TY - JOUR
T1 - Tracking the COVID-19 pandemic in Australia using genomics
AU - Seemann, Torsten
AU - Lane, Courtney R.
AU - Sherry, Norelle L.
AU - Duchene, Sebastian
AU - Gonçalves da Silva, Anders
AU - Caly, Leon
AU - Sait, Michelle
AU - Ballard, Susan A.
AU - Horan, Kristy
AU - Schultz, Mark B.
AU - Hoang, Tuyet
AU - Easton, Marion
AU - Dougall, Sally
AU - Stinear, Timothy P.
AU - Druce, Julian
AU - Catton, Mike
AU - Sutton, Brett
AU - van Diemen, Annaliese
AU - Alpren, Charles
AU - Williamson, Deborah A.
AU - Howden, Benjamin P.
N1 - Publisher Copyright:
© 2020, The Author(s).
PY - 2020/12/1
Y1 - 2020/12/1
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/85090052879
U2 - 10.1038/s41467-020-18314-x
DO - 10.1038/s41467-020-18314-x
M3 - Article
C2 - 32873808
AN - SCOPUS:85090052879
SN - 2041-1723
VL - 11
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 4376
ER -
