On how the Genome Center collected these samples
So we actually start off by doing what I call the primary test – a COVID-19 saliva test for UC Davis … that allows us to have access to a good sampling of the community’s COVID cases.
We were able to do a million tests by tapping into some of the high throughput technology from the agricultural sector, which lets us do a lot of qPCRs. Once we have the positive test, we can take those samples and look for the mutations that define these variants.
So the CDC and WHO decide which variety of COVID is of concern … [there are] a lot of different ones.
Delta [is the most prominent variant]. But, we take a look at 11 places in the genome and see if there is a mutation or not. Then that pattern of mutation versus not mutated sites tells us which variant it is. We look for all the variants that the CDC has identified …
And as our capacity at the genome center has increased, we have increased our spread. So it started with the Davis community, now we’re at the Yolo level, especially in schools.
We do get some positive samples from neighboring counties, just for genotyping, not for testing.
On the most significant challenges UC Davis researchers face with tracking COVID-19 mutations
I think the challenge is really keeping up with the speed of the changes and the speed that these variants move.
That’s where genotyping is really an advantage. So once we know what mutations are present in a variant of concern … we can look for those mutations and then get results in a couple of days and pass those results on to the county in real-time — unlike sequencing, which has its advantages in other respects.
We’re lucky because genotyping is a lot faster, so we can tell our county health officer when we see something within days, not weeks.
On what UC Davis’ lab can tell us about omicron and other variants in our region
I have to say, pathogens are always surprising. I always am amazed at how much variation they can create. So delta came into our region, well, became dominant in our region in late July, August.
Most of the samples that I get are delta, and that’s continuing to dominate the trends.
I mean, we see more and more news stories about people having omicron that did not internationally travel, so it’s obvious that it’s here and it’s just a matter of time.
On if the omicron variant has increased the demand for their lab in other counties
So the demand for just COVID testing is independent of omicron, but the demand for genotyping has increased. We’re hoping to get some counties back that were interested before delta.
They were sending us samples, but then when delta was dominant, they didn’t really care so much. Everybody knows they have delta.
I think it’s definitely too early to tell the impacts. I don’t think we know what omicron is going to look like. I do think we will see some spread of omicron [throughout the holidays].
