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Science and Innovations

Weekly Update With Dr. Paul Keim: Tracking The Spread Of COVID-19

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CDC
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A union of scientists in Arizona is tracking the spread of the coronavirus disease through the state’s population with state-of-the-art genetic techniques. It’s a kind of detective work that reveals where the virus came from and when it appeared. In KNAU’s weekly update on the science of COVID-19, Melissa Sevigny speaks with Dr. Paul Keim, founder of the Arizona COVID-19 Genomics Union.

How do you use genetics to track the spread of a disease like COVID-19?

DNA fingerprinting has really evolved from the early 1990s into a very sophisticated tool where we can identify people, plants, animals, and even viruses to their relatives. So when we generate the whole genome sequence of multiple isolates of the CoV-2 virus, we can look at that genomic sequence and we can reconstruct its family history. If you can understand the ancestors of a virus, in this case the coronavirus, well then we can use that to help track the disease as it moves across the landscape and moves across time.

You can actually see how the disease is moving through a landscape just by looking at its genetics?

What you can do is look for common features in animals and plants, and say that those common features are indicative of a common ancestry. Now the virus, what we do, is we have much more robust and comprehensive approach to identifying these shared features, and that’s the nuclide sequence…. And so in this particular case what we’re able to do is we’re able to track the coronavirus around the world and we can trace it right back to its origins in Wuhan. We can do this in such a robust fashion, we can actually put a time stamp or a real clock number on when these events occurred. This is what we call a molecular clock. It doesn’t work all the time for all organisms in all situations, but it seems to be working pretty well for the coronavirus.  

What have you found out so far?

One of the most interesting events in this whole thing is when did this thing start? So it looks like from the molecular clock that the origin of this virus is somewhere around the first part, maybe the last part of November. There’s a little bit of error in this, but not much… Likewise we can look at it on a more regional basis…. So for example, very early on in late January we had one case of COVID-19 in Maricopa County. Turned out this was a person who traveled from China, and sure enough the genome sequence of the isolate from that person traces very clearly back to China… But most of the cases we’re seeing in Arizona actually trafficked through Europe. It really looks like New York in particular got slammed by viruses that came in from Europe, and from there they started spreading across the United States… What we’re able to see is they really started arriving in Arizona in mid to late February.

How specific can you get with the geography? If you take a sample from a patient can you see they got the virus from someone in California verses someone next door?

We can’t at this point…. To do it on a scale where we could actually start to contribute to contract tracing, we’ve got to start sequencing a lot more virus. And we’re going to do that. We’re playing with the laboratory methods to improve the laboratory methods so we can start sequencing thousands of isolates, and then we also have to handle the data, because this is a massive amount of data… It’s like drinking out of a firehouse! You need something to regulate that flow and help you create a flow of information that is interpretable and usable for public health. 

Paul Keim, great to talk to you as always.

Thanks, Melissa.

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