Illumina CEO on sequencing an evolving pandemic

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In this episode of Facing Forward, Margaret Brennan talks with Illumina CEO Francis deSouza for a look at the science behind the spread of the Coronavirus pandemic and how agencies like the CDC and the White House can better understand how infectious diseases evolve.

Highlights

On sequencing a virus: "I think more sequencing is important in terms of fighting the pandemic. And you're right, although, you know, in the US we are a source of some of the innovations in sequencing. We have lagged behind over 40 countries, as you point out, in terms of just how much we're sequencing. So on average in the US right now, we are sequencing about 0.3% of the positive cases that we're seeing. Now to get a good understanding of what's happening, you really need to be sequencing about 5% of the positive cases as well as sampling the negative cases. Now, for comparison, you know, countries like the U.K. that are leading are closer to sequencing, about 10% of all positive cases."

On new strains of COVID-19: "We're going to continue to find new strains around the world and the ones that will propagate are going to be the ones of the most transmissible. And so, you know we'll- that- this will just continue to emerge. The important thing is to watch the results of the tests that the vaccine developers are doing and some of the therapy developers, and again, it's inevitable and this may be, you know, days. This could be weeks. This could be months from now or even years from now. But it's inevitable that there will be some strains that do require modifications of the vaccines that we have today. The vaccine developers know that. They understand what it would take to modify, you know, their vaccines. And so we just have to- we have to stay on top of it though, because at this point, it's a footrace between how fast we're rolling out the virus and how fast the virus is mutating and spreading around the world."

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"Facing Forward": Francis deSouza transcript

Producers: Richard Escobedo, Kelsey Micklas

Research producer: Shani Benezra

Illumina CEO Francis deSouza  / Credit: DISNEY/ABC/ Heidi Gutman
Illumina CEO Francis deSouza / Credit: DISNEY/ABC/ Heidi Gutman

MARGARET BRENNAN: I'm MARGARET BRENNAN and welcome to FACING FORWARD, a new podcast featuring in-depth interviews with the business leaders and policy makers shaping your world. There's a new administration in the White House, and President Biden will now have to figure out how to conquer the pandemic that continues to claim US lives and choke the US economy.

A highly contagious new strain of the virus is complicating matters. And now there are other new virus mutations spreading around the world and possibly here in the US. Today, we'll be talking to Francis deSouza, the CEO of Illumina. Through its work with the CDC, Illumina has helped to detect some of the very first cases of the U.K. variant or B117 reported here in the US. We're excited to have you on the podcast, Francis. How are you?

PRESIDENT & CEO OF ILLUMINA FRANCIS DESOUZA: Hi, I'm doing well. Thanks for having me, MARGARET. I'm excited to be here.

MARGARET BRENNAN: Your company Illumina, which is a public company, it's in the private sector, you conduct genomic sequencing, which is what scientists use to understand how infectious diseases spread and how they evolve. So for all of us who weren't science majors in college, how do you actually do that?

DESOUZA: Sure. So what we do at Illumina is we provide the machines and the software that allows our customers to start with biological samples. So it could be, you know, blood, saliva and you take those biological samples and our machine then reads sort of the DNA- the genomic data in that sample. So that could be DNA, and in the case of this virus, it's RNA. And then we'll spit out on the other side a report with all the sequences in that biological sample. There's an awful lot that goes into the machines we build, a lot of molecular biology, a lot of chemistry, a lot of A.I. and, you know, computer processing to go from that biological sample to the report that we provide.

MARGARET BRENNAN: And you do this for all sorts of different viruses?

DESOUZA: Yeah, we do it for any biological sample. And so, you know, today we serve at Illumina, about over 7,000 customers in 130 countries. And our customers include CDC's who are looking for pathogens and trying to identify emerging pathogens. And we were in Wuhan in December 2019 involved when the team- the CDC team there was trying to identify the cause of what was then called this, you know, pneumonia of unknown origin. And the first viral genome that was published on January 10th was actually published by a team at the Shanghai Public Health Clinic using our sequencers.

MARGARET BRENNAN: On COVID generally, how many different types of it exist in the world? Do we know?

DESOUZA: Well, the virus is continually mutating, and so, you know, a coronavirus typically mutates about two to three times a month. And so you can expect to see, you know, many, many different types of virus with different mutations on them. Now, you know, two to three times a month sounds like a lot. It's not as frequent as influenza virus, for example, that mutates on average 10 times a month. And- and- and we follow those strains to try and identify not only just how the virus is mutating, which is important information to have, because you're trying to figure out does that mean our diagnostic tools will fail because the virus has mutated enough? Does that mean our vaccines will continue to be effective, our therapies? But you also want to track these mutations to try and identify how is this virus spreading? And that gives you insight that you can use to make policy decisions for example. For example, you could decide to shut down travel to a region if, you know, that's the place where, you know, your infections are coming from.

MARAGARET BRENNAN: And by most accounts the U.S. hasn't been doing a very good job of this. We've reported more deaths due to COVID than any country in the world, and according to one ranking we're about 43rd in the world for genetic sequencing. If we had better sequencing, would that help us avoid further death?

DESOUZA: I think more sequencing is important in terms of fighting the pandemic. And you're right, although, you know, in the US we are a source of some of the innovations in sequencing. We have lagged behind over 40 countries, as you point out, in terms of just how much we're sequencing. So on average in the US right now, we are sequencing about 0.3% of the positive cases that we're seeing. Now to get a good understanding of what's happening, you really need to be sequencing about 5% of the positive cases as well as sampling the negative cases. Now, for comparison, you know, countries like the U.K. that are leading are closer to sequencing, about 10% of all positive cases.

MARGARET BRENNAN: Why aren't we doing this already?

DESOUZA: One of the challenges here in the US is that there hasn't been a coordinating force. There hasn't been a central coordinating force across the nation. And so what's happening is you're seeing pockets of sequencing and so, you know, different labs, different health systems are making their own decisions about whether to sequence or not. And then some of them are uploading the data that they sequence into the public domain. Now, that's different in other countries. In the- in the UK, for example, because they have a national health system, you know, there is a coordinated effort happening around sequencing. And so that's one of the things I think that we really need here. You know, we need a- a national initiative around genomic surveillance. We need a coordinating central body around how to manage the- the flow of samples, you know, and then also the funding associated with- with those labs actually sequencing, you know, the samples they get.

MARGARET BRENNAN: So the Biden administration says it wants to do some of that by investing in both sequencing and surveillance. So, how would that work? Does the CDC need to ask private companies like yours to help them do it?

DESOUZA: You know, there is hope as you said. If you look at the Biden American Rescue Plan, in it there are details around increasing funding for surveillance capacity at levels demanded by the crisis. And so there's definitely a thought that we need to- to increase funding for surveillance, that's one aspect of it, and also create a- a central group that- that will coordinate this. And then the central group will also help make sure that the- the samples from infected patients are getting to the right labs and that the data is being shared in the public domain.

MARGARET BRENNAN: If we did more sequencing, could we then do things like say, hey Montana, shut down your restaurants, but Wyoming, you can stay and continue working, thus your economy can continue to grow. Is it that simple?

DESOUZA: It's- it's that straightforward. However, I'd say one of the most eye opening moments here in the US of this pandemic was the realization early last spring that we had the virus circulating in the US for weeks and we didn't know it. And what that meant was we had no idea that there was, you know, a pandemic starting and building, and it- it created the realization that we do need this genomics-based pathogen surveillance network. We need a network that will tell us if there is another coronavirus circulating, or if we're even under a bioterrorist attack, or if there is emerging antimicrobial resistance anywhere in the world, or if there's another zoonotic transmission, you know, from an animal into- into the human population, you know, that's spreading uncontrolled. And so there is this moment, this realization that we actually wouldn't even know if we were under attack. So, instead of waiting weeks and months before we know we're under attack, it could be hours or days. And that makes a huge amount of difference in terms of being able to control an outbreak, you know, before it becomes a pandemic. Also, if you are sequencing earlier and getting the genomic data of the pathogen earlier, that gives vaccine developers and therapy developers a head start. You know, if you talk to companies like, you know, Moderna or BioNTech, they'll tell you that it was the publication of the viral genome on January 10th, 2020 that really kicked them off in terms of developing the vaccine. And so the earlier you catch it, the earlier you get vaccines and therapies.

MARGARET BRENNAN: I want to ask you next about the mutations of the virus. Is it 'B' one one seven or 'B' one seventeen? What do you call the U.K. strain?

DESOUZA: We call it 'B' one one seven.

MARGARET BRENNAN: You call it that. So, that's the technical name for what you refer to as the strain that was first detected in the United Kingdom. It's highly contagious, but it's here in America now. The CDC says it's going to be the dominant strain by March. Exactly how much of the virus is here? Do we know?

DESOUZA: Well, working with our partners like the CDC and Helix, we have now identified 74 cases of B117. You know, that's up from 51 cases that were reported on the 6th of January. We've identified cases now in seven states, so, you know, Texas, Minnesota, Indiana, in addition to California, Florida, Pennsylvania and Georgia. And it appears to be on the rise. So last week, B117 infections represented 0.17%, you know, of the total infections that we're seeing here in the U.S. And in a week that's gone from 0.17 to 0.27. Now, we know it's much more transmissible than some of the other strains we're seeing, so we fully expect that it'll start to become a more dominant strain in terms of the infections we're seeing here in the US.

MARGARET BRENNAN: So the U.K. found this mutation because they do sequencing. But correct me if I'm wrong, that doesn't mean that's where the virus actually came from. Right?

DESOUZA: That's exactly right. They found it because they have more sequencing and- and are just looking better than other places. It absolutely doesn't mean that it came from there necessarily.

MARGARET BRENNAN: Do we know where it came from? And is answering that question important to how you treat it?

DESOUZA: At this point we're not sure where it came from. And, you know, over time, it will be important to sort of track, you know, the spread of this virus. However, at this point, especially in terms of treating it, it isn't essential to know where it came from. What is essential and is- is taking place is to understand, you know, with every one of these new strains that we're seeing whether it'll impact the efficacy of our tools to fight the pandemic, whether it will affect the efficacy of our diagnostic tools and- and our vaccines and our therapies. And so you have the- the manufacturers of the tools and the vaccines and the therapies testing against these strains as they emerge and reporting their results. That's important.

MARGARET BRENNAN: And what we know to date is that the U.K. strain seems to be responsive to our current therapies, but it's the strain out of South Africa that there is early reporting on that indicates it may be resistant to certain treatments. That's 'B' one three five one, right?

DESOUZA: Yeah, 'B' one three five one, exactly. And--

MARGARET BRENNAN: How much of it's here? Do we know?

DESOUZA: Well, you know, it's early at this point. You know, we have more data, as you said, on B117. And the data there is encouraging that, you know, our existing, you know, therapies hold up against B117 is the data we're seeing so far. You know it's- we're getting very early data on 3151. And at this point it's too early to call whether it escapes. Now, the vaccines are targeting, you know, the- the spike protein of the virus and it will take, you know, a lot of mutations for the- the vaccines to fail. And so we'll have to see, you know, what the results with B1351 are. And, you know, at some point it- there may emerge a strain that the vaccines aren't effective for. Now, the good news is, you know, those vaccines can be updated pretty quickly, but then they'll have to go through the, you know, the testing before they get released.

MARGARET BRENNAN: We spoke on FACE THE NATION to the incoming CDC director on who emphasized she wants to focus on sequencing and surveillance. She mentioned the Brazilian strain. She mentioned a strain out of Nigeria. How worried should we be about those? What do we know about them?

DESOUZA: You know, we're going to continue to find new strains around the world and the ones that will propagate are going to be the ones of the most transmissible. And so, you know we'll- that- this will just continue to emerge. The important thing is to watch the results of the tests that the vaccine developers are doing and some of the therapy developers, and again, it's inevitable and this may be, you know, days. This could be weeks. This could be months from now or even years from now. But it's inevitable that there will be some strains that do require modifications of the vaccines that we have today. The vaccine developers know that. They understand what it would take to modify, you know, their vaccines. And so we just have to- we have to stay on top of it though, because at this point, it's- it's a footrace between how fast we're rolling out the virus and how fast the virus is- is mutating and spreading around the world.

MARGARET BRENNAN: The nominee to be the Treasury secretary, Janet Yellen, testified this week that the Biden administration is going to try to raise corporate tax rates, but she said they're not going to return them to where they were. So right now, they're at 21%, this flat rate. And before President Trump lowered them, they were in a range between 15% to- to an effective rate of as high as 39%. What would raising the rate above current levels do to your business?

DESOUZA: That's a- it's a complicated question to answer without knowing all the puts and takes. So, for example, you know, we want to see the specifics around not just, you know, the headline number of what the tax rate- corporate tax rate is on average, but also things like, you know, how- how does the proposed, you know, tax code work around things like research and development credit, you know, revenue from outside the US, for example, or profits? So, you know, there's a lot of details that we'd have to work through to really assess what the implications would be.

MARGARET BRENNAN: But the argument against it often is that that would hurt your ability to hire or, you know, any- any bite taken out of corporate profits comes at a cost ultimately somewhere. The other argument against it from the left is, you know, that corporations should pay their fair share. Do you see this as an argument that's going to dominate the next four years? Is- are you concerned about it?

DESOUZA: You know, I definitely think it will be a- a topic of conversation and debate and as- as it should be, both in terms of what the fair rate should be, as well as what the uses of those funds are. You know, how are we going to think about investing in America, whether it's on training or education? And so both in terms of sources and uses of funds, I think there should be sort of a very vigorous debate. Candidly, though, I think the more urgent conversations in the near-term are going to be around the pandemic and how we, you know, get people through the pandemic safely and quickly. I think there are going to be conversations, too, around, you know, how we continue to, you know, drive American leadership in key areas globally of- of the global economy, but also in things like climate change, for example. And so I think there are going to be a lot of very important conversations that play out. And in the near-term, I think the pandemic is probably going to be the single most important.

MARGARET BRENNAN: Yeah. On the pandemic front, the Treasury secretary nominee also testified that having a paid leave and childcare policy in the US would help the jobs crisis that women in particular have felt. Do you agree with that? And what are you doing at your own company on those policies?

DESOUZA: Yeah, I think there's a lot more we can do to support, you know, to support flexibility in the workplace, especially in times of need, specifically, you know, in times of illness, or if- if- you know, families have a baby, for example. So, you know, from our perspective as a company for this pandemic, you know, what we're doing is about a third of our employees come into an Illumina workplace to build the machines, you know, that- that we need to build to support customers that are- whether they're fighting the pandemic or in cancer centers. And so, you know, the work we do is- is essential for, you know, for those efforts. And so about a third of our employees do come in. We've done a lot in terms of retooling our workplaces, you know, in terms of social distancing and- and just lots, you know, cleaning the office, upgrading the ventilation, just a lot we've done in terms of ensuring that workplaces are safe. And then for two thirds of our employees, they work from home. And so, you know, we have enabled them to, you know, to be remote and be productive from home

MARGARET BRENNAN: But should there be a government mandate on some of those specifics?

DESOUZA: I think in- in some cases there should be. You know and again, that's going to be the- the- the- debate that plays out--

MARGARET BRENNAN: Yeah.

DESOUZA: --on how much and for what and for how long. But I do think, you know, we need to look harder at, you know, supporting- supporting, you know, the- the people that work.

MARGARET BRENNAN: The Trump administration strongly suspected that patient zero came from a research lab in Wuhan. Maybe it was an accident. How important is it to find out the origin of this virus? You called it zoonotic, meaning it went from an animal to a human. What is pinning that down exactly when it happened, prove or give us? And can you tell something like that from the work that you do?

DESOUZA: I think over time it will be important to understand, you know, how this pandemic started but at this point, it's not the priority. At this point the priority has to be, you know, understand how the virus is spreading, get the vaccines out as fast as possible, stay on top of strains as they emerge so that we know that our tools will continue to be effective, adjust our tools, you know, if the virus continues to mutate. So right now, you know, my perspective is it's really all hands on deck to get us out of the pandemic. And then once we get out of the pandemic, I think there's very important research we can do to prepare us for the next one, including understand the- understanding the origins of this one. But that is not the priority right now. The priority right now is- is get through this pandemic.

MARGARET BRENNAN: Do you think we'll ever know?

DESOUZA: I think I'm hopeful. There's lots and lots of, you know, the beautiful thing about, you know, RNA is, you know, you can start to track history as you can see mutations and you can go back and see well what came from what and you start to build up these trees. So I- I'm hopeful.

MARGARET BRENNAN: Francis deSouza, thank you for sharing your insights and for your time today.

DESOUZA: Thank you, MARGARET.

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