Illumina CEO explains what scientists are studying to determine if Omicron variant is more transm…

Hello there.

Yeah, we're making progress and we're 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've probably sequenced over the course of 2020 on about three percent of the positives that we've seen this year. Now, best practices are to do between five and ten percent, but if you look at the last three months, we're now in that five to ten percent range. So I think overall we're starting to get the right amount of sequencing done in the U.S. The challenge is that it's very variable across the states. And so you have some states that are close to 30 percent of positives, and you have some states that are closer to one percent. 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.

It absolutely is, and 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 out a global genomics epidemiological infrastructure. So they have been doing surveillance since April of 2020. So they were one of the first countries in the world to recognize the value of doing genomic sequencing of the positives, identifying how the virus was mutating. And so they started in April of 2020, and frankly, not many other countries followed until December of 2020 when we started to see 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, right, in terms of how this virus mutated.

Yeah, what really is surprising about 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 makes the S protein, and that's important. 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, transmitted to an animal, if it 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 was it for so long mutating undetected. The other thing that's important is that the mutations we're seeing, the 30 mutations 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 we've seen with other variants of concern 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. The second reason it's important is that the S protein is actually a target for some of the vaccines. So the question now is, is it mutated enough that it would escape some of the vaccines? Right, and we will be watching what the South African scientists find on that.

I think we're starting to put it together. Clearly there wasn't at the beginning of the pandemic, and there are lots of elements of a national strategy that are essential. So, you know, one is sort of understanding what are we trying to shoot for in terms of percentage of positives that we want to sequence. Two, how is that going to happen? So how are the samples going to go from clinics where testing is happening to labs that can do the sequencing, and those connections needed to be made. And then there's got to be more work around how is the data going to be shared. And so all of that, I think there are ideas and they're being put together, but there's still work being done.