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Jan 27 • 12 tweets • 5 min read
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
Jan 27
Here's the latest variant picture for Australia.

BA.1 (Omicron) is still very dominant. The new sub-lineage BA.1.1 (with the Spike R346K mutation) is significant, but not growing rapidly. ImageImage
It is noticeable that the sampling volume has been lower since last year - not very representative of an extremely intense outbreak.

It is likely heavily skewed towards hospitalisations, and no longer offers a "surveillance" view of the cases (30-150K per day), outside of WA.
Here's more on the global picture for BA.1.1, including some explainer links.
Read 9 tweets
Mike Honey 💉💉💉 Profile picture
Jan 27
Victoria outbreak update for 27 Jan 22:

Here's the distribution of recent cases by Age Group.

After schools closed, the <20 Age groups quickly shrunk, while the 20-29 age group expanded over the holiday season.

As childcare re-opened, cases in the 0-9 age group increased.
🧵 Image
Here's the Term 4 2021 period.

Many still seem unaware of the scale of the outbreak among children during that term - the main reason why Victoria's cases never dropped below ~1,000/day. Image
Forgive me for being skeptical about the announced mitigations for schools to re-open.
- little emphasis on clean air
- RAT testing is even less accurate against Omicron, and compliance will be difficult
- Surgical and cloth masks are ineffective against Delta, let alone Omicron
Read 5 tweets
Mike Honey 💉💉💉 Profile picture
Jan 27
BA.2 (Omicron) samples with a Spike R346K mutation (shared with BA.1.1 & Mu) are on the rise.

Still quite rare, this combination seems to be gaining some momentum in Denmark and the UK.
🧵
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.

Hong Kong also reported 6 samples of BA.2 + Spike R346K, collected on 3 Jan.
BA.2's set of distinct mutations are usually described as having an advantage in transmissibility (over BA.1 Omicron).

The Spike R346K mutation is usually characterised as giving increased immunity escape.

Those two changes packaged together will probably be quite successful.
Read 7 tweets
Mike Honey 💉💉💉 Profile picture
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 💉💉💉 Profile picture
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
🧵
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.
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 💉💉💉 Profile picture
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

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