. The other alterations (blue in Figure) are further down in the spike protein structure and their effect is less clear. Therefore, while it would be interesting to look at the function of this variant spike protein and see whether antibodies (immunity) induced by the current vaccine will still neutralize this virus (they should), it really does not look like a major change!

Also arguing against a significant problem from VUI 202012/01 is the fact that most of these amino acid variants have been present in viral isolates since last May! In addition, there are currently 24,746 SARS-CoV-2 virus isolates identified from the U.K. (reported to the GISAID EpiCoV collection since November 1). Only a small fraction of them, about 6% (all from clade GR) share several of these mutations, meaning 94% of the COVID-19 isolates in the U.K. right now don’t have these mutations!

GSAID concludes that, “As seen on many occasions before, mutations are naturally expected for viruses and are most often simply neutral regional markers useful for contact tracing. The mutations seen have rarely been affecting viral fitness and almost never affect clinical outcome.” While investigations into the detailed effects of these amino acid changes should be done, there is no reason to think they will result in a “super strain.”

The U.K. might better focus on other causes of the current surge in infections, like keeping the pubs open!