The new SARS-CoV-2 mutant (VOC 202012/01) has become the dominant variant in the United Kingdom (UK) with the first known case in the United States identified on December 29, 2020. Over sixty percent of COVID-19 infections in the UK are now attributed to the new variant. The new variant is defined by 23 mutations, 13 of which are non-synonymous point mutations. In addition, there are 4 deletions and 6 synonymous point mutations.
Viral mutations are not unexpected, this is an unusually large number of mutations in a single cluster. Mutations that enhance the virus’s capacity to spread among people provide a new variant with an advantage over the ancestral strain and enable the new variant to become dominant is its capacity to spread. Commercially available SARS-CoV-2 molecular assays often target the ORF region, as well as genes encoding for envelope protein (E), S and/or nucleoprotein (N). Therefore, the mutations in the new SARS VOC could theoretically impact the accuracy of assays that target ORF8 and S.
Our high throughput platform (Roche cobas 6800) targets the ORF1ab region and E gene,
Our rapid point-of-care platform similarly targets the ORF1ab region, but also detects the N gene.
The selection of ORF1ab and N targets is due to their highly conserved nature (i.e., less likely to mutate) and their unique sequence specific for SARS-CoV-2. In contrast, the use of the E gene serves as a pan-Sarbecovirus marker. It must be noted that N and E mutations do exist but have not increased in prevalence since these variants appear to be no more infectious than non-mutants. Situations may arise where only one out of two targets are detected. Detection of only one gene does not necessarily indicate the presence of a new variant and may be the result of low viral load.
