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Sequencing COVID-19: What It Can Tell Us About The Delta Variant In Nevada

Dr. Mark Pandori is in a white lab coat, a blue surgical mask and green gloves. He is looking down at a tray with a sample collection of vials placed vertically in individual slots.
Courtesy of Brin Reynolds
University of Nevada, Reno School of Medicine
Nevada State Public Health Laboratory (NSPHL) Director Dr. Mark Pandori performing testing for detection of SARS-CoV-2 at the NSPHL located at the University of Nevada, Reno School of Medicine on Jan. 5, 2021.

The Delta variant of COVID-19 is the most common strain found in Nevada, making up more than 68% of the COVID-19 cases sampled over the last two weeks, according to the Nevada State Public Health Laboratory. KUNR’s Lucia Starbuck spoke with the head of the lab, Dr. Mark Pandori, to learn more about studying the genetics of the virus and what this work can tell us about the Delta variant.

Lucia Starbuck: To get us started, what exactly is a COVID-19 variant?

Dr. Mark Pandori: A COVID-19 variant is a version of the SARS-CoV-2 virus that’s circulating. Initially, there was what you call the reference strain, or the strain that started this, in what we think is Wuhan, China, and that was the original SARS-CoV-2. Now over time, as the virus infects people, its genome changes; that’s its genetic blueprint, its DNA. As the DNA changes, as it goes from person to person, it starts to spread out into different versions of itself. So just like there’s people that look different and have different traits, the virus now has many versions of itself that each have different traits.

Starbuck: So once the virus is detected in a laboratory test, how do you determine it’s a variant? What goes into that process?

Pandori: The next thing that we can do is to take the genetic information of the virus, its RNA, which is really very similar to DNA. What we can do is run chemical reactions on the RNA to determine its sequence. Therefore, it’s called sequencing. And it’s the order of the RNA that defines what kind of variant it is.

Starbuck: What can sequencing tell us about the coronavirus?

Pandori: First, you find out whether something’s positive or negative, and when it’s positive, sequencing can tell you what variant caused that infection. Sequencing also can tell you, if you look at, let’s say, a cluster, if there’s a cluster of cases and we sequence all of them, we can see if a cluster is an outbreak or a coincidence. So you can use sequencing to essentially do investigations, like disease control investigations. That can be very helpful because if you see suddenly 50 cases, let’s say, of the Delta variant, you might think, “Oh, there’s an outbreak,” but, you might, by sequencing, find that, well, there’s different versions of the Delta virus involved in this cluster, and that you’ll realize that there were actually multiple different outbreaks with different point sources.

Starbuck: What have you learned about the Delta variant?

Pandori: Well, we’ve learned that it certainly seems to have some advantage compared to the other variants in circulation because it has crawled up the frequency charts, in terms of how often we see it, and it did so in a rather rapid manner. We do see that a lot of our clusters now are associated with the Delta variant. We’ve also seen variation within the Delta variant. So in Nevada, we’ve seen, let’s say, new variants of that variant. You know, we’ve seen Delta variants that have other changes in them. We’ve learned that this variant seems to be pretty, pretty infectious relative to other versions of the SARS-CoV-2 virus, and it seems to be changing pretty notably in a small timeframe.

Starbuck: So what kind of protection does the vaccine offer if there are these breakthrough cases or infections amongst people who are fully vaccinated?

Pandori: Certainly, yes, there are vaccinated individuals that are getting infected with the Delta variant. A vaccine is not a 100% anyway, so when this vaccine was trialed last summer, and even then, even against the so-called early strains or reference strains of this virus, the vaccine was not 100%. So, seeing vaccine breakthroughs is not a traumatic surprise to anyone in public health. In fact, this vaccine works a lot better than certain other vaccines; even the flu vaccine doesn’t protect everyone. So, seeing breakthroughs does not in and of itself mean that something is failing.

Starbuck: How can the COVID-19 vaccine protect the community against variants?

Pandori: The virus can only change when it goes from person to person to person, and right now, unvaccinated individuals are driving that. So, the idea of these variants being a problem for us, or the future variants being a real problem for us, which is a real possibility that we’ll have a variant that’s a real serious variant, that’s only occurring because the virus is able to stay in the population and continue to infect people. This is yet another reason to seriously consider vaccination because what you’re doing then is you’re eliminating or slowing down the virus’ ability to change. You’re giving it that one less opportunity to roll its genetic dice.

Lucia Starbuck is a corps member with Report for America, an initiative of the GroundTruth Project.

Lucia Starbuck is an award-winning political journalist and the host of KUNR’s monthly show Purple Politics Nevada. She is passionate about reporting during election season, attending community events, and talking to people about the issues that matter most to them.
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