Revealing COVID-19 Transmission by SARS-CoV-2 Genome Sequencing and Agent Based Modelling

  1. Rebecca J Rockett
  2. Alicia Arnott
  3. Connie Lam
  4. Rosemarie Sadsad
  5. Verlaine Timms
  6. Karen-Ann Gray
  7. John-Sebastian Eden
  8. Sheryl Chang
  9. Mailie Gall
  10. Jenny Draper
  11. Eby Sim
  12. Nathan L Bachmann
  13. Ian Carter
  14. Kerri Basile
  15. Roy Byun
  16. Matthew V O’Sullivan
  17. Sharon C-A Chen
  18. Susan Maddocks
  19. Tania C. Sorrell
  20. Dominic E Dwyer
  21. Edward C Holmes
  22. Jen Kok
  23. Mikhail Prokopenko
  24. Vitali Sintchenko
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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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