Media release

From: Doherty Institute for Infection and Immunity

Genomics-informed public health action leads to control of COVID-19

Funding: Victorian Government, National Health and Medical Research Council and Medical Research Future Fund
A world-leading genomic sequencing and public health effort located the source of Victoria’s second COVID-19
wave and demonstrated the successful control of the virus in Australia for a second time.

Described today in The Lancet Public Health, the team from the University of Melbourne’s Microbiological
Diagnostic Unit Public Health Laboratory (MDU PHL) at the Peter Doherty Institute for Infection and Immunity
(Doherty Institute) in collaboration with the Victorian Department of Health revealed, through combined
epidemiological and genomic data, that 98 per cent of locally acquired cases during Victoria’s second wave (June
to October 2020) came from a single incursion in hotel quarantine.

A genomic sequence is a list of what’s in our DNA and RNA – like a barcode – and genomic sequencing is how
scientists generate that barcode. By combining epidemiological investigation and genomic sequencing, scientists
and public health professionals can see how pathogens, like viruses, are changing and spreading over time,
providing valuable insights to public health decision makers.

In Victoria, all positive samples for SARS-CoV-2 are forwarded to MDU PHL at the Doherty Institute for
sequencing and analysis. It’s usually completed in five to seven days but can be completed within one day for
urgent cases.

From 25 January 2020 to 31 January 2021, 20,451 cases of laboratory-confirmed COVID-19 were diagnosed in
Victoria, 75 per cent of these were sent to MDU PHL for sequencing, of which 76 per cent met the criteria* and
were included for analysis.

“Our genomic ‘enhanced outbreak detection’ system revealed a rapid escalation of an outbreak originating from
a single breach of hotel quarantine. The outbreak strain spread very rapidly within Victoria and was quickly seen
in other Australian states and territories," said first author of the paper, the University of Melbourne’s Courtney
Lane, MDU PHL Epidemiology Section Lead.

"This led to a major overhaul of Victoria’s hotel quarantine system and immediate public health response,
including a lockdown. Our data also showed that prior to the second wave, Victoria successfully eliminated all
earlier circulating strains, providing confidence in the effectiveness of these decisive public health actions.
“Further sequencing over time showed that once the second wave was over in October, the circulating strain
responsible had again disappeared.”