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Mike Honey 💉💉💉 Profile picture
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Jan 17,, 8 tweets, 3 min read
Here's the latest variant picture for BA.1 (Omicron) with the Spike R346K mutation. That mutation helps with immunity escape.

This combination was recently identified as a new sub-lineage BA.1.1, but that will take some time to filter through to databases and websites.
🧵
The global analysis (above) of BA.1 with the Spike R346K mutation shows it's frequency was low, but has been steadily increasing (as a proportion of all BA.1 samples).
In the United Kingdom, the frequency of BA.1 with the Spike R346K mutation has been steadily growing, recently at ~25% (of all BA.1 samples).
Samples from Switzerland show BA.1 with the Spike R346K mutation has been quite frequent: ~50% (of all BA.1 samples).
In the USA, the frequency of BA.1 with the Spike R346K mutation has been steadily growing, recently at ~40-50% (of all BA.1 samples).
Japan's Omicron outbreak has predominantly been BA.1 with the Spike R346K mutation, recently at 90-100% (of all BA.1 samples).
Kenya's Omicron outbreak has predominantly been BA.1 with the Spike R346K mutation, recently at 90-100% (of all BA.1 samples).
Interactive dataviz and more info here:
github.com/Mike-Honey/sar…

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More from @Mike_Honey_

Mike Honey 💉💉💉 Profile picture
Jan 17,
Here's the latest variant picture for BA.2 (Omicron). Globally it is far less common than it's sibling BA.1 lineage.

BA.2 has 28 unique mutations so very different.

The frequency of BA.2 is rising in several countries, notably India, Denmark & Singapore.
🧵
Note the Frequency is calculated for each country independently, comparing to all the recent samples sequenced in that country.
Here's the latest variant picture for India.

BA.2 (Omicron) appears to have recently passed BA.1 and reached 40% frequency. Recent sample sizes are very low.
Read 7 tweets
Mike Honey 💉💉💉 Profile picture
Jan 17,
Here's the latest variant picture for Australia.

Detailed genomic sequencing data shared via GISAID shows the BA.1 (Omicron) variant has stabilised at ~92% frequency.

Samples from the state of Victoria have recently been shared, to give a more complete picture.
🧵
Here's the latest variant picture for New South Wales, where Omicron superspreader events in mid-December sparked the current wave.

This is my first look at samples shared for January. BA.1 (Omicron) variant is steady at ~92% frequency..
After a delay of a month, samples have finally been shared for Victoria, up to 7 January.

This shows Omicron rose steadily through December and reached 88% frequency.
Read 7 tweets
Mike Honey 💉💉💉 Profile picture
Jan 11,
Here's the latest variant picture for BA.2 (Omicron), the lesser-known sibling of BA.1 (Omicron).

It has started to appear at surprisingly high frequencies in several countries - those who shared the most samples are shown here.
🧵
Note the Frequency is calculated for each country independently, comparing to all the recent samples sequenced in that country.
Here's the latest variant picture for the Philippines.

Perhaps this startling picture can be discounted, as the sample sizes are very small. They have reported 20 samples of BA.2 (Omicron).
Read 10 tweets
Mike Honey 💉💉💉 Profile picture
Jan 11,
Here's my weekly analysis of cases, deaths, vaccinations and restrictions.

At the global level, Omicron has driven an amazing surge in the last 2 weeks.

I've added a % Positive chart - this helps to spot when testing is overwhelmed (so infections are likely under-reported).
🧵
Australia is one of the worst affected countries (on a population basis). Restrictions were dropped in mid-December, ignoring the risk from multiple Omicron super-spreader events.

Testing has effectively collapsed - % Positive has soared to 31%, many infections are undiscovered.
In Denmark, both the cases and % positive appear to have peaked.

Deaths are at ~100 per week or ~170 per 10M. But as they typically lag cases by 3 weeks, we can expect them to increase, sadly.
Read 11 tweets
Mike Honey 💉💉💉 Profile picture
Jan 10,
Victoria time-shifted distribution update for 10 Jan 22:

A forecast of outcomes from severe COVID-19, based on active cases:

- hospitalisations (2,210* by 15 Jan)
- ICU (737 by 20 Jan*)
- cases needing ventilation (246 by 25 Jan*)
- deaths (2,304 by 30 Jan)
🧵
* As actual numbers had drifted from the forecasts for some series, I've adjusted the settings:
- hospitalisations now 0.9% (was 1.4%)
- ICU now 0.3% with 10-day lag (was 8-day)
- ventilation now 0.1% with 15-day lag (was 10-day)

A big drop in the hospitalisation % - good news!
The lags for ICU and ventilation have now returned to their pre-Delta settings, which appear to give a closer fit.
Read 4 tweets
Mike Honey 💉💉💉 Profile picture
Jan 10,
New South Wales time-shifted distribution update for 10 Jan 22:

A forecast of outcomes from severe COVID-19, based on active cases:
- hospitalisations (3,387* by 15 Jan)
- ICU (677 by 20 Jan*)
- cases needing ventilation (339 by 25* Jan)
- deaths (3,291 by 30 Jan)
🧵
* As gaps were opening up between the actual and forecast for some series, I've adjusted the % Expected:
- hospitalisations now 1.0% (was 1.4%)
- ICU now 0.2% with 10-day lag (was 8-day)
- ventilation now 0.1% with 15-day lag (was 10-day)
The lags for ICU and ventilation have now returned to their pre-Delta settings, which appears to give a closer fit.
Read 5 tweets

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