Tracking the COVID-19 pandemic in Australia using genomics

T Seemann; CR Lane; NL Sherry; S Duchene; A Gonçalves da Silva; L Caly; M Sait; SA Ballard; K Horan; MB Schultz; T Hoang; M Easton; S Dougall; TP Stinear; J Druce; M Catton; B Sutton; A van Diemen; C Alpren; DA Williamson; BP Howden

Journal article

Tracking the COVID-19 pandemic in Australia using genomics

T Seemann, CR Lane, NL Sherry, S Duchene, A Gonçalves da Silva, L Caly, M Sait, SA Ballard, K Horan, MB Schultz, T Hoang, M Easton, S Dougall, TP Stinear, J Druce, M Catton, B Sutton, A van Diemen, C Alpren, DA Williamson Show all

Nature Communications | NATURE PORTFOLIO | Published : 2020

DOI: 10.1038/s41467-020-18314-x

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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-..

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University of Melbourne Researchers

Torsten Seemann Author

Courtney R Lane Author

Norelle Sherry Author

Sebastian Duchene Garzon Author

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Grants

Awarded by National Health and Medical Research Council

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).