HAS AUSTRALIA REALLY HAD 60,000 UNDIAGNOSED COVID-19 CASES? – 21 September 2020
A preliminary study, posted online this week by researchers at the Australian National University and elsewhere, estimates 71,000 Australians had COVID-19 by mid-July — 60,000 more than official number of cases diagnosed by that stage. UTS Biostatistics Professor Andrew Hayen, and Gregory Dore from UNSW in The Conversation.
ON THE ROAD TO COVID NORMAL: THE EASING OF REGIONAL VICTORIA’S RESTRICTIONS SIGNALS HOPE FOR MELBOURNE TOO – 16 September 2020
UniSA Professor of Biostatistics and Epidemiology Adrian Esterman in The Conversation.
NOW EVERYONE’S A STATISTICIAN. HERE’S WHAT ARMCHAIR COVID EXPERTS ARE GETTING WRONG – 14 September 2020
If we don’t analyse statistics for a living, it’s easy to be taken in by misinformation about COVID-19 statistics. University of Sydney biostatistician Jacques Raubenheimer in The Conversation.
COMPARING COVID-19 DATA AND POLICY RESPONSES BY COUNTRIES – 8 September 2020
University of Oxford’s Coronavirus Government Response Tracker (OxCGRT): online tool tracks and compares policy responses around the world, rigorously and consistently, using data from 180 countries.
PROBABILITY OF THE 6-WEEK LOCKDOWN IN VICTORIA ACHIEVING ELIMINATION OF COMMUNITY TRANSMISSION OF SARS-COV-2 – 8 September 2020
Modelling suggests that elimination could have been achieved if Victoria had gone into full stage 4 lockdown
immediately from 9 July. Blakely T, Thompson J, Carvalho N, et al. in MJA.
LARGE-SCALE TESTING IS KEY TO CONTROLLING COVID-19 – 7 September 2020
Statistical modelling shows that analysing grouped samples can give a better and more efficient indication of the prevalence of disease: Dr Daryl Holland article featuring Professor Aurore Delaigle in Pursuit.
MODELLING BUILT TO SUPPORT VIRUS ELIMINATION – 7 September 2020
The Financial Review’s Tom Burton asserts that modelling by University of Melbourne and UNE researchers found that Victoria was unlikely to have aggressively suppressed the virus by September 13, when stage four restrictions were meant to expire.
Read more in the Financial Review [Nine Media paywall access required].
‘SLOW AND STEADY’ EXIT FROM LOCKDOWN AS VICTORIAN GOVERNMENT SETS SIGHTS ON ‘COVID-NORMAL’ CHRISTMAS – 7 September 2020
Expert University of Melbourne epidemiology and biostatistics commentary from Laxman Bablani and Driss Ait Ouakrim
in ‘The Conversation’.
FINDING THE SOURCE OF AN OUTBREAK IS IMPORTANT. BUT THE TERM ‘PATIENT ZERO’ IS A PROBLEM… – 17 August 2020
Commentary and terminology clarified by UniSA Professor of Biostatistics, Adrian Esterman in ‘The Conversation’.
NEW ZEALAND IS ON ALERT AS COVID-19 RETURNS. THIS IS WHAT WE NEED TO STAMP IT OUT AGAIN – 13 August 2020
Michael Plank, Professor in Mathematics at the University of Canterbury, on the swift and decisive action needed to control resurgent COVID-19.
Read more in ‘The Conversation‘.
IT LOOKS LIKE VICTORIA HAS PASSED THE PEAK OF ITS SECOND WAVE. IT PROBABLY DID EARLIER THAN WE THINK – 13 August 2020
University of Sydney Biostatistics Professor Ian Marschner data analytics commentary in ‘The Conversation’.
ENGAGING MORE WITH MATHS IS THE NUMBER ONE LESSON FROM THE CRISIS – 11 August 2020
Asha Rao AMSI commentary on data and decision-making in the Financial Review
Read more — Nine Media paywall access required
APRA PUBLISHES WEEKLY DATA ON THE SUPERANNUATION EARLY RELEASE SCHEME – 27 July 2020
The Australian Prudential Regulation Authority (APRA) has released its latest statistics on the Early Release Initiative enabling access to superannuation contributions during the COVID-19 emergency.
Read more with infographics at the APRA website.
DISRUPTED RECOVERY: PROFESSOR JODIE MCVERNON OF THE DOHERTY INSTITUTE ON THE ABC’S Q+A PANEL – 22 July 2020
Suppression v. Elimination? Is it working, or are some states being left behind? The path to our new normal is changing rapidly. As life opens up for much of the country, our two most populated states are battling to contain a growing number of COVID cases. View the Q+A podcast of this week’s discussion and debate, hosted by Hamish Macdonald.
WHAT HAVE WE LEARNT FROM THE RECENT RETRACTION OF THE LANCET AND NEJM ARTICLES? – 22 July 2020
What does this mean for research using big data? Follow the Twitter conversation with ANU’s Research School of Population Health and be part of the online panel discussion 12:30–1:30pm this Thursday 23 July.
LIFE BEYOND CORONAVIRUS: THE WAY OUT OF LOCKDOWN – 20 July 2020
Encore discussion and ‘The Expert View’ hosted by the University of Melbourne’s Professor Shitij Kapur, featuring statistical interpretation and commentary by the Doherty Institute’s Professor Sharon Lewin.
WE’RE TESTING 50,000 AUSTRALIANS A DAY FOR COVID-19; SHOULD IT BE 6.5 MILLION? – 10 July 2020
Analysis and commentary on the mathematics of mass testing by UNSW’s Professor Richard Holden in ‘The Conversation’.
VICTORIA IS UNDENIABLY IN A SECOND WAVE OF COVID-19. IT’S TIME TO PLAN FOR ANOTHER STATEWIDE LOCKDOWN – 7 July 2020
There’s no formal definition of what constitutes a second wave, but a reasonable one might be the return of an outbreak where the numbers of new daily cases reach a peak as high or higher than the original one. By that definition, a second wave has arrived in Victoria. Continuing Adrian Esterman commentary in ‘The Conversation’.
SUPERSPREADERS, ASYMPTOMATICS AND COVID-19 ELIMINATION – 6 July 2020
Estimates of the risk of lifting lockdown at various times near the end of the epidemic in Medical Journal of Australia preprint
Read more at MJA.
VICTORIA IS ON THE PRECIPICE OF AN UNCONTROLLED CORONAVIRUS OUTBREAK. WILL THE NEW MEASURES WORK? – 3 July 2020
Further biostatistical observations and insight into infection transmission and control from UniSA’s Professor Adrian Esterman in ‘The Conversation’.
HOW AUSTRALIA’S SUPERCOMPUTERS CRUNCHED THE NUMBERS TO GUIDE OUR BUSHFIRE AND PANDEMIC RESPONSE – 30 June 2020
Data-driven models running on supercomputers can provide earlier and more accurate warning of firestorms, floods, hailstorms, cyclones and other extremes. ANU’s Professor Sean Smith and Mark Stickells of the Pawsey Supercomputing Centre on Australia’s high-performance research computing infrastructure in ‘The Conversation’.
ANU-DEVELOPED AI TOOL TO DETECT VIRAL CO-INFECTIONS – 19 June 2020
Professor Eduardo Eyras, along with his team and collaborators at the Australian National University’s John Curtin School of Medical Research has developed a tool to detect viral co-infections in COVID-19 patients to help develop informed strategies for antiviral treatment, vaccination and epidemiological control in the COVID-19 pandemic.
Various studies report that around 20 percent of SARS-CoV-2-positive individuals had a co-infection with other respiratory viruses and that these coinfections may increase the severity of the disease by altering disease progression and response to treatment.
Professor Eyras said identifying those co-infections will be relevant for treatment and prognostic purposes, however, the current standard of viral detection is based on PCR assays directed to SARS-CoV-2 only, which will miss possible co-infecting viruses. The new method, called PACIFIC, can identify SARS-CoV-2 and 361 other viruses at a sample concentration as low as 0.03%, with high specificity (low false-positive rate). “With PACIFIC, we are trying to provide a fast and easy-to-use, end-to-end tool that will enable researchers to monitor viral infections and co-infections to help manage the global COVID-19 pandemic.”
The new computational tool, based on artificial intelligence for natural language processing, detects viral co-infections from COVID-19 patient samples analysed with high-throughput sequencing (HTS). HTS enables the unbiased detection of RNA molecules present in a patient sample and can be performed on blood, sputum or any other patient sample.
Professor Eyras and his colleagues decided to develop a tool to identify SARS-CoV-2 and other potential viruses from the pool of HTS reads (i.e.: the fragments of the RNAs measured from the sample). To achieve this, the tool had to be able to identify the virus type from the RNA sequencing reads, and do this confidently enough for as many reads as possible.
“This is similar to language processing, where you recognise and classify texts, and organise them into organised groups,” Professor Eyras said. “We trained this model with examples of sequences that come from multiple viruses and from humans, and the model learns to separate them.”
MODELLING SHOWS NEW ZEALAND HITS A 95% CHANCE OF ELIMINATING CORONAVIRUS – 5 June 2020
New Zealand is now very close to its elimination target, but a 5% chance of undetected cases remains according to university researchers.
Read more in The Conversation.
COSTS OF CORONAVIRUS AND NEW METHOLOGIES REVEALED IN MARCH QUARTER NATIONAL ACCOUNTS – 3 June
Data released today by the Australian Bureau of Statistics reveals a 0.3 percent contraction in Australia’s economy for the March quarter..
The ABS has also flagged changes in the seasonal adjustment process, with series influenced by significant and prolonged impacts from COVID-19 using forward seasonal factors to produce seasonally adjusted estimates instead of the standard concurrent seasonal factors method.
Read more at the ABS website.
HOUSEHOLD IMPACTS OF COVID-19: ABS SURVEY – 2 June 2020
Latest ABS snapshot about how Australian households are faring in response to the changing social and economic environment caused by the COVID-19 pandemic.
PREDICTING THE PANDEMIC’S PSYCHOLOGICAL TOLL: MECHANISTIC AND STATISTICAL MODELLING – 1 June 2020
Jayashri Kulkarni, Professor of Psychiatry at Monash University, on the challenges of modelling in health.
Read more in The Conversation
“A FORECASTING MODEL IS AN OPINION COLUMN WITH MORE MATHS” – 26 May 2020
What will happen when we lose faith in modelling? Parnell Palme McGuinness in today’s Financial Review (Nine Media paywall access required).
AUSTRALIA’S COVID-19 LIFESTYLES REVEALED IN LATEST ABS REPORTING – 25 May 2020
One in five Australians is eating more snack foods with a similar proportion increasing alcohol consumption. Household chores, hobbies and cooking participation levels increased. Read the latest Australian Bureau of Statistics weekly report here.
BEFORE EPIDEMIOLOGISTS BEGAN MODELLING DISEASE, IT WAS THE JOB OF ASTROLOGERS – 20 May 2020
We turn to epidemiologists and infectious disease models; during the Bubonic plague people turned to astrologers.
[Read more history from UQ’s Michelle Pfeffer at The Conversation]
SWEDISH MODEL TRADES MORE DISEASE FOR LESS ECONOMIC DAMAGE – 20 May 2020
“If we are to reach a new normal, in many ways Sweden represents a future model.”
[Analysis and statistics in today’s AFR (Nine Media paywall access required)]
THE POSITIVES AND NEGATIVES OF MASS TESTING FOR CORONAVIRUS – 18 May 2020
No test is perfect and all carry a risk of harm of some kind … we must recognise this is also true for coronavirus. Jennifer MacLachlan and Benjamin Cowie of the Doherty Institute on “false positives”.
[Read more in The Conversation]
THE COSTS OF THE SHUTDOWN ARE OVERESTIMATED – THEY’RE OUTWEIGHED BY ITS $1 TRILLION BENEFIT – 18 May 2020
Economists Richard Holden (UNSW) and Bruce Preston (University of Melbourne) counter the movement advocating more rapid relaxation of containment measures on the basis of economic costs, and the notion of placing a dollar value on one person’s life.
[Read more about the value of a “statistical life” in The Conversation]
WHAT IMPACT IS THE COVID-19 PANDEMIC HAVING ON WOMEN IN THE STEM WORKFORCE? – 17 May 2020
Rapid Research Information Forum response from Australia’s Chief Scientist
[Read more through the Australian Academy of Sciences]
APRIL LABOUR MARKET STATISTICS FOR AUSTRALIA: “THE SCALE AND SPEED ARE DIFFICULT TO COMPREHEND” – 15 May 2020
University of Melbourne economist Professor Jeff Borland overview in ‘The Conversation’ this morning.
‘AS AUSTRALIA REOPENS, STAYING ON TOP OF TRANSMISSIONS REQUIRES BETTER DATA’: – 13 May 2020
Silent infections often carry similar levels of the COVID-19 virus, and modelling data shows they can contribute significantly to transmission. University of Melbourne Medical Dean Shitij Kapur’s insight into data and definitions in today’s AFR
[Read more in the Financial Review (Nine Media paywall access required)]
CORONAVIRUS: ELIMINATION IS NOT ERADICATION – 11 May 2020
UniSA Biostatistics Professor Adrian Esterman explains in ‘The Conversation’ why COVID-19 will probably be eliminated but never completely eradicated.
SAFELY RELAXING SOCIAL DISTANCING COMES DOWN TO HOUSE NUMBERS: QUT – 7 May 2020
Your house number could be the key to the safe relaxation of COVID-19-related restrictions if government follow a new exit strategy use an ‘odds-and-evens’ approach to allowing people to head back to work and enjoy other activities after weeks of lockdown.
A paper co-authored by QUT’s Professor Adrian Barnett published in the British Medical Journal.
Co-authored by Professor Adrian Barnett, a statistician with QUT’s School of Public Health and Social Work, the paper suggests governments around the globe are seeking to balance competing priorities.
“Social distancing has certainly been proven to reduce the rate of transmission of COVID-19 but has had a negative impact on the economy and created other health issues,” said Professor Barnett.
“A major problem with relaxing restrictions too quickly is the limited evidence on how this will affect transmission of the virus and no-one wants to see another wave of infection and deaths which would lead to a return to lockdown.
“We propose an interim solution in which allowing people to return to a less-restricted life should be based on odd or even house numbers. For example, people in odd numbered houses have relaxed restrictions on odd days in the month (1st, 3rd, etc) and people in even number houses on even days (2nd, 4th, etc).
“This halves the population mixing, which reduces the risk of a new wave occurring, and it creates useful data for judging whether restrictions can be further relaxed or should be tightened.”
‘LIFE BEYOND CORONAVIRUS’: THE EXPERT VIEW [PODCAST]; PART 2 OF 6 – 4 May 2020
Professor Jodie Mcvernon and a panel experts from across the University of Melbourne explore how mathematical modelling got us to this point, the new trace-and-track app, how it works and if it has a role to play in lifting restrictions, and just how long can Government keep us at home? Hosted by Professor Shitij Kapur.
LIFE BEYOND CORONAVIRUS: THE EXPERT VIEW – 21 April 2020
Professor James McCaw joins an expert panel of University of Melbourne researchers and academics in an online Pursuit video review of the latest COVID-19 data. Features Doherty Institute chief Sharon Lewin, and hosted by Shitij Kapur.
PROFESSOR JODIE MCVERNON ON ABC TV’S ‘Q+A’ – 20 April 2020
Doherty Institute epidemiologist delivering modelling to government joins Neville Power (Chairman, National COVID-19 Coordination Commission), ACTU Secretary Sally McManus,ethicist Simon Longstaff and UNSW economist Gigi Foster. Hosted and moderated by Hamish Macdonald.
VICTORIA SAW DIRE WARNING IN MODELLING AND ‘CHANGED THE FUTURE’ – 20 April 2020
Michaela Whitbourn in the Sydney Morning Herald
Victoria’s Chief Health Officer, Professor Brett Sutton, said the state would have faced 650 deaths per day at its peak if it had not introduced tough measures to curb the spread of the virus.
Modelling done by the University of Melbourne, Monash University and the Victorian Health Department suggested the state would have recorded 58,000 infections per day at its peak if action had not been taken to flatten the curve, Professor Sutton said on Monday.
Victoria’s Chief Health Officer Brett Sutton said the state “changed the future” by heeding warnings in modelling. He said the modelling “uses assumptions based on the experience of countries overseas as well as data from Australia to inform what might have occurred had we only had a case isolation and contact [tracing] process in place without social distancing measures”.
“We saw this modelling and we changed the future two months ago by virtue of what we saw. We changed the assumptions in the modelling by virtue of the measures that have been many place for weeks at different levels,” he said.
DOHERTY INSTITUTE AND UNIVERSITY OF MELBOURNE MODELLING GUIDING COVID-19 RESPONSE – 8 April 2020
AMSI members are the forefront of the complex modelling behind the Government’s response to this deadly coronavirus pandemic, with mathematicians creating models of the population to predict the course and impact of the virus.
But how does this work, and why do governments act upon such predictions?
Professors James McCaw and Jodie McVernon of the University of Melbourne / Doherty Institute provided an insight into their COVID-19 modelling to ABC News today.
Professor McCaw said “they put some ‘very scary numbers’ to the Government early on, and they were not dismissed. We don’t have an overwhelmed hospital system yet, and we may well never have one if we continue to base our responses on the best available data.”
Professors McCaw and McVernon both feature in the AMSI Maths Delivers video: ‘The Spread of Disease’ providing an insight into the mathematical modelling of susceptibility, infection spread and recovery of disease in populations.
“We cannot promise lives will not be lost”:
Modelling expert Professor Jodie McVernon interviewed by Sabra Lane on AM ABC Radio
James McCaw is a mathematical biologist and infectious diseases epidemiologist with a PhD in theoretical physics from the University of Melbourne. He holds a joint appointments at the University of Melbourne in Mathematics and Statistics within the Faculty of Science (alongside his role as Associate Dean – Research) and at the University’s School of Population and Global Health
Professor McCaw’s interests span from modelling host-pathogen-drug dynamics, focusing on influenza and malaria, to developing public health control strategies for emerging and re-emerging infectious diseases. One of his current projects is Household Transmission Investigation for Novel Coronavirus (COVID-19) Infection Aka Ffx Full Implementation.
Professor Jodie McVernon is a physician with subspecialty qualifications in public health and vaccinology based at the Doherty Institute. Jodie possesses extensive expertise in clinical vaccine trials, epidemiologic studies and mathematical modelling of infectious diseases.
These focus on the application of a range of cross-disciplinary methodological approaches including mathematical and computational models, to synthesise insights from basic biology, epidemiological data and sociological research. Such models advance understanding of the observed epidemiology of infectious diseases and inform understanding of optimal interventions for disease control.
AMSI ONLINE RESOURCES EXPLAIN THE MATHEMATICS OF DISEASE – 8 April 2020
AMSI is offering free online resources including videos informing the community of the power of mathematics, statistics and data modelling in the epidemeological response to the COVID-19 crisis
The Spread of Disease is a video produced as part of AMSI’s Maths Delivers intitiative, providing an overview of the application of mathematical sciences in modelling the susceptibility, infection spread and recovery of disease in populations.
Presenters include Professor James McCaw of the University of Melbourne’s School of Mathematics and Statistics who holds a joint appointment with the School of Population and Global Health, and Professor Jodie McVernon, an expert in public health and vaccinology at the renowned Doherty Institute.
AMSI also offers a significant range educational resources for teachers enhancing understanding of the mathematical sciences. Beyond enhancing knowledge of mathematical modelling of disease, AMSI Calculate provides a diverse range of engaging multimedia materials explaining maths concepts and enhancing learning. These online resources are easily accessed online and available free to teachers seeking to optimise digital delivery of lessons.
WINTER SCHOOL 2020 UPDATE
AMSI and Winter School 2020 hosts The University of Queensland are conforming to public health directives aimed at reducing the spread of infection throughout the community.
Therefore the AMSI Winter School on New Directions in Representation Theory will not be staged in accordance with the intended July 2020 schedule.
We are currently exploring all possibilities to host this program at a later date and will provide updates via AMSI web, Facebook and Twitter.
Students will be contacted directly regarding refund of registration fees.
We thank all of our partners including The University of Queensland, SMRI and MSRI for their support during this challenging time.
A PERSONAL UPDATE FROM PROFESSOR TIM BROWN, DIRECTOR AMSI, 1 April 2020
Dear AMSI Stakeholders and Friends,
Thanks so much for all your good wishes. I regret that I have not yet been able to reply to these individually given the pressure of the many changes at AMSI caused by COVID-19 (as everywhere!).
Fortunately, I have been fit enough to work throughout and I want to say a huge public thank-you to the AMSI Executive and the Board for their wonderful support and encouragement in this time of personal and professional challenge. Adelle Howse as Chair of the AMSI Board has played the crucial role leading the Board and giving me daily support, guidance and encouragement to face the challenges as best as I can.
The good news is that I received a phone call and subsequent letter this morning from the Victorian Department of Health and Human Services confirming that I met their criteria to end isolation. Of course, I will continue to be in contact with my medical advisors should there be a need and will carefully practice the recommendations of the government more generally.
There is another person to whom I want to say a special thank-you. During their illness, my close contact has worked tirelessly and wisely on the project that brought them to AMSI. This is to the great benefit of mathematical sciences in Australia. As I said to this person repeatedly, I consider myself lucky to have contracted the virus early whilst medical facilities in Australia have capacity to deal with people diagnosed as COVID-19 positive.
Please all stay safe – I just hope that my experience of the infectiousness of the virus can add a tiny bit to the public awareness.
A PERSONAL MESSAGE FROM PROFESSOR TIM BROWN, DIRECTOR AMSI, 24 March 2020
In the changed world that we face AMSI operations are continuing as normal, albeit online rather than face-to-face. Staff are successfully working from home across all our programs.
Last night I was confirmed as positive with COVID-19 having had close contact with someone at AMSI’s Parkville offices last Tuesday. The person was subsequently diagnosed as positive.
At that time, the person I had contact with displayed no symptoms. We did not touch and remained 1 to 1.5 metres apart for the duration of our 90 minute meeting. It is important for as many people as possible to know how infectious this disease is.
Fortunately, my symptoms so far have been mild, and I’m fit for work. I remain focused on delivering AMSI’s mission and plans. The key to this is our AMSI staff and their welfare remains a primary concern to me as operations continue as normal but with changed methodologies.
I’m very confident that together the strong, powerful and focused AMSI team can get through this well and that we will seize any opportunity we have to assist Australia with all the health, social and economic challenges that face us.
UPDATE 23 March 2020
Please note that further to this statement, access to AMSI Building 161 has been restored however staff normally domiciled in this building continue to work remotely until further notice.
STATEMENT 19 March 2020
Dear AMSI members, friends and stakeholders,
Please be reassured in these difficult times that AMSI and our team are committed to sustaining business continuity and maintaining our mission.
The dispersed nature of our business relationships and delivery combined with the significant IT capability of the University of Melbourne enables us to continue in as close to a ‘business as usual’ manner as possible with revised work practices.
In accordance with evolving University of Melbourne policy and procedures (based on Chief Medical Officer advice) our office [Building 161] at the Parkville campus is closed until further notice. AMSI staff continue operating at dispersed locations — often from at home. There are also travel restrictions in place in accordance with this policy.
During this period AMSI team members remain contactable via email and mobile phone, and in most instances office phones will divert seamlessly to remote locations. Zoom video conferencing is also available enabling ‘face-to-face’ contact to continue electronically.
We are also working through education delivery, PhD internship and business relationship management issues with a view to minimising disruption and providing policy clarity.
AMSI will issue periodic updates on our response to this situation via our website amsi.org.au and our social media channels.
The mathematical sciences have a great part to play in managing and resolving this challenge to humankind.
I thank you for your understanding and flexibility regarding this evolving situation and assure you that AMSI will continue to adapt and function effectively throughout this period.