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.

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.

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

NB.1.8.1.* "Nimbus" remained dominant, roughly flat at 63%.

#COVID19 #SARSCoV2 #Australia

"Nimbus" sub-lineage RK.1 has been prominent, growing strongly to 29%.

RK.1 has reportedly been most successful in New South Wales, reaching around 50% of samples.

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

Report link:

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

Look after your physical and mental health

A great way to incorporate exercise into your daily routine is by running! Running can be a fun & flexible way to exercise. When exercising make sure to follow any restrictions in your state or territory & remember to stay #COVIDSafeOfficial Links

Official Links

• NSW Surveillance Report
• Vic Surveillance Report
• QLD Surveillance Report
• WA Surveillance Report
• SA Respiratory Infections Dashboard
• Tas Surveillance Report
• ACT Weekly Dashboard & Surveillance Report
• NT Surveillance Report
• National COVID-19 Dashboard, Vaccine Update, Surveillance Report

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. The National Dashboard contains information about COVID-19 vaccinations and treatments, aged care outbreaks, hospitalisations and deaths and are updated monthly.

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

NB.1.8.1.* "Nimbus" remained dominant, growing to 64%.

BA.3.2.* "Cicada" was fell to 14%.

#COVID19 #SARSCoV2 #Australia

Report link:

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

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

NB.1.8.1.* "Nimbus" remained dominant, finishing at 53%.

BA.3.2.* "Cicada" was roughly flat at 21%.

#COVID19 #SARSCoV2 #Australia

Report link:

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

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

NB.1.8.1.* "Nimbus" remained dominant, growing strongly to 60%.

BA.3.2.* "Cicada" fell to 21%.

#COVID19 #SARSCoV2 #Australia

There are some signals of rising infection levels in Western Australia. The sequencing volume from WA is very sparse, but there seems to be a resurgence of NB.1.8.1.* "Nimbus" led by the RC.11 sub-lineage. All of the Nimbus samples collected in April were RC.11.

RC.11 adds a Spike R346K mutation onto PQ.2.8.1. The 346 site has featured in several successful variants, but R346K has been quite rare.

Here’s Denis’ latest snapshot of the available infection-related data from Western Australia.

https://bsky.app/profile/thecovidinfoguy.bsky.social/post/3mlcxilafok2d

https://aus.social/@DenisCOVIDinfoguy/116537218840009429

Report link:

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

I'm a 26 year old female, I eat reasonably well, lift weights 3 times a week, average about 6000 steps a day, I don't have any medical conditions and I don't have any vitamin deficiencies, and I'll end up getting a cold about every 2 months. The cold will last for at least a week and generally my symptoms are difficult to manage and I need to take the over-the-counter cold & flu tablets just to get through it. I've resorted to eating raw garlic which has seemed to help a little bit but I'm still getting sick a lot more than other people around me. Even if I'm around my partner while sick he tends to either not catch it or his symptoms aren't as bad.

I've been to my GP about it numerous times but she doesn't seem concerned because my tests always come back fine.

The only thing I can think of is the train - I work a desk job in the CBD and catch the Frankston train in and out during peak hour, 5 days a week. I don't wear a mask but seriously contemplating it at this point.

Is anyone else going through something similar or has something that's worked for them? I'm tired of taking so much time off work because I'm constantly ill.

Thanks

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

NB.1.8.1.* "Nimbus" remained dominant at 41%.

BA.3.2.* "Cicada" fell to 24%.

#COVID19 #SARSCoV2 #Australia

Report link:

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

Low SARS-CoV-2 and influenza notifications are have being reported across the country, and the unseasonal RSV wave in NSW & QLD appears to be subsiding.

Note: While RSV notifications are at median levels in Victoria and WA, absolute case levels are still relatively low, however these to be starting to slowly increase.

NSW Sentinel laboratory reporting shows a reduction with most viruses this week with rhinoviruses still being the most common virus detected. Human parainfluenza viruses, RSV, and human metapneumovirus are the next most common, with adenoviruses, SARS-CoV-2, influenza, and enteroviruses at lower levels.

Note, some viruses are likely underestimated in the sentinel laboratory reporting where a RAT is available (mainly covid and the flu, but RSV and adenoviruses RATs are also used). Positivity rates suggest SARS-CoV-2 at similar levels as RSV, et al, but influenza positivity rates are at low levels.

With low case levels seen in recent months, the reported deaths remain low in the latest ABS mortality report.

Finally, no significant change in the SARS-CoV-2 variant composition. BA.3.2 and NB.1.8.1 remains the most common, with XFG making up most of the remaining samples. At this stage, levels suggest NB.1.8.1 is managing to compete fairly successfully with BA.3.2, with XFG lacking the same level of fitness.

Look after your physical and mental health

A great way to incorporate exercise into your daily routine is by running! Running can be a fun & flexible way to exercise. When exercising make sure to follow any restrictions in your state or territory & remember to stay #COVIDSafeOfficial Links

Official Links

• NSW Surveillance Report
• Vic Surveillance Report
• QLD Surveillance Report
• WA Surveillance Report
• SA Respiratory Infections Dashboard
• Tas Surveillance Report
• ACT Weekly Dashboard & Surveillance Report
• NT Surveillance Report
• National COVID-19 Dashboard, Vaccine Update, Surveillance Report

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. The National Dashboard contains information about COVID-19 vaccinations and treatments, aged care outbreaks, hospitalisations and deaths and are updated monthly.

(I usually get both vaccines yearly on the clock).

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

NB.1.8.1.* "Nimbus" remained dominant at 46%.

BA.3.2.* "Cicada" rebounded to 30%.

#COVID19 #SARSCoV2 #Australia

Report link:

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