rt-from-frequency-dynamics VS pango-designation

Although several XBB.1.5 descendants are growing marginally faster, all variants that aren't XBB+486P are on the decline nationwide. This includes CH.1.1, which has been the clear #2 VOC behind XBB.1 since ~October and which has gotten some press recently.

State or national variant numbers can currently be best accessed at cov-spectrum; in this link by clicking on "show regions". Covariants provides an even easier-to-read version, but it only separates a few classes of variants and in 2-week intervals. And Bedford labs variant tracker provides a unique perspective of different variant growth, but currently does not separate by states and has irregular updating.

With variant tracking the main place to follow is the pango-designation project on github (but please do not post there if you go). Cov-spectrum is great for following the epidemiology of variants, as well as bedford labs. And before that covariants, but they haven't kept up with cov-spectrum's development. All of it's very simple from a modelling perspective, but applying the gisaid data to the case data is massively enlightening.

Though they update even more infrequently, I really like the new Bedford labs graphs. These make it very clear just how complicated trying to model the next several months would be.

For a national perspective you can see Trevor Bedford’s GitHub. https://github.com/blab/rt-from-frequency-dynamics/tree/master/results/pango-countries

Bedford labs splits it up into specific case counts, and shows the same thing. Here we see that BA.5 cases just stopped declining and started rising. Unfortunately they update irregularly. I'm looking specifically at the third graph here, and what makes me not want to be certain is the dark gray dots that are rising rapidly at the right. These aren't on the legend but I believe mean "other".

Bedford labs this week has added several new graphs. This looks in detail at just the US at a lot of different lineages. This looks at many countries with fewer lineages. Note that they do not have XBB.1 (everything's grouped as XBB giving variable results) and their updates are very irregular.

4 Bedford labs variant tracker is following XBB now, but not XBB.1. This isn't very useful to see growth in many countries where XBB has been spreading for a bit and XBB.1 has just been introduced, though the r~0.19 (3.8-fold weekly growth) is probably pretty accurate for Singapore.

covariants, cov-spectrum, outbreak.info, blab

But my best source, when it's updated, is Bedford labs variant tracking project.

And don't miss this news as well as the link that goes to the discussion.