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Mike Honey Profile picture
@Mike_Honey_
Jan 27, 2022 • 12 tweets • 5 min read • Read on X
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Here's the latest variant+mutation picture for the new BA.1.1 (Omicron) lineage. This was formerly BA.1 with the Spike R346K mutation.

That mutation is understood to give increased immunity escape.

The BA.1.1 definition is now flowing out to databases and websites.
🧵
Note the Frequency is calculated for each country independently, comparing to all the recent samples sequenced in that country.

Linear and Log Y-axis presented - log axis helps compare growth rates.
BA.1.1 has quickly reached 65% frequency in the USA. Here are the leading 7 states (by volume of BA.1.1 sequences shared).

Colorado (79%) and Washington (75%) are reporting the highest frequencies.
Here are the next 7 US states reporting BA.1.1.

Georgia (84%) and Ohio (82%) are reporting the highest frequencies
BA.1.1 is now the leading lineage in Canada at 51%. Here are the leading provinces.

The sample sizes are very small after late-December, and some provinces are lagging by weeks, making it hard to compare.
Across Africa, BA.1.1 has not reached high frequencies in most countries, besides Nigeria (76%).
Across Asia, BA.1.1 has reached the highest frequency in Japan (99%) and Singapore (53%)
Here are the other top countries reporting BA.1.1 across Europe.

The Netherlands (46%) and Switzerland (43%) have reached the highest frequency.
Across South America, BA.1.1 has reached the highest frequency in French Guina (92%) and Argentina (85%)
Interactive dataviz here:
github.com/Mike-Honey/cov…
The study discussed in this pre-print noted:
"...the entire panel of antibodies [every combination of natural immunity and/or vaccine] was essentially rendered inactive against this minor form of the Omicron variant."
news-medical.net/amp/news/20211…
* [at that time] minor form

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More from @Mike_Honey_

Mike Honey Profile picture
Dec 20, 2025
A recent scientific paper compared long-term mortality by vaccination status.

I noticed that Table 2 drew a lot of attention, but was actually included in the paper as a static image. So I built a quick dataviz project to explore.
🧵 Image
On the first page, I've added a % Incidence change (vaccinated vs unvaccinated) and emphasised that with data bars. This is quicker for general readers to grasp than hazard ratios.
🧵
You can click on any column header to sort the rows, e.g. as shown by % Incidence change. The starkest difference was deaths from COVID-19 at +372%.

Other causes with significant differences were diseases of the skin & blood, pregnancy and childbirth.
🧵 Image
Read 19 tweets
Mike Honey Profile picture
Dec 19, 2025
A recent scientific paper included an antigenic map, comparing the immune status of individuals vaccinated with a range of vaccines "… vaccinated sera", against a collection of significant variants "Virus …".

The map was very informative, so I built a quick dataviz project.
🧵 Image
The map shows starkly that BA.3.2 "Cicada" is a wild outlier, way out on its own in the south-west corner. This suggests the current vaccines and/or disease-acquired immunity will not offer strong protection against infection.
🧵
Another point of note is how the XFG "Stratus" variant is the furthest away from BA.3.2, at the extreme south, compared to other recent variants.

This might help explain how BA.3.2 has been able to drive significant waves in Europe, following their recent waves of XFG
🧵
Read 12 tweets
Mike Honey Profile picture
Dec 14, 2025
Here's the latest variant picture for Europe (excluding the UK), to late November.

BA.3.2.* "Cicada" is showing a very strong growth advantage of 7.9% per day (55% per week) over XFG.* "Stratus", which predicts a crossover in late December.

#COVID19 #EUR #BA_3_2 #Cicada #XFG
🧵 Image
To include the latest BA.3.2.* samples, I have rolled my reporting window forward an extra week or so. So the most recent data is even less representative than usual. The picture for those dates might change as more data is shared.
🧵
Here are the leading European countries reporting BA.3.2.* .

The Netherlands leapfrogged Germany to report the highest frequency at 31%. Germany also grew sharply to 25%. Denmark grew to 16%.
🧵 Image
Read 6 tweets
Mike Honey Profile picture
Dec 14, 2025
Here's the latest variant picture for the United Kingdom, to late November.

For the UK, BA.3.2.* "Cicada" is showing a strong growth advantage of 5% per day (35% per week) over XFG.* "Stratus", which predicts an imminent crossover.

#COVID19 #SARSCoV2 #UK #BA_3_2 #Cicada
🧵 Image
To include the latest BA.3.2.* samples, I have rolled my reporting window forward an extra week. So the most recent data is even less representative than usual. The picture for those dates might change as more data is shared.
🧵
BA.3.2.* accelerated sharply in Scotland to 16% of recent samples.
🧵 Image
Read 7 tweets
Mike Honey Profile picture
Dec 8, 2025
A recent scientific paper explored the impact of mass SARS-CoV-2 infections on Lymphocytes (crucial to the body’s immune system).

I noticed the authors had shared the data behind their charts in the Appendix Supplementary materials, so I built a quick dataviz project.
🧵 Image
Above, I’ve re-cast the data behind their Figures 3 and 5 in terms of % change from the baseline. Hopefully this is useful to help compare the subsets, whose results vary in scale.
🧵
I added interactive filter controls and a trend line (dashed pink). You can use those to explore for example the trends in the last 12 months measured in the paper, for the CD3, 4 & 8 series.
🧵 Image
Read 8 tweets
Mike Honey Profile picture
Dec 7, 2025
Australian Influenza update:

It became clear during November that a unusual second wave is underway in Australia, driven by the new "clade K" (H3N2 clade 2a.3a.1, subclade K).

Tasmania, New South Wales and South Australia are currently the hardest-hit.

#Influenza #Australia
🧵
Western Australia had been spared the worst of this second wave until the last week or so. But now there’s a signal of a sharp change in case momentum there also.
🧵
The latest Australian Respiratory Surveillance Report confirms my earlier speculation that the new "clade K" (H3N2 clade 2a.3a.1, subclade K) is driving the "unusual" second wave of influenza in Australia.

🧵 health.gov.au/resources/publ…Image
Read 11 tweets

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