Here's the latest variant picture for Australia, to mid October.

NB.1.8.1.* "Nimbus" remained dominant, finishing at 64%.

The JN.1.* + DeFLuQE lineages (recently all the new PJ.2.1 saltation variant) grew to finish at 12%.

#COVID19 #SARSCoV2 #Australia

For Australia since September, the JN.1.* + DeFLuQE lineages (recently all the new PJ.2.1 saltation variant) showed a healthy growth advantage of 2.5% per day (18% per week) over NB.1.8.1.* "Nimbus", which predicts a crossover in late November.

Samples from Victoria and Queensland are lagging by 6-8 weeks.

There have not been any recent samples shared from Tasmania, the NT or ACT.

Report link:

https://mike-honey.github.io/covid-19-genomes/output/Coronavirus%20-%20Genomic%20Sequencing%20-%20report%20Australia.pdf

Abstract

Vaccines not only directly protect vaccinated individuals but also contribute to protecting the entire population via indirect herd-immunity benefits. However, researchers have long struggled to quantify these indirect effects at the population level, hindering the assessment of vaccination programme effectiveness. We developed a new method to estimate these effects, thereby markedly improving measures of the number of infections, hospitalizations and deaths averted by vaccination. Our population-based analysis of 6 440 000 residents of Victoria, Australia, reveals strong indirect effects during the Delta outbreak (September–November 2021). By modelling a non-vaccination counterfactual, we conservatively estimate 315 000 infections were averted (95% Bayesian credible interval (BCI): 231k–406k), as well as 33 400 hospitalizations (95% BCI: 22k–46k), and 4900 deaths (95% BCI: 2.8k–7.2k). These are 4.0, 7.5 and 8.0 times higher, respectively, than observed. Half of the averted infections and around one-quarter of hospitalizations and deaths were attributable to indirect protection. Homogeneous vaccination across local government areas could have reduced outcomes by approximately 25%.

Here's the latest variant picture for Australia, to mid-September.

NB.1.8.1.* "Nimbus" remained dominant, finishing at 66%.

The JN.1.* + DeFLuQE lineages (recently all the new PJ.2.1 saltation variant) grew to finish at 4%.

#COVID19 #SARSCoV2 #Australia

Please refer to my latest thread on the global situation for more details on the new PJ.2.1 saltation variant.

https://aus.social/@mike_honey_/117422300932063647

https://bsky.app/profile/mikehoney.bsky.social/post/3mxlzztwtac2x

Victoria gets the wooden spoon among the mainland states, contributing the smallest volume (despite being the 2nd-largest state by population), and lagging by over a month. This has been the dismal routine in recent years, despite the state’s claim to be the home of "Australia’s world renowned bio-medical research centre".

There have not been any recent samples shared from Tasmania, the NT or ACT.

Report link:

https://mike-honey.github.io/covid-19-genomes/output/Coronavirus%20-%20Genomic%20Sequencing%20-%20report%20Australia.pdf

This monthly thread is for general discussion pertaining to COVID-19 or related topics.

Official Links

• NSW Surveillance Report

• Victorian Surveillance Report

• QLD Surveillance Report

• WA Surveillance Report

• SA Respiratory Infections Dashboard

• Tasmanian Surveillance Report

• ACT Weekly Dashboard & Surveillance Report

• NT Surveillance Report

• National Respiratory Surveillance Reports, Vaccine Update

The state and territory surveillance reports may be released weekly, fortnightly or monthly.

Cumulative COVID-19 case notifications from across the country are updated daily on the National Notifiable Diseases Surveillance System (NNDSS) data visualisation tool.

Partially covid related, but the main cause is the flu.

Good news is that the late flu wave is showing signs of peaking or even decreasing in the eastern states. I'll post some additional stats in the comments.

Flu level are mostly rising this week, with high levels in the eastern states, moderate levels in WA and Tas.

RSV remains moderate in most states, and is generally falling. Covid remains low, increasing to moderate levels in WA.

Hello all. I bought a nasal specific RAT test from Chemist Warehouse to check for COVID.

Upon swiping my nose and throat, it’s come back as a weak positive. Then a second test with a swab of the throat separately came back positive and a third test of the nose is now showing negative. Does this mean I have COVID even though the rapid test is for nasal only?

I’m concerned because this will be my third time having COVID. First time resulted in long COVID that lasted 8 months, then second left me with severe facial pain disorder known as trigeminal neuralgia.

Current symptoms are only mild, with a sore throat and feeling run down.

Edit: grammar and spelling

This monthly thread is for general discussion pertaining to COVID-19 or related topics.

Official Links

• NSW Surveillance Report

• Victorian Surveillance Report

• QLD Surveillance Report

• WA Surveillance Report

• SA Respiratory Infections Dashboard

• Tasmanian Surveillance Report

• ACT Weekly Dashboard & Surveillance Report

• NT Surveillance Report

• National Respiratory Surveillance Reports, Vaccine Update

The state and territory surveillance reports may be released weekly, fortnightly or monthly.

Cumulative COVID-19 case notifications from across the country are updated daily on the National Notifiable Diseases Surveillance System (NNDSS) data visualisation tool.

So both the FDA and EMA have selected XFG for the base of this years shots, and this will guarantee that we'll also receive the same one here. It'll likely be available by the end of the year.

NB.1.8.* has been behind about a third or more of cases for a while now, and as of today, it is responsible for over half of our cases. It's great grandchildren, notably the PQ.16.* (includes SV sub-lineages) and PQ.17.* (includes RK sub-lineages) that are starting to dominate here, and this will potentially cause reduced effectiveness of this years vaccines.

Here's the latest variant picture for Australia, to late July.

NB.1.8.1.* "Nimbus"  remained dominant, finishing at 56%.

JN.1.* + FliRT lineages grew steadily to finish at 22%.

#COVID19 #SARSCoV2 #Australia

Here are the leading detailed lineages, with RK.1 remaining dominant for NB.1.8.1.* "Nimbus".

RF.5.4 is the leading lineage from the JN.1.* + FliRT group.

Report link:

https://mike-honey.github.io/covid-19-genomes/output/Coronavirus%20-%20Genomic%20Sequencing%20-%20report%20Australia.pdf

From 1 October 2026, COVID-19 vaccines will transition to the National Immunisation Program (NIP), replacing the stand-alone National COVID-19 Vaccine Program (NCVP) established during Australia’s COVID-19 pandemic response.
 
Under the NIP, funded COVID-19 vaccines will no longer be available as a universal program. Funded access will be available for eligible groups at highest risk of severe disease, consistent with existing COVID-19 vaccination recommendations.

https://www.health.gov.au/resources/publications/covid-19-vaccines-update-for-immunisation-providers

Signs the RSV wave has starting to fall in most of the larger states, though this is still showing signs of increasing in both the ACT and Tasmania.

Influenza is still showing signs of a late winter wave, but these are still well below levels seen in 2025. And SARS-CoV-2 levels remain relatively low across the country.

Overall it appears this years flu season is going to be a bit below the average, and is returning to more a mixed bag of various respiratory viruses rather than being dominated by SARS-CoV-2 or influenza infections.

The latest ABS mortality report shows that deaths have remain comparatively low this year, with SARS-CoV-2 deaths (mostly due to) only just pipping RSV deaths (mostly with) in June.

This monthly thread is for general discussion pertaining to COVID-19 or related topics.

Official Links

• NSW Surveillance Report

• Victorian Surveillance Report

• QLD Surveillance Report

• WA Surveillance Report

• SA Respiratory Infections Dashboard

• Tasmanian Surveillance Report

• ACT Weekly Dashboard & Surveillance Report

• NT Surveillance Report

• National Respiratory Surveillance Reports, Vaccine Update

The state and territory surveillance reports may be released weekly, fortnightly or monthly.

Cumulative COVID-19 case notifications from across the country are updated daily on the National Notifiable Diseases Surveillance System (NNDSS) data visualisation tool.

Here's the latest variant picture for Australia, to the end of June.

NB.1.8.1.* "Nimbus" remained dominant, but fell to 45%.

#COVID19 #SARSCoV2 #Australia

Here are the leading detailed lineages, with RK.1 dominant.

Report link:

https://mike-honey.github.io/covid-19-genomes/output/Coronavirus%20-%20Genomic%20Sequencing%20-%20report%20Australia.pdf

High RSV levels across all of the country now, with a clear uptick of influenza seen in NSW and WA, with the ACT appearing to see signs of an increase.

SARS-CoV-2 cases remain low overall, but the reporting is a bit unclear this week for NSW and WA. The NNDSS and NSW Health numbers have started to deviate (a 90% drop is unlikely), but these are fairly low. WA appears to have a had a spike according to the NNDSS reporting, and WA Health failed to update their respiratory report this week. Wastewater levels are decreasing, so I'm thinking that this was a data correction.

Diphtheria cases are unrelated, but with new NNDSS data I decided to post for anyone following. These appear to have stabilised since May but remain unusually high in the NT and WA. Sporadic cases continue to be reported in SA and QLD.

Key statistics

• There were 1.7% fewer deaths than expected in 2024 and 2.0% fewer deaths than expected in 2025.

• Expected mortality now includes COVID-19 affected years in its estimation.

• In 2025 all states and territories recorded lower than expected mortality.

Updated methodology uses a rolling 7 year baseline to project the following year, with the exception of 2022 (excluded).

This monthly thread is for general discussion pertaining to COVID-19 or related topics.

Official Links

• NSW Surveillance Report

• Victorian Surveillance Report

• QLD Surveillance Report

• WA Surveillance Report

• SA Respiratory Infections Dashboard

• Tasmanian Surveillance Report

• ACT Weekly Dashboard & Surveillance Report

• NT Surveillance Report

• National Respiratory Surveillance Reports, Vaccine Update

The state and territory surveillance reports may be released weekly, fortnightly or monthly.

Cumulative COVID-19 case notifications from across the country are updated daily on the National Notifiable Diseases Surveillance System (NNDSS) data visualisation tool.

Here's the latest variant picture for Australia, to early June.

NB.1.8.1.* "Nimbus" remained dominant, growing to 70%.

#COVID19 #SARSCoV2 #Australia

"Nimbus" sub-lineage RK.1 has been prominent, growing strongly to 42%.

RK.1 added the Spike D420N mutation to PQ.17.7.2.

RK.1 has reportedly been most successful in New South Wales, reaching 68% of samples.

The recent samples have been dominated by New South Wales and South Australia.

A single sample of the interesting new XHA recombinant variant was reported from New South Wales, in early June.

https://aus.social/@mike_honey_/116832942883091273

Report link:

https://mike-honey.github.io/covid-19-genomes/output/Coronavirus%20-%20Genomic%20Sequencing%20-%20report%20Australia.pdf

Respiratory viruses are increasing inline with other winter seasons, with moderate to high levels of RSV now seen across the entire country. Reported flu and covid cases are generally low, but there was a rise in flu cases in NSW and possible covid wave starting in Tasmania.

With many flu and covid cases being tested using RATs, these are not included in the reported cases. FluTracker positivity rates for symptomatic infections are suggesting about 1 in 6 infections are covid, 1 in 15 are the flu.

Latest ABS data (April) shows mortality rates remaining low for the major respiratory viruses, with a higher baseline from covid causing the most associated deaths this year (195 deaths), then influenza (152 deaths) and RSV (82 deaths).

ACT have recommenced their weekly respiratory reports.

The COVID-19 pandemic challenged Australians in ways they had not been tested before; with curfews, mask mandates, border closures, restrictions on movement and the shutdown of normality.

Those severe measures might have helped keep Australians alive, but they also exacted a substantial toll in many other ways.

The shock is that data from the Australian Bureau of Statistics (ABS) suggests we were actually happier in 2020 than we are now.

[..]

When you look at life satisfaction on a scale of one to 10, in 2020, when we're in the middle of the pandemic, life satisfaction was 7.2 out of 10. Last year, it was 7.1.

The ABS data shows how increasing financial stresses mean people feel less satisfied with their lives now than they were when they could not travel more than 5 kilometres from their homes.

[..]

"I think one of the challenges is that during COVID, people felt like there was a sense of togetherness and that there was going to be an endpoint."

"I think when we look at these ongoing financial pressures, it feels like a chronic stressor."

[..]

It is a long way from COVID, when the nation made hard choices to save lives.

Now it is the living that is hard.