The SARS-CoV-2 UK variant (B.1.1.7) strain has recently emerged as the dominant strain in the UK and has been found to be more infectious. Studies from France and the UK have shown that S gene dropout predicts the B.1.1.7 strain with near-perfect accuracy. Last week, we reported observing ~0.5% of recent positive HelixⓇ COVID-19 Tests in the US with S gene dropout that may be attributed to B.1.1.7.
S gene dropout derives from a deletion mutation in the gene that overlaps the RT-PCR probes, and because several strains with the same deletion variant have been reported worldwide, confirmation that these US strains were indeed B.1.1.7 requires genomic sequencing to scan for the unique combinations of variants that specifically distinguish this strain from others.
With the support of the CDC, in partnership with Illumina, we have sequenced the viral genomes from a subset of our SARS-CoV-2-positive samples with S gene dropout. Of the initial 31 samples with high quality sequencing data, four match the B.1.1.7 strain. Three of these samples were from infected individuals in California (CA), and one from Florida (FL). Together with recent reports from CA and Colorado (CO), this brings the number of states having confirmed B.1.1.7 strains to three. We have notified the relevant public health departments and submitted these sequences to public research repositories, which should be available in the next couple of days.
Our previous report showed relatively high rates of S gene dropout in viral samples collected from Massachusetts (MA), Ohio (OH), and FL. However, in our initial sequencing analysis, we find that these do not directly correlate with B.1.1.7 strain detection in the US. Of the samples with S gene dropout that were sequenced, only one of twelve in FL, and zero of seven in MA were B.1.1.7. We have not yet obtained viral sequences from samples in OH.
The results of this analysis highlight that while S gene dropout may be a reliable predictor of B.1.1.7 in the UK and France, it is a less specific indicator in the US today, given the current viral landscape. Furthermore, while the B.1.1.7 strain is present in multiple US states, other strains that cause S gene dropout are more prevalent in the US. However, with the overall high incidence of viral transmission and the higher transmissibility (here and here) of this strain, the proportions of different strains in the US could readily change.
Leveraging our nationwide SARS-CoV-2 testing footprint, with Illumina and the CDC, we will continue to sequence additional samples to monitor the spread of B.1.1.7 and/or the emergence of other strains in the US.