@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

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18+ mike_honey_, to australia
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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 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

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_,
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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_,
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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_,
@mike_honey_@aus.social avatar

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

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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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.

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

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

Samples from India dried up during January, so it's unclear if KP.2 is still spreading there.

As the lineage designation has not yet flowed through to Nextclade, I'm approximating it by searching for samples with the characteristic mutations.

Interactive mutation matching dataviz, code, acknowledgements and more info here:
https://github.com/Mike-Honey/sars-cov-2-genomes#gisaid---mutation-matches

🧵ends

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.

18+ mike_honey_, to australia
@mike_honey_@aus.social avatar 
The detailed daily PCR test & case data for Queensland has been updated, up to January 30.

PCR Cases (7-day running average) have been falling steadily since January 10.

As Test volumes have also been falling, % Positive is up slightly to around 16%.

#COVID19 #Australia #QLD #Brisbane @auscovid19@a.gup.pe   
🧵
mike_honey_,
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@auscovid19 ```markdown
% Positive was generally falling since late December, down to a trough around 14% on January 18. However it has since rebounded to around 16%.

mike_honey_,
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@auscovid19 ```markdown
Among the South East region LGAs, Somerset is the new outlier with extremely high cases per capita (466/M) combined with the highest % Positive (21%) for the latest week. This implies the rate of infections is far higher than the reported cases would indicate.

Last week's outlier was the Gold Coast. Case rates have fallen marginally there, but the % positive remains high so undiscovered infections abound.

18+ mike_honey_, to australia
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Australian COVID-19 stats update for the period ending 10 January 2024:

I've revived an old Vaccination progress infographic, looking at the doses since 11/12/2023. I assume they are all for the XBB.1.5 vaccines, and that no-one has received 2 doses since that date.

Up to January 10, just under 0.5M doses were given, so 2.4% of the Adult population (or 1.9% of the total population) had received an XBB.1.5 vaccination dose.

@auscovid19
🧵

image/png

mike_honey_,
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@musubhai @auscovid19 I don’t see any direct connection between the two.

mike_honey_,
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@musubhai @auscovid19 there's almost no reporting of COVID case trends in Australian media now, so the vast majority of the population are clueless about the current wave (largest in a year).

There is a portion of "the public" who are aware of cases, keen to get the new vaccines (and eligible) who drove the sharp rise in vaccination rates in late 2023.

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

Here's the latest variant picture for Australia.

As of late December, BA.2.86.* "Pirola" (62%) was dominant - led by the JN.1 sub-variant.

EG.5.* "Eris" (30%) was in sharp decline.

The growth of BA.2.86.* accelerated from late November onwards, in a now-familiar pattern.

@auscovid19
🧵

mike_honey_,
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Here are the most common sub-lineages of the BA.2.86.* variant in Australia. Sub-lineage JN.1 (42%) reached a critical mass and began growing rapidly during late November.

mike_honey_,
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For Australia, the JN.1 sub-lineage had a strong growth advantage of 9% per day (62% per week) over EG.5.* since mid-November.

18+ mike_honey_, to india
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Here's the latest variant picture for India.

As of late December, BA.2.86.* "Pirola" (97%) seemed dominant. The JN.1 and JN.1.1 sub-lineages are the most common among the reported data.

This confirms the recent pattern from travellers out of India, e.g. arriving in Singapore.


🧵

image/png

mike_honey_,
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The sharing of samples from India dried to a trickle in September, but seems to have recently resumed. The volume is still very low for such a massive population.

All of the samples reported as 1 December have incomplete Collection dates.

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

🧵ends

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

Here's the latest variant picture for the Netherlands.

As of late November, EG.5.* "Eris" (32%) was still dominant, but fading quite rapidly.

BA.2.86.* "Pirola" (28%) began rising strongly during November.

There's also a significant late resurgence of XBB.1.5.* "Kraken" (20%).


🧵

mike_honey_,
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The "Pirola" sub-lineage JN.1 (16%) began accelerating the growth of the BA.2.86.* clan in the Netherlands during November.

mike_honey_,
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For the Netherlands, the JN.1 sub-lineage had a very strong growth advantage of 15% per day over EG.5.* during November, with a crossover in mid-November.

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

Here's the latest variant picture for the United Kingdom.

As of late November, EG.5.* "Eris" (35%) was still dominant.

BA.2.86.* "Pirola" (28%) began rising strongly during November.


🧵

mike_honey_,
@mike_honey_@aus.social avatar

The "Pirola" sub-lineage JN.1 (12%) began accelerating the growth of the BA.2.86.* clan in the UK during November.

The classic exponential growth curve of JN.1 is quite striking.

mike_honey_,
@mike_honey_@aus.social avatar

The leading country reporting JN.1 is England (14%).

The other countries are still dominated by the other sub-variants of BA.2.86.*. That will probably switch shortly to follow the pattern of England, with accelerated growth.

image/png

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

Here's the latest variant picture for Switzerland.

As of late November, EG.5.* "Eris" (49%) was still dominant, although falling rapidly.

BA.2.86.* "Pirola" (34%) began rising sharply during November.


🧵

mike_honey_,
@mike_honey_@aus.social avatar

The "Pirola" sub-lineage JN.1 (25%) began leading the growth of the BA.2.86.* clan in Switzerland during November.

The first sample of JN.1 was detected in Austria on October 5, so it has achieved that result in just over 6 weeks - remarkable.

18+ mike_honey_, to australia
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The detailed daily PCR test & case data for Queensland has been updated, up to November 27.

The Reff (case momentum) was falling in previous weeks, but in the latest week it rebounded to around 1.1.

PCR Cases (7-day running average) showed a "false peak" then continued to grow to around 260/day. That "false peak" might've been what the Queensland CHO saw when he recently predicted the wave would peak within a week.

@auscovid19
🧵

mike_honey_,
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The % Positive (from PCR tests) has increased to around 14% - a level not seen since late June.

DenisCOVIDinfoguy, to random
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🇦🇺Australia's weekly reported COVID numbers: 17 November 2023

Jurisdiction / Cases / Deaths

🔹SA: 2,496 / NR
🔹TAS: 1,044 / 7
🔹ACT: 582 / 0
🔹VIC: (No data) / 25

🔹WA: (No data)
🔹NSW: (No data)
🔹QLD: (No data)
🔹NT: (No data)

NR = Not Reported

mike_honey_,
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@DenisCOVIDinfoguy @auscovid19 Here are the recent trends in the cases and hospitalisations per capita for SA, TAS and the ACT:

image/png

DenisCOVIDinfoguy, to auscovid19
@DenisCOVIDinfoguy@aus.social avatar

SA COVID weekly update: 8 November to 14 November

🔹PCR cases only: 2,496 (+3)
🔹Deaths: NR
🔹Total deaths: 1,624 (+0)
🔹Hospital: 109 (+76)
🔹ICU: 7 (+4)

NR = Not reported

@auscovid19

mike_honey_,
@mike_honey_@aus.social avatar

@DenisCOVIDinfoguy @auscovid19 Here are the recent trends in the key stats for SA (log axis):

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