Revealing COVID-19 Transmission by SARS-CoV-2 Genome Sequencing and Agent Based Modelling
Type
PreprintAuthor/s
Rockett, Rebecca JArnott, Alicia
Lam, Connie
Sadsad, Rosemarie
Timms, Verlaine
Gray, Karen-Ann
Eden, John-Sebastian
Chang, Sheryl
Gall, Mailie
Draper, Jenny
Sim, Eby
Bachmann, Nathan L
Carter, Ian
Basile, Kerri
Byun, Roy
O'Sullivan, Matthew V
Chen, Sharon C-A
Maddocks, Susan
Sorrell, Tania C
Dwyer, Dominic E
Holmes, Edward C.
Kok, Jen
Prokopenko, Mikhail
Sintchenko, Vitali
Abstract
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 ...
See moreCommunity 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 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.
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See moreCommunity 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 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.
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Date
2020Funding information
New South Wales Ministry of Health, NHMRC Centre for Research Excellence in Emerging Infectious Diseases (GNT1102962) and Australian Research Council grant DP200103005
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