Thread by @NathanGrubaugh

🧬10/21 Connecticut #SARSCoV2 variant surveillance
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH | @Yalemed

👑Delta - 99.7% (336/337)

📊Top lineages
39% = B.1.617.2
22% = AY.25
13% = AY.39
7% = AY.3
4% = AY.4 (not UK AY.4.2)
4% = AY.20

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

Effective reproductive number (Rt) estimates for the top Delta lineages in Connecticut.

➡️All are now <1, suggesting that transmission is 📉.

➡️The relative similar Rt values suggest that they are of similar transmissibility. (2/12)

Last week we reported AY.4 was ~27%, and this week its 4%. The sudden 📉 is not due to more refined classifications. Its hard to distinguish between closely related sequences, and a dropout in some Delta spike sequences makes it even harder. (3/12)

https://twitter.com/NathanGrubaugh/status/1448748730316906498?s=20

A tweet from Dr. Gottlieb last week created a media frenzy around the idea of a more transmissible "Delta+" AY.4 lineage. While I think that this was good intentioned, and we should characterize it, IMO it created more panic than what it deserved. (4/12)

https://twitter.com/ScottGottliebMD/status/1449803423906418691?s=20

👆 was in reference to AY.4.2, and Dr. Barrett has a nice thread on this. AY.4.2 is slightly 📈 in England, but we haven't seen much spread out of the region. Certainly worth watching, but not anything to panic about in Connecticut or the US yet. (5/12)

https://twitter.com/jcbarret/status/1450408485829718039?s=20

AY.4.2 is defined by 2 spike mutations: A222V and Y145H. As noted by Dr. Rambaut, the latter can be difficult to assess from sequences using the V3 or earlier primers.

*I strongly encourage everyone sequencing Delta to switch the the V4 primers* (6/12)

https://twitter.com/arambaut/status/1448780478677504005

You can learn more about the spike drop out when sequencing Delta with V3 primers by reading Dr. Sanderson's preprint. (7/12)

https://twitter.com/theosanderson/status/1450131544773910542?s=20

We've switched the the V4 primers and have yet to sequence a AY.4 with the Y145H mutation. And so far no AY.4.2 sequences or AY.4 + A222V have been identified in Connecticut, only a few with A222S from August (see 👇). (8/12)

While not in AY.4, we identified other Delta lineages with A222V - B.1.617.2, AY.26, AY.37 - but they are not growing in frequency after being very common during the early emergence in our region.

👇 shows the Connecticut Delta clade and the allele at spike 222. (9/12)

In Connecticut at least, and probably for most of the US, we are not *yet* concerned about any particular Delta lineage. The AY.4.2 situation in England is worth following though, and so is our continued vigilance for anything changing locally. (10/12)

AY.39 is now #3 on the leaderboard in Connecticut. Its sudden emergence is likely due to its new classification.

It's predominately found in the US and looks to be defined by synonymous mutations. So probably not a concern. (11/12)

cov-lineages.org/lineage.html?l…

I'd like to introduce y'all to Kien Pham, an outstanding @yaleemd MPH student who is helping us on the bioinformatic side of our surveillance system. He's not on Twitter yet, but [/doom-scrolls through my feed] perhaps that's for the best 🤷‍♂️ (12/12)

grubaughlab.com/team/kien-pham/

**clarification. drop is due to more refined classifications. Rouge "not" in there. I need a tweet proofreader or edit function.