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Genetic Sleuthing Reveals Multiple Introductions Of Coronavirus To Arizona


A new study shows the virus that causes COVID-19 arrived in Arizona in at least eleven separate introductions in February and March. That’s the result of genetic detective work done by scientists at Arizona’s three state universities and the Translational Genomics Research Institute in Flagstaff. KNAU’s Melissa Sevigny spoke with Jolene Bowers of TGen North about how sequencing the genome of the coronavirus can help public health professionals track the disease through time and space.

What can you learn from looking at the genetic material of the coronavirus?

What we’re doing is we’re sequencing a whole bunch of virus genomes to try to understand how the virus is spreading in and around Arizona. The way we do that is we’re sequencing these genomes and looking for these small mutations that will tell us who is related to whom. These mutations are constantly happening. They’re being passed down from generation to generation. So when we see two viruses that share a certain mutation, then we can be confident that they’re related.

So you sequenced the genome of the very first case in Arizona, and what did you learn from that?

Actually the CDC sequenced that first case… This was in late January. A young man was returning from travel and he presented to a health care center with mild symptoms…. He was very quickly diagnosed and quarantined… We were able to show that none of the viruses that we sampled in Arizona were related to that virus genome at all… So public health response efforts really work.

So you’ve sequenced many more genomes since that first case happened in January. What have you learned since then?

What we were able to show is a lot of our viruses in Arizona are most closely related to other viruses that are circulating in other states in the United States…. And we determined that very likely the virus was introduced into Arizona probably in mid to late February, but we didn’t start seeing it until cases starting coming to light in early and mid-March…. This was when the virus really started taking off in Arizona, and it probably all arrived here through domestic travel. Probably not surprising because that was when some of the travel restrictions were put in place and international travel was being discouraged.

One of the things your team discovered was that there were at least 11 separate introductions of the virus to Arizona. I’m curious, did that surprise you or were you expecting that?

It’s not surprising at all that we had that many virus introductions into Arizona. Arizona’s not in a bubble and people are still moving around. What did surprise me is we were able to detect at least 11 different introductions to the virus. Because the way we’re doing that, we’re comparing the genomes of the virus, so these genomes have to be different enough to detect these differences in the virus, so we can trace these lineages or these variants of these viruses back to different ancestors. That’s how we determined there were probably at least 11 introductions. We think that’s probably an underestimate really.

What are the next steps, or questions you still want to answer?

We definitely want to take another big picture look now that we have thousands of genomes sequenced and see how the pandemic has evolved in Arizona, Do we see any of these super spreader events? One of our major goals is really to demonstrate the value of this genomic epidemiology and make it routine, so that it becomes an everyday thing.

Jolene Bowers, thank you for speaking with me today.

Thank you for having me.


Melissa joined KNAU's team in 2015 to report on science, health, and the environment. Her work has appeared nationally on NPR and been featured on Science Friday. She grew up in Tucson, Arizona, where she fell in love with the ecology and geology of the Sonoran desert.
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