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How genomic sequencing gives authorities a ‘high resolution’ understanding of COVID-19 outbreaks

“That just means that in terms of community outbreak in NSW, that hasn’t come from within NSW,” he said. “It just means that we understand the nature of the problem there and that’s helping them get on top of that very quickly.”


Virologist Dr Megan Steain reiterated the PM’s sentiment.

“The fact they can trace it from one particular source, gives us more confidence that what is not happening is cryptic transmission throughout the community,” she said.

“The fact we know it’s got one source is reassuring and hopefully means we can contain the outbreak.”

Professor Vitali Sintchenko, director of the Centre for Infectious Diseases and Microbiology-Public Health at the University of Sydney and a microbiologist with NSW Health Pathology, said whole genome mapping provides the fingerprints of each virus sample, which can be compared with other samples to provide a deeper understanding of the spread of the disease.

“With genomics, you have this high-resolution capability to understand transmission pathways,” he said.

“Epidemiologists generate hypotheses about contacts by talking to people, microbiologists or scientists can generate this hypothesis without talking to people but by comparing genomes.”

Professor Sintchenko said this has been particularly helpful in cases where epidemiologists had not been able to link cases due sometimes to people forgetting to mention things that may help trace the source.

“Public health officials want to see high-level scientific evidence that cases are linked, not that people said they were at the same pub.”

But whole genome sequencing is not without shortcomings – it works best when a patient has a high viral load, and quality of the sample is also high, both these factors can affect the University of Sydney and NSW Health Pathology’s ability to map the virus.

“In clinical samples for people with minimal disease, the viral yield is very, very low,” Professor Sintchenko said. “And it’s very challenging to extract that full genome from those samples.”

The grant is focused on this challenge and because of it Professor Sintchenko’s team has begun a project to improve the sensitivity in genome mapping, with the aim to further strenghen outbreak tracing in NSW.

“We are hopeful that we will have a significantly higher proportion of samples being genome sequenced, and less gaps in the understanding of transmission pathways,” he said.

The project is one of six projects worth $2.3 million that have been granted funding under the first round of the NSW government’s COVID-19 Research Grants program.

NSW Chief Health Officer Dr Kerry Chant said local research was important as the pandemic continued.


“The world’s population has no pre-existing immunity to COVID-19 and whilst there are significant global collaborative efforts under way to develop an effective vaccine, this could still be some time away,” Dr Chant said.

Dr Rebecca Rockett, virologist at the University of Sydney’s Marie Bashir Institute for Infectious Diseases and Biosecurity at Westmead Hospital, said the genome sequencing will remain a critical part of the transmission solving toolkit.

“Genome sequencing is the key to unlocking the puzzle of local transmission, and it’s critical that we continue to invest in this research to advance our ability to contain the virus in the long-term not just to trace locally acquired cases, but also to identify new cases once border restrictions are lifted and travel resumes,” she said.

With Kate Aubusson

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