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
Link:
Tableau public.tableau.com/profile/helix6…
Helix web helix.com/pages/helix-co…
🧵 with results for CA, FL, MA...
So far, you can check trends in by states for:
- % of SGTF by positives
- Ns & % of B117
Link:
Tableau public.tableau.com/profile/helix6…
Helix web helix.com/pages/helix-co…
🧵 with results for CA, FL, MA...
2/
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
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
3/
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)
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)
4/
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
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
- % 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?)
- % 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?)
7/ MA
We saw our first case of B117 in MA. Reported here: boston.com/news/coronavir…
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.
We saw our first case of B117 in MA. Reported here: boston.com/news/coronavir…
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
% 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
9/
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
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
10/
As always this was a big team effort. Dashboard and data wrangling led by @simonjwhite71 & @genesareclever . + @ETCirulli @kellyschiabor & many others @my_helix .
Also @illumina @fdesouza , @CDCgov, @K_G_Andersen lab
& inspiration from @firefoxx66 @AineToole @trvrb et al
As always this was a big team effort. Dashboard and data wrangling led by @simonjwhite71 & @genesareclever . + @ETCirulli @kellyschiabor & many others @my_helix .
Also @illumina @fdesouza , @CDCgov, @K_G_Andersen lab
& inspiration from @firefoxx66 @AineToole @trvrb et al
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