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Tracking the COVID-19 pandemic in Australia using genomics

Author

Listed:
  • Torsten Seemann

    (The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
    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
    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
    The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
    Victorian Infectious Diseases Reference Laboratory 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
    The University of Melbourne at The Peter Doherty Institute for Infection and Immunity
    The University of Melbourne at The Peter Doherty Institute for Infection and Immunity)

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.

Suggested Citation

  • 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 & M, 2020. "Tracking the COVID-19 pandemic in Australia using genomics," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-18314-x
    DOI: 10.1038/s41467-020-18314-x
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    Cited by:

    1. Hafiz Suliman Munawar & Sara Imran Khan & Fahim Ullah & Abbas Z. Kouzani & M. A. Parvez Mahmud, 2021. "Effects of COVID-19 on the Australian Economy: Insights into the Mobility and Unemployment Rates in Education and Tourism Sectors," Sustainability, MDPI, vol. 13(20), pages 1-17, October.
    2. Tuyet Hoang & Anders Gonçalves Silva & Amy V. Jennison & Deborah A. Williamson & Benjamin P. Howden & Torsten Seemann, 2022. "AusTrakka: Fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic," Nature Communications, Nature, vol. 13(1), pages 1-4, December.
    3. Jessica E. Stockdale & Kurnia Susvitasari & Paul Tupper & Benjamin Sobkowiak & Nicola Mulberry & Anders Gonçalves da Silva & Anne E. Watt & Norelle L. Sherry & Corinna Minko & Benjamin P. Howden & Cou, 2023. "Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Dinesh Aggarwal & Ben Warne & Aminu S. Jahun & William L. Hamilton & Thomas Fieldman & Louis Plessis & Verity Hill & Beth Blane & Emmeline Watkins & Elizabeth Wright & Grant Hall & Catherine Ludden & , 2022. "Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    5. Dinesh Aggarwal & Andrew J. Page & Ulf Schaefer & George M. Savva & Richard Myers & Erik Volz & Nicholas Ellaby & Steven Platt & Natalie Groves & Eileen Gallagher & Niamh M. Tumelty & Thanh Viet & Gar, 2022. "Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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