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Alexandre Bolze Profile picture
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24 Feb, 7 tweets, 5 min read
SARS-CoV-2 surveillance data from @my_helix updated on Github and Tableau.

public.tableau.com/profile/helix6…

Last collection date:
- Feb 20 for testing
- Feb 7 for seq

Florida: >20% of positives are B117 📈

🧵 with more results incl. B1429
2/
You can see the raw numbers for FL here: github.com/myhelix/helix-…

Screenshot with numbers.
- results based on many (>100 positives per day)
- clear that now ~100% of SGTF are B.1.1.7 in FL.

Rise of B.1.1.7 following what was shown in UK, Denmark & other places.
3/
 B117 also on the rise in California.

~ all SGTF are B117
- On Feb 20 (not looking at Feb 21 that is incomplete data): 17% of positives are SGTF.
- 12.8% 5-day avg.
4/
 Georgia is another state where numbers are increasing.

See 👇 the table you can get from Github.

Like for FL, CA & other states, near all SGTF sequenced turned out to be B.1.1.7.
5/
Some discussions on Twitter about the need to write papers to show results, methods etc. Fully agree.

This is our preprint from a few weeks ago: medrxiv.org/content/10.110…

You can also see everyone who contributed :)
6/
 What about the other variants? The B.1.429 variant making the headlines recently?

You can track on dashboard: public.tableau.com/profile/helix6…

Ex: on Feb 6, B.1.429 represented 17% of the 81 non-SGTF sequences.

=> soon, will be able to assess competition between B117 & B1429
7/
 Overall we see cases go down, B117 goes up. & B.1.429??

We keep testing, sequencing and tracking to hopefully help keep numbers down.

& analyzing with help + inspiration from @firefoxx66 @jcbarret @K_G_Andersen @trvrb @ewanbirney @AineToole + many more

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More from @alexbolze

Alexandre Bolze Profile picture
24 Feb
Love @GeneticsSociety journal club series

Today @jacobkitzman presented work to *functionally* test ~all possible missense variants in MSH2.

=> important to provide accurate information to people about their risk for Lynch syndrome

paper: sciencedirect.com/science/articl…

quick 🧵
2/
 Variant interpretation is a limiting step for genomic medicine.

Most missense variants are classified as VUS (aka we have no clue what to say to the individual who carries it)

Best way would be to test them experimentally but that is hard!
3/
 @jacobkitzman & team functionally tested >16,000 missense vars in MSH2.

16,000! 94% of all possible missense in gene. And ~100X more than all vars tested so far (& in literature)

=> 90% of missense were neutral.
Read 4 tweets
Alexandre Bolze Profile picture
18 Feb
SARS-CoV-2 surveillance by @my_helix update

- 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/helix6…
- SGTF info up to Feb 15
- Seq info up to Jan 30

🧵 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.

Check it out
github.com/myhelix/helix-…

- Info on >300,000 positive tests in last 2.5 months
- Info on 2,843 sequences (2/3 are random non-SGTF)
Read 9 tweets
Alexandre Bolze Profile picture
15 Feb
SARS-CoV-2 surveillance data from @my_helix is here: github.com/myhelix/helix-…

Stats on
>300,000 positives from last 4 months
2,503 sequences (1/3 SGTF, 2/3 random non-SGTF)

🧵on vars of concerns & interest in 7 states

>2% of positives are B.1.1.7 in: CA, FL, GA, PA & TX
@my_helix tests (PCR tests) in all states & all available on Github.

Analysis here limited to states with >100 positives PER DAY (and with N gene Cq<27) in December & January.
7 states: CA, FL, GA, IN, NC, PA, TX.

AZ, MA, MI were just under cutoff.
And analysis is focused on variants of concerns
B.1.1.7
B.1.351 (not present)
P.1 (not present)

variants of interest
B.1.427
B.1.429

See outbreak.info/situation-repo… from @K_G_Andersen or covariants.org from @firefoxx66 for info on these variants.
Read 12 tweets
Alexandre Bolze Profile picture
8 Feb
Thread about our preprint on the study of emergence and increased prevalence of SARS-CoV-2 B.1.1.7 variant in the US.

medrxiv.org/content/10.110…
2/
 First, my Conflict of Interest: I am an employee of Helix.

We do a lot of COVID testing (PCR tests) and also receive funding for the viral surveillance program.

See the other COIs from authors of this preprint. Image
3/
Methods are very similar to the ones used in the regular @my_helix updates with the dashboard.
public.tableau.com/profile/helix6…

The study is based on >500,000 positives PCR tests. We test in all 50 US states, but it is not homogeneous. See map 👇 Image
Read 13 tweets
Alexandre Bolze Profile picture
5 Feb
Latest numbers from @my_helix SARS-CoV-2 surveillance.

Data on PCR test positives & SGTF (S-gene target failure) up to Feb 3.
Stats on sequences and B117 up to Jan 22.

Link: public.tableau.com/profile/helix6…

Thread on Florida and California
2/
For each graph, numbers are provided for each day and as 5-day moving average.

n SGTFs and n positives come from PCR tests -> based on large numbers.

n SGTFs seq & n B117 come from sequencing -> smaller numbers. => 5-day avg important for these to reduce noise
3/
Florida first
- latest avg (n SGTF) / (n positives): 8.6%
- latest avg (n B117) / (n SGTF seq): 78%

Extrapolating the seq data, estimate (likely under estimate) is: B117 represents 6.7% of positives

Trend 📈
Read 7 tweets
Alexandre Bolze Profile picture
4 Feb
In @my_helix SARS-CoV-2 dashboard, we show that in Massachusetts, ~5% of positives are SGTF (= have del69/70). It has been consistent since November.

BUT, they are not B117. So what are these SGTF?

Majority are B.1.375.

More details in 🧵

public.tableau.com/profile/helix6…
B.1.375 is a SARS-CoV-2 variant with the following defining mutations:

Gene: protein change
ORF1a: T1828A
ORF1b: E1264D
ORF3a: T151I
Spike: del69/70 -> this is why it is a SGTF
M: I48V

Some details about the variant in this paper: virological.org/t/detection-of…
As far as I know, this is not a variant of concern.

In our sequences of SGTF samples, we also see this variant a lot in Florida. Following the fraction B1.1.7/B.1.375 in Florida over time will be informative to assess whether B.1.375 has any impact on transmissibility
Read 4 tweets

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