Illumina shines in Covid genetics battle

Melbourne-educated Tom Berkovits is a senior executive in the Asia-Pacific for $105bn global DNA-sequencing firm Illumina, at the front line in resisting Covid-19.

Tom Berkovits says Illumina ‘continues to sequence the virus to monitor the changes that happen over time’. Picture: Greg Bowker

Tom Berkovits is proud of his Australian heritage, being educated at Melbourne High School and Monash University before moving abroad 15 years ago to pursue his dream to work for some of the world’s biggest healthcare and medical industry companies.

Today he is a senior executive in the Asia-Pacific for $105bn global DNA-sequencing firm Illumina, the biotech responsible for more than 90 per cent of the world’s data generated from genome sequencing, which has become critical in the battle against Covid-19 virus and its variants.

When he looks across the Tasman the now Auckland-based Berkovits laments the low vaccination rates – until recently – in his homeland, which are causing ongoing damaging lockdowns in its biggest cities.

Low vaccination rates are also leaving his adopted home vulnerable after New Zealand plunged into a snap lockdown this week.

In particular, Berkovits wonders about the misinformation and shifting official advice on the AstraZeneca vaccine – now known in Australia as Vaxzevria – which has fuelled vaccine hesitancy across this country.

“I am no expert in this, but the different vaccines work very differently … My personal belief is any vaccine that provides you with protection is valuable. Unfortunately the statistics (on AstraZeneca) were beaten up. I don’t know quite why,’’ says Berkovits, who is Illumina’s director of market development and clinical genomics in the Asia-Pacific and Japan.

Yet despite its challenges in managing the pandemic, he believes Australia is at the forefront of leveraging genomic research throughout the region to revolutionise public health contact tracing and pandemic control for not only Covid-19 but other infectious diseases.

Genome sequencing analyses the genetic information contained in human cells. Such data can help improve disease testing and develop more personalised treatments for cancer and other illnesses.

“We are doing a great job and well ahead, setting the standard quite frankly for what is to come,” he says. “Many other countries are looking at the Australian model and are using genome sequencing for surveillance.

“We have had significant sequencing efforts in Indonesia, The Philippines, India, and we are just trying to stand it up Bangladesh. Most of the Covid samples from Papua New Guinea are being sequenced in Queensland.”

The Nasdaq-listed Illumina, whose share price has risen more than 2400 per cent over its 21-year history and which boasts partnerships with the Bill & Melinda Gates Foundation, started its Australian operations in 2008.

In the six years since Berkovits joined the company, it has secured partnerships in the Australasian market with the University of Melbourne, AgResearch and The Doherty Institute.

In February Illumina announced a collaboration with the University of Melbourne and the Victorian government to set up a $60m Genomics Hub in Melbourne to bring together the best of genomic expertise and technology in Australia.

Its vision is to improve public health outcomes through research and diagnostics in areas such as infectious diseases.

“Asia-Pacific has more than two-thirds of the world’s population. It is a very diverse region but has issues with the prevention of disease,’’ Berkovits says.

“By 2030 India, China and Indonesia will spend the most on the planet on healthcare. We need to be able to conceive and create products and services that meet their needs. That is really where we see this (the greater use of genome sequencing) being a bit different from what has come before.”

Earlier this year Illumina revealed plans to collaborate with the Communicable Disease Genomics Network (CDGN) – a collection of the nation’s public health laboratory organisations – to track Covid in Australia using real-time data sharing and integration to better understand the transmission and spread of the virus.

It represented the first national implementation of a pathogen surveillance program in Australia.

“Since then we have enabled collective access to technology in all states so we now have sequencing tech in all states,’’ Berkovits says.

The partners are using AusTrakka, a national platform for real-time analysis of integrated pathogen genomic information which now hosts data for more than 20,000 Covid-19 samples from all the states and territories, as well as New Zealand.

The CDGN program is being funded by the federal government with a $3.3m Medical Research Future Fund (MRFF) grant through the University of NSW School of Medical Sciences. Illumina has also contributed more than $2m of its genomic sequencing systems and related consumables.

More recently the emergence of the Delta variant has heightened awareness of genomic surveillance in the fight against Covid-19 and future pathogens.

“One of the things that gets a bit lost is that viruses are living organisms and they mutate over time. We continue to sequence the virus at significant depth to monitor the changes that happen over time,” Berkovits says.

The Australasian operations of Illumina have access to every piece of technology available at the company’s flagship facilities in California to fight Covid-19.

“Where things start to differ is in terms of what people can access and what is funded. So when I look at the US or a lot of Europe, comprehensive genomic profiling in oncology is becoming a standard of care,’’ he says.

“In Australia we are still in the one-test, one-result way of thinking.”

He said there was scope for more detailed biological work to provide more genomic information to patients, allowing them to make more informed decisions about treatments and care.

But funding for the work remains a challenge.

“My impression is we take a lot of things for granted. Covid vac­cines aren’t free, the tests aren’t free. All of that is being funded by government, as are contact tracing apps. The fact that at least from a healthcare perspective, Covid hasn’t cost us money in our pockets is a plus for the government,’’ Berkovits says.

Illumina has been working to get more private equity and venture capital funds into the sector by focusing on partnering with entrepreneurs to build start-ups.

In 2014 it launched the Illumina Accelerator, which works with Illumina research and development sites in San Francisco and Cambridge in Britain.

The Accelerator has invested in 45 genomics start-ups around the globe, which have collectively raised nearly $US600m in venture capital.

“We have had some discussions already with people with funds in the US to invest in Australia. But nothing has happened yet,” Berkovits says.

“The entrepreneurial environment in Australia is different from the US. Here a degree of seed money gets people started. But companies are forced to IPO earlier than they should, because they don’t have access to enough money.”

He also says there are different standards from country to country.

“With something like this, particularly in Australia, it feels like there is still an expectation this is something governments are responsible for. I also worry if too much private equity comes in, people will be seen to be profiting from something like this. It is a delicate balance.”

In May Illumina announced a venture with Brisbane-based precision microbiome science firm Microba Life Sciences to advance understanding of the human gut microbiome.

There are other initiatives looking at infectious disease monitoring.

Genome sequencing is being used to determine which strains of tuberculosis are likely to be resistant to antibiotics, to treat patients faster. Tuberculosis is the largest infectious killer in the world and drug resistance is becoming a global problem.

“One of the things we are also looking at is health economics. A lot of the measures used to decide if something is economically viable in the healthcare setting use older standards. There are new models out there,” he says.

In the post-Covid world, genome sequencing even looks set to be used in new contexts to help improve environmental monitoring.

“We have been asked to partner with an ARC (Australian Research Council) Centre of Excellence in environmental monitoring looking not just at wastewater, but sampling air in an airport or a shopping mall. So you get to a point where you can see if pathogens are floating around to determine if a space is safe or not,’’ Berkovits says.

More broadly he believes the COVID pandemic should prove to be a turning point in better educating the community around genome sequencing and its greater adoption in the world.

“What has legitimately happened is the pandemic has made genome sequencing part of our everyday vernacular. We know it is important. There has been a flow-on effect from that. It has accelerated the border adoption of genome sequencing into infectious diseases by 5-10 years,’’ he says.

“The response to COVID has shown governments around the world were unprepared for a pandemic. I am hoping that with the evolution of genome sequencing, we will see improved preparedness as we move forward.”