I've added a page for a fresh take on a Risk Analysis - trying to estimate the % Currently Infectious now from Aged Care Staff Cases in combination with the seroprevalence survey result.
It comes out at 1.8% or 1-in-56, which implies a 42% chance that there is someone infectious in a group of 30.
An encouraging uptick in the rate of vaccination deliveries, nudging the coverage up to ~6% of adult Australias with an XBB.1.5 vaccine does. I'm a bit puzzled as to why there would be an uptick?
@RcjWaz@auscovid19 yes, probably. Ofc makes no sense as the big JN.1 wave was in Dec-Jan, but that’s people, I guess.
VIC Health department started pushing for double shots yesterday. Not how I would do it, but again, I am not “people”.
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.
The designated lineages so far are JN.1.16.1, KP.1.1., KP.2., KR.1, KS.1, KU.2 and KZ.1.1. So 7 different evolutionary paths to arrive at the same advantageous combination, in just a few months.
It's still a bit hard to pick a frontrunner out of that swarm. My best guess is the KP.2.* lineages, descended from JN.1.11.1.
The analysis will become clearer as the Nextclade update has just dropped, providing accurate classification of all the new lineages. It will take me a few days to re-process the data using that update.
The lineage diagrams by Daniele Focosi are an excellent resource for making sense of the dynamic evolution picture. They currently show the "FLiRT" lineages at top-right. https://twitter.com/dfocosi/status/1775858186764861898
It seems the first wave of the JN.1.* + "FLiRT" lineages started in Nigeria (43%) during February. Note the end of that series in late February is currently the end of all available sample data from Nigeria, so JN.1.* + "FLirt" lineages are likely more dominant there by now.
The second wave was in several Asian countries in early March, notably: India (62%), Singapore and more recently Qatar (78%).
Qatar recently resumed sharing samples after a gap of several months, so presumably there was a lot of unreported growth before the samples shown here.
Across Europe, JN.1.* + "FLiRT" lineages are showing sharp growth in several countries, led by the UK (35%) and the Netherlands (reaching 31%). Recent sample sizes are often thin and patchy, which can distort the recent results.
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 New Zealand, across North America, Europe, Asia and Australia.
Here's an animated map showing the spread of the KP.2 lineage.
Locations are approximate - typically country and state/province.
PS:
KP.2 adds the Spike R346T mutation to JN.1.11.1.
Globally, KP.2 is showing a very strong growth advantage of 14% per day (101% per week) over other BA.2.86.* "Pirola" (including JN.1.*) since February. That predicts a crossover in late March.
The detailed daily PCR test & case data for Queensland has been updated, up to January 30.
PCR Cases (7-day running average) have been falling steadily since January 10.
As Test volumes have also been falling, % Positive is up slightly to around 16%.
#COVID19 #Australia #QLD #Brisbane @auscovid19@a.gup.pe
🧵
@auscovid19 ```markdown
% Positive was generally falling since late December, down to a trough around 14% on January 18. However it has since rebounded to around 16%.
@auscovid19 ```markdown
Among the South East region LGAs, Somerset is the new outlier with extremely high cases per capita (466/M) combined with the highest % Positive (21%) for the latest week. This implies the rate of infections is far higher than the reported cases would indicate.
Last week's outlier was the Gold Coast. Case rates have fallen marginally there, but the % positive remains high so undiscovered infections abound.
Australian COVID-19 stats update for the period ending 10 January 2024:
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.
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.
@musubhai@auscovid19 there's almost no reporting of COVID case trends in Australian media now, so the vast majority of the population are clueless about the current wave (largest in a year).
There is a portion of "the public" who are aware of cases, keen to get the new vaccines (and eligible) who drove the sharp rise in vaccination rates in late 2023.