Microbiology & Immunology - Research Publications

Permanent URI for this collection

http://hdl.handle.net/11343/226

Filters

2020 1
Reset filters

Settings
Statistics
Citations
Author: Batt, Susan × Author: Williamson, Deborah × Start date: 2020 × Type: Preprint ×

Search Results

Now showing 1 - 1 of 1
  • Item
    Thumbnail Image
    Tracking the COVID-19 pandemic in Australia using genomics
    Seemann, T ; Lane, C ; Sherry, N ; Duchene, S ; Goncalves da Silva, A ; Caly, L ; Sait, M ; Ballard, S ; Horan, K ; Schultz, M ; Hoang, T ; Easton, M ; Dougall, S ; Stinear, T ; Druce, J ; Catton, M ; Sutton, B ; van Diemen, A ; Alpren, C ; Williamson, D ; Howden, B ( 2020)
    BACKGROUND: Whole-genome sequencing of pathogens can improve resolution of outbreak clusters and define possible transmission networks. We applied high-throughput genome sequencing of SARS-CoV-2 to 75% of cases in the State of Victoria (population 6.24 million) in Australia. METHODS: Cases of SARS-CoV-2 infection were detected through active case finding and contact tracing. A dedicated SARS-CoV-2 multidisciplinary genomic response team was formed to enable rapid integration of epidemiological and genomic data. Phylodynamic analysis was performed to assess the putative impact of social restrictions. RESULTS: Between 25 January and 14 April 2020, 1,333 COVID-19 cases were reported in Victoria, with a peak in late March. After applying internal quality control parameters, 903 samples were included in genomic analyses. Sequenced samples from Australia were representative of the global diversity of SARS-CoV-2, consistent with epidemiological findings of multiple importations and limited onward transmission. In total, 76 distinct genomic clusters were identified; these included large clusters associated with social venues, healthcare facilities and cruise ships. Sequencing of sequential samples from 98 patients revealed minimal intra-patient SARS-CoV-2 genomic diversity. Phylodynamic modelling indicated a significant reduction in the effective viral reproductive number (Re) from 1.63 to 0.48 after the implementation of travel restrictions and population-level physical distancing. CONCLUSIONS: Our data provide a comprehensive framework for the use of SARS-CoV-2 genomics in public health responses. The application of genomics to rapidly identify SARS-CoV-2 transmission chains will become critically important as social restrictions ease globally. Public health responses to emergent cases must be swift, highly focused and effective.