Tracking the COVID-19 pandemic in Australia using genomics

Torsten Seemann, Courtney R. Lane, Norelle L. Sherry, Sebastian Duchene, Anders Gonçalves 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 Diemen, Charles Alpren, Deborah A. Williamson and Benjamin P. Howden ()
Additional contact information
Torsten Seemann: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
Courtney R. Lane: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
Norelle L. Sherry: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
Sebastian Duchene: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
Anders Gonçalves da Silva: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
Leon Caly: Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection and Immunity
Michelle Sait: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
Susan A. Ballard: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
Kristy Horan: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
Mark B. Schultz: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
Tuyet Hoang: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
Marion Easton: Victorian Department of Health and Human Services
Sally Dougall: Victorian Department of Health and Human Services
Timothy P. Stinear: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
Julian Druce: Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection and Immunity
Mike Catton: Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection and Immunity
Brett Sutton: Victorian Department of Health and Human Services
Annaliese Diemen: Victorian Department of Health and Human Services
Charles Alpren: Victorian Department of Health and Human Services
Deborah A. Williamson: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
Benjamin P. Howden: The University of Melbourne at The Peter Doherty Institute for Infection and Immunity

Nature Communications, 2020, vol. 11, issue 1, 1-9

Abstract: 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-patient SARS-CoV-2 genomic diversity. Phylodynamic modelling indicates a significant reduction in the effective viral reproductive number (Re) from 1.63 to 0.48 after implementing travel restrictions and physical distancing. Our data provide a concrete framework for the use of SARS-CoV-2 genomics in public health responses, including its use to rapidly identify SARS-CoV-2 transmission chains, increasingly important as social restrictions ease globally.

Date: 2020
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DOI: 10.1038/s41467-020-18314-x

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