@mike_honey_@aus.social
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mike_honey_

@mike_honey_@aus.social

Data Visualisation and Data Integration specialist - Melbourne, Australia
tiktok.com/@mike_honey_
#covid19 #australia #fedi22

This profile is from a federated server and may be incomplete. Browse more on the original instance.

mike_honey_, to australia
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Here's an update on my metric for Australia and it's states and territories:

"Days since Health Leadership faced the public on COVID".

I'm tracking the last date that CMOs/CHOs etc in each jurisdiction last held a press conference or similar and took questions from the media on COVID.

I'm not aware of any events of that type in the last week.

@auscovid19
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18+ mike_honey_, to random
@mike_honey_@aus.social avatar

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 an imminent crossover.


🧵

mike_honey_,
@mike_honey_@aus.social avatar

The designated lineages so far are JN.1.16.1, KP.1.1., KP.2., KR.1, KS.1, KU.2 and KZ.1.1. So 7 different evolutionary paths to arrive at the same advantageous combination, in just a few months.

It's still a bit hard to pick a frontrunner out of that swarm. My best guess is the KP.2.* lineages, descended from JN.1.11.1.

The analysis will become clearer as the Nextclade update has just dropped, providing accurate classification of all the new lineages. It will take me a few days to re-process the data using that update.

mike_honey_,
@mike_honey_@aus.social avatar

The lineage diagrams by Daniele Focosi are an excellent resource for making sense of the dynamic evolution picture. They currently show the "FLiRT" lineages at top-right.
https://twitter.com/dfocosi/status/1775858186764861898

mike_honey_,
@mike_honey_@aus.social avatar

It seems the first wave of the JN.1.* + "FLiRT" lineages started in Nigeria (43%) during February. Note the end of that series in late February is currently the end of all available sample data from Nigeria, so JN.1.* + "FLirt" lineages are likely more dominant there by now.

mike_honey_,
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Across Europe, JN.1.* + "FLiRT" lineages are showing sharp growth in several countries, led by the UK (35%) and the Netherlands (reaching 31%). Recent sample sizes are often thin and patchy, which can distort the recent results.

mike_honey_,
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The second wave was in several Asian countries in early March, notably: India (62%), Singapore and more recently Qatar (78%).

Qatar recently resumed sharing samples after a gap of several months, so presumably there was a lot of unreported growth before the samples shown here.

mike_honey_,
@mike_honey_@aus.social avatar

In North America, JN.1.* + "FLiRT" lineages have been reported with strong growth in the US (22%) and Canada (13%).

The frequency for both countries has doubled in a week, and the familiar curves of exponential growth have become clear.

mike_honey_, to auscovid19
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Here's the latest variant picture for South Australia.

The "Deltacron" XBC.1.6 variant (35%) has been dominant since early April - a unique scenario globally.

95% of the XBC.* samples shared recently have come from Australia, and South Australia seems the only state where it is anywhere near dominant.

XBB.1.16 "Arcturus" (14%) looks like the next challenger. Be alert for conjunctivitis symptoms, which seem more common with that variant.

The sample volumes seem representative up to May 14.

@auscovid19
🧵

mike_honey_, to australia
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The ABS' Provisional Mortality statistics have been updated, up to March 2023. These are the COVID-19 deaths. Each individual death is represented by a single point, spread out across the years of the pandemic. The latest wave of COVID-19 deaths since March are still to be added.

Can spot the point where "hybrid immunity" kicks in?

Interactive Australian covid stats dataviz, code, acknowledgements and more info here:
https://github.com/Mike-Honey/covid-19-au-vaccinations#death-toll-page

@auscovid19

mike_honey_, to auscovid19
@mike_honey_@aus.social avatar

Here's a new metric for Australia and it's states and territories:

"Days since Health Leadership faced the public on COVID".

I'll be tracking the last date that CMOs/CHOs etc in each jurisdiction last held a press conference or similar and took questions from the media on COVID.

@auscovid19
🧵

mike_honey_, to australia
@mike_honey_@aus.social avatar

Here's the latest variant picture for South Australia.

The next challenge to EG.5.* "Eris" (56%) looks like either XBB.1.5.* "Kraken" (16%) or BA.2.86.* "Pirola" (10%), which looks to have started community transmission.

@auscovid19
🧵

mike_honey_, to australia
@mike_honey_@aus.social avatar

Here's an update on my metric for Australia and it's states and territories:

"Days since Health Leadership faced the public on COVID".

I'm tracking the last date that CMOs/CHOs etc in each jurisdiction last held a press conference etc and took questions from the media on COVID.

I'm not aware of any events of that type in the last week.

At the Federal level, Australia has reported over 2,000 deaths and almost 400,000 cases since the last press conference.

@auscovid19
🧵

mike_honey_, to australia
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Here's the latest variant picture for the EG.5.1 variant in Australia. There are signs of growth in Queensland (6%), NSW (5%) and SA (5%).

EG is an alias for XBB.1.9.2.1, from the "Hyperion" clan. Along with several prior generations of mutations, EG.5 added the Spike F456L mutation, then EG.5.1 itself added the Spike Q52H mutation.

EG.5 was the first lineage mentioned last month's edition of the Neher Lab's variant report:
https://github.com/neherlab/SARS-CoV-2_variant-reports/blob/main/reports/variant_report_latest_draft.md

EG.5 was recently designated a "Variant Under Monitoring" (VUM) by the WHO.
https://www.who.int/activities/tracking-SARS-CoV-2-variants

Note data sharing from some states and territories lags significantly - the dismal routine:

  • Victoria - no report for 3 weeks
  • Tasmania - no report since mid-May
  • NT - only 6 random samples reported since April 2022

@auscovid19

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

mike_honey_, to Tasmania
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Here's the latest variant picture for Tasmania, Australia.

The "Deltacron" XAY.* variant (33%) has put on a surprising sudden surge from late July onwards. This might explain the rise in cases and hospitalisations during that period.

XAY is a recombinant of Omicron BA.2 and Delta AY.45. XAY.* has been slowly evolving: XAY.1 added the Spike D253G mutation, then XAY.1.1 added Spike R346T and ORF1a K2108N. XAY.1.1.1 added Spike D1153Y and finally child lineage GL.1 added Spike D420N. GL.1 is the only sublineage present in the recent data from Tasmania.

🧵

@auscovid19

image/png

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

Here are the deaths where the underlying cause of death was certified by a doctor as COVID-19 (14,000 deaths). Each individual death is represented by a single point, spread out across the years of the pandemic.

The latest wave of COVID-19 deaths is building in this view.

This visual is also available as a vertical scrolling page, which gives a more detailed perspective:
https://mike-honey.github.io/australia-covid-19-death-toll.html

@auscovid19

Interactive Australian covid stats dataviz, code, acknowledgements and more info here:
https://github.com/Mike-Honey/covid-19-au-vaccinations#death-toll-page

mike_honey_, to random
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Here's an animated map showing the spread of the new BA.2.86 "Pirola" variant.

123 samples have been reported so far, over 5 continents (in GISAID (as of a couple of hours ago), based on Nextclade lineage calls).

Locations are approximate - typically country and state/province.


🧵

video/mp4

18+ mike_honey_, to random
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The new KP.2 lineage of SARS-CoV-2 is showing signs of spread. It was first detected in samples collected in early January from Assam, India. It has since showed up in New Zealand, across North America, Europe, Asia and Australia.

Here's an animated map showing the spread of the KP.2 lineage.

Locations are approximate - typically country and state/province.


🧵

video/mp4

mike_honey_,
@mike_honey_@aus.social avatar

PS:
KP.2 adds the Spike R346T mutation to JN.1.11.1.

Globally, KP.2 is showing a very strong growth advantage of 14% per day (101% per week) over other BA.2.86.* "Pirola" (including JN.1.*) since February. That predicts a crossover in late March.

mike_honey_, to auscovid19
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Here's the latest variant picture for South Australia.

Recently classified "Deltacron" XBC.1.6 (32%) is continuing to extend it's dominance.

XBB.1.5 "Kraken" (13%) continues to decline.

XBB.1.9.1 "Hyperion" (11%) and XBB.1.16 "Arcturus" (10%) are both continuing to rise.

XBB.1.16 looks a bit more rapid lately, so it might be the next challenger. Be alert for conjunctivitis symptoms, which seem more common with that variant.

The sample volumes seem representative up to April 25.

@auscovid19
🧵

18+ mike_honey_, to australia
@mike_honey_@aus.social avatar

Australian COVID-19 monthly stats update.

A new pack of the stats that are updated monthly.

An encouraging uptick in the rate of vaccination deliveries, nudging the coverage up to ~6% of adult Australias with an XBB.1.5 vaccine does. I'm a bit puzzled as to why there would be an uptick?

Report link:
https://mike-honey.github.io/covid-19-au-vaccinations/output/covid-19-au%20-%20report%20Monthly.pdf

@auscovid19

mike_honey_,
@mike_honey_@aus.social avatar

@RcjWaz @auscovid19 yes, probably. Ofc makes no sense as the big JN.1 wave was in Dec-Jan, but that’s people, I guess.
VIC Health department started pushing for double shots yesterday. Not how I would do it, but again, I am not “people”.

mike_honey_, to australia
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Here's the latest variant picture for Western Australia.

The EG.5.* "Eris" variant (32%) has been challenged by the "Deltacron" XBC.* (16%).

@auscovid19

Sample volumes seem representative up to September 20.

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

mike_honey_, to australia
@mike_honey_@aus.social avatar

Here's the latest variant picture for New South Wales, Australia.

The EG.5.* "Eris" variant (40%) has become dominant. XBB.2.3.* "Acrux" (23%) is also rising.

@auscovid19
🧵

mike_honey_, to auscovid19
@mike_honey_@aus.social avatar

Here's an update on my metric for Australia and it's states and territories:

"Days since Health Leadership faced the public on COVID".

I'm tracking the last date that CMOs/CHOs etc in each jurisdiction last held a press conference or similar and took questions from the media on COVID.

A minor tweak to the method this week - deaths and cases are now only counted from the day after the last press conference. This mainly affects the ACT results.

I also had a stray filter in last week's results, which affected the VIC, TAS & NT results.

@auscovid19
🧵

mike_honey_, to brisbane
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Here's the latest variant picture for Queensland, Australia.

XBB.1.16.* "Arcturus" (32%) has surged to dominance.

The XBB.1.9.* "Hyperion" (24%) and XBB.1.5.* "Kraken" (19%) variants are still significant.

The "Deltacron" XBC.* variant (11%) and CH.1.1.* "Orthrus" (14%) are still in the frame.

Be alert for conjunctivitis symptoms, particularly associated with the Arcturus variant.

The vigorous mix of very different variants poses a raised immediate re-infection risk for anyone relying on natural immunity from a recent infection.

The sample volumes seem representative up to May 3. There are almost no sequences shared since that date - hopefully only a temporary bottleneck.

@auscovid19

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

mike_honey_, to australia
@mike_honey_@aus.social avatar

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

Here are the deaths where the underlying cause of death was certified by a doctor as COVID-19 (13,389 deaths). Each individual death is represented by a single point, spread out across the years of the pandemic.

The latest wave of COVID-19 deaths after April are still to be added, but you can already see the density starting to increase during April.

This visual is also available as a vertical scrolling page, which gives a more detailed perspective:
https://mike-honey.github.io/australia-covid-19-death-toll.html

@auscovid19

Interactive Australian covid stats dataviz, code, acknowledgements and more info here:
https://github.com/Mike-Honey/covid-19-au-vaccinations#death-toll-page

mike_honey_, to random
@mike_honey_@aus.social avatar

"CO2 Levels" project launch:

I've started a new project to provide interactive data analysis on CO2 levels. The data is gathered from Aranet monitors or can be entered manually.

I have started gathering a public dataset of files and can now accept submissions via GitHub. That dataset is presented in a public dashboard for analysis by anyone.

If you prefer a private analysis, you can clone this project and run it on your own machine, using the free Power BI Desktop tool.

Over time, I hope to add features for tagging of location and categorisation.

Project page:
https://github.com/Mike-Honey/co2-levels?tab=readme-ov-file#readme

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