Banner image: Members of the Infectious Disease Modelling team at the University of Melbourne. From left to right: Punya Alahakoon (PhD student), Ke Li (PhD student), Dr Rob Moss, Prof James McCaw, Dr Freya Shearer, Dr David Price, Yang Yue (PhD student). Image: Ed Sloane/ARDC
From the moment COVID-19 was detected in Australia in 2020, Australia’s state and federal governments have relied on weekly epidemic assessment reports — underpinned by infectious disease modelling and epidemiological analytics — to guide decisions on keeping Australians safe. The capability in infectious diseases modelling had been developed over many years, supported by Australia’s investment in national research infrastructure.
In early 2020, the COVID-19 pandemic arrived in Australia. The Biosecurity Act was invoked, and Prof James McCaw and Prof Jodie McVernon were called upon to sit as invited experts on the Australian Health Protection Principal Committee (AHPPC), a subcommittee of the National Cabinet. The Committee is chaired by the Chief Medical Officer of Australia and includes the Chief Health Officers from Australia’s states and territories.
James and Jodie support the AHPPC with advice on all aspects of COVID-19 epidemiology, assessment of emerging international literature, and expert interpretation of model-based analyses of COVID-19. Jodie and James co-lead scenario analyses informing policy, including the 2021 Doherty Institute modelling commissioned by the Australian Government to advise on the National Plan to transition Australia’s National COVID Response.
James, a Professor of Mathematical Biology at the University of Melbourne who holds an honorary appointment at the Doherty Institute, says, “I’m one of 3 invited experts on the AHPPC, appointed for my expertise in infectious disease modelling and dynamics and data analytics. I lead the weekly epidemic assessments and forecasting, and contribute to the work on scenario modelling.”
In weekly reports, James and his team provide updates on the effective reproduction number and transmission potential for COVID-19, anticipated future caseload from COVID-19, along with estimates of the impact of the vaccine, and how much it is suppressing transmission.
The modelling relies in part on the computing power of Australia’s national research cloud, the ARDC Nectar Research Cloud (Nectar), which was launched in 2012 to provide Australia’s research community with on-demand computing infrastructure and software.
Although James said he mainly talks to committees and writes reports these days, he leads a team of modellers, epidemiologists and biostatisticians.
“There are 30 to 40 people doing all this work across Australia who find Nectar a very accessible and well supported system.”
Supporting Australia’s Neighbours During the Pandemic
James and his team have done more than just support the Australian government’s response to the pandemic.
“We do work on an international level, particularly in our region. Under the leadership of Professor Jodie McVernon we’ve done a lot of work for French Polynesia, Fiji and a number of other nations in the Asia Pacific as part of their COVID response, working through the World Health Organization to support them.
“In late 2020, our analyses supported the French government’s decision-making on how to manage the epidemic in French Polynesia. Those analyses were supported and run on the Nectar cloud resources.”
Modelling Infectious Diseases on Nectar Since 2012
As an Australian Research Council Future Fellow from 2011 to 2015, James expanded and consolidated the emergent infectious disease modelling and mathematical epidemiology capability within the University of Melbourne School of Population and Global Health. Jodie and James had benefited from earlier investment through an NHMRC Capacity Building Grant 2005 to 2010, and worked with the Department of Health in response to the 2009 H1N1pdm09 ‘swine flu’ pandemic.
“The field of infectious disease modelling and mathematical epidemiology is very computational. It doesn’t require the massive computational power delivered by supercomputers like in particle physics and astronomy. However, we run extensive simulations and make a lot of use of Bayesian computational statistics,” said James.
James needed computing resources, and the launch of Australia’s national research cloud, Nectar, in 2012 came at just the right time. James’ group started using Nectar within months of its launch.
“It was revolutionary because of its ease of use, and it didn’t cost anything as a user.”
James said that without Nectar, he would have needed to continue to buy expensive high performance computers every few years, and spend considerable time administering those systems.
“Nectar made money available, which is an incredibly precious resource for mid-career researchers in a computational field. So instead of spending $15,000 on another computer, I was able to go to conferences, pay open access charges and better support my PhD students. Those little things add up to be a real financial burden.
“It completely changed my ability to develop my career because the system was merit-based, not dollar-based.
“If this resource [Nectar] was not there, it would be a nightmare. A lot of my work is absolutely contingent on this resource or equivalent resources continuing to exist. That it has been so stable and reliable over the last almost decade has been very important.
“It has been essential to support and grow the computational capability of my research team, which has continued to grow since 2012,” said James.
Basic Science Prepared Us for the Future
Nectar has also supported fundamental basic science in mathematical biology over the last decade, said James.
“I’ve had 5 students studying the fundamental mathematical aspects of infection and immunity who’ve done their whole PhD work and computations through the Nectar Research Cloud resource allocation. This has resulted in important contributions to scholarly knowledge in mathematical biology.
“That has also laid the foundation for being ready to respond to events like the COVID-19 pandemic and support the response.”
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The infectious disease and COVID-19 modelling is conducted primarily on the University of Melbourne node of the ARDC Nectar Research Cloud. The project also draws on resources from across the 7 nodes of Nectar due to the federated model and national provision.
The ARDC is funded through the National Collaborative Research Infrastructure Strategy (NCRIS) to support national digital research infrastructure for Australian researchers.