School of Mathematics and Statistics - Research Publications
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ItemNo Preview AvailableCOVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting(ROYAL SOC, 2023-08-30)Since the emergence of SARS-CoV-2 in 2019 through to mid-2021, much of the Australian population lived in a COVID-19-free environment. This followed the broadly successful implementation of a strong suppression strategy, including international border closures. With the availability of COVID-19 vaccines in early 2021, the national government sought to transition from a state of minimal incidence and strong suppression activities to one of high vaccine coverage and reduced restrictions but with still-manageable transmission. This transition is articulated in the national 're-opening' plan released in July 2021. Here, we report on the dynamic modelling study that directly informed policies within the national re-opening plan including the identification of priority age groups for vaccination, target vaccine coverage thresholds and the anticipated requirements for continued public health measures-assuming circulation of the Delta SARS-CoV-2 variant. Our findings demonstrated that adult vaccine coverage needed to be at least 60% to minimize public health and clinical impacts following the establishment of community transmission. They also supported the need for continued application of test-trace-isolate-quarantine and social measures during the vaccine roll-out phase and beyond.
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ItemNo Preview AvailableIndividual variation in vaccine immune response can produce bimodal distributions of protection(ELSEVIER SCI LTD, 2023-10-26)The ability for vaccines to protect against infectious diseases varies among individuals, but computational models employed to inform policy typically do not account for this variation. Here we examine this issue: we implement a model of vaccine efficacy developed in the context of SARS-CoV-2 in order to evaluate the general implications of modelling correlates of protection on the individual level. Due to high levels of variation in immune response, the distributions of individual-level protection emerging from this model tend to be highly dispersed, and are often bimodal. We describe the specification of the model, provide an intuitive parameterisation, and comment on its general robustness. We show that the model can be viewed as an intermediate between the typical approaches that consider the mode of vaccine action to be either "all-or-nothing" or "leaky". Our view based on this analysis is that individual variation in correlates of protection is an important consideration that may be crucial to designing and implementing models for estimating population-level impacts of vaccination programs.
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ItemNo Preview AvailableValue of information analysis for pandemic response: intensive care unit preparedness at the onset of COVID-19(BMC, 2023-05-13)BACKGROUND: During the early stages of the COVID-19 pandemic, there was considerable uncertainty surrounding epidemiological and clinical aspects of SARS-CoV-2. Governments around the world, starting from varying levels of pandemic preparedness, needed to make decisions about how to respond to SARS-CoV-2 with only limited information about transmission rates, disease severity and the likely effectiveness of public health interventions. In the face of such uncertainties, formal approaches to quantifying the value of information can help decision makers to prioritise research efforts. METHODS: In this study we use Value of Information (VoI) analysis to quantify the likely benefit associated with reducing three key uncertainties present in the early stages of the COVID-19 pandemic: the basic reproduction number ([Formula: see text]), case severity (CS), and the relative infectiousness of children compared to adults (CI). The specific decision problem we consider is the optimal level of investment in intensive care unit (ICU) beds. Our analysis incorporates mathematical models of disease transmission and clinical pathways in order to estimate ICU demand and disease outcomes across a range of scenarios. RESULTS: We found that VoI analysis enabled us to estimate the relative benefit of resolving different uncertainties about epidemiological and clinical aspects of SARS-CoV-2. Given the initial beliefs of an expert, obtaining more information about case severity had the highest parameter value of information, followed by the basic reproduction number [Formula: see text]. Resolving uncertainty about the relative infectiousness of children did not affect the decision about the number of ICU beds to be purchased for any COVID-19 outbreak scenarios defined by these three parameters. CONCLUSION: For the scenarios where the value of information was high enough to justify monitoring, if CS and [Formula: see text] are known, management actions will not change when we learn about child infectiousness. VoI is an important tool for understanding the importance of each disease factor during outbreak preparedness and can help to prioritise the allocation of resources for relevant information.
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ItemRapid assessment of the risk of SARS-CoV-2 importation: case study and lessons learned(ELSEVIER, 2022-03)During the early stages of an emerging disease outbreak, governments are required to make critical decisions on how to respond, despite limited data being available to inform these decisions. Analytical risk assessment is a valuable approach to guide decision-making on travel restrictions and border measures during the early phase of an outbreak. Here we describe a rapid risk assessment framework that was developed in February 2020 to support time-critical decisions on the risk of SARS-CoV-2 importation into Australia. We briefly describe the context in which our framework was developed, the framework itself, and provide an example of the type of decision support provided to the Australian government. We then report a critical evaluation of the modelling choices made in February 2020, assessing the impact of our assumptions on estimated rates of importation, and provide a summary of "lessons learned". The framework presented and evaluated here provides a flexible approach to rapid assessment of importation risk, of relevance to current and future pandemic scenarios.
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ItemCOVID-19 in low-tolerance border quarantine systems: Impact of the Delta variant of SARS-CoV-2(AMER ASSOC ADVANCEMENT SCIENCE, 2022-04)In controlling transmission of coronavirus disease 2019 (COVID-19), the effectiveness of border quarantine strategies is a key concern for jurisdictions in which the local prevalence of disease and immunity is low. In settings like this such as China, Australia, and New Zealand, rare outbreak events can lead to escalating epidemics and trigger the imposition of large-scale lockdown policies. Here, we develop and apply an individual-based model of COVID-19 to simulate case importation from managed quarantine under various vaccination scenarios. We then use the output of the individual-based model as input to a branching process model to assess community transmission risk. For parameters corresponding to the Delta variant, our results demonstrate that vaccination effectively counteracts the pathogen's increased infectiousness. To prevent outbreaks, heightened vaccination in border quarantine systems must be combined with mass vaccination. The ultimate success of these programs will depend sensitively on the efficacy of vaccines against viral transmission.
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ItemNo Preview AvailableAssessing the risk of spread of COVID-19 to the Asia Pacific region( 2020)During the early stages of an emerging disease outbreak, governments are required to make critical decisions on how to respond appropriately, despite limited data being available to inform these decisions. Analytical risk assessment is a valuable approach to guide decision-making on travel restrictions and border measures during the early phase of an outbreak, when transmission is primarily contained within a source country. Here we introduce a modular framework for estimating the importation risk of an emerging disease when the direct travel route is restricted and the risk stems from indirect importation via intermediary countries. This was the situation for Australia in February 2020. The framework was specifically developed to assess the importation risk of COVID-19 into Australia during the early stages of the outbreak from late January to mid-February 2020. The dominant importation risk to Australia at the time of analysis was directly from China, as the only country reporting uncontained transmission. However, with travel restrictions from mainland China to Australia imposed from February 1, our framework was designed to consider the importation risk from China into Australia via potential intermediary countries in the Asia Pacific region. The framework was successfully used to contribute to the evidence base for decisions on border measures and case definitions in the Australian context during the early phase of COVID-19 emergence and is adaptable to other contexts for future outbreak response.