Omicron BA.4.6 at 4 percent of all US sequences

America, Australia, BA.4, BA.4.6, BA.5, Denmark, Europe, France, Genome, Infection, Iowa, Kansas, Missouri, Nebraska, New York State, Science, Testing, Transmission, UK, USA

Omicron BA.4.6, a subvariant of BA.4, has been attracting some media attention over the past few days. The subvariant of BA.4 is prevalent in Iowa, Kansas, Missouri, and Nebraska, making up 10.7% of all local cases in that region.

BA.4 is the quiet half-brother of the BA.5 subvariant which has been rampaging across the globe for the last two months. Now, it looks like BA.4 may have finally found a purpose. 

According to CoVSPectrum, with nearly 3,000 samples, BA.4.6 currently represents just over 4% of sequences nationally in the US, and is seeing steady growth.

BA.4.6 accounts for nearly 5% of sequences in the UK, and around 6% of sequences in Canada. France and Denmark have just over 1% of sequences showing as BA.4.6. The new strain has also been detected in 43 other countries.


Internationally, BA.4.6 accounts for about 2.4 percent of all sequences.



The relative growth rate of BA.4.6 has been picking up, perhaps in response to the slow decay of BA.5. 


The CDC variant tracker is showing growth in BA.4.6 (in dark blue):


Data from New York is showing BA.4.6 (in brown) at over 5% of sequences:


Raj Rajnarayanan’s Covid tracker is showing that BA.4.6 is already the 9th most frequent subvariant in the USA:


In the UK, BA.4.6 seems to be easily outcompeting BA.2.75 (in blue) according Sanger:


An interesting thread from Diego Bassani about the BA.4.6 situation in Australia:







** Based on past experience, for the next winter wave, Coronaheadsup is expecting a completely different variant to Omicron to appear. We don’t think this subvariant is it. **




** This post was originally published on August 5, 2022 **