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Alexandre Bolze Profile picture
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3 May, 4 tweets, 3 min read
Great thread from @trvrb on growth of P.1 in the US.

We can see it in @my_helix data. See this dashboard: public.tableau.com/profile/helix6…

In all US, we see ~20% of non-SGTF tests that are P.1 & 📈.
2/ on sampling:
- we do more tests in some states. & N sequenced also based on pos rate. => can click on a state, or scroll on bar to see actual count.
- we do not select for SGTF or non-SGTF.
- we show fraction of P.1. to non-SGTF.
3/
 Ex: in Florida (a state where we test a lot)

- P.1 represents ~25% of non-SGTF as of April 14.
- % of pos that are SGTF in FL is stable in FL at ~70% from April 14 to April 27.

So far does not look like P.1. replacing B117. But more granular analysis & context necessary
P.1 is the green bar in the plots above. ☝️

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More from @alexbolze

Alexandre Bolze Profile picture
8 Apr
Weekly update from @my_helix SARS-CoV-2 surveillance program.

Check dashboards here: public.tableau.com/profile/helix6…

As reported by @CDCDirector, B.1.1.7 represents more than 50% of cases in US. And fraction still increasing.

See 7 states where Helix tests a lot. Details in 🧵
2/
 Before going in details on B.1.1.7, here are some stats on vaccinations in US from @CDC. What an effort! I am very optimistic for the US.

Also important to note that all vaccines work very well against the B.1.1.7 variant. It is really incredible how well they work.
3/
 California

Fraction of B.1.1.7 is still increasing. Numbers are small, but I think we may have enough information to look closely at direct competition between B.1.429 and B.1.1.7. Hypothesis is that B.1.1.7 is more transmissible.
Read 11 tweets
Alexandre Bolze Profile picture
28 Mar
Update on @my_helix SARS-CoV-2 surveillance program

- Dashboards here: public.tableau.com/profile/helix6…

Some analysis on 7 states where we (Helix) have most positive tests 👇

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-tra…
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.
Read 13 tweets
Alexandre Bolze Profile picture
20 Mar
Update on @my_helix SARS-CoV-2 surveillance

- Seq data up to Feb 26. >15,000 sequences since Jan 1.
- Check dashboard for stats on tests & variants of concerns in your state. public.tableau.com/profile/helix6…

Re B.1.1.7, Michigan 📈 fast. MN too but we have less data.

More in🧵
2/
On Method:
- Numbers of positives, SGTF etc. are only reporting those with N gene Ct <27 (we use this threshold to select samples for sequencing).
- In Jan, we enriched sequences for SGTF to get grasp of % of SGTF that are B117. Now we don't enrich for SGTF anymore.
3/
Michigan.
SGTF (pretty much all of the ones we sequenced in MI were B117) represent now more than 60% of positives in MI.
And total cases in MI also on rise based on CDC tracker. 👇
Read 7 tweets
Alexandre Bolze Profile picture
10 Mar
Update on @my_helix SARS-CoV-2 surveillance program

Check public.tableau.com/profile/helix6…

~50% of cases in Florida, Georgia & Texas are B.1.1.7.

in FL: Overall cases continue to 📉 but 52.8% of pos were SGTF (S-gene target failure) on March 7.

=> We will track closely evolution
2/
 In Georgia

54% of positives were SGTF on March 7.

While still ~90% of these are likely B.1.1.7, interesting to note that B.1.525 also sequenced several times in GA and also leads to SGTF

(note: B.1.525 is not a variant of concern)
3/
 Texas

53% of positives were SGTF on March 7. Overall cases still going down. Again, we will keep testing, sequencing and tracking to see what happens as things reopen, and vaccinated population increases.
Read 4 tweets
Alexandre Bolze Profile picture
6 Mar
Update from @my_helix SARS-CoV-2 surveillance program

Check public.tableau.com/profile/helix6…

🧵 with FL, TX, GA, CA & MA + results on identification of B.1.351 & P.1 !!

FL: B.1.1.7 is ~40% of positives. 📈 about as predicted

Absolute numbers of B117 up despite overall 📉 in cases
2/
Texas

March 3: B117 were ~30% of positive tests.
26% with 5-day avg.

Absolute numbers of SGTF (a great proxy for B117 now) also going up despite big decrease in overall cases (as seen overall in US)

Note: this is only based on Helix data
3/
Georgia

March 3: B117 represents ~26% of positive tests.

Absolute numbers of SGTF (a great proxy for B117 now) also going up despite big decrease in overall cases (as seen overall in US)
Read 8 tweets
Alexandre Bolze Profile picture
2 Mar
Data drop from @my_helix SARS-CoV-2 surveillance

Check any state public.tableau.com/profile/helix6…

Or download from github.com/myhelix/helix-…

To see if large vaccination effort can keep overall cases from📈again -> important to monitor FL

See @ScottGottliebMD for perspective
2/
With overall number of cases 📉 quickly => important to look at % of positives that are B1.1.7
AND also the evolution of the absolute number of B1.1.7

Can do this based on Helix numbers,
or by multiplying % from Helix by overall number of cases reported by states and CDC
3/
 CA: % of positives that are B117 now ~15-17%

Increase in absolute numbers of B117 is slower (compared to FL).
Still N of B117 is not decreasing, unlike the non-SGTF SARS-CoV-2 variants including B.1.429 & B.1.427 who are decreasing fast.

Note: Y-axis truncated in right 👇
Read 6 tweets

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