Setting and data sources

In this observational, genomic epidemiological study, we did genomic sequencing of all laboratory-confirmed cases of COVID-19 in Victoria, Australia between Jan 25, 2020, and Jan 31, 2021. The state of Victoria, which has a population of approximately 6·24 million people, has a consistently high testing rate for SARS-CoV-2.¹¹ All samples testing positive for SARS-CoV-2 by RT-PCR are forwarded to the Doherty Institute Public Health Laboratories (Melbourne, VIC, Australia)¹² for real-time, prospective, genomic surveillance of COVID-19, with sequencing usually completed within 7 days. For urgent cases, rapid sequencing and analysis is completed within 24 h. Epidemiological data, including detailed information on demographics, risk factors, and exposure were collected for each case through an interview done by the Victoria Department of Health. Mode of acquisition was categorised as: travel overseas if the individual reported travel in the 14 days before symptom onset; contact with a confirmed case if no overseas travel was reported and case contact had occurred within the same period; or source unknown. A COVID-19 genomics response team was established to integrate and review genomic epidemiological data, as previously described.² Data were collected in accordance with the Victorian Public Health and Wellbeing Act 2008. Ethical approval was received from the University of Melbourne Human Research Ethics Committee (study number 1954615.3).

Since June, 2020, rapid sharing of SARS-CoV-2 genomic sequence data between Australian states has occurred via AusTrakka, a national sequence sharing programme governed by the Communicable Diseases Genomics Network. All publicly available SARS-CoV-2 sequences available in AusTrakka on Feb 11, 2021, were included, and epidemiological data were obtained from the submitting laboratories.