Update on @my_helix SARS-CoV-2 surveillance program
- Dashboards here: public.tableau.com/profile/helix6β¦
Some analysis on 7 states where we (Helix) have most positive tests π
Details in following tweets
(1 / n)
- Dashboards here: public.tableau.com/profile/helix6β¦
Some analysis on 7 states where we (Helix) have most positive tests π
Details in following tweets
(1 / n)
2/
How did I pick these 7 states?
- Each had >50 positives (Cq N gene <27) per day in recent Helix tests
- Alternative could be to use a threshold for % of positives in state coming from Helix
~5% of pos in these 7 states come from Helix
State Ns: covid.cdc.gov/covid-data-traβ¦
How did I pick these 7 states?
- Each had >50 positives (Cq N gene <27) per day in recent Helix tests
- Alternative could be to use a threshold for % of positives in state coming from Helix
~5% of pos in these 7 states come from Helix
State Ns: covid.cdc.gov/covid-data-traβ¦
3/
California
Looking at absolute counts. Restricting graph to Feb 1st to March 23rd to better see the trend.
Note: in CA, majority of our tests are done in San Diego county.
California
Looking at absolute counts. Restricting graph to Feb 1st to March 23rd to better see the trend.
Note: in CA, majority of our tests are done in San Diego county.
4/
Florida
Overall cases starting to increase based on CDC. From what we see, it is mostly the counts of SGTF (~B.1.1.7) that is increasing.
Yet, this increase is not super fast (compared to some states). Note the difference in Y-axis π
Florida
Overall cases starting to increase based on CDC. From what we see, it is mostly the counts of SGTF (~B.1.1.7) that is increasing.
Yet, this increase is not super fast (compared to some states). Note the difference in Y-axis π
5/
Georgia
64% of positives are SGTF (~B.1.1.7). And importantly counts of SGTF are increasing right now.
Georgia
64% of positives are SGTF (~B.1.1.7). And importantly counts of SGTF are increasing right now.
6/
Massachusetts
It used to be the poster-child state to show that SGTF is not the same as B.1.1.7. For a long time MA, had 3-5% of positives that were SGTF and NOT B.1.1.7
Now, >90% of SGTF in MA are B.1.1.7. And SGTF counts increasing like in many states (still low numbers)
Massachusetts
It used to be the poster-child state to show that SGTF is not the same as B.1.1.7. For a long time MA, had 3-5% of positives that were SGTF and NOT B.1.1.7
Now, >90% of SGTF in MA are B.1.1.7. And SGTF counts increasing like in many states (still low numbers)
7/
Michigan
It is 1 of the states with fastest case π based on CDC. In our tests, we see fast π in counts of SGTF & also increase in non-SGTF.
Note: testing is from multiple places across state, done at a national retail pharmacy
Follow @LauringLab for experts in MI.
Michigan
It is 1 of the states with fastest case π based on CDC. In our tests, we see fast π in counts of SGTF & also increase in non-SGTF.
Note: testing is from multiple places across state, done at a national retail pharmacy
Follow @LauringLab for experts in MI.
8/
North Carolina
Overall, 35% of positives are SGTF.
Counts definitely low, but looks to flatten, or even increase slightly.
North Carolina
Overall, 35% of positives are SGTF.
Counts definitely low, but looks to flatten, or even increase slightly.
9/
Pennsylvania
- a great example to visualize how B.1.1.7 is more transmissible than most other variants. non-SGTF counts are flat, but SGTF π
- Based on covid.cdc.gov/covid-data-tra⦠there were 15,103 positives in PA from 03/19-03/23.
& 1,043 in Helix with Cq<27 (~1,500 total)
Pennsylvania
- a great example to visualize how B.1.1.7 is more transmissible than most other variants. non-SGTF counts are flat, but SGTF π
- Based on covid.cdc.gov/covid-data-tra⦠there were 15,103 positives in PA from 03/19-03/23.
& 1,043 in Helix with Cq<27 (~1,500 total)
10/
A question for the experts to end this series on B.1.1.7.
When does B.1.1.7 stops being a variant of concern because it is the dominant variant, and therefore becomes the reference?
Or this does not influence nomenclature?
@K_G_Andersen @dmaccannell
A question for the experts to end this series on B.1.1.7.
When does B.1.1.7 stops being a variant of concern because it is the dominant variant, and therefore becomes the reference?
Or this does not influence nomenclature?
@K_G_Andersen @dmaccannell
11/
1 more thought
Looking at the US & France (I am π«π·): the US have the big advantage of vaccines. Both supply and well orchestrated distribution.
I saw live a mass vaccination event in San Mateo. It was beautiful
=> Optimistic for US & I hope France copies πΊπΈ re vaccines
1 more thought
Looking at the US & France (I am π«π·): the US have the big advantage of vaccines. Both supply and well orchestrated distribution.
I saw live a mass vaccination event in San Mateo. It was beautiful
=> Optimistic for US & I hope France copies πΊπΈ re vaccines
Lastly, this program is result of big effort from many teams @my_helix (including lab and operations teams, engineering team, research etc.) as well as teams @illumina and many other partners including all the people involved in collecting testing samples
+ support from CDC.
+ support from CDC.
Thread on variants of concerns (B.1.351, P.1, B.1.427, B.1.429)
& vars of interests (B.1.525, B.1.526) tomorrow.
but you can check some of these here: public.tableau.com/profile/helix6β¦
Tip: scroll over bars to see total counts & be careful with most recent day (usually incomplete)
& vars of interests (B.1.525, B.1.526) tomorrow.
but you can check some of these here: public.tableau.com/profile/helix6β¦
Tip: scroll over bars to see total counts & be careful with most recent day (usually incomplete)
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