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Mike Honey

@Mike_Honey_

Oct 4 • 10 tweets • 3 min read • Read on X

The Provisional Mortality statistics have been updated by the Australian Bureau of Statistics (ABS), up to June 2024.

COVID-19 deaths quickened during June 2024 as the FLuQE KP.3.* wave began to have an impact.
🧵

These are the deaths where the underlying cause of death was certified by a doctor as COVID-19 (18,557 deaths). Each individual death is represented by a single point, spread out across the years of the pandemic.
🧵

The visual is also available as a vertical scrolling page, which gives a more detailed perspective.

🧵mike-honey.github.io/australia-covi…

Comparing the waves of weekly COVID-19 deaths as a line chart, late June was hopefully the peak of deaths from this wave, or close to it. Of course that leaves around half the deaths from this wave still to be revealed in this data series.
🧵

It's clear this latest wave was more severe than the prior double-wave over summer of Eris EG.5.* closely followed by Pirola JN.1.*, breaking trend of decreasing waves.

This might be due to waning vaccination coverage, or the relative severity and impact of the variants.
🧵

Comparing Aged Care Staff Cases (our most reliable proxy for infection levels), it does seem the peak of the latest wave was a lot higher. Infections seemed to peak in early June, so hopefully late June was indeed the peak for the associated deaths.
🧵

It seems a new wave of infections is starting, driven by XEC and other new variants. Protections e.g. mask mandates are currently very relaxed in most Australian healthcare settings.
🧵

The pattern has been that protections are only increased *after* a large wave has already been allowed to build, and is affecting staff capacity. Assuming those patterns continue, we can expect to see a fresh wave of deaths show in this series in a few months time.
🧵

Audio credit:
Djúpalónssandur beach waves.wav by tim.kahn -- -- License: Attribution NonCommercial 4.0
🧵 endsfreesound.org/s/349133/

Interactive Australian covid stats dataviz, code, acknowledgements and more info here:

🧵 endsgithub.com/Mike-Honey/cov…

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Mike Honey

@Mike_Honey_

Oct 4

https://twitter.com/SolidEvidence/status/1841557426296013029

This thread by @SolidEvidence gives an update on the Bavarian BA.5 chronic case that has apparently been evolving in an 18-month-plus infection.

It was detected in wastewater samples by @LongDesertTrain.

I will try to add some context on the sharing of wastewater samples.
🧵

https://twitter.com/SolidEvidence/status/1841557426296013029

Sharing of wastewater samples via GISAID makes discoveries like this by expert variant trackers like Marc and Ryan possible. But the data is extremely sparse.

Here's a map of all the wastewater samples shared via GISAID this year.
🧵

There are just a handful of places sharing data, mostly in Europe and India.

There is no data at all this year from North America, Oceania or Africa.

Locations are approximate - typically country and state/province.
🧵

Read 11 tweets

Mike Honey

@Mike_Honey_

Sep 20

Here's the latest variant picture with a global scope.

DeFLuQE variants (KP.3.1.1 and descendants) continue to dominate FLiRT and FLuQE variants.

XEC.* is now visible and starting to grow.
🧵

Here are the leading countries reporting XEC.*. There is strong growth reported from Germany, France, the Netherlands and Denmark.
🧵

H/t to @CorneliusRoemer and the Nextclade team who have shared how to access their nightly builds - no more waiting to get the latest variants classified! All the latest variants/lineages now appear in these PDF reports and the backing dataviz.
🧵

Read 4 tweets

Mike Honey

@Mike_Honey_

Sep 19

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.
🧵

Now a possible confounder is that the AFLW (Womens) league started in 2018 and has expanded since. But as you can see below, that can explain a trivial fraction of the growth in "illness", even assuming that the illness of AFLW players was covered evenly.
🧵

Read 25 tweets

Mike Honey

@Mike_Honey_

Sep 15

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.
🧵

In North America, MV.1 has mostly been reported in the north-east US. In Canada; Ontario and BC have reported the first samples.
🧵

Read 13 tweets

Mike Honey

@Mike_Honey_

Sep 15

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.
🧵

https://x.com/EricTopol/status/1829905374583181806

XEC is a mix of KS.1.1 (FLiRT, although XEC did not get the R346T mutation) and KP.3.3 (FLuQE). XEC might have an advantage from it's unusual T22N mutation, in combination with the FLuQE mutations.

Eric Topol shows it's mutations here:

🧵

https://x.com/EricTopol/status/1829905374583181806

Read 6 tweets

Mike Honey

@Mike_Honey_

Aug 29

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.
🧵

Read 6 tweets

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