We will aim to update @my_helix dashboards even more frequently

SGTF updated with stats up to June 7

Info from UK + early stats on @GISAID & outbreak.info point to Delta driving part (most) of recent📉 in SGTF in US. But seq data is lagging. Image
To read more on B.1.617.2 and its rise in UK: assets.publishing.service.gov.uk/government/upl…

- B.1.617.2 overtook B.1.1.7 recently. Observed by sequencing, & also by looking at SGTF data 👇

Something to keep in mind when looking at SGTF in US

- Also US had similar path to UK for B.1.1.7 Image
Pro tips to look at @my_helix dashboard:
- be aware that most recent day may have very small sample size.
- You can exclude it by clicking on bar & moving mouse up. See picture. Image
As always, this is a huge team effort: supply chain, lab, engineering etc. @simonjwhite71 for always optimizing the tableau.

& thanks to many in UK for the inspiring work + the many discussions & explanations on Twitter
@jcbarret @theosanderson @kallmemeg @PHE_uk
With today's update, we now have data on 126 positive samples for June 7. And SGTF (~B.1.1.7) represent 41% of these.

So decrease of B.1.1.7 in favor of other variants is continuing. Likely driven by B.1.617.2, the delta variant. Image

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More from @alexbolze

10 Jun
When will B.1.617.2 (Delta) be the dominant variant in the US?

Could be next week (or next 2 weeks) based on trends in our testing data & sequences available.

SGTF (~B.1.1.7) now < 50% based on last 5 days.

source: @my_helix @DiseaseOutbreak Image
P.1 (Gamma)
B.1.526/.1 (Iota)
B.1.617.2 (Delta)
are the other main variants

Based on recent small numbers (check outbreak.info), Delta is trending up, but Gamma and Iota are not increasing anymore.

More sequences will provide more accurate info. Image
This needs to be put in perspective with fact that vaccines work very well against all (incl. B.1.617.2).

Read 4 tweets
13 May
We updated @my_helix viral surveillance dashboards.

- SGTF dashboard still here => important to see in real time if a variant is outcompeting B.1.1.7 in some states

- Selected variants dashboard. You can see P.1, B.1.617.2 & others. public.tableau.com/profile/helix6…
Using the SGTF dashboard:

In some states like FL, SGTF 5-day avg is 📉 66% on May 9 compared to 71% 10 days before. & SGTF likely still >95% B.1.1.7

So what is the 34% and maybe growing?
You can look at the variants dashboard. It shows sequencing results.
See overall trend. And counts by state (click on specific variant).

Here, we observed 237 counts of P.1. in FL.
Read 9 tweets
3 May
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.
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
Read 4 tweets
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 🧵
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.

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
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)
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…

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
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🧵
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.
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

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