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Mike Honey 💉💉💉

@Mike_Honey_

Jan 24

Here's an analysis of cases and deaths, for Australia, then state-by-state.

I couldn't bear to post this last week as the case rate was one of the worst in the world (with WA at near-zero). That seems to have been the peak.

The death rate continues to increase.

New South Wales is the worst affected state, where the case rate rose to just under 4,000 per 100K population. If NSW was a country, that would've been the highest rate globally for any comparable country.

Victoria rose to a similar level, just slightly lower on this "per population" basis.

The rise in cases was even steeper than in NSW, so the impact of that on deaths is likely yet to come.

Read 10 tweets

Mike Honey 💉💉💉

@Mike_Honey_

Jan 24

Here's the latest variant picture for Australia.

BA.1 (Omicron) is perhaps more dominant in Australia than in any other country.

While there was an existing Delta outbreak in 2 states, the arrival of Omicron was just before most NPIs were abandoned, with most not reinstated
🧵

https://twitter.com/Mike_Honey_/status/1485408294038810624?s=20

The BA.2 sibling Omicron lineage is present, but at relatively low frequency.

BA.2 is out-competing BA.1 in several countries around the world, as shown on this thread.

https://twitter.com/Mike_Honey_/status/1485408294038810624?s=20

The Australian states each have fairly discrete outbreaks with quite different profiles.

Here's New South Wales, where NPIs were first dropped as BA.1 arrived, and multiple super-spreader events in mid-December. Together that paved the way for the total dominance at ~95%.

Read 9 tweets

Mike Honey 💉💉💉

@Mike_Honey_

Jan 24

Here's the latest variant picture for New Zealand.

The lineage (BA.1) Omicron is dominant globally, also recently in NZ samples. The BA.2 sibling lineage is also present at significant frequencies.
🧵

An Omicron community outbreak was just reported, but those samples will not be sequenced for a few more days yet.

Hopefully this analysis provides some guidance on the likely composition of that outbreak.

TL/DR; it depends.

BA.1 with the Spike R346K mutation was classified quite recently as BA.1.1. That mutation is understood to give increased immunity escape.

That lineage change has not yet flowed out to databases and websites.

Here's the frequency of BA.1.1 in NZ samples:

Read 5 tweets

Mike Honey 💉💉💉

@Mike_Honey_

Jan 24

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 many unique mutations.

The frequency of BA.2 is rising in several countries, on similar trajectories.
(Linear then log scales)
🧵

I'm now presenting these charts with both a linear Y-axis scale, together with a version using a log scale. A log axis helps compare growth rates.

The Frequency is calculated for each country independently, comparing to all the recent samples sequenced in that country.

Here are the other top countries in Europe, by BA.2 samples.

Although their frequencies are lower so far, Belgium, France, Germany, Norway and the Netherlands appear to be on a similar trajectory.

Read 11 tweets

Mike Honey 💉💉💉

@Mike_Honey_

Jan 17

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).

Read 8 tweets

Mike Honey 💉💉💉

@Mike_Honey_

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

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