Journal article
Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling
RJ Rockett, A Arnott, C Lam, R Sadsad, V Timms, KA Gray, JS Eden, S Chang, M Gall, J Draper, EM Sim, NL Bachmann, I Carter, K Basile, R Byun, MV O’Sullivan, SCA Chen, S Maddocks, TC Sorrell, DE Dwyer Show all
Nature Medicine | NATURE PORTFOLIO | Published : 2020
Abstract
In January 2020, a novel betacoronavirus (family Coronaviridae), named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of a cluster of pneumonia cases occurring in Wuhan City, Hubei Province, China1,2. The disease arising from SARS-CoV-2 infection, coronavirus disease 2019 (COVID-19), subsequently spread rapidly causing a worldwide pandemic. Here we examine the added value of near real-time genome sequencing of SARS-CoV-2 in a subpopulation of infected patients during the first 10 weeks of COVID-19 containment in Australia and compare findings from genomic surveillance with predictions of a computational agent-based model (ABM). Using the..
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Awarded by Australian Research Council
Funding Acknowledgements
Members of the ICPMR SARS-CoV-2 Study Group include L. Donovan, S. Kumar, T. Tran, H. Rahman, D. Ko, T. Sivaruban, E. Martinez, A. Ginn, Q. Wang and K. Pey. Members of the ABM team include N. Harding, C. Zachreson and O. Cliff. We acknowledge the Sydney Informatics Hub and use of the University of Sydney's high-performance computing cluster, Artemis. We thank the NSW Pathology partner laboratories, ACT Pathology, Douglass Hanly Moir, Australian Clinical Laboratories and Laverty Pathology for referring samples for genomic surveillance. Expert advice and epidemiological information provided by the NSW public health surveillance units at the NSW Health Protection are also gratefully acknowledged. The authors are indebted to all researchers and their organizations who have shared SARS-CoV-2 genome data on GISAID. This study was supported by the Prevention Research Support Program funded by the NSW Ministry of Health and the National Health and Medical Research Council Centre for Research Excellence in Emerging Infectious Diseases (no. GNT1102962). V.S. and M.P. are supported by an Australian Research Council grant (no. DP200103005). The funders of this study had no role in study design, data collection, data analysis and interpretation, or writing of the article.