π§¬7/15 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @YaleMed
Alpha (B.1.1.7) = 27% (π8%)
Delta (B.1.617.2) = 64% (π11%)
**Delta is now likely the dominant variant in CT**
short 𧡠| Report π
covidtrackerct.com/variant-surveiβ¦
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @YaleMed
Alpha (B.1.1.7) = 27% (π8%)
Delta (B.1.617.2) = 64% (π11%)
**Delta is now likely the dominant variant in CT**
short 𧡠| Report π
covidtrackerct.com/variant-surveiβ¦
2/10 Our data combined with the CDC indicates that Delta was ~64% by 6/28 in Connecticut and may have been as high as 80% by 7/6 (remember that sequencing data always has a bit of a lag). Also, the rise in Delta is replacing almost all other variants. 
3/10 In addition to B.1.617.2, we are also seeing the sub-lineages AY.1, AY.2, and AY.3, which are all classified as Delta. Some AY.1's have K417N and some AY.2's have V70F. AY.3 is defined by mutations outside of spike. The functional differences between these are unknown.
4/10 The increase in Delta combined with low vaccination rates has caused a resurgence of COVID-19 cases in some states. In Connecticut, we are only seeing a very slight increase so far, which is also reflected in the wastewater data.
Data π yalecovidwastewater.com/reports
Data π yalecovidwastewater.com/reports
5/10 Follow @thehowie for a regular breakdown of the case numbers in Connecticut π
6/10 If Delta is up, but not so much the cases - how do we estimate the potential impact of Delta?
To help answer this question, we added a new function to our reports: Variant-specific effective reproduction numbers (Rt)
To help answer this question, we added a new function to our reports: Variant-specific effective reproduction numbers (Rt)
7/10 We estimate Rt by combining the variant frequency estimates from our sequencing data with daily reported COVID-19 cases. @MaryPetrone10 + @jessroth95 developed this method to compare the transmissibility of Alpha vs Iota.
Here Mary explains it:
Here Mary explains it:
https://twitter.com/MaryPetrone10/status/1411306664775532547?s=20
8/10 We estimate that the Rt for Delta is > 1 (1.55, indicating that cases are π), and is ~2X greater than Alpha (0.67) in CT. Unless we drive the Delta Rt < 1 though vaccinations and NPIs, we should absolutely expect to see an increase in local cases.
9/10 Delta is now dominant in CT, and only monitoring its frequency will become less informative (at least until something new emerges...). Following Rt trends will tell us a lot more about what to expect. Currently the Delta Rt is going in the wrong direction.
10/10 This week I'd like to thank @rtobiaskoch, @kendallbillig, @jessroth95, @ChaneyKalinich, @RebeccaEarnest1 for quickly implementing the Rt plots to our reports this week. It's still a work in progress (e.g. need to add CIs), and we appreciate constructive feedback π»
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