Tracking the COVID-19 pandemic in Australia using genomics
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
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.
Article activity feed
-
-
SciScore for 10.1101/2020.05.12.20099929: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethical approval was received from the University of Melbourne Human Research Ethics Committee (study number 1954615.3). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources For phylogenetic analysis, a single sequence was selected per patient, and genomic clusters defined as two or more related sequences using Cluster Picker14; additionally, recently proposed lineages were also determined. Clustersuggested: (Cluster, RRID:SCR_013505)17 Data sharing and availability: Consensus sequences and Illumina sequencing reads were deposited into … SciScore for 10.1101/2020.05.12.20099929: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethical approval was received from the University of Melbourne Human Research Ethics Committee (study number 1954615.3). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources For phylogenetic analysis, a single sequence was selected per patient, and genomic clusters defined as two or more related sequences using Cluster Picker14; additionally, recently proposed lineages were also determined. Clustersuggested: (Cluster, RRID:SCR_013505)17 Data sharing and availability: Consensus sequences and Illumina sequencing reads were deposited into GenBank under BioProject PRJNA613958 (Supplementary Data). BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
-
