Thread by @alexbolze

Latest numbers from @my_helix SARS-CoV-2 surveillance.

Data on PCR test positives & SGTF (S-gene target failure) up to Feb 3.
Stats on sequences and B117 up to Jan 22.

Link: public.tableau.com/profile/helix6…

Thread on Florida and California

2/
For each graph, numbers are provided for each day and as 5-day moving average.

n SGTFs and n positives come from PCR tests -> based on large numbers.

n SGTFs seq & n B117 come from sequencing -> smaller numbers. => 5-day avg important for these to reduce noise

3/
Florida first
- latest avg (n SGTF) / (n positives): 8.6%
- latest avg (n B117) / (n SGTF seq): 78%

Extrapolating the seq data, estimate (likely under estimate) is: B117 represents 6.7% of positives

Trend 📈

4/
California
- latest avg (n SGTF) / (n positives): 2.83%
- latest avg (n B117) / (n SGTF seq): 76%

Extrapolating the seq data, estimate is: B117 represents 2.1% of positives.

Trend is up but still noisy.

5/
Also more and more B117 from the latest sequences in Georgia. We will keep monitoring.

Check out other states on the dashboard. Note: when the number of positives per day, we don't show (n SGTF) / (n positives) because it is too noisy.

6/
Map with number of non-SGTF sequences done as of Jan 22. All of these are already on GISAID or on their way. And you can also find a great visualization of where they fall on @nextstrain nextstrain.org/groups/neherla…

built by @firefoxx66

7/
Feedback is welcome.

Credit to many teams @my_helix @illumina @CDCgov .
@simonjwhite71 @Maglaar @genesareclever @ETCirulli @kellyschiabor

and to many scientists around the world for collaboration / help & discussions. @K_G_Andersen @ewanbirney