Update on @my_helix SARS-CoV-2 variant surveillance program.
Data from testing with n positives & SGTF (S-gene target failure)
Stats on sequences (SGTF & non-SGTF)
Stats on B117
2/
First, the dashboard is still focused on B117. Because B117 is more infectious & had large impact in many UK, Ireland, Denmark...
But, looking for other variants is also super important. covariants.org
=> we are increasing sequencing of random positives. see map
3/ Back to SGTF & B117 analyses. Knowing there is a bias in selection, we estimate % of positives that are B117 by looking at 2 metrics:
- (n SGTF) / (n positives)
- (n B117) / n SGTF sequenced)
And all numbers are from positives with a N-gene Cq < 27.
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One more thing on method. We updated to have 5-days moving average instead of 7-days.
In current update, last collection date is:
- Jan 31 for PCR testing (n positives and n SGTF
- Jan 18 for sequencing data
extrapolating the seq data, estimate is that B117 represent ~5.2% of positives
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Georgia is another state with n of B117 that is rising. Numbers a bit small for real estimates but one to watch.
8/
MA numbers
Massachusetts is still the perfect example to show that not all SGTF are B117. For 3 months, it had a very stable 5% of positives that are SGTF and almost no B117.
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
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
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
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.