- New dashboard: you can check all lineages now
Random ex: B.1.1.64 in 4 states (note: I don't know anything about this variant). public.tableau.com/profile/helix6…
- SGTF info up to Feb 15
- Seq info up to Jan 30
🧵 with more results
2/
Of the variants of concern, so far we only identified B.1.1.7 (666 times up to Jan 30). No B.1.351 and no P.1
We identified many B.1.429, a variant of interest. It represents about 20% of the sequences we do every day. But sampling is still biased for SGTF
3/
To assess fraction compared to non-SGTF sequenced, you can also get that info from the 2 files on Github with ALL of the data.
- Info on >300,000 positive tests in last 2.5 months
- Info on 2,843 sequences (2/3 are random non-SGTF)
4/
Tip: if you want to quickly download the 2 files on your computer.
- Click on the file on home page (github.com/myhelix/helix-…).
- Then click on "Raw". see picture.
- Then on your Chrome toolbar: File/Save Page as
=> your turn to play.
5/
It is very rewarding to see many use this information.
Example: @scottleibrand analysis of what might happen in next few months
9/ So we made it a little easier. There is now a page with the fraction of B.1.427 or B.1.429 compared to non-SGTF sequences. public.tableau.com/profile/helix6…
- check US or by state.
- look at total non-SGTF seq per collection day
Jan 29, 18% of non-SGTF we sequenced were B.1.429
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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.