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.
Hmm latest wave well on track to match or even exceed the Omicron BA.1 wave, judging from the wastewater surveillance data here in BE. Current wave still mostly result of waning immunity & behavioural change/seasonality. Variant pressure will come on top of this in November...
Here latest variant picture for Belgium... Emerging Omicron BQ.1.1, XBB and BA.2.3.20 lineages all have the potential to drive a new infection wave, given their observed growth rate advantage over the current BA.5.2 type.
In Singapore the recombinant XBB is currently driving an infection wave. As yet little info on severity. In all likelihood, higher population immunity will cause infection fatality rate & infection hospitalisation rate to go down. But I got a new updated booster, just in case...
Agree: the chance of experiencing long-term health consequences after Covid is definitely not an independent Bernoulli "flip of the coin" / "Russian roulette" type constant chance. It is concentrated in particular risk groups & risk is also decreasing due to better immunity.🧵
The same no doubt applies to rare vaccine adverse effects: these will be concentrated in a very specific group of people with particular predispositions, that most likely also partly overlaps with predispositions for severe or long Covid.
Was looking for studies that tried to quantify this degree of overlap in (genetic) predispositions for vaccine adverse effects & severe or long Covid. Anybody any pointers? Any good GWAS studies on this? Or twin studies? @chrischirp@kallmemeg@andrew_croxford@macroliter
Repost of estimates of growth advantage of some emerging SARS-CoV2 variants (fixing mistake in my XBB annotation). Overall growth rate estimates, averaged across continents, has BQ.1.1 at nr 1, followed by BA.2.3.20, BQ.1, XBB and BA.2.75.2. BQ.1.1 currently looks like winner.🧵
In Asia, the XBB recombinant is currently the one with the largest growth advantage though, and it may also become so in Europe (I'm not showing estimate for Europe because of small sample size, but it's also growing fast there).
Short-term projections predict mostly BQ.1.1 to take off in Europe & the US, while XBB is causing an infection wave right now in Singapore & Bangladesh. These should be countries to watch to get info on severity. In many countries, XBB will likely get established as well though.
Politicization of science & the whole antivax movement was pretty deadly: in the US anti-vaxx sentiment killed 2.5 times more Republicans than Democrats due to the large differences in vaccination rates. Almost like a cluster randomized trial. 300K lives were lost unnecessarily.
New news piece in Nature magazine by @ewencallaway, with a bit of input from myself: "Will there be a COVID winter wave? What scientists say" 🧵nature.com/articles/d4158…
For anyone interested in the dynamics of new variants it is worth mentioning that the R code to carry out multinomial fits on all of the @GISAID & @CovidGenomicsUK data is freely & openly available at github.com/tomwenseleers/… & can be re-used by anyone.
The script carries out multinomial fits & calculates the share of different variants through time by country & their growth advantage in a computationally efficient way. It returns plots like in the thread below.