Laura PionekJan 7, 2023
Mike Honey

The new XBB.1.5 "Kraken" lineage continues to spread around the world, as shown in this updated animated map. New York state continues to be the epicentre with over 50% of the shared lineages. Note that this does not directly represent cases, as jurisdictions share sequences at wildly differing rates and times

As well as showing a few more days of recent data, I now have integrated global data for the nextclade.org lineage classifier. Most experts say nextclade lineages are more precise and they also are quicker to include new lineages as they are defined.

On the map page I added a counter to give the number of sequences, and tweaked the map settings to get better positioning for the points.

Please note the locations are not precise - I'm using the country and state/province (where available), as geocoded by Bing Maps.

You can download the original video file here - please feel free to share and re-use anywhere:
https://github.com/Mike-Honey/covid-19-genomes/raw/main/covid-19-genomes-map-XBB-1-5.mp4

#COVID19 #XBB_1_5 #Kraken
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Jan 6, 2023 at 12:25pmWeb
Show threadMike HoneyJan 6, 2023

Here are the US states reporting the most XBB.1.5 samples. The north-east region dominates, led by New York at 54% frequency up to 24 December.

The growth rates are impressive - consider it was around 1% frequency in New York in mid-November.

Show threadMike HoneyJan 6, 2023

Here are the non-US countries reporting the most XBB.1.5 samples.

Israel is reporting the highest frequency (3%), followed by the UK (1.5%), then other European countries and Canada.

Show threadMike HoneyJan 6, 2023

For Israel, XBB.1.5 is showing a growth advantage of 6% per day against the BQ.* lineages, which predicts a crossover in early February.

For the UK: 10% growth, predicts a crossover in late January.

Show threadMike HoneyJan 6, 2023

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

Here are some alternative versions of diagrams showing the new lineages among the swarm of the "great convergence":

https://twitter.com/dfocosi/status/1609105670523047937

https://twitter.com/SolidEvidence/status/1608050436073832453

https://twitter.com/rquiroga777/status/1610061860451110912

Here's a good thread for more detail on XBB.1.5
https://twitter.com/jbloom_lab/status/1610002767904669698

Here's a comparison the Immune Escape vs ACE2 Binding Scores for a range of current lineages. XBB.1.5 sits in the top-right corner. It looks ideally balanced between the two attributes needed to overcome immunity and then bind to a new host.
https://twitter.com/RajlabN/status/1610791830580494337

Here's more info on why those two attributes of XBB.1.5 are important:
https://twitter.com/jbloom_lab/status/1610002767904669698

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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
Show threadMike HoneyJan 7, 2023
Here's a version just showing the US samples of XBB.1.5 "Kraken". They represent the majority of samples globally to this point.
https://github.com/Mike-Honey/covid-19-genomes/raw/main/covid-19-genomes-map-XBB-1-5-USA.mp4
Show threadLorraineJan 6, 2023

@mike_honey_
That “trend” map is wild
Aside from being a horrible & terrible subject matter, it’s fascinating to see exactly the order in which it travels
Could watch it for an inordinate amount of time

Decades?ago some lecture about fashion talked about how trends moved across🇺🇸& it bounced around seemingly in non-sensical manner. Reminds me of this world map

Also🌎Fashion Month is in March…so just as things calm down,they will fuel🔥fire

Show threadMike HoneyJan 7, 2023
@Lorrrraaaaine thanks - I'm glad it's useful