Thread by @NathanGrubaugh

🧬8/12 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @Yalemed

Delta - 95% (📈7%)
B.1.621 - 4% (📉4%)
Gamma - <1% (📉3%)
Alpha - 0% (📈1%)

State infections = 55/100k pop/day
State Rt = 1.2

short 🧵 | Report 👉
covidtrackerct.com/variant-survei…

217 days ago we reported the first B.1.1.7 (now called Alpha) cases in Connecticut. For the first time since then we report 0⃣ Alpha cases.

Lets quickly recap Alpha's reign (2/10)

https://twitter.com/NathanGrubaugh/status/1347273096689016835?s=20

Alpha is the first variant to hit the news, and concern over its emergence was the primary motivating factor for the construction of our state genomic surveillance system. Because of our rapid increase in sequencing, we've been able to detect other variants much earlier. (3/10)

Alpha initially raised more questions than we had answers, and subsequently caused quite a bit of panic in our community. I tried to address some of these to the best that I could. (4/10)

https://twitter.com/NathanGrubaugh/status/1349019541574189057?s=20

Alpha peaked at ~64% in Connecticut, much lower than what it reached in the UK. Its rapid rise in early 2021 was only surpassed by its recent fall.

I don't know why this is making me think 'Game of Thrones', but the 👑 is dead (eaten by a Delta-shaped 🐲). RIP (5/10)

The new 👑 is obviously Delta (first of its name), and it now makes up >95% of the sequenced cases in Connecticut.

We find it in 2 primary flavors: AY.3 (~15%) and B.1.617.2 (~80%). Its still not clear if one of these is more transmissible. (6/10)

The challenger, and second most common variant, is B.1.621 (& B.1.621.1 - Blue). I'm not yet sure if it will suffer the same fate as the other variants, but for now at least its still hanging around. (7/10)

BTW, the B.1.621 GISAID data submission issue has been fixed. As backlogged data gets uploaded, we should have a better picture of its national/global prevalence (8/10)

https://twitter.com/NathanGrubaugh/status/1425113760881053699?s=20

Our variant-specific Rt plots confirm that for the last 1.5 months, Delta, and to some extent B.1.621, has been driving transmission (i.e. Rt > 1). Cases for all other variants are decreasing even during this resurgence. Thus cases wont come down until we bring Delta down. (9/10)

Thanks to our friends in Puerto Rico (@fabyhealthyle ), Dominican Republic (@PaulinoRobert ), and USVI, we are producing reports and custom Nextstrain builds for the Caribbean too. We'll start generating weekly threads in the near future. (10/10)

covidtrackerct.com/caribbean/