September BA Update

 President Biden says the pandemic is over. Maybe, but still ~400 Americans are dying each day from COVID-19 and excess deaths are still 10% above “expected.” It seems SARS-CoV-2 is not done with us. See the wonderful Your Local Epidemiologist blog for details. In fact, I would like to put in a plug for Katelyn Jetelina's blog. It's one of the best sources for explanations of the current epidemiological situations that I have encountered.

On September 13 2022, I downloaded a metadata file from GISAID containing 13,061,086 rows and 22 columns.  For this post, I take a brief look at the progress of the BA variants in the US. It's hard to know if the GISAID data gives a representative sample of the COVID-19 situation as, like other dats sources, it's likely that the actual situation is underreported. Still, the data you have is the dats that you have.

Here's what the data shows for variants of concern.

As we have seen before the Omicron variant is firmly established in the US.

Among the BA variants, we see a mixture of the common subvariants.

BA.5 hasn't yet taken over. There are still other variants circulating.

BA.4.6 has been in the news lately. It has an additional mutation in the spike protein that appears to increase its ability to escape the immune response.

GISAID lists BA.5.2.1, BA.2.75, BE.1.1, BA.5.2, BA.5.6, BA.5.1, and BA.5 as emerging variants. You can see their progress here.

Is the pandemic over? I'm not sure. We'll see. As they say on Game of Thrones: Winter is coming.

Code is available on GitHub.