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.
Highlights
Genomic sequencing has significant potential to inform public health management for SARSCoV-2
We provide a detailed picture of the emergence and limited onward spread of SARS-CoV-2 in Australia, and demonstrate how genomic data can be used to inform public health action directly
The sheer scale and rapidity of the COVID-19 pandemic have necessitated swift and unprecedented public health responses, and the high proportion of cases with associated sequence data in our study provides unique genomic insights into the effects of public health interventions on the spread of SARSCoV-2
Summary
Genomic sequencing has significant potential to inform public health management for SARSCoV-2. Our data provide a concrete framework for the use of SARS-CoV-2 genomics in public health responses, including its use to rapidly identify SARSCoV-2 transmission chains, increasingly important as social restrictions ease globally. In addition to facilitating the development of diagnostic tests, wholegenome sequencing (WGS) can be used to detect phylogenetic clusters of SARS-CoV-25, with many laboratories making genomic data publicly available[6,7]. Genomic surveillance has been used to detect and respond to putative transmission clusters[8,9] and to provide information on the possible source of individual cases[10]. This report describes the key findings from the first 1333 cases of COVID-19 in our setting and demonstrates the integration of genomics-based COVID-19 surveillance into public health responses
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