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Mike Honey

@mikehoney.bsky.social

10K followers 100 following 3K posts

Data Visualisation and Data Integration specialist - Melbourne, Australia https://linktr.ee/mike_honey_ Support my projects by sponsoring me on Github: https://github.com/sponsors/Mike-Honey

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Mike Honey @mikehoney.bsky.social · 3d

With the NB.1.8.1.* "Nimbus" and XFG.* "Stratus" variants carving up dominance around the globe, it is time to ponder which variant might drive the next wave.

The leading contender at this point is PY.1.1.1.

#COVID19 #SARSCoV2 #PY_1_1_1 #XFG_1_1
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Mike Honey @mikehoney.bsky.social · 2d

Yes I think thats right. There was a small Nimbus wave in Scotland, but it was crushed by Stratus.

Mike Honey @mikehoney.bsky.social · 2d

Report link:
mike-honey.github.io/covid-19-gen...
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mike-honey.github.io

Mike Honey @mikehoney.bsky.social · 2d

Here are the leading European countries reporting XFG.* "Stratus".

The frequency reached 96% in Italy recently.
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Mike Honey @mikehoney.bsky.social · 2d

Here's the latest variant picture for Europe (excluding the UK), to late September.

The XFG.* "Stratus" variant continued to dominate, growing to 85% frequency.

NB.1.8.1 "Nimbus" grew slightly to 10%.

#COVID19 #SARSCoV2 #EUR #LP_8_1 #XFG #Stratus #NB_1_8_1 #Nimbus
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Mike Honey @mikehoney.bsky.social · 2d

Report link:
mike-honey.github.io/covid-19-gen...
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mike-honey.github.io

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Mike Honey @mikehoney.bsky.social · 2d

Here's the latest variant picture for the United Kingdom, to late September.

The XFG.* "Stratus" variant remained dominant, but fell back to 75%.

NB.1.8.1 "Nimbus" grew to 17%.

#COVID19 #SARSCoV2 #UK #XFG #Stratus #NB_1_8_1 #Nimbus
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Mike Honey @mikehoney.bsky.social · 2d

Report link:
mike-honey.github.io/covid-19-gen...
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mike-honey.github.io

Mike Honey @mikehoney.bsky.social · 2d

On this thread I gave an update on PY.1.1.1 and other new lineages.
bsky.app/profile/mike...
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Mike Honey @mikehoney.bsky.social · 2d

The recent rebound in the JN.1.* +FLiRT variant was driven by the PY.1.1.1 sub-lineage, mostly reported from Ontario.
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Mike Honey @mikehoney.bsky.social · 2d

Here's the latest variant picture for Canada, to late September.

XFG.* "Stratus" continued to dominate, but fell back to 71%.

NB.1.8.1 "Nimbus" grew slightly to 14%.

JN.1.* + "FLiRT" rebounded suddenly to 7%.

#COVID19 #Canada #XFG #Stratus #NB_1_8_1 #Nimbus #FLiRT
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Mike Honey @mikehoney.bsky.social · 2d

You may say I'm a dreamer
But I'm not the only one

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Mike Honey @mikehoney.bsky.social · 3d

Interactive genomic sequencing dataviz, code, acknowledgements and more info here:
github.com/Mike-Honey/c...
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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.com

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Mike Honey @mikehoney.bsky.social · 3d

Huge thanks to all the dedicated variant hunters who persevere with their crucial work away from the limelight, especially to Federico Gueli for his tips on new lineages, eg
bsky.app/profile/siam...
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Federico Gueli @siamosolocani.bsky.social · 3d

Quick Sars cov2 variant update.
XFG.17.2.1 ( 219S 679R) is the fastest then there PE.1.4/PE.1.7 but still an Oceania only lineage.
After them some new designations are to watch XFG.10.4 first XFG designated with 435S
PQ.2.8.1 has S:H445P.

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Mike Honey @mikehoney.bsky.social · 3d

The usual caveats apply - recent sample sizes are smaller which might skew these results, and “global” sequencing data is dominated by wealthy countries, with many under-sampled regions.
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Mike Honey @mikehoney.bsky.social · 3d

I will hold with PY.1.1.1 as my leading contender, based on it’s broader geographical distribution, and sharp recent growth.

Also there have been more samples of PY.1.1.1 reported in the International Traveller samples – the most representative sample set with a global perspective.
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Mike Honey @mikehoney.bsky.social · 3d

Here are the International Traveller samples of PY.1.1.1, XFG.1.1.1 and XFV.

India has been the source of the most PY.1.1.1 with 8 samples.

This dataset (mostly arrivals in the US and Japan) is arguably more random, as it is not skewed by sequencing volumes.
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Mike Honey @mikehoney.bsky.social · 3d

Here's a map showing the spread of the XFG.1.1 variant. The first sample was reported from Denmark in June. It seems very broadly spread across North America, especially considering the patchy sample volumes over this period.

Locations are approximate - typically country and state/province.
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Mike Honey @mikehoney.bsky.social · 3d

XFG.1.1 was recently defined, characterised by a reversion to Spike W452R, which captured the attention of the Variant Hunters.

XFG.1.1 has mostly been reported from North America, with sharp recent growth showing for the US to 3% and Canada to 2%.

It has also been detected in US wastewater.
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Mike Honey @mikehoney.bsky.social · 3d

Here's a map showing the global spread of the PY.1.1.1 variant. The first samples were reported simultaneously from Manipur, India and New South Wales, Australia in late May.

Locations are approximate - typically country and state/province.
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Mike Honey @mikehoney.bsky.social · 3d

Singapore has shared almost 60 samples since then so the final level of 6% is a more reliable gauge.
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Mike Honey @mikehoney.bsky.social · 3d

Here’s the latest variant picture for Singapore. The wild spike in the PY.1.1.1 frequency (included in the FLiRT series) looks to be an artefact of a gap in the sequencing data from Singapore, from mid-August to mid-September. 🧵

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Mike Honey @mikehoney.bsky.social · 3d

Here’s the latest variant picture for India. There was a burst of sequencing data in late May, probably prompted by their XFG.* wave. But the data soon slowed and then came to a complete stop during July.
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Mike Honey @mikehoney.bsky.social · 3d

PY.1.1.1 has also shown signs of growth in several other countries, notably rising to 8% in Canada and finishing at 6% in Singapore.
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Mike Honey @mikehoney.bsky.social · 3d

PY.1.1.1 is descended from "FLiRT" variant LF.7.9.1. PY.1.1 added the K679R mutation, then PY.1.1.1 added A435S (same mutation that characterised NB.1.8.1).

PY.1.1.1 is presumed to have originated from India, rising sharply to 11% frequency there by mid-July.
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Mike Honey @mikehoney.bsky.social · 3d

I added some other contenders for monitoring, although they don’t seem significant so far: XEC.27.2.*, XFV, XFW, XFZ and XGA.
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