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Illumina Helped the World Fight COVID-19. Now, CEO Francis deSouza Has Monkeypox in His Sights

Time logo Time 8/14/2022 John Simons
Francis deSouza, CEO, Illumina © Courtesy of Illumina Francis deSouza, CEO, Illumina

As 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. mRNA treatments are also under development for other infectious diseases like malaria, Ebola and HIV, as well as for cancer. “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 a veteran of the digital revolution, having spent the bulk of his career in the tech sector. At the age of 16, he entered MIT, where he studied computer science and electrical engineering. Later, he co-founded two companies that made collaborative software for large corporate clients. Symantec acquired one of the startups, and Microsoft bought the other. He did stints in executive positions at each of the acquiring companies and joined Illumina in 2013 as president. He became CEO in 2016.

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 business has also faced steep challenges, including a costly patent lawsuit and an E.U. antitrust probe into its acquisition of biotechnology company Grail. 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. At the same time, the company drastically lowered its full-year outlook.

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.

This interview has been condensed and edited 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?

Over the last few months, we have been engaged with health systems around the world to understand the spread of monkeypox and the evolution of the monkeypox virus. Fortunately, now many countries over the last two to three years have been standing up a genomics-based pathogen surveillance program to help fight COVID. And so, they had a bit of a head start and were able to start to repurpose some of the infrastructure that was focused on COVID to look at monkeypox.

We still have big blind spots when it comes to monkeypox. So for example, over 50% of the countries that have reported a monkeypox outbreak have yet to share any data on the genomics of the monkeypox outbreak they have. 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. So, we still have work to do to truly have this global pan-pathogen, genomic surveillance network.

It must be an interesting time for a company like yours. The world is trying to emerge from the COVID-19 pandemic, and suddenly monkeypox emerges.

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] outbreaks, for example. We’re seeing polio reemerge in some communities where we haven’t seen it. And it really does emphasize the need for a sort of early identification of disease outbreaks and the value that a genomics infrastructure would 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. How does the business landscape look from where you sit?

At a very top level, there are certainly some challenges that businesses and consumers are facing right now that are likely going to continue to play out in the coming quarters. The rising interest rates and the threat of inflation, the challenges to the supply chain, the impact of the war in Ukraine, are all going to continue to be headwinds to business as a whole.

So, Illumina is doing battle with COVID, monkeypox, and cancer. What’s the latest on those fronts?

Video: Illumina CEO Francis DeSouza on sequencing monkeypox to develop vaccines, diagnostics (CNBC)


We launched a viral surveillance panel that can do sequencing of 66 of the most critical viruses that are of public health concern, including 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. We have now, for example, more than 700 customers around the world that are doing COVID surveillance using our sequencing. 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?

The way the company responded to monkeypox was similar to the way we responded to the COVID outbreak. When we were in the early stages of the [COVID] outbreak, our teams got to work immediately on coming up with a panel to sequence the virus. The teams worked seven days a week, often around the clock, to go from the idea of what that product would look like to having a product that received emergency use authorization from the FDA in under 60 days. That’s unprecedented and it just took a huge amount of work from hundreds of people across Illumina to make that happen. We did that back in 2020.

When we saw monkeypox emerge, we activated that same approach. We had a team come together, create the content so that the panel would be able to identify monkeypox, as well as 65 other pathogens now, and the team worked really quickly to make this panel available. We benefited from the experience of having done it before for COVID so we knew what it took, and we also now benefit from the fact that we have infrastructure in place that we can leverage to make this panel accessible more broadly.

Monkeypox comes at a time when Illumina is introducing a lot of other products, right? Can you talk about that and how you insert something very quickly into the product chain, when these new viruses come along?

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. We need to look for the evolution and spread of COVID-19, SARS-CoV-2, but also for the next coronavirus, for emerging antimicrobial resistance, for a bio-terrorist attack, the next zoonotic transmission.

So, for example, we are starting to see the emergence of wastewater surveillance, where counties and cities are starting to sample their wastewater regularly and sequence it to get an understanding of the viral load and the emerging strains in a community. What we are able to do is provide additional technology. 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. So, we get this advanced warning system about how pathogen outbreaks are emerging and evolving.

I think that positions us as a global community much better to address the next outbreak. While we may not ever be able to prevent an outbreak, we should commit to making this our 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. How do you weigh those dual concerns?

Our mission from the beginning has always been to improve human health by unlocking the power 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. Our focus has been to drive innovation that makes sequencing cheaper, faster, easier to use.

About a decade ago we started to see some of the first discoveries translated to clinical applications. We saw, for example, clinical applications like noninvasive prenatal testing emerge, also, therapy selection for cancer patients. We want to accelerate the adoption of those technologies because it improves health outcomes for people, and it is good for our business as well and it takes costs out of the healthcare system. 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.

We create our own tests as well to help catalyze the market. We also created a group that focuses on getting reimbursement for patients for 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. What are your biggest challenges to accomplishing it all?

One of the challenges that we have to address is making genomics accessible to everyone. We need to increase awareness of the benefits of genomic testing and the availability of testing by patients and physicians. 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. Our teams at Illumina have helped deliver reimbursement for one billion people around the world for genomic testing. 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?

There is a shortage of educational material and training available for physicians, patients, and even in academic environments. 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.

The GRAIL Galleri test that was launched last June is a huge breakthrough in terms of cancer screening. It is a single blood test that can identify if a patient has one of 50 types of cancer, across stages. Forty-five out of the 50 cancers that GRAIL can identify have no other screen. We know that if you identify a cancer early, your five-year survival odds are much higher than if you discover a cancer late. The challenge is that the majority of cancers don’t have any screen. Over 70% of the people who die from cancer, die of cancer that has no screen. The GRAIL test promises to be quite transformative.

I have always wondered how someone in your position motivates scientists who are trained to plod slowly through research over many years and not operate on corporate timetables. How do you handle that, inspiring scientists, lighting a fire under them?

The kind of people that work at Illumina are typically drawn by the mission, the idea that the work we do improves human health by unlocking the power 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. What that means is there is a huge amount of self-motivation among our employees to do the work right. We take the right amount of diligence. We recognize that delivering a diagnostic is a sacred responsibility, that people make important decisions with the output of our products.

And then there’s also a visceral acknowledgement of the fierce urgency of what we do. We know that in the U.S., somewhere between 1,500 to 2,000 people a day die of cancer. If we can get our products to the market faster while doing them right, that makes a difference. Similarly, we have customers working on improving food security or helping develop synthetic fuels that will help combat 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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