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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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.
- 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. 👇
~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.
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.