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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.”

The MDU PHL team were well placed at the beginning of the COVID-19 pandemic to sequence all the positive samples that were coming in, as well as sharing the data in real-time with colleagues across Australia and the world.

“Effectively combining epidemiological and genomic data to inform policy is the holy grail of public health pathogen genomics,” said University of Melbourne Professor Benjamin Howden Director of the MDU PHL and a senior author on the paper.

“Through established relationships with the Victorian Department of Health we were able to form a comprehensive team of bioinformaticians, genomic epidemiologists, lab technicians and collaborate with the Department from the start and throughout this pandemic. Our team was able to hit the ground running.”

Ms Lane said the rapid sharing of data helps with the identification of interstate spread from Victoria, and conversely other states and territories can be prepared if they have a case appear in their jurisdiction.

“Our interstate colleagues can see our data within one hour of it coming off the sequencing instrument, and as we have shown, real time data is so important during a pandemic,” she said.

AusTrakka, developed by University of Melbourne’s Associate Professor Torsten Seemann, Lead Bioinformatician and University of Melbourne’s Dr Anders Gonçalves da Silva, Senior Bioinformatician, both of MDU PHL, is the pathogen genomics surveillance system used by the team to rapidly share genomic sequencing data. The platform facilitates nationally integrated genomics epidemiology in Australia and is underpinned by the Communicable Diseases Genomics Network (CDGN).

*Not all cases can be sequenced as viral load could be too low (either at the start or end of the virus) and some asymptomatic and symptomatic cases may never get tested.