Overview

In 2020, AusTrakka was rapidly developed in response to key reports to the Office of Health Protection and Response on the need to better facilitate public health genomics data sharing and analysis in Australia and New Zealand. AusTrakka serves as Australia’s national genomics surveillance platform for SARS-CoV-2 and as a coordinator of genomics outbreak investigations across jurisdictions.

National Genomics Data Sharing

All state and territory public health laboratories upload genomic sequences and agreed epidemiological metadata to AusTrakka on a dedicated server for nationally aggregated genomics analysis and visualisation of sequences.

• Access Control: Managed at a user level, overseen by the Communicable Diseases Genomics Network (CDGN) and the Public Health Laboratory Network (PHLN).

• Data Security: Ensures secure data sharing while maintaining custodianship with the submitting laboratory.

Public Health Surveillance & Bioinformatics

For public health surveillance, AusTrakka supports:

• Bioinformatic analysis

• Genomic epidemiology

• Reporting of genomic findings within and between jurisdictions

Platform Functions & Architecture

The AusTrakka platform accepts sequence and epidemiological data from public health laboratories and performs several functions.

Outlined below is:

1. The platform architecture and functions

2. Team functions

3. Outputs of the AusTrakka system

Operational Governance

The AusTrakka Governance is operated by the CDGN and is maintained by the AusTrakka Development Team at the University of Melbourne. An agreement on data governance for AusTrakka, which covers the sharing of pathogen sequences/isolates and minimal metadata with pre-defined recipients, has been established between key partners within the Office of Health Protection and the CDGN public health laboratory members, who will be the main contributors of genomic sequencing data.

The overarching governance of AusTrakka is accessible here. This framework describes the AusTrakka governance for all bacterial and viral pathogens, with steering groups established for specific pathogens as required.

AusTrakka's governance framework ensures proper oversight and management of genomic data sharing across Australian jurisdictions while maintaining data security and appropriate access controls.

Currently, the AusTrakka Advisory Group comprises of representatives from leading genomics public health laboratories in NSW, QLD, SA, VIC and WA, who are responsible for overseeing the AusTrakka National Analysis Team (ANAT), structure and workforce as well as the facilitation of analysis requests and reporting of AusTrakka outputs.

Governance Framework for national genomics surveillance in AusTrakka

The Framework for SARS-CoV-2 data sharing and analysis using AusTrakka was rapidly developed early in the COVID-19 pandemic to provide a mechanism for rapid data sharing and genomic analysis under various operational situations within and between jurisdictions and nationally.

This Framework formalised the endorsement from public health laboratories and public health units represented on key Australian Government committees to rapidly share all SARS-CoV-2 genomics data with the AusTrakka platform through their nominated public health laboratory for national real-time surveillance. It also describes supporting mechanisms to request genomic data and analysis between jurisdictional public health laboratories in Australia and New Zealand.

This Framework was endorsed by the AHPPC on Thursday, 1 October 2020.

The Governance Framework for National Genomic Surveillance in AusTrakka is currently under review and endorsement by the CDNA, PHLN, and AHPPC. This framework applies the same principles in data custodianship and describes the mechanisms for data sharing for national surveillance and outbreak investigation of pathogens identified as priorities by national committees.

AusTrakka Governance Groups

AusTrakka Advisory Group

• Prof Vitali Sintchenko, ICPMR (NSW)

• A/Prof Amy Jennison, QH PEHRL (QLD)

• Dr Lex Leong, SA Pathology (SA)

• Prof Benjamin Howden, MDU PHL (VIC)

• A/Prof Torsten Seemann, AusTrakka and MDU PHL (VIC)

• Prof David Speers, PathWest (WA)

• Ms Amy Black, Australian Government (Cth)

• Dr Michel Watson, Australian Government (Cth)

• Ms Tuyet Hoang, AusTrakka

• Dr Ceyhun Güngör, AusTrakka

AusTrakka National Analysis Team (ANAT)

• Dr Shona Chandra, Genomic Epidemiologist, AusTrakka (NSW)

• Dr Krystalyn Martin, Genomic Epidemiologist, AusTrakka (QLD)

• Ms Mathilda Wilmot, Genomic Epidemiologist, AusTrakka (VIC)

• Dr Alicia Arnott, Genomic Epidemiologist, AusTrakka (VIC)

• A/Prof Torsten Seemann, Lead Bioinformatician, AusTrakka (VIC)

• Ms Linh Nguyen, Bioinformatician, AusTrakka (QLD)

• Dr Erin Flynn, Bioinformatician, AusTrakka (SA)

• Dr Caitlin Selway, Bioinformatician, AusTrakka (SA)

• Dr Kristy Horan, Bioinformatician, AusTrakka (VIC)

• Dr Daniel Knight, Bioinformatician, AusTrakka (WA)

• Dr Ceyhun Güngör, Program Manager, AusTrakka

AusTrakka Development Team

• A/Prof Torsten Seeman, Lead Bioinformatician

• Dr Clare Sloggett, Lead DevOps

• Sam Carswell, DevOps

• Vi Phu, Software Engineer

• Mann Sheth, Software Engineer