Thread by @TWenseleers

The SARS-CoV2 lineage soup was becoming a bit too complex to plot nicely, so here some simplified plots with lineages grouped by number of key mutations present, as suggested by @CorneliusRoemer (with some help from @rquiroga777).

With the exception of Singapore, that is experiencing an XBB driven wave now, level6+ variants (BQ.1.1, XBB, etc) would appear to still be at a relatively low level & not to exert a lot of pressure on case nrs yet, but this might soon change,...

considering that the Omicron XBB variant is clearly driving up infections in Singapore...

and that the estimated growth rate advantage of level6+ variants (BQ.1.1, XBB, etc) over resident type BA.5.2 is in excess of 10% per day. All this means a resurgence is likely later in November, even if cases currently start to flatten a bit...

Western European countries are seeing rising hospital and ICU admissions, with especially Germany already seeing figures that are higher than expected. If you get your invitation for a booster it might be a good idea to go and get it...

Here a plot of estimated cases by lineage in a few selected countries.

Here also shown as a stacked area chart.

And estimated share of different variant lineages in a few countries: in the UK...

In Denmark...

In Austria... (this excudes pre-selected targeted sequencing)

In Belgium...

And Singapore, where XBB has become dominant...

In W Europe, level 6+ lineages are still too rare to have much of an effect on case nrs - the resurgence we saw so far was mostly driven by waning immunity & a change in contact patterns. Only in Belgium BF.7 might have played some role as well. But effect of BQ.1.1 yet to come.

R code of plots & analysis of global @GISAID & @CovidGenomicsUK data can be found here: github.com/tomwenseleers/…. Some more plots can be found here github.com/tomwenseleers/….