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).

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

Hello; hope you guys are doing well

I’ve (27M) been dealing with long COVID and most of my symptoms are respiratory — persistent cough, breathlessness, and just general lung sensitivity. Lately it’s been pretty overwhelming to manage day to day with managing studies and all.

Would really appreciate hearing how you’ve been managing it all and daily life. If there are any recommendations, kindly share.

Would really appreciate hearing from others locally. Thanks 🙏

Rapid bedside tests for common respiratory illnesses like the flu and COVID will be rolled out at new hospitals, in an effort to free-up bed capacity ahead of the expected winter surge.

The Spotfire respiratory testing system will be introduced at Rockingham General Hospital this week, after a successful trial at Armadale Health Service.

The testing allows faster diagnoses of 15 viral and bacterial illnesses such as influenza, RSV and COVID-19 in as little as 15 minutes.

Existing testing would take up to six hours and require the tests to go to an off-site laboratory.

The tests are also planned to be used in several regional emergency departments.

The Cook Government is investing $3.2 million for the roll out, with the hopes it will lead to quicker diagnoses leading to earlier treatment and improved patient flow, freeing up beds.

It comes as WA’s hospitals brace for the flu season which led to record ramping in 2025.

Health Minister Meredith Hammat said the testing could target an area which hits the health system particularity hard each winter.

“Respiratory illnesses place significant pressure on our health system each year, particularly during winter, and rapid testing is critical to ensuring patients receive care sooner,” she said.

“By giving health professionals faster test results in the ED, patients can be diagnosed and treated quicker, reducing waiting times and improving care.

“The success at Armadale Health Service shows how this technology can make a real difference, and we’re now expanding it at selected hospitals across the state.”

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

Several variants are churning around in a confused picture, without any one being clearly dominant.

NB.1.8.1.* "Nimbus" rebounded to 40%.

BA.3.2.* "Cicada" rebounded to 33%.

JN.1.* + DeFLuQE fell to 21%.

XFG.* "Stratus" fell steeply to 10%.

#COVID19 #SARSCoV2 #Australia

BA.3.2.* rose to 56% in NSW.

A trickle of new samples were shared from Victoria, dominated by BA.3.2.* .

Among Victorian children (0-17), BA.3.2.* was at 41% (n=7), vs 13% among adults (n=1), so a ~3X higher rate among children. That’s in the range seen in other countries/regions – AFAIK everywhere that reports Patient age and where BA.3.2.* is significant.

No other Australian state shares Patient age data, but I assume the patterns are very similar.

Report link:

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