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REVEALING COVID-19 TRANSMISSION BY SARS-CoV-2 GENOME SEQUENCING AND AGENT BASED MODELLING [article]

Rebecca J Rockett, Alicia Arnott, Connie Lam, Rosemarie Sadsad, Verlaine Timms, Karen-Ann Gray, John-Sebastian Eden, Sheryl Le Chang, Mailie Gall, Jenny Draper, Eby Sim, Nathan L Bachmann (+12 others)
2020 bioRxiv   pre-print

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https://web.archive.org/web/20201109003502/https://www.biorxiv.org/content/biorxiv/early/2020/04/24/2020.04.19.048751.full.pdf

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Community transmission of the new coronavirus SARS-CoV-2 is a major public health concern that remains difficult to assess. We present a genomic survey of SARS-CoV-2 from a during the first 10 weeks of COVID-19 activity in New South Wales, Australia. Transmission events were monitored prospectively during the critical period of implementation of national control measures. SARS-CoV-2 genomes were sequenced from 209 patients diagnosed with COVID-19 infection between January and March 2020. Only a
more » ... quarter of cases appeared to be locally acquired and genomic-based estimates of local transmission rates were concordant with predictions from a computational agent-based model. This convergent assessment indicates that genome sequencing provides key information to inform public health action and has improved our understanding of the COVID-19 evolution from outbreak to epidemic.
doi:10.1101/2020.04.19.048751 fatcat:plv3qpty2bdl5dehd4gnb6w4r4
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Rebecca J Rockett, Alicia Arnott, Connie Lam, Rosemarie Sadsad, Verlaine Timms, Karen-Ann Gray, John-Sebastian Eden, Sheryl Le Chang, Mailie Gall, Jenny Draper, Eby Sim, Nathan L Bachmann, Ian Carter, Kerri Basile, Roy Byun, Matthew V O Sullivan, Sharon C-A Chen, Susan Maddocks, Tania C Sorrell, Dominic E Dwyer, Edward C Holmes, Jen Kok, Mikhail Prokopenko, Vitali Sintchenko. "REVEALING COVID-19 TRANSMISSION BY SARS-CoV-2 GENOME SEQUENCING AND AGENT BASED MODELLING." bioRxiv (2020)