PERTH, Australia – Australia is employing some new genomic tools to help identify SARS-CoV-2 infections and track them within communities.
Illumina Inc. and the University of Melbourne have partnered to establish the Illumina-University of Melbourne Genomics Hub – a first for the Asia-Pacific region – which will bring together the best of genomic expertise and technology in Australia. The move aims to drive better public health outcomes in research and diagnostics in areas like infectious diseases, such as the coronavirus.
The hub will give local researchers access to world-class genomics, bioinformatics and health economics technologies to better understand the human genome and translate that knowledge to new commercial applications.
The AU$60 million (US$45.4 million) project is the first of many proposals from universities to secure funding from the Victorian Higher Education State Investment Fund, which was developed in response to the COVID-19 pandemic.
The Melbourne Genomics Hub will leverage existing infrastructure and make it accessible to more people, not just for sequencing but for other things as well, said Tom Berkovits, director of market development and clinical genomics for Illumina in the Asia-Pacific region.
“We’ve seen this genomics industry transform Cambridge and San Francisco. By housing in Parkville and leveraging the state, hopefully, it will spur the genomics industry and take it to a global scale.”
Illumina makes the technology, and it has an idea and a roadmap on what it thinks is technically feasible, Berkovits said, “but we rely on research in terms of what we can do with it. Our role is as an enabler, and we try to make the technology as accessible as we possibly can.”
But making technology accessible has become more complicated in this data-driven area, he said, and Illumina is trying to continuously push the boundaries of what the technology can do.
“What has been transformative with COVID is we have used these tools to track the virus in the community… we’ve sequenced almost 80% of the 20,000 strains of COVID in Victoria, so we could track where the virus came from, and it only takes 48-72 hours to track the virus,” said Sharon Lewin, director of the Peter Doherty Institute for Infectious Diseases.
“We had a full-on escalating exponentially increasing COVID outbreak, so what we have achieved in Australia is incredible, particularly Melbourne, because we really did have a widespread community transmission, and I personally never thought we’d get to zero, and here we are having eliminated COVID.
“People trusted the science, the modeling, we had strong leadership, clinical leadership, and it shows you that it can be done,” said Lewin, who is an infectious diseases physician and virologist.
“Genomics has been a big part of virology for a very long time. For years, we’ve looked at the genetic sequence of the [HIV] virus. Sequencing is incredibly important, because the bits that go into hiding, most of it is chopped up virus, because there’s very little intact virus. There’s a lot of work we do in sequencing the virus to understand how the virus persists. If you find the identical virus in multiple cells, it tells you the cells have divided.
“For me, it’s been exciting to see genomics move into the field of public health. You can do the detective work much easier if you know the genetic sequence of the virus.”
The partnership with Illumina will look at the host response to COVID, identifying who gets sick and who doesn’t, she said, explaining that treatments to date have not been that effective, and it’s been frustrating that antivirals haven’t done much. “If you don’t know who’s going to get sick, you treat hundreds of people to help one person,” she added. “If we could pick early on, we could tailor therapeutics better than we have.”
CRISPR technology is making some of these available that never were before, she said.
“We have the potential to treat a lot of conditions, but now we have the potential to pick up people earlier. We can’t prevent it, but we can catch and treat much earlier.”
Yet another advantage of genomics is health economics and the ability to gain evidence to show when something is working well, as well as whether it will be efficient in the health care system.
“Genomics has transformed the way we perform our research and the discoveries we make. We’re trying to understand the cells of the immune system – what the immune system is composed of – and how we can harness the power to fight infectious disease like COVID and cancer,” said Shalin Naik, a researcher at the Walter and Eliza Hall Institute of Medical Research.
“In particular, we’ve discovered how dendritic cells are made. Dendritic cells are what I call the ‘James Bond’ of the immune system, and they educate the soldier T cells and B cells to rid the body of infection and cancer.
“Using genomics, we’ve been able to understand how they’re made from stem cells and the genes that help define their characteristics. We’re trying to use this information to find new ways to boost the immune system.”
Speeding up genomic sequencing
Pinpointing SARS-CoV-2 transmission quickly is crucial, and New South Wales Health Pathology has teamed up with the Garvan Institute of Medical Research and the Kirby Institute at the University of New South Wales to develop faster SARS-CoV-2 genome sequencing capabilities, enhancing the ability of contact tracing to take faster action.
A nanopore genome sequencing technology was developed by researchers at the Garvan Institute and the Kirby Institute and is the most rapid coronavirus genome sequencing strategy in Australia.
Garvan researchers have fine-tuned the protocols for cutting-edge Oxford Nanopore Technologies to sequence SARS-CoV-2 in less than four hours. Garvan’s Kinghorn Centre for Clinical Genomics is the first facility in Australia to apply this nanopore technology for the genomic surveillance of SARS-CoV-2.
The current gold-standard method reads short genetic sequences of just 100 to 150 genetic letters at a time; whereas nanopore technologies have no upper limit to the length of DNA fragments that can be sequenced and are able to more rapidly determine the complete sequence of a viral genome.
The nanopore sequencing method was found to be highly accurate, with variants detected with more than 99% sensitivity and more than 99% precision in 157 SARS-CoV-2-positive patient specimens.
“Every time the SARS-CoV-2 virus passes from person to person, it may make copying errors that change a couple of its 30,000 genetic letters. By identifying this genetic variation, we can establish how different cases of coronavirus are linked – to know where a case was potentially picked up from and who they may have given it to,” said Rowena Bull, a postdoc research fellow from the Kirby Institute.
Genomic testing is crucial for tracking virus transmission in cases where the source remains unclear from investigating known epidemiological contacts alone, she said.
“By reconstructing the virus’s evolutionary history, or family tree, we can understand the behaviors that help spread COVID-19 and identify so-called super-spreaders.”
Nanopore sequencing also has the potential to enhance SARS-CoV-2 surveillance by enabling point-of-care sequencing and improved turnaround times for critical cases.
Nanopore devices are cheaper, faster, portable and don’t require the lab infrastructure needed by current standard pathogen genomics tools, she said.