mikehoney.bsky.social
Data Visualisation and Data Integration specialist - Melbourne, Australia
https://linktr.ee/mike_honey_
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2,012 posts
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Getting Started
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Interactive genomic sequencing dataviz, code, acknowledgements and more info here:
github.com/Mike-Honey/c...
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Huge thanks to all the dedicated medical and scientific experts around the world, who continue to share their data to enable the classification of new variants.
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Audio credit:
Swarm_Bees_outdoor_stereo by leonseptavaux -- freesound.org/s/573839/ -- License: Attribution 4.0
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LF.7 was descended from JN.1.16.1 – a FLiRT characterised by the Spike R346T mutation. The collection of FLiRT lineages have not been very successful in most places. But they have been given the opportunity to spread and mutate further for over a year, leading to PY.1, just classified last week.
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PY.1 is descended from LF.7.9.1, both of which are only characterised by nucleotide mutations – no spike changes. So it’s success will be challenging to explain.
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Here’s the map of PY.1 samples from India. It looks to be fairly evenly distributed there, from a geographic perspective.
Locations are approximate – to the state level.
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Here are the leading individual variants for India. PY.1 reached an impressive 40% frequency in recent sequences, while facing stiff competition from the XFP and XFG* "Stratus" variants.
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Here’s the Global picture, comparing PY.1 (shown as “JN,1.* + FLiRT”) vs the leading NB.1.8.1 "Nimbus" and XFG* "Stratus" variants.
I show them here using a log scale, so you can compare their growth rates. PY.1 looks quite competitive so far, reaching 8% frequency.
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Locations are approximate - typically country and state/province.
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Interactive genomic sequencing dataviz, code, acknowledgements and more info here:
github.com/Mike-Honey/c...
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Here are the recent International Traveller samples originating from China (arriving in the US and Japan). This confirms the recent dominance of the NB.1.8.1 "Nimbus" variant.
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The geographical coverage of the recent data from China is incomplete – almost all the data came from the provinces of Yunnan (capital: Kunming) and Hubei (Wuhan).
Locations are approximate - to province level only.
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Note the only other significant group is XDV.*, which are the ancestors and cousins of NB.1.8.1.
It’s quite striking to see that level of dominance confirmed again, across a far larger set of samples. I haven’t seen this pattern anywhere, since BA.2.86/JN.1 took over globally in late 2023.
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There are parallel waves of both, in different places. The Nimbus zone is roughly from the Himalayas and Myanmar border east to the Rocky Mountains.
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XFG.* doesn't look very significant in NZ - yet. Certainly one to watch!
There's also a late rebound in XEC.* - mostly the PU.1 sub-variant. XEC.* never reached dominance in NZ, so there would still be plenty of susceptibles around for it.
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Yes it was a bit unexpected to see XFG seemingly going backwards in the Netherlands recently - thanks for digging in to explain Josette!
It has me pondering rapid reinfections, especially for immune-compromised people ...
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Report link:
mike-honey.github.io/covid-19-gen...
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China rose to share the highest recent volume, followed by Singapore, Brazil and Japan.
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XFG.* "Stratus" made up 100% of recent samples from Bangladesh and 89% for Myanmar. India grew strongly to 64%.
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With the resumption of sequence data sharing from China, the takeover of the NB.1.8.1 "Nimbus" parallels that in Hong Kong, rising to 100% frequency.
Growth in Thailand and Japan rose above 80%.
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For the "Global - Other" countries, the XFG.* "Stratus" variant is showing a strong growth advantage of 6.4% per day (45% per week) over the NB.1.8.1 "Nimbus" variant. That predicts a crossover in mid-June (the data routinely lags).
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This perspective excludes all the high-volume countries and regions that I routinely report on: Australia, NZ, Europe, Canada and the US. The remaining countries are aggregated into this report.
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Report link:
mike-honey.github.io/covid-19-gen...
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Here are the leading European countries reporting XFG.* "Stratus". It has reached 33% in Italy and Spain.
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For Europe (excluding the UK), the XFG.* "Stratus" variant shows a strong growth advantage of 4.7% per day (33% per week) over LP.8.1.*. That predicts a crossover in early June (the data routinely lags).
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mike-honey.github.io/covid-19-gen...
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For the UK, the XFG.* "Stratus" variant shows a slowing growth advantage of 2.9% per day (20% per week) over LP.8.1.*. That now predicts a crossover in early July.
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Report link:
mike-honey.github.io/covid-19-gen...
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Data volumes shared from the US have slowed noticeably in recent weeks. The data from many states is lagging, and data from some larger states like Texas and Florida is extremely thin.
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NB.1.8.1 "Nimbus" has mainly been reported among the International Traveller samples, at around 20-40% frequency.
It has been dominant among patchy samples from Maryland.
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For the US, the NB.1.8.1 "Nimbus" variant shows a slowing growth advantage of 5.9% per day (41% per week) over LP.8.1.*, which predicts a crossover in early June (the data routinely lags).
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XFG.* "Stratus" has mainly been reported from New York state, rising to 50% frequency. It has also been very common among the International Traveller samples. It rose in Colorado to 25%.
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For the US, the XFG.* "Stratus" variant shows a strong growth advantage of 6% per day (42% per week) over LP.8.1.*, which predicts a crossover in early June (the data routinely lags).
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Report link:
mike-honey.github.io/covid-19-gen...
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Data from Tasmania was updated, but still lags to the end of March.
Volumes from Victoria continue to lift, but it is still woefully under-represented.
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Here are the states reporting NB.1.8.1 "Nimbus". Putting aside a patchy data point from Queensland, tt has been most successful in Western Australia, surging as high as 83% frequency. NSW, Victoria and Queensland finished at 44-60%.
Growth is slower in SA, at just 20%.
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Report link:
mike-honey.github.io/covid-19-gen...
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The highest frequencies of XFG.* "Stratus" have been reported from India, reaching 64%. It has also shown sustained growth in the US to 33%, and Spain to 27%.
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Globally, the XFG.* "Stratus" variant is showing a stronger and accelerating growth advantage of 6.6% per day (46% per week) over the LP.8.1.* variant. That predicts a crossover in late May (the data routinely lags).
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With the resumption of sequence data sharing from China, the takeover of the NB.1.8.1 "Nimbus" parallels that in Hong Kong, rising to 100% frequency.
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Globally, the NB.1.8.1 "Nimbus" variant is showing a slowing growth advantage of 4.1% per day (29% per week) over the LP.8.1.* variant, with a crossover in mid- May.
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Here are the trends across all the International Traveller samples, with a roughly similar picture. However both NB.1.8.1.* and XFG.* are a bit higher.
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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