Illumina CEO Francis deSouza Has Monkeypox in His Sights
s chief executive of San Diego-based genomic sequencing company Illumina, Francis deSouza feels well-placed to witness the world’s next great scientific transformation.
“I really believe that just like the 20th century was the era of the bit and the digital revolution, the 21st century is likely to be remembered as the era of the genome,” he says. “We’re seeing that play out in terms of genomic-based screening and diagnostics emerging, like Illumina’s offerings, but we’re also seeing the emergence of genomic-based medicine.”
DeSouza’s excitement is understandable. Well over a billion doses of mRNA vaccines—developed in record-time with the help of gene sequencing—have been safely deployed around the world to help fight the COVID-19 pandemic. Ebola, HIV, and malaria are all being treated with mRNA therapies. “We’re really seeing a huge expansion in the number of personalized therapies, gene therapies, and those are likely to have a huge impact in the coming years,” deSouza says.
DeSouza (51), is an experienced participant in the digital revolution. He has spent most of his professional life working in the technology sector. DeSouza entered MIT as a 16-year-old to study computer science and engineering. He co-founded two software companies for corporate clients that produced collaborative software. Symantec bought one startup, while Microsoft purchased the other. He held various executive roles at the acquired companies, and he was elected president of Illumina in 2013. In 2016, he became the CEO.
In that time, Illumina’s products have been central to many of the field’s advancements. “Already, any academic, commercial or pharmaceutical lab focused on doing genomics work likely owns one if not several Illumina sequencers,” wrote TIME’s Alice Park in 2021, when the company was chosen among the “TIME100 Most Influential Companies”.
The company has faced many challenges including an expensive patent lawsuit, and an E.U. Antitrust investigation into the acquisition of Grail, a biotechnology company. On Aug. 11, Illumina surprised Wall Street analysts, posting worse-than-expected second quarter earnings that showed it had swung to a loss—something deSouza attributed to a “complex macroeconomic environment” in a statement accompanying the results. However, Illumina also dramatically lowered its outlook for full-year earnings.
DeSouza spoke to TIME recently about motivating scientists, finding ways to make COVID-19 “our last pandemic,” and the company’s role in the fight against monkeypox.
The following interview was edited and condensed for clarity.
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Illumina has sequenced monkeypox, but there’s still work to be done. What’s been keeping you busy lately?
In the last months we’ve been working with global health systems in order to better understand monkeypox spread and evolution. Many countries have established a genome-based surveillance program for COVID over the past two or three years. They had an advantage and could repurpose some infrastructure which was originally focused on COVID in order to focus on monkeypox.
There are still many blind spots in the world of monkeypox. More than 50% of all countries reporting a monkeypox epidemic haven’t shared data about the genomes. And so they may not be doing the surveillance yet or they may not be in the position yet to upload that data, so we still don’t know how it’s evolving in at least 50% of the countries that already have reported it. To truly establish a global pan-pathogen surveillance network, there is still much to be done.
This must be a very exciting time for companies like yours. The COVID-19 pandemic is over, but suddenly there’s monkeypox.
You’re right. We’re not only still dealing with the pandemic and seeing the emergence of monkeypox, but if you look around the world, there are countries that are grappling with [tuberculosis]Examples of outbreaks are: We’re seeing polio reemerge in some communities where we haven’t seen it. It really highlights the importance of early detection of diseases and the role that genomics infrastructure could play.
The other thing that’s becoming clear is that identifying and fighting outbreaks early is not just a public health priority, but it’s also a national defense priority for countries because the same infrastructure that can help you identify a monkeypox outbreak can also help you identify a bioterrorist attack. And so, there’s a growing awareness that this is both a public health priority, as well as a defense priority.
As if that wasn’t enough, most CEOs see a recession coming, according to recent surveys. What does it look like from your seat?
Businesses and consumers face many challenges right now, which will continue to be a challenge in the next quarter. Rising interest rates, inflation threats, challenges in the supply chain and the effects of war in Ukraine will all continue to pose obstacles to businesses.
Illumina continues to fight COVID, monkeypox and cancer. What’s the latest on those fronts?
The panel can sequence the sequences of all 66 most serious viruses, which include monkeypox. One of the important takeaways from the pandemic is that it’s important for us to do pathogen surveillance routinely so that we can identify outbreaks when they first emerge, but also how they spread and how the viruses mutate. There are now more than 700 COVID monitoring customers using our sequences. We’re enabling those customers to use the existing infrastructure by adding to it our viral surveillance panel so that they can look for outbreaks across any one of those 66 viruses. As far as monkeypox, we want to track how it’s spreading and how it’s evolving, and this will allow our customers to do that. And so, we’re making that viral surveillance panel available for early access, and then commercializing it as quickly as possible after that.
What was the sequence of events that went into developing Illumina’s monkeypox test?
Monkeypox response by the company was very similar to how we responded to COVID. In the early days of the epidemic, we didn’t know what to do. [COVID]Our teams immediately set about creating a panel that would sequence the virus. In less than 60 days, the teams were able create an emergency product authorization by the FDA. This was achieved after they worked for seven days straight, sometimes around the clock. That’s unprecedented and it just took a huge amount of work from hundreds of people across Illumina to make that happen. That was in 2020.
We used the same strategy when monkeypox was discovered. It was easy to get the group together to produce the content needed to allow the panel to correctly identify monkeypox. Because we had done this before with COVID, we were familiar with the process and now have an infrastructure to help make the panel more accessible.
The introduction of Monkeypox coincides with Illumina’s own products. Talk about how to quickly insert something into the product chain when new viruses are introduced.
Yeah, I think all of us have learned from the pandemic that there is a need for a global genomic pathogen surveillance infrastructure—that we need to have the capability to identify when an outbreak is happening, as quickly as possible. Not only should we be looking for COVID-19 and SARS-CoV-2’s evolution, but also the next coronavirus to detect emerging antimicrobial resistance for bioterrorism attacks, zoonotic transmission.
We are beginning to notice the rise of wastewater surveillance. This is where cities and counties are now starting to collect wastewater and then sequence it in order to understand the virus load and emerging strains within a given community. Our ability to provide technology enhancements is what we can do. So, it’s not just SARS-CoV-2 now, but we’ve given them signatures around these 66 viruses to say any one of these, if you see it, report it back, report the load associated with it. We now have an advanced warning system on how new and emerging pathogen outbreaks evolve.
This will position us better as global communities to tackle the next epidemic. Although we might not be able stop an outbreak entirely, it is important that we make this the last pandemic.
I wonder how a company like Illumina balances helping the world fight viruses and other medical concerns, while also showing investors that you’re growing revenue and increasing profitability, et cetera. These dual concerns are what you need to weigh.
Since the very beginning, our mission has been to enhance human health through unlocking the potential of the genome. One of the important roles we play is to drive innovation aggressively to make genomic sequencing more accessible to everyone—to make it accessible to more researchers, initially, to enable them to do larger experiments so they could uncover the discoveries around how a human genome or a plant genome or an animal genome translates into health disease characteristics. Innovation that improves sequencing’s speed, efficiency, and affordability has been our focus.
Some of our first discoveries were translated into clinical applications around a decade back. For example, we saw noninvasive prenatal screening and therapy selection for patients with cancer emerge as clinical applications. Because it has positive health outcomes, it’s good for business and reduces healthcare costs. We are trying to speed up the adoption of these technologies. To do that, we realized that we need to make sure that we are creating and supporting an ecosystem of partners that will create the applications that the clinicians want across a variety of different healthcare conditions—in noninvasive prenatal testing, in genetic disease testing for kids in the NICU, in helping cancer patients select the right therapies.
Our tests are also created to catalyze market growth. The group also focuses on obtaining reimbursement for patients who have undergone genomic testing. By creating, nurturing, and supporting an ecosystem of partners that leverage our platform—as well as catalyzing support from other stakeholders, like regulatory bodies, like reimbursement authorities—that expands the market for genomics and is good for patients, is good for our customers, and is good for Illumina.
That’s a lot. How do you overcome these challenges?
Making genomics available to all is one of our challenges. Patients and physicians need to be more aware of the many benefits of genome testing. A lot of physicians, for example, went to medical school before the first human genome was sequenced and so there’s a need for education and awareness.
There’s also a need for expanded reimbursement. Illumina has helped to provide reimbursements for over one billion individuals worldwide through its genomic testing programs. That’s a huge amount of progress in the last few years and we have reimbursement now in some regions for things like genetic disease testing, especially for children, for cancer therapy selection, for noninvasive prenatal testing. But there’s still a long way to go to make reimbursement broadly available around the world.
It’s surprising to hear that some doctors find it difficult to change their ways and accept some of these new technologies. You’re essentially saying “Hey, we have this test that can look for 50 types of cancers.” Where’s the barrier for a doctor?
It is difficult to find educational materials and training for patients and physicians. There’s still a need to expand genomics education in medical schools, in undergrad, and a lot of that is just because the field is emerging so quickly. We’re all sort of helping catch up in terms of education and awareness of genomic testing.
Over the last year, Illumina’s stock has fallen by almost half. Is there something investors aren’t quite understanding about the company and its vision?
I think investors appreciate the long-term opportunity for genomics to really transform healthcare and that’s a big opportunity in terms of improving patient outcomes The need is to accelerate the adoption of genomics technology in a healthcare system and continue to make sure that the benefits of genomics are understood and are absorbed at a pace that investors would like to see investors are continuing to look at how quickly genomics is being adopted in cancer, for example, whether it’s for cancer therapy selection or identification of minimal residual disease, or for screening.
GRAIL Galleri is a major breakthrough in the field of cancer screening. It was released last June. The test is one blood test and can tell if someone has any of the 50 kinds of cancer. GRAIL can detect 45 percent of all 50 kinds of cancer. Our research shows that early detection of cancer is better than late diagnosis. Your five-year survival rate is much greater if you catch it before it’s too late. The challenge is that the majority of cancers don’t have any screen. More than 70% of people who are diagnosed with cancer die because they don’t have a screen. GRAIL is a promising test that promises great results.
It has always intrigued me how scientists in your situation motivate those who have been trained to work slowly over long periods of time and not on corporate schedules. Is it possible to ignite a flame under scientists by inspiring them and allowing them to do the same?
People who work for Illumina are often drawn to the mission. It is the belief that our work improves health and unlocks the potential of the genome. When you talk to our employees, they will tell you personal stories about why they’re here, whether it’s a person in their family that was impacted by cancer, or somebody in their family that has a genetic disease. This means that our employees are highly motivated to succeed in their jobs. The right amount of effort is required. It is our belief that diagnosing patients with a product can be a holy responsibility.
And then there’s also a visceral acknowledgement of the fierce urgency of what we do. It is estimated that between 1500 and 2,000 Americans die from cancer each day in America. We can make a significant difference by getting our products to market quickly and doing it correctly. We also have customers who work to improve food security and develop fuels for combating climate change. These are not only some of the biggest challenges humanity faces, but they’re also some of the most urgent challenges humanity faces, and everybody at Illumina gets that viscerally.
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