Prepare for and respond to emerging infectious disease threats

Aim 2

This project will design simulation-estimation (computer modelling) studies to determine optimal proportion of samples to sequence during different stages of a public health emergency for pandemic preparedness, accounting for stakeholder priorities and resource constraints. It will also analyse >269,000 Australian SARS-CoV-2 genomes collated in AusTrakka during the COVID-19 pandemic to investigate mutation modelling approaches, and develop adaptable sampling decision matrix for early detection, rapid characterisation, and ongoing monitoring of emerging epidemic/pandemic threats.

Outcome:

An agile decision-making protocol for genomics-informed pandemic response.

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Published by 
Australian Pathogen Genomics Program

Program Aims 2026-2026

Aim 1
Implement, optimise and evaluate pathogen genomics in national surveillance
Develop and integrate genomic and epidemiological data analysis and reporting for priority pathogens nationally. Evaluate the utility of genomics-enabled surveillance and define future priorities.
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Aim 2
Prepare for and respond to emerging infectious disease threats
Develop decision-making frameworks for genomics-informed pandemic response and establish approaches for integrating genomic surveillance into public health preparedness efforts.
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