S-Gene Target Failure is Proxy for VOC 202012/01 COVID-19 strain

 The new COVID-19 variant, designated "Variant of Concern" or VOC 202012/01 by Public Health England, now accounts for the majority of transmission in the UK. The strain is characterised by the fact that the PCR used in most places in the UK- TaqPath by Thermo Fisher, has a dropout where the S gene should be. This is called S-Gene Target Failure, or simply SGTF.

The new variant has 23 mutations- 13 non-synonymous mutations, 4 deletions and  6 synonymous mutations- compared with the wild type variant, and one extra stop codon. Most of these mutations are in the gene for Spike protein, as shown below from the relevant PHE document.. One of these mutations, present at the N-terminal domain of the S-protein, is a deletion of 6 nucleotides- from 21765-21770, resulting in the loss of two amino acids- Histidine and Valine at position 69-70 of the Spike protein. It is the latter deletion that causes the characteristic SGTF on the TaqPath PCR. 

(Synonymous mutations lead to base pair substitutions which leave the amino acid unchanged, while non-synonymous mutations alter the coded amino acid)

TaqPath uses a 3-target PCR- it amplifies the S-gene, the N-gene (called N) and and Open Reading Frame called Orf1ab. COVID-19 has a further Orf called Orf8, which is not a target for TaqPath and therefore not amplified. (Open Reading Frames are DNA sequences without stop codons. When they are long, they are likely to code for protein, rather than being non-coding sequences).

For the VOC, the PCR cannot read the S-gene sequence due to deletion at 69-70, and so the S-gene "drops out", resulting in S-gene target failure. Only the other 2 targets, i.e. N and Orf1ab are amplified. 

Fully 99.7% of variants sequenced in the UK with SGTF belong to the new VOC strain. SGTF is thus used as a reliable proxy for the new strain.

However, as referred to elsewhere in this blog, the increased transmissibility of the new strain- between 40%-70% more than the wild type strain- is owed to another mutation in the Spike protein, namely N501Y, which affects the RBD, and is thought to increase the strength with which the S-protein binds to its cognate receptor on human cells- ACE2. 

Incidentally, the 69-70 deletion was seen in the Danish Cluster 5 variant, the one that led to a cull of millions of minks. Its clinical significance, unlike that of N501Y, is unknown.

The New VUI-202012/01 COVID-19 Variant Found in the United Kingdom

 The UK has just tightened its COVID tiers based on a fast spreading variant of the virus picked up by the COVID-19 Genomic Consortium. So far 1108 cases with this variant has been described. Apparently it is 70% more infectious than the prevalent D614G strain. Several European countries have imposed a summary bans on flights originating in the UK as a result.

It is fair to say that as a RNA virus, COVID-19 mutates continuously. A WHO analysis found that the rate of mutations for COVID-19 is 1.12 x 10^-3 mutations per site year, which is quite similar to the range of 0.80 x !0^-3 to 2.38 x 10^-3 per site year for the original SARS virus in 2003.

To put this into some context, the mutation rate in human beings is 1.2 x 10^-8 per generation. This translates to around 72 new mutations in a newborn. Mutagenesis is therefore an inevitable vicissitude of the genetic code.

You may be aware that the current circulating clade- D614G- originated in China in January 2020 and replaced the existing clade within 3 months. It is likely that VUI-202012/01 will become the dominant strain if allowed to spread.

Concern about emergence of new strains is reflected in the Danish government's recent decision to cull 17 million minks because they harboured a variant of the virus that was apparently not well neutralised by existing human antibodies.

The new variant VUI-202012/01 has 17 new mutations- the most important of which is N501Y involving the spike protein (which means that tyrosine has replaced asparagine in the 501st amino acid of the spike protein).

Looking at the DNA code, asparagine has 2 codons- AAC and AAT. Tyrosine also has two- TAC and TAT. This new strain is therefore due to A to T transversion at the first position of the putative codon. 

When a purine is replaced by a purine or pyrimidine by a pyrimidine, it is called a transition. Crossovers between purine and pyrimidine is called transversion. In general mutations caused by transition outnumber those due to transversions manyfold. The commonest mutations are due to C to T transition as cytosine bases are prone to be methylated at the 5'position and thence are spontaneously deaminated to thymine. Thus, the WHO database for COVID 19 in Feb 2020 showed 1670 C to T transitions compared with only 128 A to T transversions.

Thus, it is fair to say that the N501Y mutation in the VUI-202012/01 has persisted because it offers a survival advantage- i.e. infectivity, much as the G614 variant was more infective than the D614 variant. However, it must be said that there is no evidence that it is more dangerous. If anything, the D614G carried a lower mortality than the original strain, although this may have been due to better established treatment protocols.

Nor is there any evidence to suggest that the current vaccines will be less effective against the new strain. The current vaccines were in fact formulated against the original COVID strain and are just as effective against the D614G strain. This is due to the fact that protective antibodies target several epitopes and unless there is a significant conformational change in the shape of a protein, the vaccine generated antibodies will still neutralise.

I do think that this particular variant will take over despite the restrictions- just as D614G did. I also think there need be no undue cause for concern. With rapidly executed vaccination programmes, it should be possible to control the virus by spring.