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Mike Honey

Oct 3 • 8 tweets • 3 min read

Here's the latest variant picture for the recently-designated BQ.1.1 lineage, nickname "Cerberus", from the BA.5.* family.

It has most commonly been reported across Europe, notably France (3%), Belgium (2%) and the UK (~2%).
🧵

The BQ.1.1 categorisation has yet to rollout to GISAID, so I'm approximating it here by searching for samples of BE.1.1 with the characteristic mutations - NSP12:Y273H, Spike:R346T and NSP13:N268S (h/t @josetteshoenma)

That method is currently catching ~260 sequences.

For the UK, BQ.1.1 is showing a growth advantage of 12% per day against all other BA.5.* lineages, which predicts a crossover in mid-October.

For France, BQ.1.1 is showing a growth advantage of 8% per day against all other BA.5.* lineages, which predicts a crossover in late October.

Interactive mutation matching dataviz, code, acknowledgements and more info here:
github.com/Mike-Honey/sar…

@dfocosi

In @dfocosi's very helpful diagram of the lineages emerging in the "great convergence", you'll find BQ.1.1 out at the far bottom-right:

https://twitter.com/dfocosi/status/1576217954013696000?s=20&t=-6oNdRWMVPbHe5aYZHrzAA

@CorneliusRoemer

In this thread on BQ.1.1, @CorneliusRoemer highlights that it overcomes all available antibody treatments.

https://twitter.com/CorneliusRoemer/status/1576729414918103044?s=20&t=-6oNdRWMVPbHe5aYZHrzAA

@siamosolocani

h/t @siamosolocani who first spotted this lineage, and the others in the "Lineage Watch" team who have contributed to our understanding of it.

Also to all the contributors around the world, sharing data for the common good.

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Mike Honey

@Mike_Honey_

Oct 3

Here's the latest variant picture for Australia:
- the BA.2.75.* "Centaurus" group is at around 9%
- BA.4.6 nickname "Aeterna" might have peaked at 8% and then fallen somewhat

Up-to-date samples from Victoria were recently shared.
🧵

Among the BA.2.75.* family, the dominant lineage shown by GISAID currently is BA.2.75.

Several more detailed child lineages have been identified e.g. BM.1.1, XBB, with their categorisations yet to flow out to GISAID. See below for details.

Breaking down Australia by state shows BA.2.75.* "Centaurus" has most frequently been reported in New South Wales, approaching 20% recently. Victoria's recent update took them to 10%.

Sampling might be skewed towards suspected BA.2.75 samples in different jurisdictions.

Read 12 tweets

Mike Honey

@Mike_Honey_

Oct 1

Here's an update on "fully vaccinated" rates for a collection of countries that Australia & NZ often compare themselves to.

I define "fully vaccinated" as the % who received a booster in the last 120 days - as recommended by US CDC, Australia's ATAGI etc for vulnerable folks.
🧵

Zooming in on recent months, it's clear that NZ and Canada are achieving far better outcomes than the US, Singapore (now below the US!), Australia and the UK.

Surely there are some lessons that could be learned?

Interactive world covid stats dataviz, code, acknowledgements and more info here:
github.com/Mike-Honey/cov…

Read 5 tweets

Mike Honey

@Mike_Honey_

Oct 1

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

- BA.2.75 "Centaurus" is showing impressive recent growth, rising from 1% to 10% frequency in just 13 days

- it's first generation of child sub-lineages are not enjoying similar success so far
🧵

For the UK, BA.2.75 "Centaurus" is showing a growth advantage of 20% per day against BA.5.* lineages, which predicts a crossover in [checks watch] late September.

The points are closely clustered along the trend line, so this seems quite likely.

AFAIK BA.2.75 hasn't shown this level of growth anywhere else.

There are further sub-lineages still to be spun out from the BA.2.75 lineage as currently defined in GISAID - see below for more details.

Read 9 tweets

Mike Honey

@Mike_Honey_

Sep 30

@TRyanGregory

Here's the latest variant picture for the recently-designated XBB lineage, nickname "Gryphon" (h/t @TRyanGregory).

It has most commonly been reported from Bangladesh, a possible origin. It recently rose to ~50% frequency.

It also showed some signs of growth in India (6%)
🧵

@siamosolocani

The XBB categorisation has yet to rollout to the GISAID database, so I'm approximating it here by searching for samples with the characteristic mutations - Spike Q183E, NSP13 S36P and E T11A (h/t @siamosolocani).

That method is currently catching 66 sequences.

@CorneliusRoemer

h/t @CorneliusRoemer who first spotted this lineage, and the others in the "Lineage Watch" team who have contributed to our understanding of it.

Also to all the contributors around the world, sharing data for the common good.

Read 11 tweets

Mike Honey

@Mike_Honey_

Sep 30

An inflection point for covid (surveillance) deaths in Australia?

Here's the largest 4 states and the national aggregate, on a per capita basis.

All increased this week, with Victoria and Queensland up ~100% week-on-week. Nationally, up 50%.
🧵

Cases in hospital and ICU continue to fall.

Reported cases continue to fall, although the rate of descent is continuing to slow.

Read 6 tweets

Mike Honey

@Mike_Honey_

Sep 29

Here's the recent curve of cases (7-day average) for Victoria.

The growth this week could be just another bobble, a super-spreader from the major event last weekend, or the start of a wave from a new variant.
🧵

Based on that data, the 4-day Reff (case momentum) for Victoria is up to 1.04.

Results above 1 indicate the outbreak is expanding.

For the weeks ending 16 and 23 September, I'm treating each day as if weekly total cases divided by 7 were reported.

Here's how that looks, among the daily counts from the current week, and days prior to September 9.

Read 5 tweets

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