Dataset Information

Tracking the COVID-19 pandemic in Australia using genomics.

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 (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.

SUBMITTER: Seemann T

PROVIDER: S-EPMC7462846 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Tracking the COVID-19 pandemic in Australia using genomics.

Seemann Torsten T Lane Courtney R CR Sherry Norelle L NL Duchene Sebastian S Gonçalves da Silva Anders A Caly Leon L Sait Michelle M Ballard Susan A SA Horan Kristy K Schultz Mark B MB Hoang Tuyet T Easton Marion M Dougall Sally S Stinear Timothy P TP Druce Julian J Catton Mike M Sutton Brett B van Diemen Annaliese A Alpren Charles C Williamson Deborah A DA Howden Benjamin P BP

Nature communications 20200901 1

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-s ...[more]

PMID: 32873808

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Project description:Since the start of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; COVID-19) pandemic in December 2019, there have been global surges of single-use plastic use. Due to the importance of personal protective equipment (PPE) and sanitation items in protecting against virus transmission and from testing, facemasks, respirators, disposable gloves and disposable wet wipes have become global staples in households and institutions. Widespread use and insufficient infrastructure, combined with improper waste management have resulted in an emerging category of litter. With widespread presence in the environment, such items pose a direct threat to wildlife as animals can interact with them in a series of ways. We examined the scope of COVID-19 pandemic-related debris, including PPE and sanitation items, on wildlife from April 2020 to December 2021. We document the geographic occurrence of incidents, debris types, and consequences of incidents that were obtained from social media searches, unpublished reports from colleagues, and reports available from the citizen science database "Birds and Debris". There were 114 unique sightings of wildlife interactions with pandemic-related debris (38 from 2020 and 76 from 2021). Within the context of this dataset, most incidents involved birds (83.3 %), while fewer affected mammals (10.5 %), invertebrates (3.5 %), fish (1.8 %), and sea turtles (0.9 %). Sightings originated in 23 countries, and consisted mostly of entanglements (42.1 %) and nest incorporations (40.4 %). We verified sightings by contacting the original observers and were able to identify replicated sightings and increase the resolution of the data collected compared with previously published results. Due to the complexities associated with global use and accessibility of digital platforms, we likely underestimate the number of animals harmed by debris. Overall, the global scope of this study demonstrates that online and social media platforms are a valuable way to collect biologically relevant citizen science data and track rapidly emerging environmental challenges.

Dataset Information

Tracking the COVID-19 pandemic in Australia using genomics.

Publications

Tracking the COVID-19 pandemic in Australia using genomics.

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