This AFL season, I've been struck by how many mentions of "illness" there have been. I assume most of these are COVID cases, and here's an analysis that confirms that assumption.

For 2024 (so far), mentions of illness are around 850% higher than the pre-COVID baseline.
#AFL
🧵 I searched the AFL website for mentions of "illness" by year, starting in 2016 (using the Tools / Custom Date Range feature).
The results were quite striking - after years of a fairly static level of 30-40, they have exploded since 2021 - when Australia #LetItRip.
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New variant MV.1 is spreading quite rapidly, and looks a potential next challenger against the now-dominant DeFLuQE variants (KP.3.1.1 and descendants), perhaps rivalling XEC.

MV.1 first appeared in Maharashtra, India in late June.
🧵 The story might've ended there, but after almost a month the next sample was recorded. It has since spread quite rapidly to 9 countries on 4 continents. Around 40 samples have now been reported.
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Recombinant variant XEC is continuing to spread, and looks a likely next challenger against the now-dominant DeFLuQE variants (KP.3.1.1.*).

Here are the leading countries reporting XEC. Strong growth in Denmark and Germany (16-17%), also the UK and Netherlands (11-13%).
🧵 XEC first appeared in Berlin in late June.  It has since spread quite rapidly across Europe, North America and Asia. Around 550 samples have now been reported, from 27 countries on 3 continents.
Poland, Norway, Luxembourg, Ukraine, Portugal and China have now reported samples.
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Recombinant variant XEC is continuing to spread, and looks a likely challenger against the now-dominant DeFLuQE variants (KP.3.1.1 and descendants).

Here are the leading countries reporting XEC. A chain of samples were reported from Slovenia during August, reaching 12%.
🧵 XEC first appeared in Berlin in late June.  It has since spread quite rapidly across Europe, North America and Asia. Around 180 samples have now been reported, from 18 countries on 3 continents. Belgium, Hong Kong and Japan reported their first samples in the last week or so.
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Having grown up in NZ and lived in the UK for a year I'm proud (and lucky) to be able to choose Australia as my home.

IMO a fair chunk of our advantage is down policy differences, but wealth is probably also significant.
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https://twitter.com/EricTopol/status/1828165310844899670

Australia was #1 in the world for median wealth (now #2 by a tiny margin), and well clear of the other anglophone countries. This gives more Australians a relaxed lifestyle, with the freedom to worry less about finances.
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visualcapitalist.com/wp-content/upl…

Recombinant variant XEC is continuing to spread, and looks a likely next challenger against the now-dominant DeFLuQE variants (KP.3.1.1 and descendants).
🧵 XEC first appeared in Berlin in late June.  It has since spread quite rapidly across Europe, North America and Asia.

Around 111 samples have now been reported, from 15 countries on 3 continents. Israel and Spain have reported their first samples in the last week.
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Here's a look at the volume of genomic sequencing data in GISAID, by submission date For 2024. It has been running at 33,000 - 53,000 per month, so over 1,000 per day. July was a relatively high-volume month, and August looks on track to also deliver strong volumes.
🧵 The chart below tracks the median delay between sample collection and submission to GISAID.  This is holding steady at 20-30 days.
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Recombinant variant XEC is continuing to spread very rapidly, and looks a likely next challenger against the now-dominant DeFLuQE variants (KP.3.1.1 and descendants).
🧵 XEC first appeared in Berlin in late June.  It has since spread quite rapidly across Europe, North America and Asia. Around 78 samples have now been reported, from 12 countries on 3 continents. Taiwan has reported it's first sample in the last week.
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With DeFLuQE variants dominant or taking over now in most places, it is time to ponder which variant will drive the next wave.

A new leading candidate is recombinant XEC - a potent mix of KS.1.1 (FLiRT) and KP.3.3 (FLuQE).

This first appeared in Berlin in late June.  
🧵 Globally, XEC is showing a robust growth advantage of 4.6% per day (32% per week) over JN.1.* + DeFLuQE variants. This is fastest growth of any contender I am aware of. As the starting frequencies are quite low, any crossover looks like happening in September or later.
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With DeFLuQE variants dominant or taking over now in most places, it is time to ponder which variant will drive the next wave.

A leading candidate at this stage is samples that combine the mutations for DeFLiRT + DeFLuQE: Spike S31del, F456L, R346T and Q493E.
🧵 These first started appearing from mid-May in British Columbia, and are still quite rare (I got 27 samples).  But there does indeed seem to be signs of growth in Spain and the US.

AFAIK no specific lineage has been designated yet for this combination.
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Here's the latest variant picture with a global scope.

The FLuQE variants (KP.3.*) appear to have taken over dominance from the FLiRT variants.

DeFLuQE variants (KP.3.1.1 and descendants) are rising to challenge next.
🧵 Following a Nextclade update, I am grouping all the KP.3.* child lineages featuring the Spike S31del mutation into a new "Lineage L2" group: JN.1.* +DeFLuQE. For now these are KP.3.1.1 and it's sub-lineage MC.1.

Here's the latest variant picture for China. Unlike many other countries, the FLiRT and FLuQE variants do not appear to have made a strong showing (yet). Instead, the XDV.* variant appears dominant.
🧵 XDV is a double-recombinant of XDE (itself a recombinant of GW.5.1 and FL.13.4), mixed with JN.1.

GW.5.1 is descended from XBB.1.19.1, while FL.13.4 is descended from XBB.1.9.1.
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With FLuQE variants dominant or taking over now in most places, it is time to ponder which variant will drive the next wave.

A leading candidate at this stage is KP.3.1.1, which is based on the FLuQE KP.3, but with a deletion of the S:S31 mutation, so a "DeFLuQE".
🧵 KP.3.1.1 has been most successful in Spain (50%), but is also rising in other countries, notably Ireland (27%) and the Netherlands (20%).

Here's the latest variant picture for FLuQE variants.

Following a Nextclade update, I am grouping the JN.1.* child lineages with the Spike Q493E mutation into a new group: JN.1.* +FLuQE.

Globally these have been most successful in Japan (74%).
🧵 Across Asia, the other country reporting significant growth of FLuQE variants is Israel (33%)

The new SARS-CoV-2 "FLiRT" lineage LB.1 has acquired the Spike S31del mutation so becoming a "DeFLiRT".
That deletion appears to be quite efficient, leading to strong growth in the US (11%), New Zealand (10%) and Singapore (7%).
🧵 At present this seems the most likely successor to KP.2 and KP.3.

LB.1 is descended from JN.1.9.2.

I've started extracting the stats on Molnupiravir and Paxlovid prescribing for Residential Aged Care facilities in Australia.

It reveals that Paxlovid is only being given to around 10-15% of Resident cases. Most cases are receiving Molnupiravir.
🧵 The data is presented in weekly PDF reports under this page, although once collated it became clear that the actual updates to this data is sporadic.
health.gov.au/resources/coll…

Globally, JN.1.* + "FLiRT" is still showing a steady, strong growth advantage of 8% per day (58% per week) over other BA.2.86.* "Pirola" (including JN.1.*) samples, since February.

That predicts an imminent crossover in mid-April.
🧵 Convergent evolution has seen several SARS-CoV-2 sub-lineages of JN.1.* acquire the Spike F456L and R346T mutations aka "FLiRT".

Convergent evolution has seen several SARS-CoV-2 sub-lineages of JN.1.* acquire the Spike F456L and R346T mutations aka "FLiRT".

Globally, JN.1.* + "FLiRT" is still showing a steady, strong growth advantage of 8% per day (58% per week) ...
🧵 ... over other BA.2.86.* "Pirola" (including JN.1.*) samples, since February.

That predicts a crossover in mid April.

The Provisional Mortality statistics have been updated by the Australian Bureau of Statistics (ABS), up to December 2023.

Here are the deaths where the underlying cause of death was certified by a doctor as COVID-19 (16,312 deaths).
🧵 Each individual death is represented by a single point, spread out across the years of the pandemic.

Convergent evolution has seen several SARS-CoV-2 sub-lineages of JN.1.* acquire the Spike F456L and R346T mutations aka "FLiRT".

The first chart shows the 9 leading countries by volume, the 2nd chart shows the next 9.
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The designated lineages so far are JN.1.16.1, KP.1.1.*, KP.2.*, KR.1, KS.1 and KU.2.  So 6 different evolutionary paths to arrive at the same advantageous combination, in just a few months.

Convergent evolution has seen several SARS-CoV-2 sub-lineages of JN.1.* acquire the Spike F456L and R346T mutations aka "FLiRT".

The JN.1.* + "FLiRT" lineages have been most successful in Japan (30%), Singapore (23%) and the United States (16%).
🧵 The frequency in the United States has grown to 16%. For recent dates (roughly March 8 onwards), "community transmission" (non-travel related) samples are now the majority.