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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

mike_honey_, to uk
@mike_honey_@aus.social avatar

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.


🧵

mike_honey_, to australia
@mike_honey_@aus.social avatar

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

As of mid-October, EG.5.* "Eris" (60%) was still dominant.

BA.2.86.* "Pirola" (4%) began rising during October.

@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
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LordsofHardwired,
@LordsofHardwired@med-mastodon.com avatar

@mike_honey_ @auscovid19 so did you figure out the mystery variant from that area that was unknown?

mike_honey_,
@mike_honey_@aus.social avatar

@LordsofHardwired @auscovid19 Yes, see 2nd post in that thread.

mike_honey_, to australia
@mike_honey_@aus.social avatar

The dismantling of the Australian COVID-19 case reporting is hiding the scale (or even existence) of the current wave of community transmission sweeping across the country.

From the health.gov.au data (faithfully extracted by @dbRaevn) here are 4 key metrics, on a log scale to compare waves:

  • Cases (reported from PCR & RAT tests)
  • Hospitalised cases
  • Aged Care Staff cases
  • PBS scripts (for oral treatments)

Its fairly clear that they each move up in down in close synchronisation as the waves and troughs have occurred. Each metric has stayed within fairly consistent ranges, apart from Cases which in a steady decline, making historical comparisons irrelevant.

I think the most consistent is Aged Care Staff cases, where there is still mostly mandating of testing and reporting. I do expect that to be eroding slowly to become less accurate, but it's probably the best we have.

@auscovid19
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mike_honey_, to australia
@mike_honey_@aus.social avatar

The detailed daily case data for NSW has been updated, up to October 18.

The Illawarra region stands out, with the highest cases per capita (284/M) combined with the highest Reff (1.34) for the week.

Interactive Australian outbreak dataviz, code, acknowledgements and more info here:
https://github.com/Mike-Honey/covid-19-outbreak-paths#readme

@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" (44%) appears to be a resurgence of XBB.1.5.* "Kraken" (18%).

@auscovid19
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mike_honey_, to australia
@mike_honey_@aus.social avatar

Here's the latest variant picture for South Australia.

EG.5.* "Eris" (33%) appears to have become dominant over "Deltacron" XBC.* (24%) and XBB.1.16.* "Arcturus" (23%), in a somewhat chaotic mix.

Sample volumes seem representative up to October 3.

@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

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

skua,
@skua@mastodon.social avatar

@mike_honey_ @auscovid19

Waiter, waiter, there's an egg in my soup!

Madame, I do not see an egg, only minestone.

EG_5 proportion has plummeted.
Maybe it thrived at winter community events?

And AIUI there hasn't been a death from Covid since the end of August, which is welcome news.

mike_honey_, to Tasmania
@mike_honey_@aus.social avatar

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

The "Deltacron" XAY.* variant (45%) has been displaced by EG.5.* "Eris" (33%).

Sample volumes have been a bit patchy.

@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

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

The EG.5.* "Eris" variant (44%) is competing with XBB.2.3.* "Acrux" (38%).

Sample volumes are a pale shadow of what they once were - now lagging, patchy and inconsistent. Under 150 samples represent a 6-week period, which likely distorts this picture.

@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

Here's the latest variant picture for Western Australia.

The EG.5.* "Eris" variant (35%) has remained dominant, with the latest challenge coming from "Deltacron" XBC.* (26%).

@auscovid19
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mike_honey_, to australia
@mike_honey_@aus.social avatar

Here's the latest variant picture for South Australia.

XBB.1.16.* "Arcturus" (26%) is growing recently, and looks about to displace EG.5.* "Eris" (21%) and the "Deltacron" XBC.* variants (27%).

@auscovid19
🧵

mike_honey_, to australia
@mike_honey_@aus.social avatar

The latest wave of COVID to hit Victoria, Australia is taking shape. Probably the most consistent stat is hospitalisations - the VIC definition is "Beds occupied by active COVID-19 cases.". These are already up 50% from the trough on August 7.

@auscovid19
🧵

mike_honey_, to random
@mike_honey_@aus.social avatar

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

mike_honey_,
@mike_honey_@aus.social avatar

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

mike_honey_,
@mike_honey_@aus.social avatar

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

88 samples have been reported so far, mostly from the UK, Denmark and Sweden.

Locations are approximate - typically country and state/province.

video/mp4

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