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Mike Honey Dec 2, 2022

Western Europe is clearly in the grip of a fresh wave of covid, with a sharp uptick in hospital admissions in several adjacent countries, not long after their recent BQ.* waves. It's difficult to find trends in the genomic sequencing data to explain this in most of these countries - the recent data is from most is quite thin.

I'm focusing on Denmark, where genomic sequencing output is prompt and dense. There, it seems BN.1.3.1 from the BA.2.75.* "Centaurus" clan is the new lineage showing the most significant growth (6%).

There's some growth from the other lineages in the BA.2.75.* "Centaurus" clan, notably BN.1.4 (2%).

#COVID19 #Europe #Denmark #BN_1_3_1 #BN_1_4 #BQ
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Mike Honey Dec 2, 2022

Here's the high-level variant picture for Denmark:

The BQ.* clan of lineages grew steadily during October to dominance (41%).

The BA.5.* clan is steadily fading (35%).

There's recent growth from the BA.2.75.* lineages (14%) - the leading challenger.

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Mike Honey Dec 2, 2022

In Denmark, the growth in the BQ.* clan is mostly driven by the BQ.1.1 "Cerberus" lineage (17%).

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Mike Honey

For Denmark, the BN.1.3.1 lineage is showing a growth advantage of 3% per day against BQ.1.1, which predicts a crossover in late December.

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Mike Honey Dec 2, 2022

A fresh wave of hospital admissions has clearly started in Denmark, and also in Belgium, France and the Netherlands, with remarkable synchronicity. The more intense genomic sequencing data from Denmark is likely a useful guide to the lineages driving the waves in other countries.

Weekly hospital admissions are up to 63/M in Denmark, following a trough around 21 November at 41/M.

As with the recent BQ.* waves, it's remarkable how a relatively low frequency of a new lineage can spark severe outcomes.

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Mike Honey Dec 2, 2022

Daily reported cases in Denmark are up to 146/1M, following a trough around 22 November at around 91/M.

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Mike Honey Dec 2, 2022

Daily reported deaths in Denmark are still falling, down to 7/M. Deaths typically lag cases and hospitalisations by a few weeks.

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Mike Honey Dec 2, 2022

Here are the key stats for Denmark in a single chart, with a log scale.

This helps align the dates and compare growth rates.

Here I'm showing the absolute values, rather than that the per capita stats used above.

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Mike Honey Dec 2, 2022

"Fully vaccinated" - received a booster in the last 120 days

Like most high-income countries, this is now very low (0.5%). At least it seems the decline bottomed out in November.

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Mike Honey Dec 2, 2022

Interactive genomic sequencing dataviz, code, acknowledgements and more info here:
https://github.com/Mike-Honey/covid-19-genomes#readme

World covid stats dataviz here:
https://github.com/Mike-Honey/covid-19-world-vaccinations#statistics-by-geography-page---pick-a-stat-and-countries-for-a-time-series

Here https://mstdn.science/@TRyanGregory pulled together a mega-thread of recent threads from various experts on the current SARS-CoV-2 variant evolution landscape:
https://twitter.com/TRyanGregory/status/1596936566626086912?s=20&t=PFJp_zs1mMu52r9UW14bhw

Here are some alternative versions of diagrams showing the new lineages:

https://twitter.com/dfocosi/status/1595740062007939072

https://twitter.com/SolidEvidence/status/1587519610324017153

https://twitter.com/rquiroga777/status/1594092136047284225

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GitHub - Mike-Honey/covid-19-genomes: Projects on COVID-19 topic of genomic sequencing - mostly DataViz

Projects on COVID-19 topic of genomic sequencing - mostly DataViz - Mike-Honey/covid-19-genomes

GitHub

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malcriada_lala_Dec 3, 2022

@mike_honey_ is this showing that people are not keeping up with the vaccine schedule?

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Mike Honey Dec 3, 2022

@Malcriada it's not intended as that and I'm not sure what the schedule is in Denmark. I think of it as a population-level measurement of booster waning.

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