Tracking the COVID-19 pandemic in Australia using genomics.
Adult
Australia
/ epidemiology
Betacoronavirus
/ genetics
COVID-19
Coronavirus Infections
/ epidemiology
Female
Genome, Viral
Genomics
/ methods
Health Personnel
Humans
Male
Middle Aged
Molecular Epidemiology
Pandemics
Phylogeny
Pneumonia, Viral
/ epidemiology
Public Health
Retrospective Studies
SARS-CoV-2
Travel
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
01 09 2020
01 09 2020
Historique:
received:
06
07
2020
accepted:
17
08
2020
entrez:
3
9
2020
pubmed:
3
9
2020
medline:
24
9
2020
Statut:
epublish
Résumé
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
Identifiants
pubmed: 32873808
doi: 10.1038/s41467-020-18314-x
pii: 10.1038/s41467-020-18314-x
pmc: PMC7462846
doi:
Types de publication
Journal Article
Observational Study
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4376Subventions
Organisme : Department of Health | National Health and Medical Research Council (NHMRC)
ID : APP1105525
Pays : International
Organisme : Department of Health | National Health and Medical Research Council (NHMRC)
ID : APP1174555
Pays : International
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