Tracking the COVID-19 pandemic in Australia using genomics

Nat Commun. 2020 Sep 1;11(1):4376. doi: 10.1038/s41467-020-18314-x.


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.

Publication types

  • Observational Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Australia / epidemiology
  • Betacoronavirus / genetics*
  • Betacoronavirus / isolation & purification
  • COVID-19
  • Coronavirus Infections / epidemiology*
  • Coronavirus Infections / transmission
  • Coronavirus Infections / virology*
  • Female
  • Genome, Viral
  • Genomics / methods
  • Health Personnel
  • Humans
  • Male
  • Middle Aged
  • Molecular Epidemiology
  • Pandemics
  • Phylogeny
  • Pneumonia, Viral / epidemiology*
  • Pneumonia, Viral / transmission
  • Pneumonia, Viral / virology*
  • Public Health
  • Retrospective Studies
  • SARS-CoV-2
  • Travel