~50% of cases in Florida, Georgia & Texas are B.1.1.7.
in FL: Overall cases continue to π 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.
4/ Also
I am amazed how this real world experiment replicated what was observed & described in UK 3 months earlier.
Different setting, knowledge, people & still same results.
2/
With overall number of cases π 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.
2/ Live-attenuated Yellow Fever vaccine is very safe & given to more than 600 million people.
But less than 1 in 100,000 have very severe disease after. And we know it is the same vaccine. So why?
Note: the COVID vaccines are NOT live attenuated vaccines.
3/ 5 of 8 had defects in type 1 IFN response.
- 2 had autosomal recessive loss-of-function variants in IFNAR1 & IFNAR2.
- 3 others had auto-antibodies to type 1 IFN. At high concentration, plasma of patients inhibits addition of IFNa2 in cells and virus can grow. See π
- 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/helix6β¦
- SGTF info up to Feb 15
- Seq info up to Jan 30
𧡠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.