More Variants

Vietnam has uncovered a new COVID-19 variant combining characteristics of the two existing variants first found in India and the UK,
~ Vietnam Health Minister Nguyen Thanh Long 

This is the one that actually gets me concerned,

Dr. Daniel Griffin, chief of infectious diseases for ProHEALTH, told CNBC, referring to the E484K mutation.

It seems like every news cycle brings stories of a new SARS-CoV-2 variant. Even though in the US cases are dropping, the world is far from putting COVID-19 behind it. The US one-dose vaccination level is about 50% at the end of May 2021. Unfortunately, much of the world is far below this level. As long as there are vulnerable populations new variants will arise.

 The B..617.3 variant has been in the news lately. Pango-Lineages lists three lineages with assigned sequences in the B.1.617 family: B.1.617.1, B.1.617.2, B.1.617.3. B.1.617.1 is the original variant in this group. I'll use the code from here and here to take a quick look at the the growth of these three variants in the US, United Kingdom, and India. This article from Nature gives a good summary of the effects of the three.

The data shown below is from metadata from GISAID downloaded on 2020-05-30.  The data table has 1,784,546 observations of 22 variables.

The growth of the B.1.617.2 variant is most dramatic in the UK data. This plot of log(counts) by data shows the exponential growth of B.1.617.2, while B.1.617.3 hasn't gained as much of a foothold yet.

The US data is similar but B.1.617.2 has not reached the level it has in the UK. Still B.1.617.2 is showing exponential growth.

The India data is a bit messier, partly because it is more sparse. It shows more growth of B.1.617.3, while B.1.617.2 continues to grow.