AusTrakka – Working towards integrated pathogen genomics for SARS-CoV-2

Clare Sloggett0, Torsten Seemann0, Anders Goncalves Da Silva0
(0) MDU-PHL, The University of Melbourne and The Peter Doherty Institute for Infection and Immunity

Find me on Wed Nov 25th, 1:30-2:50pm AEDT in Remo, table 132

Abstract
The COVID-19 pandemic has highlighted the need for SARS-CoV-2 genomics sequencing and analysis to track transmission and identify emerging clusters and outbreaks. Simultaneously, the need to share genomic data between jurisdictions has become apparent to highlight inter-jurisdictional spread of SARS-CoV-2. Here we describe the development and early implementation of the AusTrakka genomic data sharing platform and describe its utility for nationally integrated SARS-CoV-2 genomics.

The development of the AusTrakka platform by the Communicable Diseases Genomics Network (CDGN) was accelerated to address the urgent need for timely SARS-CoV-2 genomic data sharing between public health laboratories to contribute meaningfully to public health intervention. Over six months, AusTrakka has built in capacity for public health laboratories to upload SARS-CoV-2 consensus genome sequences that are analysed by bioinformatic pipelines and tools integrated into the platform, as well as capability to generate and visualise national phylogenetic trees that identify and notify relevant jurisdictional public health laboratories of genomic ‘matches’ that may infer interstate transmission or emerging clusters for further investigation.

Since its endorsement as the national SARS-CoV-2 genomic data sharing platform, over 13,000 SARS-CoV-2 genomic sequences have been uploaded to the platform from every state and territory, as well as New Zealand and has been used for national reporting against the Australian National Disease Surveillance Plan for COVID-19. The next phase of its development sees the integration of genomic and epidemiological data, required for SARS-CoV-2 to enable optimal high-resolution genomic clustering and determination of putative transmission events. The development of AusTrakka continues to be a highly consultative process, leveraging on Australia’s genomic and bioinformatics expertise to remove the barrier of entry into SARS-CoV-2 genomics for public health laboratories by bridging the gap between raw genomic sequence data, bioinformatic analysis and epidemiology for real-world application of public health pathogen genomics.