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Publication: Genome Medicine
Funding: This work was supported by a National Health and Medical Research Council (NHMRC), Australia Partnership Grant.

The Pathogen Genomics in Public HeAlth Surveillance Evaluation (PG-PHASE) Framework published in Genome Medicine today, uses an adaptable, whole-of-system approach towards understanding the utility of pathogen genomics and whole-genome sequencing (WGS) in disease control and measuring the impact on public health processes and outcomes.

Pathogen WGS is being integrated into public health surveillance and disease control systems worldwide as a tool for infectious disease surveillance, outbreak investigation, and infection prevention and control. While the take up of WGS is on the rise, there is limited data available outlining the optimal model for using pathogen genomics in epidemiological investigations or how to effectively measure the impact on public health.

Developed by a team from the Doherty Institute and the Melbourne School of Population and Global Health, led by University of Melbourne Dr Angeline Ferdinand, Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL) Research Fellow at the Doherty Institute, the PG-PHASE Framework design was informed by findings from extensive literature reviews and in-depth key stakeholder interviews.

The framework consists of a three-phased approach that aims to assist public health laboratories, health departments and authorities to understand their current capacity in utilising WGS to detect and respond to infectious disease outbreaks, as well as the associated costs, challenges and facilitators required.

“PG-PHASE was designed to give assessors a holistic view of how genomic data is utilised in public health practice across all stages, from the decision to send an isolate or sample for sequencing, to the use of sequence data in public health surveillance, investigation and decision-making,” Dr Ferdinand said.

“We divided the framework into three phases which can be used separately or in conjunction with one another, fully adaptable to the unique need of the assessor in understanding WGS laboratory processes, analysis, reporting and data sharing.”

Applicability of the PG-PHASE Framework was demonstrated in a real-life case scenario, having been applied to the initial public health implementation of SARS-CoV-2 sequencing in Victoria, completed by the MDU PHL at the Doherty Institute.

Findings that arose during the assessment are being implemented to provide guidance on appropriate investment for future pandemic preparedness planning, particularly for emerging pathogens.

“Ultimately, it is our hope and expectation that utilisation of the PG-PHASE framework will support more effective and efficient integration of pathogen WGS in public health, leading to improved resource allocation, strengthened and more responsive surveillance systems and improved public health outcomes,” Dr Ferdinand said.

The PG-PHASE Framework is publicly available for use. Users are encouraged to contact lead author Dr Angeline Ferdinand, for collaborative support and guidance. Dr Ferdinand has had a wide-ranging academic career that has focused on applied research that addresses complex problems of health equity, social determinants of health and the implications of new technologies in public health practice.