Thread by @DiseaseEcology

Why hasn't B.1.1.7 fully displaced other variants in US? What other variants are persisting/growing?
Thread
B.1.1.7 has risen to relatively high frequencies in many states, but hasn't exceeded 90% in any of them & may be falling in several.
Data here from @my_helix

GISAID sequences via fantastic outbreak.info for US as a whole suggest B.1.1.7 now stable @70%, P.1 is growing, B.1.526 frequencies are stable. But variable sequencing means finer resolution is better for understanding frequency dynamics, spatial variability & nuance.

Statewide scale is still too large but better than whole US.
Here's FL. Similar pattern as whole US - P.1 growing & B.1.526 stable, leading to slight recent decrease in B.1.1.7

Here's MA. Similar to FL, whole US. Rising P.1, B.1.526 stable. B.1.1.7 barely rising.

Here's CA. A little different. B.1.1.7 is still increasing in frequency (increasing in N CA now; earlier spread in S CA). As elsewhere, P.1 increasing. B.1.526 stable or slightly increasing. B.1.427, B.1.429 being displaced. B.1.617.2 increasing.

Given situation in UK, many folks are watching B.1.617.2 (1st det in India) in US. Low freq (~2%) overall.
Here is CA. Growing, but not exponentially, possibly due to spatial heterogeneity in sampling, variation in # of introductions & traveller cases, etc.

In UK B.1.617.2 is displacing B.1.1.7 (follow @chrischirp @arambaut for 2 perspectives on rise), likely due to increased transmissibility & partial immune escape, especially for 1-dose vaccine protection. How this will play out in US w/ most receiving both doses is unclear to me.

I'll be watching both P.1 & B.1.617.2 & hoping we can get remaining folks vaccinated & prevent resurgence due to either of these variants. Full vaccine protection against both appears solid (e.g. gov.uk/government/new…).

Would love to hear what folks like @K_G_Andersen @trvrb think is happening.