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 ( R e ) 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.
【저자키워드】 SARS-CoV-2, viral infection, Epidemiology, Viral genetics, 【초록키워드】 public health, Sequencing, Transmission, SARS-CoV-2 transmission, management, healthcare, Patient, Travel, Effectiveness, Cluster, physical distancing, epidemiological, phylodynamic, pathogen transmission, genomic, COVID-19 cases, Support, Victoria, Public health responses, sequence, effective, identify, can be used, indicate, reducing, reveal, reduction in, reproductive, increasingly, 【제목키워드】 COVID-19 pandemic,