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.