Working with @my_helix and @illumina, we recently sequenced 31 SARS-CoV-2 TaqPath S dropouts (SGTF) from 5 across states, collected roughly between December 19th and 21st. Data are being submitted to GISAID, Genbank and SRA now, and I'm commenting here in a personal capacity.

Of the 31 SGTFs that successfully sequenced, we did find four confirmed B.1.1.7 variants. (Reported https://twitter.com/SanDiegoCounty/status/1344817187639365632 and here https://twitter.com/HealthyFla/status/1344815068479954944?s=20). So... hunt successful.

But another interesting aspect of this pilot data set may be this: setting aside the four B.1.1.7s that we picked up, most of the SGTFs sequenced in this first set were of other lineages, and almost half were B.1.346 ( https://virological.org/t/identification-of-a-novel-sars-cov-2-spike-69-70-deletion-lineage-circulating-in-the-united-states/577/1).

Can we draw any meaningful conclusions from a set of 31 geographically diverse SGTF samples from a single timepoint? ¯\\_(ツ)_/¯

But when added to all the other recent SGTF-directed sequencing going on across the country, it does suggest that a significant proportion of dropouts we're currently seeing nationally is associated with other del69/70 lineages, and in a number of places, predominantly B.1.346.

We'll see if these observations hold. Could be good news, or we could just be at the leading edge of the curve. I do think a del69/70 assay could be useful for prioritizing sequencing. But for the time being at least, the value of SGTF as a direct proxy for B.1.1.7 seems unclear