PERTH, Australia – Australian public health laboratories are collaborating to sequence the virus genomes of all positive COVID-19 tests in Australia to track the virus using genomics across the country.

The Communicable Disease Genomics Network (CDGN) and Illumina Inc. will track COVID-19 by using next-generation genomic sequencing technology, enabling real-time data sharing and integration to better understand the transmission and spread of the virus.

The Australian government provided an AU$3.3 million (US$2.4 million) Medical Research Future Fund (MRFF) grant through The University of New South Wales (UNSW) Sydney’s School of Medical Sciences. As part of the research project, Illumina has contributed more than AU$2 million worth of its genomic sequencing systems.

Coordinated by the CDGN, this will be the first national implementation of pathogen surveillance and a critical step forward in Australia’s pandemic response.

“The CDGN is a collaborative network of public health labs around the country, and improving integration and the way we do things will help support the whole country so we can have one of the best sequencing efforts in the world, University of Melbourne Professor Ben Howden, and co-chair of the CDGN, told BioWorld.

“The CDGN has been working to establish a nationally integrated pathogen genomics initiative that will facilitate the rapid implementation of this project, ensuring national access and consistency in genomics analyses. Information on the national transmission of the virus that causes COVID-19 will be important to informing future public health responses in Australia,” said Howden, who is also the director of the Microbiological Diagnostics Unit Public Health Laboratory at the Peter Doherty Institute for Infection and Immunity.

The public health lab at the Doherty Institute has been working on sequencing a number of public health pathogens, and it started working on the SARS-COV-2 pathogen when it arrived in Australia in February.

This collaboration will assist in developing a national, coordinated and integrated effort for bringing in SARS-COV-2 genomics to optimize the approach to getting the genomic sequence data, as well as implementing more consistent approaches to analyzing, interpreting and reporting the data, Howden said.

He acknowledged that funding to date has been state-based, so a national fund helps to integrate those efforts. This system will also help better predict future pandemics, and could lead to new approaches in the future, he said.

Using genomics will also help identify mutations of COVID-19 in the Australian population to inform the design of treatments and vaccines and to precisely identify persistent infection vs. reinfection or inactive infection.

“It can also tell if you have new importation of cases. As the borders hopefully open up within the country, we can use genomics to track the movement between jurisdictions of cases,” he said, noting that genomic data can be used for looking at mutations that emerge over time and if these have an impact on the behavior of the virus and whether vaccines will work and which drugs might be effective.

“We share a lot of our genome data internationally, so there are large databases of COVID genome data from around the world, and the people who are designing diagnostic tests need to understand the genome sequence to target their diagnostics to parts of the genome, and if mutations are arising in some areas, those diagnostic approaches may need to adapt to that.”

Vaccine developers are mostly targeting particular parts of the genome of the virus that encode for the surface proteins, and if mutations are detected within that, it might have an impact on potential targets of the vaccine.

“We have no evidence at this stage that there are changes in the behavior of the virus, but if there were some mutations that changed the way it spreads or the dynamics of spread, we might be able to measure that through the genomic work, and that could be important for control issues.”

Genetic signature of virus a ‘passport stamp’

There are mutations in the virus that can tell where an incursion has come, and these genetic signatures provide a “passport stamp” to map out where these mutations have come from, Howden said.

“Pathogen genomics is pretty revolutionary technology in public health surveillance and response, because it gives you so much information and it’s all about integration, data sharing and then wrapping that around public health labs.

He said the Illumina systems will help increase capacity across the country.

San Diego-based Illumina’s systems are being delivered to the Doherty Institute, Westmead Hospital, UNSW at the Prince of Wales Hospital and Queensland Health Forensic and Scientific Services, expanding the capacity of the four major public health laboratories in New South Wales, Victoria and Queensland to sequence pathogens, including COVID-19 samples.

“The technology will be used to sequence the genome of the virus, SARS-COV-2, which causes COVID-19, and the genomic information will then be used to further our understanding of the virus’ behavior, evolution and transmission,” Tamsin Eades, market development manager at Illumina, told BioWorld.

“Illumina hopes that the data will be used by our partners to further understand the transmission of the SARS-COV-2 and to help with contact tracing efforts that may resolve cases where the source of infection is unknown,” she said.

“As a partner in the grant, Illumina will contribute to the development, assessment and optimization of NGS-based methodologies to both sequence and analyze the SARS-COV-2 genome.”

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