B.1.1.7 is there. Last 7 days have shown at least 1 or 2 SGTF per day (of 80-100 positives).
Still noisy, but lower case count overall may favor a quicker expansion of B.1.1.7 in coming weeks.
North Carolina
Among the states where Helix tests the most, this is the state with the fewer SGTF and therefore fewer B.1.1.7 cases.
Pennsylvania
SGTF is present. Recently the fraction of SGTF that were B.1.1.7 has been increasing. Our best estimate is that B.1.1.7 represents just above 2% of positive cases in PA.
Texas
SGTF numbers have been increasing rapidly in the last 2 weeks. And the large majority of SGTF we sequenced from Texas are B.1.1.7.
Texas and Georgia are now at levels similar to California for B.1.17.
Few B.1.429 (nothing like California for this variant)
This is a huge team effort. In addition to lab, bioinformatics, research teams ... this is only possible thanks to a great engineering team. @EmreColak_Sr@Maglaar
As far as I know, this is not a variant of concern.
In our sequences of SGTF samples, we also see this variant a lot in Florida. Following the fraction B1.1.7/B.1.375 in Florida over time will be informative to assess whether B.1.375 has any impact on transmissibility
Update on @my_helix SARS-CoV-2 variant surveillance program.
Data from testing with n positives & SGTF (S-gene target failure)
Stats on sequences (SGTF & non-SGTF)
Stats on B117
2/
First, the dashboard is still focused on B117. Because B117 is more infectious & had large impact in many UK, Ireland, Denmark...
But, looking for other variants is also super important. covariants.org
=> we are increasing sequencing of random positives. see map
3/ Back to SGTF & B117 analyses. Knowing there is a bias in selection, we estimate % of positives that are B117 by looking at 2 metrics:
- (n SGTF) / (n positives)
- (n B117) / n SGTF sequenced)
And all numbers are from positives with a N-gene Cq < 27.
Update. @my_helix launched a dashboard with our results re virus surveillance
So far, you can check trends in by states for:
- % of SGTF by positives
- Ns & % of B117