Globally, JN.1.* + "FLiRT" is still showing a steady, strong growth advantage of 8% per day (58% per week) over other BA.2.86.* "Pirola" (including JN.1.*) samples, since February.

That predicts an imminent crossover in mid-April.
🧵 Convergent evolution has seen several SARS-CoV-2 sub-lineages of JN.1.* acquire the Spike F456L and R346T mutations aka "FLiRT".

Convergent evolution has seen several SARS-CoV-2 sub-lineages of JN.1.* acquire the Spike F456L and R346T mutations aka "FLiRT".

Globally, JN.1.* + "FLiRT" is still showing a steady, strong growth advantage of 8% per day (58% per week) ...
🧵 ... over other BA.2.86.* "Pirola" (including JN.1.*) samples, since February.

That predicts a crossover in mid April.

The Provisional Mortality statistics have been updated by the Australian Bureau of Statistics (ABS), up to December 2023.

Here are the deaths where the underlying cause of death was certified by a doctor as COVID-19 (16,312 deaths).
🧵 Each individual death is represented by a single point, spread out across the years of the pandemic.

Convergent evolution has seen several SARS-CoV-2 sub-lineages of JN.1.* acquire the Spike F456L and R346T mutations aka "FLiRT".

The first chart shows the 9 leading countries by volume, the 2nd chart shows the next 9.
🧵

The designated lineages so far are JN.1.16.1, KP.1.1.*, KP.2.*, KR.1, KS.1 and KU.2.  So 6 different evolutionary paths to arrive at the same advantageous combination, in just a few months.

Convergent evolution has seen several SARS-CoV-2 sub-lineages of JN.1.* acquire the Spike F456L and R346T mutations aka "FLiRT".

The JN.1.* + "FLiRT" lineages have been most successful in Japan (30%), Singapore (23%) and the United States (16%).
🧵 The frequency in the United States has grown to 16%. For recent dates (roughly March 8 onwards), "community transmission" (non-travel related) samples are now the majority.

Convergent evolution has seen several SARS-CoV-2 sub-lineages of JN.1.* acquire the Spike F456L and R346T mutations aka "FLiRT".

The JN.1.* + "FLiRT" lineages have been most successful in Singapore (23%) and the United States (10%).
🧵 The designated lineages so far are JN.1.16.1, KP.1.1, KP.2, KR.1 and KS.1.

Convergent evolution has seen several SARS-CoV-2 sub-lineages of JN.1.* acquire the Spike F456L and R346T mutations aka "tiLT".

The designated lineages so far are KP.1.1, KP.2 and KR.1.

The "tiLT" lineages have been most successful in Singapore (24%) and the USA (7%).
🧵 Here's a map showing the remarkable global spread of JN.1.* + "tiLT". Just under 200 samples have been reported mostly since January, from 23 countries on every continent.

Locations are approximate - typically country and state/province.

The new KP.2 lineage of SARS-CoV-2 is showing signs of spread. It was first detected in samples collected in early January from Assam, India. It has since showed up in NZ, across North America, Europe and Asia.

Here's an animated map showing the spread of the KP.2 lineage.
🧵 Locations are approximate - typically country and state/province.

The new XDQ lineage of SARS-CoV-2 is showing signs of spread. It was first detected in a sample collected in mid-November from Berlin. Within a week it appeared in South Korea, where it has been most successful (30%).
🧵 Here's the variant picture for South Korea. While XDQ's growth against BA.2.86.* "Pirola" looks dramatic, note that the sample volumes are quite low for those recent dates (grey column chart).

The detailed daily PCR test & case data for Queensland has been updated, up to February 5.

PCR Cases (7-day running average) have started rising again in the latest week, driving the Reff (case momentum) back above 1.0.

% Positive was steady in the 14%-15% range.
🧵 % Positive was generally falling since late December, down to a trough around 15% on January 18. However it rebounded to around 17% on January 26, before falling again to around 14%-15%.

Note this is still an very elevated rate compared to the lull in September at around 4%.

Here's the latest variant picture for the sub-lineages of BA.2.86.* "Pirola", at the "Global" level.

JN.1 (46%) has been dominating growth, benefitting from it's Spike:L455S mutation.
🧵 This version of the chart uses a log scale, which helps clearly compare growth rates.

Australian COVID-19 stats update for the period ending 10 January 2024:

Up to January 10, just under 0.5M doses were given, so 2.4% of the Adult population (or 1.9% of the total population) had received an XBB.1.5 vaccination dose.
🧵

I've revived an old Vaccination progress infographic, looking at the doses since 11/12/2023. I assume they are all for the XBB.1.5 vaccines, and that no-one has received 2 doses since that date.

Here's the latest variant picture for Indonesia

As of mid-December, BA.2.86.* "Pirola" (73%) was dominant, led by the JN.1 sub-variant.
🧵 Here are the most common sub-lineages of the BA.2.86.* variant in Indonesia. Sub-lineage JN.1 (55%) grew rapidly during early December. There is also a significant contribution from child lineage JN.1.1 (15%).

Here's the latest variant picture for Tasmania, Australia.

As of mid-December, EG.5.* "Eris" (47%) was generally declining.

BA.2.86.* "Pirola" (50%) began rising steadily from mid-November onwards, led by the JN.1 sub-variant.
🧵 Here are the most common sub-lineages of the BA.2.86.* variant in Tasmania. Sub-lineage JN.1 (32%) reached a critical mass and began growing rapidly during late November.

Here's the latest variant picture for Australia.

As of mid-December, EG.5.* "Eris" (49%) was about to be overrun by BA.2.86.* "Pirola" (48%), led by the JN.1 sub-variant.

The growth of BA.2.86.* accelerated from late November onwards, in a now-familiar pattern.
🧵 Here are the most common sub-lineages of the BA.2.86.* variant in Australia. Sub-lineage JN.1 (32%) reached a critical mass and began growing rapidly during late November.

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

BA.2.86.* "Pirola" (45%) now seems dominant, rapidly displacing EG.5.* "Eris" (30%) during November.
🧵 Here are the most common sub-lineages of the BA.2.86.* variant in the UK. JN.1 (18%) began accelerating the growth of this variant during November.

It's new sub-lineage JN.1.1 (6%) is also growing rapidly. JN.1.1 is characterised by the ORF1a:F499L mutation.

Here's the latest variant picture for the United States.

As of late November, EG.5.* "Eris" (42%) was still dominant, although falling rapidly.

BA.2.86.* "Pirola" (25%) began rising sharply during November.
🧵 The "Pirola" sub-lineage JN.1 (22%) began leading the growth of the BA.2.86.* clan in the US during November.

A new sub-lineage XCT.1 was recently classified and is showing some growth, notably in Germany (5%) and Switzerland (4%).

XCT is a recombinant of JG.4 (via EG.5.1.3 of the "Eris" clan) and DV.7.1 (via CH.1.1.1 of the "Orthrus" clan).

XCT.1 adds the Spike S704L mutation.
🧵 Here's an animated map showing the spread of the XCT.1 lineage in Europe.

Starting from the presumed origin in Vienna in late Septermber, almost 50 samples have been reported so far from 11 countries.

Locations are approximate - typically country and state/province.

The dismantling of the Australian COVID-19 case reporting is hiding the scale (or even existence) of the current wave of community transmission sweeping across the country.
🧵 From the data (faithfully extracted by @dbRaevn) above are 4 key metrics, on a log scale to compare waves:
- Cases (reported from PCR & RAT tests)
- Hospitalised cases
- Aged Care Staff cases
- PBS scripts (for oral treatments)health.gov.au

Here's the latest variant picture for the EG.5.* "Eris" variant, recently upgraded by the WHO from a "Variant Under Monitoring" to a "Variants Of Interest" .

The leading countries across Asia reporting EG.5.* are China (61%), Hong Kong (46%) and Taiwan (32%).
🧵 The leading countries across Europe reporting EG.5.* are Austria (50%), Ireland (40%) and Portugal (40%).

I'm observing most of Asia has now descended into the chaotic variant mix observed in Australia for much of 2023.

Each place has 3+ variants, each at 15-30% frequency.

This is quite different to the pattern in earlier years, when a single variant dominated for months.
🧵 This implies an increased immediate re-infection risk, as whichever variant an individual catches is in the minority.

As soon as their immune system calms, they are certain to encounter new variants that can overcome their natural immunity.