Transcript: Francis deSouza on

The following is a transcript of an interview with Illumina CEO Francis deSouza that aired Sunday, December 5, 2021, on “Face the Nation.”

MARGARET BRENNAN: We’re going to go now to Francis deSouza, CEO of Illumina, a company that identifies and tracks COVID variants through genomic sequencing. Good morning to you.

PRESIDENT & CEO OF ILLUMINA FRANCIS DESOUZA: Hello, there. 

MARGARET BRENNAN: From what you are seeing, the $2 billion that US taxpayers just helped allocate towards improving sequencing in this country. Is America better now than we were at the start of this pandemic at figuring out exactly where the virus and the variants are?

DESOUZA: Yeah, we’re making progress, and we are in a lot different position than we were at the beginning of the pandemic and certainly even a year ago. We were sequencing very little in terms of the positives that we were seeing in this country. But over the last year, we started to see sequencing infrastructure being rolled out. And now if you look at the course of all of 2021, we’re probably sequenced- probably sequenced over the course of 2021, about 3% of the positives that we’ve seen this year. Now best practices to do between five and 10%. But if you look at the last three months, we’re now in that five to 10% range. So, I think overall we’re starting to get the right amount of sequencing done in the US. The challenge is that it’s very variable across the states. And so, you have some states that are close to 30% of positives. You know, some states that are closer to 1%. And so overall, I think we have the capacity we need. It’s just that we clearly have blind spots in parts of the country where we need to do more.

MARGARET BRENNAN: And to that point, in the United Kingdom, within 48 hours of the first cases they knew after South Africa sounded the alarm the UK detected, they had Omicron on their shores. Here in the United States, it was out of Minnesota. It took a week of time to pass between when the patient was tested and state health officials in Minnesota confirmed it. Why are we slower? Isn’t that more dangerous?

DESOUZA: It absolutely is, and you want to be- you want to be ahead of this. There’s no question that the UK specifically has been one of the leaders in terms of rolling, rolling out a global genomics epidemiological infrastructure. So, they have been doing surveillance since Apr of 2020. So, they were one of the first countries in the world to recognize the value of doing genomic sequencing of the positives and identifying how the virus was mutating. And so, they started in Apr of 2020. And frankly, not many other countries followed until Dec of 2020, when we started to see new and new variants emerge, and it became clear that there was huge value in understanding how this virus was mutating, that we needed to understand it so we could track how it was spreading, but also to know if the tools we were using to fight the pandemic, the vaccines, the diagnostics, the therapies, whether they were still going to be effective.

MARGARET BRENNAN: Right. In terms of how this virus mutated, there’s speculation that it either jumped back and forth between animals and humans, or that there was something unique to its mutation within immunocompromised individuals. Do you have any insight into why Omicron seems to be so uniquely threatening?

DESOUZA: Yeah, what really is surprising about the- the genome of this variant is that it is so heavily mutated. So, we have over 50 new mutations, 30 of which are in the S-gene, which- which makes the S-protein, and that’s important. But- but the fact that there are so many that we haven’t seen before coming from a virus that only mutates two to three times a month tells us that it’s been somewhere mutating for a long time, and we haven’t seen it. And so, there are a number of hypotheses. One, it could have been as part of a chronic illness that somebody who was perhaps immunocompromised had over a year and so they weren’t ever really able to clear the virus. And so, they had it and it was mutating. And then for some reason, it started transmitting again over the last couple of weeks. Or it could have been, as you said, you know, transmitted to an animal, mutated there and then come back into humans. Or it could have been circulating in a part of the global population that’s just not being sequenced. And so, we’re trying to figure out, you know, where it was for so long mutating undetected. The other thing that’s important is that the mutations we’re seeing, the 30 mutations in the- on the S-gene are important because the S-gene codes for the S-protein, and that’s important for two reasons. One, that is how the virus interacts with human cells and gets into human cells and–

MARGARET BRENNAN: Right.

DESOUZA: –we’ve seen with other variants of concerns that certain mutations make variants more transmissible. And so, there’s an indication and we’re seeing that with some of the early data that this variant might be more transmissible. 

MARGARET BRENNAN: Right.

DESOUZA: The second reason it’s important is that the S-protein is actually a target for some of the vaccines. And so, the question now is is it mutated enough that it escapes some of the vaccines. 

MARGARET BRENNAN: Right. And we will be watching what the South African scientists find on that, of course. In this country, though, do you think there is a national strategy to go along with the money we talked about, the 2 billion, to improve sequencing.

DESOUZA: I think we’re starting to put it together. Clearly that wasn’t the beginning of the pandemic and there are lots of elements of a national strategy that are essential, so, you know, one sort of understanding, you know, what are we trying to shoot for in terms of percentage of positives that- that we want to sequence. Two, how is that going to happen? So how are the samples going to go from, you know, clinics where testing is happening to labs that can do the sequencing and those connections needed to be- to be made.

MARGARET BRENNAN: Yeah. 

DESUZA: And then there’s got to be more work around, you know, how is the data going to be shared? 

MARGARET BRENNAN: Yeah. 

DESOUZA: And so, all of that- I think there are ideas and they’re being put together. 

MARGARET BRENNAN: OK.

DESOUZA: But there’s still work being done to get it together.

MARGARET BRENNAN: All right. Thank you very much, Mr. deSouza, for your time this morning. We’ll be back in a moment.