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
Link: blog.helix.com/sars-cov-2-uk-…
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
Link: blog.helix.com/sars-cov-2-uk-…
2/
Context: a new strain of SARS-CoV-2, B.1.1.7, was identified in the UK, and has been shown to be more transmissible.
-> need to track & monitor the variant in the US
See this thread for our initial work re B.1.1.7
Context: a new strain of SARS-CoV-2, B.1.1.7, was identified in the UK, and has been shown to be more transmissible.
-> need to track & monitor the variant in the US
See this thread for our initial work re B.1.1.7
https://twitter.com/alexbolze/status/1341955114043662336?s=20
3/
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.
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.
4/
Method:
we sequenced in partnership with @illumina (cc @fdesouza) 31 samples with S-gene drop outs from Helix RT-PCR testing assay.
These are all recent samples (last 10 days).
from States:
FL: 12
MA: 7
CA: 6
IN: 3
PA: 3
Method:
we sequenced in partnership with @illumina (cc @fdesouza) 31 samples with S-gene drop outs from Helix RT-PCR testing assay.
These are all recent samples (last 10 days).
from States:
FL: 12
MA: 7
CA: 6
IN: 3
PA: 3
5/
1st result:
Of the 31, the large majority did carry the H69 deletion.
This confirms that majority (probably all if restrict to samples with low Ct for N & ORF1 genes) of S gene drop outs are caused by H69del/V70del variant.
1st result:
Of the 31, the large majority did carry the H69 deletion.
This confirms that majority (probably all if restrict to samples with low Ct for N & ORF1 genes) of S gene drop outs are caused by H69del/V70del variant.
6/
2nd result:
4 of the 31 mapped to the 20B/501Y.V1 clade. This means there were 4 with the B.1.1.7 variant (sometimes called the UK variant).
by State:
- 3 of 6 in CA.
- 1 of 12 in FL.
- 0 of 7 in MA.
2nd result:
4 of the 31 mapped to the 20B/501Y.V1 clade. This means there were 4 with the B.1.1.7 variant (sometimes called the UK variant).
by State:
- 3 of 6 in CA.
- 1 of 12 in FL.
- 0 of 7 in MA.
7/
The result from Florida was reported yesterday by @HealthyFla.
See:
The result from Florida was reported yesterday by @HealthyFla.
See:
https://twitter.com/HealthyFla/status/1344815068479954944?s=20
8/
This means that so far, B.1.1.7 variant was identified in 3 states in the US: 1 in CO, 1 in FL, and 4 in CA.
Follow @K_G_Andersen & @firefoxx66 for a lot more details on where this variant is identified in the World.
This means that so far, B.1.1.7 variant was identified in 3 states in the US: 1 in CO, 1 in FL, and 4 in CA.
Follow @K_G_Andersen & @firefoxx66 for a lot more details on where this variant is identified in the World.
9/
It also means that unlike the UK, S gene drop out is not yet a perfect proxy for B.1.1.7 in the US.
In UK, it is now a great proxy (@jcbarret):
In the US, not YET. It is a good proxy only If variant becomes dominant in the US.
It also means that unlike the UK, S gene drop out is not yet a perfect proxy for B.1.1.7 in the US.
In UK, it is now a great proxy (@jcbarret):
https://twitter.com/jcbarret/status/1343863095123435521?s=20
In the US, not YET. It is a good proxy only If variant becomes dominant in the US.
10/
We saw ~0.5% of positive tests in early December with S gene drop outs, and that 4 of 31 were B.1.1.7, a very very rough estimate would be that:
about 1 in 1,000 of positives in the US may be B.1.1.7.
Of course varies by state etc.
We saw ~0.5% of positive tests in early December with S gene drop outs, and that 4 of 31 were B.1.1.7, a very very rough estimate would be that:
about 1 in 1,000 of positives in the US may be B.1.1.7.
Of course varies by state etc.
11/
There is a clear need to continue tracking this variant in US. And to track new variants, or other like the other 501Y first identified in South Africa.
@my_helix will continue our effort to look into this with Illumina.
There is a clear need to continue tracking this variant in US. And to track new variants, or other like the other 501Y first identified in South Africa.
@my_helix will continue our effort to look into this with Illumina.
12/
This was another big sprint by many teams at Helix lead by @jameslu20 & @genesareclever. The lab team, Bioinfo, Research, QA ... + @illumina and with support from @CDCgov
Thanks also to @ewanbirney @firefoxx66 @trvrb @K_G_Andersen & other experts for help and resources.
This was another big sprint by many teams at Helix lead by @jameslu20 & @genesareclever. The lab team, Bioinfo, Research, QA ... + @illumina and with support from @CDCgov
Thanks also to @ewanbirney @firefoxx66 @trvrb @K_G_Andersen & other experts for help and resources.
13/
1 more question is whether the 4 samples we identified (or the 6 in the US) come from the same introduction.
Clear answer will be when these sequences get added to @nextstrain. First look seems to suggest that the FL sample is different than the 3 CA samples.
1 more question is whether the 4 samples we identified (or the 6 in the US) come from the same introduction.
Clear answer will be when these sequences get added to @nextstrain. First look seems to suggest that the FL sample is different than the 3 CA samples.
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