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20 Mar, 7 tweets, 4 min read
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🧵
2/
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.
3/
Michigan.
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. 👇
4/
Florida.
SGTF (~B117) represent a little over 50% of positives. Increase is slower. And number of cases is stable. That is good news. Vaccines and other efforts are working.
5/
California.
Current proportion of SARS-CoV-2 seems to be:
- 45% B.1.427 / B.1.429 (fairly stable in last month)
- 30% B.1.1.7 (increasing slowly in last month)
- 25% other

note: Our numbers are enriched for San Diego County in CA.
6/
 The 2 other variants of concern:
- 24 B.1.351 in CT, FL, GA, MA, NC, TX
- 11 P.1 in FL & MA

btw, we optimized the seq file on Github so that it matches the virus name on GISAID

Credit: @my_helix research platform team @simonjwhite71 et al

Check: github.com/myhelix/helix-…
7/
To finish, today is the 3-months anniversary since @CovidGenomicsUK & others in UK reported on B.1.1.7.

See


So much happened in 3 months!

glad we were able to learn & contribute to B117 tracking & overall virus surveillance effort.

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More from @alexbolze

Alexandre Bolze Profile picture
10 Mar
Update on @my_helix SARS-CoV-2 surveillance program

Check public.tableau.com/profile/helix6…

~50% of cases in Florida, Georgia & Texas are B.1.1.7.

in FL: Overall cases continue to 📉 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.
Read 4 tweets
Alexandre Bolze Profile picture
6 Mar
Update from @my_helix SARS-CoV-2 surveillance program

Check public.tableau.com/profile/helix6…

🧵 with FL, TX, GA, CA & MA + results on identification of B.1.351 & P.1 !!

FL: B.1.1.7 is ~40% of positives. 📈 about as predicted

Absolute numbers of B117 up despite overall 📉 in cases
2/
Texas

March 3: B117 were ~30% of positive tests.
26% with 5-day avg.

Absolute numbers of SGTF (a great proxy for B117 now) also going up despite big decrease in overall cases (as seen overall in US)

Note: this is only based on Helix data
3/
Georgia

March 3: B117 represents ~26% of positive tests.

Absolute numbers of SGTF (a great proxy for B117 now) also going up despite big decrease in overall cases (as seen overall in US)
Read 8 tweets
Alexandre Bolze Profile picture
2 Mar
Data drop from @my_helix SARS-CoV-2 surveillance

Check any state public.tableau.com/profile/helix6…

Or download from github.com/myhelix/helix-…

To see if large vaccination effort can keep overall cases from📈again -> important to monitor FL

See @ScottGottliebMD for perspective
2/
With overall number of cases 📉 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.

Note: Y-axis truncated in right 👇
Read 6 tweets
Alexandre Bolze Profile picture
1 Mar
Response to live-attenuated vaccines is a great way to study human response to infectious diseases.

Great paper from @casanova_lab studying 8 patients with life-threatening disease after live-attenuated yellow-fever vaccine.

rupress.org/jem/article-ab…
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 👇
Read 4 tweets
Alexandre Bolze Profile picture
24 Feb
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.
Read 7 tweets
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

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