Tracking the COVID-19 pandemic in Australia using genomics

Torsten Seemann; Courtney R Lane; Norelle L Sherry; Sebastian Duchene; Anders Goncalves da Silva; Leon Caly; Michelle Sait; Susan A Ballard; Kristy Horan; Mark B Schultz; Tuyet Hoang; Marion Easton; Sally Dougall; Timothy P Stinear; Julian Druce; Mike Catton; Brett Sutton; Annaliese van Diemen; Charles Alpren; Deborah A Williamson; Benjamin P Howden

Journal article

Tracking the COVID-19 pandemic in Australia using genomics

Torsten Seemann, Courtney R Lane, Norelle L Sherry, Sebastian Duchene, Anders Goncalves da Silva, Leon Caly, Michelle Sait, Susan A Ballard, Kristy Horan, Mark B Schultz, Tuyet Hoang, Marion Easton, Sally Dougall, Timothy P Stinear, Julian Druce, Mike Catton, Brett Sutton, Annaliese van Diemen, Charles Alpren, Deborah A Williamson Show all

NATURE COMMUNICATIONS | NATURE RESEARCH | Published : 2020

DOI: 10.1038/s41467-020-18314-x

Download PDF

Abstract

Genomic sequencing has significant potential to inform public health management for SARS-CoV-2. Here we report high-throughput genomics for SARS-CoV-2, sequencing 80% of cases in Victoria, Australia (population 6.24 million) between 6 January and 14 April 2020 (total 1,333 COVID-19 cases). We integrate epidemiological, genomic and phylodynamic data to identify clusters and impact of interventions. The global diversity of SARS-CoV-2 is represented, consistent with multiple importations. Seventy-six distinct genomic clusters were identified, including large clusters associated with social venues, healthcare and cruise ships. Sequencing sequential samples from 98 patients reveals minimal intra-..

View full abstract

University of Melbourne Researchers

Torsten Seemann Author Microbiology and Immunology

Sebastian Duchene Garzon Author Microbiology and Immunology

Ben Howden Author Microbiology and Immunology

Norelle Sherry Author Microbiology and Immunology

Anders Goncalves Da Silva Author Microbiology and Immunology

Related Projects (4)

GENOMIC APPROACHES IN HUMAN HEALTH MICROBIOLOGY

This project uses latest genomic technologies to advance our understanding of how bacteria cause disease and finding new antibiotics/approac..

IMPROVING PREVENTION, TRACKING AND TREATMENT OF MAJOR HUMAN BACTERIAL PATHOGENS

This research fellowship will lead to a detailed understanding of the mechanisms by which bacteria become resistant to antibiotics and cause..

AN EVIDENCE BASED FRAMEWORK FOR ESTABLISHING PUBLIC HEALTH MICROBIAL GENOMICS IN AUSTRALIA

Microbial genomics is a powerful laboratory tool to characterise human pathogens at the highest level, allowing greater understanding of the..

APPLYING PATHOGEN GENOMICS TO THE PREVENTION AND CONTROL OF ANTIMICROBIAL RESISTANCE

Grants

Awarded by National Health and Medical Research Council, Australia (NHMRC)

Funding Acknowledgements

We thank the public health, clinical, and microbiology staff across Victoria who have been involved in the testing, clinical care, and public health responses to COVID-19. The data collected through public health officers and microbiology laboratories are critical for public health genomics investigations. We also thank Nick Loman, Jonathon Jacobs, Duncan Maccannell, and Karthik Gangavarapu for bioinformatics advice, and Josh Quick, George Taiaroa, and Sara Zufan for assistance with obtaining ARTIC primers early in the pandemic. The authors gratefully acknowledge the contributions from other laboratories to GISAID (Supplementary Data 3). The Victorian Infectious Diseases Reference Laboratory (VIDRL) and the Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL) at The Doherty Institute are funded by the Victorian Government. This work was supported by the National Health and Medical Research Council, Australia (NHMRC); Partnership Grant (APP1149991), Practitioner Fellowship to B.P.H. (APP1105905), Investigator Grant to D.A.W. (APP1174555), Research Fellowship to T.P.S (APP1105525).