Thread by @NathanGrubaugh

⚡️4/15 Connecticut #SARSCoV2 variant surveillance report 🧬
@CovidCT | @jacksonlab | @CTDPH | @YaleSPH

- B.1.1.7 📈
- B.1.526 📉
- Still not much P.1 & B.1.351

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

2/9 While we continue to see the rapid decline of non-VOCs/VOIs, the competition between B.1.1.7 & B.1.526 is quite interesting, and could have significant public health importance. Currently B.1.1.7 is "winning", though things could rapidly change as more people get vaccinated.

3/9 For the first time we saw B.1.1.7 📉 from TaqPath data, which could mean that it is slowing down (it has to at some point). Below I also plotted the B.1.1.7 frequency estimates from our sequencing data, which has tracked with TaqPath and importantly still shows B.1.1.7 📈

4/9 So I am hesitant to say that the 📈 trajectory of B.1.1.7 is starting to slow down based on the TaqPath data. We now have enough data to expect B.1.1.7 to keep 📈 until it completely dominates (>90%), or until the selection landscape changes w/ 💉

5/9 The B.1.526 story is interesting. 1st, it is a complicated lineage, with 2 new sub-lineages ("sister" lineages?) and 3 primary mutations within the spike RBD:

L452R, S477N, E484K

As you can see, they have very different patterns which could be functionally relevant.

6/9 What's interesting is that B.1.526 (+E484K or S477N) and B.1.526.2 (+S477N) were 📈 as fast as B.1.1.7, but now both are on the 📉.

B.1.526.1 (+L452R), meanwhile, is still 📈. Perhaps this is a blip in the data, or perhaps their is something real to this.🤷‍♂️

7/9 The L452R mutation on B.1.526.1 is notable as it is also found on the VOCs B.1.427/9 (first detected in CA) that are known to reduce the efficacy of some monoclonal antibodies. However, B.1.427/9 haven't been much of an issue in CT, and are collectively <3% since March.

8/9 The decline in B.1.526, and the fact that B.1.351 & P.1 have taken hold in CT, means that the frequency of viruses in CT with the E484K mutation has also 📉. I'll take this as good news with the caveat that other mutations are also likely important for immune evasion.

9/9 This week I'd like to highlight the work by @AndersonBrito_ who was instrumental in setting up our weekly reports. I am so grateful to have Anderson on our team 🙏

His amazing data processing python scrips and nextstrain code can be found here:
github.com/andersonbrito/…