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

Rockett, R. J.; Arnott, A.; Lam, C.; Sadsad, R.; Timms, V.; Gray, K.-A.; Eden, J.-S.; Chang, S. L.; Gall, M.; Draper, J.; Sim, E.; Bachmann, N. L.; Carter, I.; Basile, K.; Byun, R.; O Sullivan, M. V.; Chen, S. C.-A.; Maddocks, S.; Sorrell, T. C.; Dwyer, D. E.; Holmes, E. C.; Kok, J.; Prokopenko, M.; Sintchenko, V.

doi:10.1101/2020.04.19.048751

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bioRxiv · 10.1101/2020.04.19.048751

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

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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 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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Rockett, R. J., Arnott, A., Lam, C., Sadsad, R., Timms, V., Gray, K.-A., Eden, J.-S., Chang, S. L., Gall, M., Draper, J., Sim, E., Bachmann, N. L., Carter, I., Basile, K., Byun, R., O Sullivan, M. V., Chen, S. C.-A., Maddocks, S., Sorrell, T. C., Dwyer, D. E., Holmes, E. C., Kok, J., Prokopenko, M., Sintchenko, V.. 2020-04-22. REVEALING COVID-19 TRANSMISSION BY SARS-CoV-2 GENOME SEQUENCING AND AGENT BASED MODELLING. https://doi.org/10.1101/2020.04.19.048751

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