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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. Genome sequencing can be used to infer pathogen transmission dynamics and inform public health responses. Here, the authors sequence >1,200 SARS-CoV-2 samples from Victoria, Australia and find genomic support for the effectiveness of social restrictions in reducing transmission. [ABSTRACT FROM AUTHOR]

Keywords: Infectious diseases; Infection control; Drug resistance, microbial; Public health; Sequence analysis EN Infectious diseases Infection control Drug resistance, microbial Public health Sequence analysis 510 510 1 06/16/20 20200615 NES 200615 Clinical record A 70-year-old man with multiple myeloma was admitted to our hospital in 2018, having been hospitalised 10 months previously in the United Kingdom. Neither patient developed clinical features of urinary tract or disseminated I C. auris i infection and antifungal therapy was not administered. In high risk settings, and where a case of I C. auris i infection has been identified, timely screening of patients is required to ensure that appropriate control measures are instituted. [Extracted from the article]