Genomic sleuths track the true origins of COVID-19 infections
Jun 25, 2020 – 6.58pm
Victoria is using world-leading genomic fingerprinting techniques to track infections and better identify cluster sources and super spreaders.
Researchers from Melbourne University's Doherty Institute have mapped the DNA of around 80 per cent of all of Victoria's COVID-19 infections since late January, using a technique known as genomic sequencing.
Doherty Institute researchers have mapped the DNA of three quarters of Victoria's COVID-19 infections. AAP
The COVID-19 virus mutates regularly, enabling Doherty researchers to work with the Victorian Department of Health and Human Services to track the source and transmission chains and to stamp them out.
Each mutation is unique and enables researchers to forensically track individual clusters and the true source of the infection.
Dr Norelle Sherry, a medical microbiologist at Doherty, said the sequencing data enabled clusters to be identified and to focus the public health interventions.
"By using the virus fingerprint we can create a map that links all the cases so we can identify where people have got the virus from," Dr Shelly said.
She said this meant health officials could with confidence focus on contacts from particular clusters and not waste time and resources chasing contacts in other clusters.
Dr Sherry said by comparing that information to a large global database researchers have been able to map where the viruses came from.
This will be increasingly important as internal and international borders are opened, enabling researchers to say whether new cases are appearing from travellers or whether they appear to be some lingering transmission in the community.
The technique was used in the initial outbreak and showed that despite a surprisingly high number of genomic clusters (76), most were "dead-end clusters", that didn't continue to spread. It also showed that the social distancing measures that were put in place were highly effective.
The results of that work have been published as a pre-print academic paper that has now been peer reviewed and expected to be published soon.
The Doherty Institute is working closely with local health officials to apply the same techniques to the current surge in cases. Victoria yesterday recorded its highest daily increase since April 7, prompting a massive increase in testing.
Dr Sherry said that by combining the genomic data with the epidemiological data, public health officials had a rich pool of insights to design their interventions.
By combining testing, genomic sequencing, aggressive contact tracing and reinforced social distancing, authorities are hoping to drive infection rates back to below levels where it is no longer reproducing at a rate to survive.
Bio-info mathematicians modelling the genomic data have also been looking at the genomic signatures of the virus to find undetected viruses, or whether most of the cases seem to be captured in the data.
The Victorian genomic sequencing is understood to be the most comprehensive sequencing coverage in the world for an infectious-disease outbreak. By comparison, 3 per cent of ebola infections were mapped.
The technique is also being used in New Zealand and other Australian states. Health agencies are following the Victorian work closely, with a view to building up enough genomic sequencing data of known infections, so they can use the same approach.
Political and health leaders have been emphasising that Australia's strategy of suppression, rather than eradication, means there will be increases in cases as the economy is reopened.
Doherty was the first research institute to clone the COVID-19 virus, after receiving an early version of the virus from Chinese researchers in Wuhan. Researchers took the decision then to try and sequence as many active infection samples as possible.
The Doherty genomic program has been under development for five years and is part of a global effort to track the many versions of the virus, which is being fed into a global site, called Nextstrain.
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Sign up now Tom Burton has held senior editorial and publishing roles with The Mandarin, The Sydney Morning Herald and as Canberra bureau chief for The Australian Financial Review. He has worked in government, specialising in the communications sector. He has won three Walkley awards. Connect with Tom on Twitter. Email Tom at tom.burton@afr.comIntroducing your Newsfeed Beta
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