Update. @my_helix launched a dashboard with our results re virus surveillance
So far, you can check trends in by states for:
- % of SGTF by positives
- Ns & % of B117
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Methods:
ALL numbers are based on positives with Ct<27.
In real life, we return positive results for Ct≥27, but we only sequence (with @illumina) samples with more virus (Ct<27) to optimize seq success.
Still Ns analyzed are large. A couple thousands positives per day
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So far, our effort was focused on B117, which is established to be more contagious.
B117 causes SGTF (S gene target failure) in PCR test. But it is not the only variant to do so.
So 2 metrics are useful to track
- (n SGTF / n positives)
- (n B117 / n SGTF sequenced)
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Overall in the US, we saw this (in the last ~4 weeks).
- only states with some SGTF sequenced are represented here.
- B117 identified in 8 states
Now trends in CA, FL, MA and PA
5/ CA
- % of positive samples that are SGTF increasing over time. Now, 7-day moving average: ~1%
- % of SGTF sequenced that are B117 has always been high. Now, ~0.9
rough estimate is that now: 1% x 0.91 ~0.9% of positives in CA are B117
6/ FL
- % of positive samples that are SGTF increasing. Big increase in last couple of days. Now, 7-day moving average: ~3%
- % of SGTF sequenced that are B117 ~ 30%.
There is a lag for seq results so it will be important to see what latest sequences will be (mostly B117?)
But trend is similar to previous.
High % of positives are SGTF (has been stable at around 3% for 2 months).
But only 1 SGTF sequenced has been B117.
8/ PA
% of positives that are SGTF has been around 0.5% for a while. But maybe (!) early signs that it is going up.
Recently sequenced 2 B117 in the state
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Hope many people can play with the data. Sequences also available on GISAID. To find them, search:
Helix/Illumina"Genomics and Discovery, Respiratory Viruses Branch, Division of Viral Diseases, Centers for Disease Control and Prevention"Peter W. Cook et al @dmaccannell
Update 🧵 on @my_helix study on the B.1.1.7 variant in the US.
Summary:
- we sequenced 31 samples with S-gene drop out in US
- 4 were B.1.1.7
- 3 from CA, 1 from FL
- Pursuing seq effort with @illumina , & work with @CDCgov
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Reminder:
- H69del/V70del variant present in B.1.1.7 likely leads to S gene drop out in RT-PCR assay.
- H69del/V70del is NOT unique to B.1.1.7. Frequent in other clusters (see pic. all of the green is NOT B1.1.7)
Need to sequence to know if S gene drop outs are B.1.1.7.