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Mike Honey Profile picture
@Mike_Honey_
Nov 29 • 7 tweets • 2 min read • Read on X
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Here's the latest variant picture for the United States, to early November.

The XFG.* "Stratus" variant continued it’s dominance, roughly flat at 83% frequency.

NB.1.8.1 "Nimbus" was down slightly to 7%.

#COVID19 #SARSCoV2 #USA #XFG #Stratus #NB_1_8_1 #Nimbus
🧵 Image
XFG.1.1 is emerging as a new contender. It is characterised by a reversion to Spike W452R, which captured the attention of the Variant Hunters.

XFG.1.1 finished at 4%.
🧵 Image
Mutations at position 452 have swung from near-zero to near-100% in a multiple-pendulum pattern, across the span of the pandemic. SL452W has been dominant since JN.1 emerged, the longest period of stability.
🧵 Image
The previous variants with S:W452R (Delta & BA.5) were generally more severe in their impact on individuals.
🧵
For the US, XFG.1.1 is showing a slowing advantage of 2.9% per day (20% per week) over other XFG.* "Stratus" lineages. At that pace, any crossover might be in the New Year.
🧵 Image
Here are the leading US states reporting XFG.1.1.

Oregon has reported the highest frequency at 19%, while California reached 11% and Minnesota hit 10%.
🧵 Image
Report link:

🧵 endsmike-honey.github.io/covid-19-genom…

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More from @Mike_Honey_

Mike Honey Profile picture
Dec 7
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
Mike Honey Profile picture
Dec 6
Here's an animated map showing the spread of the BA.3.2.* variant, nicknamed "Cicada".

The other main hotspots have been South Africa, Western Australia (since July) and Germany (from mid-October).

Locations are approximate - typically country and state/province.
🧵
Audio credit:

Crickets Cicada Catbirds Ephemeral Wetland by KevinSonger -- -- License: Attribution 4.0
🧵freesound.org/s/687109/
Here's the latest variant picture with a global scope, to mid-November.

BA.3.2.* has continued to show signs of growth. Recent samples have been reported from South Africa, Australia, across Europe, and a traveller entering the US from Kenya.

#COVID19 #Global #BA_3_2
🧵 Image
Image
Read 10 tweets
Mike Honey Profile picture
Nov 23
Here's the latest variant picture with a global scope, to early November.

BA.3.* (mostly BA.3.2.2) has started showing significant signs of growth. Recent samples have mostly been reported from Germany and Australia.

#COVID19 #SARSCoV2 #Global #BA_3_2 #XFG #Stratus
🧵 Image
Image
Note I have rolled my reporting window forward an extra week, to capture this development. So recent samples are even thinner than usual.
🧵
Here are the sub-lineages of BA.3.*. BA.3.2.2 is driving the recent growth, rising to 2.5% frequency. It features the Spike K356T and A575S mutations.

The Variant Hunters expect that these will be superseded by further child lineages with added mutations.
🧵 Image
Read 16 tweets
Mike Honey Profile picture
Oct 26
I’ve used WA Health’s COVID-19 wastewater surveillance page to estimate the number of infections of BA.3.2.

I estimate ~400 BA.3.2.* infections in Perth for the latest week, and ~4,600 over the 9 weeks since BA.3.2.* was first detected.

#BA_3_2 #Australia #WA #Perth
🧵 Image
WA Health revamped their dashboard using Power BI, so it is more interactive now and a bit easier to get precise values. However they paused the wastewater variant analysis for 3 weeks, so I’ve estimated the values in that gap.

🧵 health.wa.gov.au/articles/n_r/r…Image
Here’s the 6 month view of their variant chart. BA.3.2.* fell to to 10.2% of wastewater for the week ending 19-Oct-2025.

XFG.* grew to 27.7%, which is probably the best hope for crushing BA.3.2.* before it has a chance to evolve further.
🧵 Image
Read 8 tweets
Mike Honey Profile picture
Sep 14
With the NB.1.8.1.* "Nimbus" and XFG.* "Stratus" variants carving up dominance around the globe, it is time to ponder which variant might drive the next wave.

The leading contenders at this point are PY.1.1.1 and XFV.

#COVID19 #SARSCoV2 #PY_1_1_1 #XFV #XFZ
🧵 Image
Both are at low frequencies globally, but are already remarkably widespread geographically. New entrant XGA might be flattered by the low recent sample volumes.

I added some other contenders for monitoring, although they are less significant: XEC.27.2(.1), XFW, XFY and XFZ.
🧵
PY.1.1.1 is presumed to have originated from India, rising sharply to 11% frequency there in by early July. It has also shown signs of growth in several other countries, notably rising to 3% in Canada.
🧵 Image
Read 15 tweets
Mike Honey Profile picture
Aug 31
For context, using Figure 17 we can estimate the number of infections of BA.3.2.

I estimate ~25K BA.3.2.* infections in Perth that week.
🧵
If you match the current level of the navy blue line to the cases/100K scale on the left, it looks like ~2.5K cases per 100K population (from all variants).

Perth's population is 2.3M, so that scales up to ~58K cases.
🧵 Image
But early-2023 testing levels were far from perfect. I'll multiply by 3 to get an estimate of ~170K infections. That's surely very conservative.

15% of 170K gives an estimate of ~25K infections with BA.3.2, in Perth that week.
🧵
Read 6 tweets

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