mike_honey_

mike_honey_, 1 month ago to random

"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

#CO2 #Aranet

mike_honey_, 6 months ago to uk

Here's the latest variant picture for the GW.5.1.1 lineage, a descendant of XBB.1.9.* "Hyperion"

It has been growing since early Sept, notably in the UK (3%) and Australia (1.5%).

The Variant Trackers have been drawing attention to this lineage, as one of the handful that have convergently acquired both the "FLip" mutations L455F + F456L as well as A475V.

#COVID19 #UK #Australia #GW_5_1_1 #FLip
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mike_honey_, 7 months ago to australia

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.

#COVID19 #Australia #SA #Adelaide #EG_5 #Eris #XBB_1_5 #Kraken #BA_2_86 #Pirola @auscovid19
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mike_honey_, 7 months ago to australia

Here's the latest variant picture for Western Australia.

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

#COVID19 #Australia #WA #Perth #EG_5 #Eris #XBC #Deltacron @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_, 8 months ago to random

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.

#COVID19 #BA_2_86 #Pirola
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video/mp4

mike_honey_, 8 months ago to australia

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.

#COVID19 #Australia #NSW #Sydney #EG_5 #Eris #XBB_2_3 #Acrux @auscovid19
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mike_honey_, 8 months ago to australia

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

#COVID19 #Australia @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_, 8 months ago to random

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

23 samples have been reported so far, over 4 continents.

Locations are approximate - typically country and state/province.

Here's a link to download the video file - feel free to share anywhere:
https://github.com/Mike-Honey/covid-19-genomes/raw/main/covid-19-genomes-map-BA-2-86.mp4

#COVID19 #BA_2_86 #Pirola

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

video/mp4

mike_honey_, 9 months ago to Tasmania

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.

🧵

#COVID19 #Tasmania #XAY #XBC #Deltacron @auscovid19

image/png

mike_honey_, 9 months ago to random

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

Just 5 samples have been reported so far - this shows their spread across time and space.

The tiny dots represent single sequences, the large dot is for the 2 sequences shared from Denmark.

Locations are approximate - typically country and state/province.

Here's a link to download the video file - feel free to share anywhere:
https://github.com/Mike-Honey/covid-19-genomes/raw/main/covid-19-genomes-map-BA-2-86.mp4

#COVID19 #BA_2_86 #Pirola

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

video/mp4

mike_honey_, 9 months ago to France

Here's the latest variant picture for France.

The new EG.5.* "Eris" variant (34%) has been rising quite rapidly during July, and is now dominant over XBB.1.9.* "Hyperion" (22%), XBB.1.16.* "Arcturus" (14%), XBB.1.5.* "Kraken" (14%) and XBB.2.3.* "Acrux" (13%).

The sample volumes seem representative up to July 17.

#COVID19 #France #EG_5

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

mike_honey_, 9 months ago to ireland

Here's the latest variant picture for Ireland.

The new EG.5.* "Eris" variant (58%) has been rising rapidly, bursting clear of the usual "XBB soup" variants.

In 2023 it has been quite unusual to see a single variant achieve > 50%, in any country. Ireland is currently reporting EG.5.* at the highest frequency seen anywhere.

The sample volumes seem representative up to July 29.

#COVID19 #Ireland #EG_5

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

mike_honey_, 9 months ago to australia

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

#COVID19 #Australia @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_, 9 months ago to random

Here's an animated map showing the spread of EG.5.1 around the world.

The earliest sample of EG.5.1 was recorded in Jakarta, Indonesia, in mid-March. From there it spread quite quickly to northern Asia and central Europe, then across North America and around the world.

Locations are approximate - typically country and state/province.

Here's a link to download the video file - feel free to share anywhere:
https://github.com/Mike-Honey/covid-19-genomes/raw/main/covid-19-genomes-map-EG-5-1.mp4

#COVID19 #EG_5_1

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

video/mp4

mike_honey_, 10 months ago to australia

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

#COVID19 #Australia #EG_5_1 @auscovid19

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

mike_honey_, 10 months ago to random

Here's the latest picture for new SARS-CoV-2 lineage EG.5 and it's descendants in Australia.

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,.

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

Here's the frequency of EG.5 in the Australian states recently. There are only a few scattered samples up to early June, so perhaps this parent lineage has died out.

No nickname has been considered for this lineage yet, but FWIW I'm thinking of EG.5 as "Egg".

#COVID19 #EG_5 #EG_5_1 #EG_5_2
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mike_honey_, 10 months ago to australia

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

#COVID19 #Australia @auscovid19

mike_honey_, 10 months ago to australia

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.

#COVID19 #Australia @auscovid19
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mike_honey_, 11 months ago to brisbane

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

It's difficult to interpret as sample volumes are very low and patchy. There's a lengthy gap where <10 samples were shared, between May 13 and May 24.

XBB.1.9.* "Hyperion" (24%) may have returned to dominance. It looks like the many sub-lineages including EG.* and FL.* are making a contribution

#COVID19 #QLD #Brisbane #XBB_1_16 #Arcturus #XBB_1_9 #Hyperion #XBB_1_5 #Kraken @auscovid19

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

image/png

mike_honey_, 11 months ago to australia

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.

#COVID19 #Australia @auscovid19
🧵

mike_honey_, 11 months ago to brisbane

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.

#COVID19 #QLD #Brisbane #XBB_1_16 #Arcturus #XBB_1_9 #Hyperion #XBB_1_5 #Kraken @auscovid19

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

mike_honey_, 11 months ago to auscovid19

Here's the latest variant picture for the Australian Capital Territory (ACT).

XBB.1.9.* "Hyperion" (23%) has rebounded back to dominance.

There's been a recent surge from the last non-recombinant clan: CH.1.1.* "Orthrus" (18%).

The XBB.1.5.* "Kraken" clan (18%) is still significant.

XBB.1.16.* "Arcturus" (17%) is also quite prominent.

"Deltacron" XBC.* (16%) has been growing recently.

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

The chaotic 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 17.

#COVID19 #Australia #ACT #Canberra #FK_1_1 #CH_1_1 #Orthrus #XBB_1_16 #Arcturus @auscovid19

mike_honey_, 1 year ago to auscovid19

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.

#COVID19 #Australia #SA #Adelaide #XBC_1_6 #XBB_1_5 #Kraken @auscovid19
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mike_honey_, 1 year ago to auscovid19

Here's the latest variant picture for Tasmania.

XBB.1.9.* "Hyperion" (38%) and XBB.1.16.* "Arcturus" (23%) have mostly displaced XBB.1.5.* "Kraken" (23%).

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

There's still a bit of XBF.* "Bythos" and CH.1.1.* "Orthrus" around, which have mostly disappeared from the rest of the world.

The sample volumes seem representative up to May 5. This is a very welcome update, after a long pause of around 6 weeks.

#COVID19 #TAS #XBB_1_9 #Hyperion #XBB_1_16 #Arcturus @auscovid19

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

mike_honey_, 1 year ago to auscovid19

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.

#COVID19 #Australia @auscovid19
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