Australia’s performance in fighting Covid has declined as scientists say researchers are set back by inadequate data systems. Deaths are rising more than predicted, strain on hospitals too. Michael Sainsbury reports the latest on a pandemic which just won’t go away, amid heightened concerns over Long Covid, vaccine impact and the threat of new strains.

Australia’s COVID researchers and epidemiologists are being hampered by inadequate national data gathering systems and databases for the virus as the pandemic presses into its fourth year. 

The lack of detailed, centralised and like-for-like data across the states and territories has been unresolved for decades and has become problematic as health experts wrestle with Long COVID and the prospect of a continuing need for new vaccines and antivirals, as the virus continues to mutate.

“The most important thing is to get excellent data systems that allow us to get this data in real time, so we really understand the impact,” said Professor Sharon Lewin, chief executive of The Peter Doherty Institute for Infection and Immunity. Based in Melbourne,  the Doherty Institute  was the first in the world to sequence the genome of SARS-COV-2  (COVID-19).

“At the moment, data management is quite fragmented around the country, because every state doesn’t share that data [so] … we don’t even have the capabilities to do the real time assessment that we need. So that’s probably the biggest area that I think we need more investment in.”

The issue has emerged as Australia’s performance in managing COVID has deteriorated with the number of people dying surging over the past year as governments across the country favoured a “let it rip” approach. This was packaged as a more digestible “living with COVID” to a nation tired of lockdowns and mask mandates and seemingly willing to let the country’s more vulnerable and at-risk  succumb to the disease – amid widespread complacency about third and fourth vaccine doses that has increased risk of infection and death.

Forty deaths a day

Countless thousands of Australians had their Christmas and New Year plans upended for the third year in a row after a year in which deaths across the country numbered 14,813. That’s 40.5 deaths per day, dramatically outstripping 909 in 2020 (3.6 per day) and 1,331 ( 2.7 per day) in 2021.

In the latest data for the week ending January 13, there were 413 deaths bringing the national total for the year already to 659, about 50% of the total deaths in 2021.

Excess deaths for the first eight months of 2022 were +15,400, or 13% more than predicted, the Actuaries Institute said. Excess deaths in August were 10% more than predicted, lower than recent months, mostly due to lower-than-expected respiratory deaths following an earlier end to the flu season.

Applying their model to Australian Bureau of Statistics (ABS) data (released 25 November), the Institute’s COVID-19 Mortality Working Group estimates that just over half of the excess mortality for the first eight months of 2022 (+8,200 deaths) is due to COVID-19 (‘from COVID-19’), with another +2,100 deaths in people who had COVID-19 listed as a contributory cause (‘with COVID-19).

Complacency rates

Much of the reason for this is complacency. For many months now, most Australian governments have pretended  – or at least hoped – that the COVID 19 pandemic is over. It’s the same for many Australians, exhausted by years of lockdowns and travel restrictions, people are prone to saying things like they are “over’ COVID. Deaths in aged care from COVID have also climbed to record numbers in 2023. 

“We have moved from a policy of anti-infection to one of pro-infection” claims epidemiologist Professor Mike Toole from the Burnet Institute.

State competition cruells national performance

The problems with Australia’s lack of detailed, centralised data have their origins in the fiercely independent health systems of Australia state and territories and extend beyond COVID 19 although that is the major focus at present as the pandemic and new variants of the virus continues to roil the country and its public health systems.

Variants can carry mutations in their genomes. These can increase the ability of the virus to transmit between people, evade the antibodies produced by immune systems, and affect the severity of the disease.

The latest variant of the Omnicron strain that became dominant internationally last year because of its high rate of infection – concerning medical experts around the globe, known as XBB1.5 and codenamed Kraken.

On January 4, the World Health Organisation (WHO) declared the XBB.1.5 sub-variant of the Omicron strain as the most transmissible seen to date and officials are working to gauge what its impact might be in the broader population. What we do know is that it is highly infectious and has an increased ability to evade immune systems, causing hospitalisations in the US to climb to their highest rate in 12 months.

Kraken marketing

Professional and citizen scientists have agreed to begin nicknaming sub-variants after mythological creatures so to keep in line with the WHO’s Greek alphabet  naming system 

“Kraken’s not actually Greek, it’s Scandinavian, but it’s pretty common in popular culture,”  T. Ryan Gregory, a professor of evolutionary biology at the University of Guelph told CTV news.

“‘Release the Kraken,’ from the campy 1980’s movie [Clash of the Titans] is what comes to mind for me, the Seattle Kraken hockey team, there’s a rum that’s popular.”

“It’s got people talking about variants again, which I think is very useful,” said Gregory.

“It seems a previous infection and vaccination don’t protect you as much as they did for previous variants. Vaccination both probably help prevent severe illness but that won’t prevent you from spreading it to other people,” Toole said.

State breakdown

An illustration as to the struggle to get harmonised, regular and even real-time data is explained by Toole:

“The situation (with variants) is not very clear at the moment. The Kirby Institute found there were 15 different omicron variants that had been reported in Australia. Now it’s impossible to interpret what is happening. Western Australia has not issued a report for more than two weeks. Last week Queensland did not issue reports. So when I look at the January 6 figures, I can’t compare them with anything except with December the 23rd which was the last Friday that all states and territories reported, ” Toole said this week.

But the issues stem way beyond timing. There are problems with the way COVID deaths are reported differently in some states. For instance, NSW does not report a death until it is registered by a doctor, meaning its figures lag other states –  so there is no harmonised, week-to-week view of what’s happening around the country.

Toole said he had previously worked for the US Centre for Disease Control and Prevention. Because the US has a lot of states and territories, more than 50, it seems easier to get collaboration than it is when you’ve got a small number, a number of which are in competition with each other. 

“That’s why setting up a CDC in Australia has always been difficult,” he added, noting the last serious attempt to set one up was in the 1980’s Hawke government.

Still, the pandemic may at least  see a fix to this gaping hole in Australia’s health system –  if not for COVID 19 then at least the next pandemic or outbreak with work now underway to create a federal Centre for Disease Control.

Will we see a CDC?

The establishment of an Australian Centre for Disease Control (CDC) is an election commitment of the Albanese government – $3.2 million was provided in the October 2023 Budget to support preparatory work to establish it.

“Once established, the CDC will ensure ongoing pandemic preparedness, lead the federal response to future disease outbreaks, and work to prevent both non-communicable and communicable diseases. No final decisions have been made by the Minister about the scope, powers or scale of the Australian CDC,” a health department spokesperson said.

“Late last year, the Department of Health and Aged Care consulted with key sector stakeholders on the design of an Australian CDC. Feedback from this consultation period will inform the department’s advice to the government on the CDC model, including initial advice on proposed scope and remit.”

Australia, once a leader, now a laggard

Meanwhile, experts say, Australia – once leader in whole-of-population vaccination, is now a laggard with vaccination rates for third doses more or less flatlining at 70 per cent for the past six months, ranking the country at 35 worldwide.

Both Lewin and Toole said it was important that this number was improved as there was data showing that the risk of severe disease decreased after a third and fourth booster.

“We worry most about and most importantly in the elderly or over 65 or people with immunosuppression,” Lewin said. “The vaccines are becoming less and less effective against transmission because of the new variants. But they are very effective against disease … and there’s no evidence that these new variants behave differently in that context.”

Toole believes there is also a problem at the other end of the demographic. 

“When you look at children, it’s even worse. Just over 50% of five to 11 year olds have had two doses of the vaccine. And yet, if you look at other vaccines, measles has around 95%. So there’s been a major failure in communication to parents about the importance of vaccinating their children, not just to protect them, but so they don’t spread it to all vulnerable people. So really, we’ve been stuck at the same point in terms of protective measures for a long time now.”

He added that recent decisions by Cricket Australia to allow COVID positive player Matthew Renshaw take the field in the Third Test against South Africa in Sydney recently and Tennis Australia’ decision to allow COVID positive players on court was “unacceptable”.

Even from an occupational health and safety perspective  he said “what if those players or any one else they infected get a severe case of the disease?”

Both Lewin and Toole believed that there is a strong case for more and better executed public health campaigns to help boost vaccination rates and drive home the idea of personal responsibility about protecting yourself and others from the virus.

“We get no messaging and see no mask wearing from our leaders,” Toole says.

Long Covid is a growing concern

Three years in we are only just beginning to see empirical evidence of how devastating the long term effects of the virus can be. A conservative estimate by the Burnet Institute is that 500,000 Australians are suffering from Long Covid.

For now, Lewin says that we will increasingly be reliant on vaccines and antivirals, something her decade long experience in HIV showed can almost completely control a virus.

Covid is continuing to play havoc with hospital waiting lists as continuing hospitalisations due to the virus continue to clog up hospitals around the nation. A report issued by the Australian Medical Association this week showed there was an estimated elective surgery backlog of 306,281 patients nationally. This will balloon to more than 500,000 by the end of the financial year if action isn’t taken.

“State premiers have talked about the dire state of the health system and the need for urgent action through national cabinet – this report highlights a key part of the system that’s struggling,” AMA president Professor Steve Robson said.

“Our analysis shows hospitals can’t meet demand or the recommended time frames for surgeries and it’s only going to get worse without intervention. This plan needs to be funded by both states and territories and the federal government and backed by long-term funding commitments that deliver permanent expanded workforce and increased capacity to deliver services in our public hospital system.”