SCANning for coronavirus

In the winter of 2019, a series of storms dubbed “Snowpocalypse” dumped more than 20 inches of snow on the Seattle area, forcing the closure of schools and businesses. This weather-induced social-distancing caused flu cases to plummet. What researchers learned from these snowstorms helped prepare them for the coronavirus pandemic and find what, at the time, were the earliest known cases of community spread. Their work has gone on to provide invaluable data that social distancing works to slow down deadly viruses.

Behind every science headline, there is a human story. Hear about the scientific advancements aiming to shape the cures of tomorrow with Lab Notes: A podcast from the Allen Institute. Streaming everywhere.

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Rob Piercy

Before the novel coronavirus became a full-blown global pandemic, there was a worldwide scramble to understand how and where it was spreading, and who was getting sick; critical information needed to guide public health decisions and save lives.

Rachel Tompa

Today, we’re going to hear about a team of researchers in the Pacific Northwest whose work on another virus gave them a head-start on SARS-CoV-2 – and helped them find what, at the time, were the earliest known cases of community spread. Their work has gone on to provide invaluable data that social distancing works to slow down deadly viruses.

Rachel Tompa

I’m Rachel Tompa.

Rob Piercy

I’m Rob Piercy. And this is Lab Notes.

Rachel Tompa

Hey Rob, do you remember the winter of 2019?

Rob Piercy

Yeah, that was what, like a decade ago now? Honestly, with the pandemic I have lost all sense of time. So, maybe it was a century ago.

Rachel Tompa

Yeah, something like that. For our listeners, we’re in Seattle and in early 2019, Seattle had this series of absolutely bonkers snowstorms.

Rob Piercy

More than 20 inches in the month of February. That’s a lot for Seattle. People make fun of Seattle-ites for our wimpy approach to snow. It’s somewhat true, but it’s also difficult to get around this city when it snows. There are a lot of hills around here! Jokingly dubbed “Snowpocalypse,” many of us were stuck working from home and schools shut down for several days.

Rachel Tompa

At the time it felt like when will my children *ever* get out of the house and go back to school. I think it was less than two weeks all together. Can you imagine? Now it’s been what, also about a century since kids have gone to school in person?

Rob Piercy

Six months.

Rachel Tompa

Right, six months. So that winter, we got this little taste of what it’s like to be stuck in your house with no end in sight. But the snowpocalypse also hinted at the events of 2020 in another way.

Jay Shendure 

We'd been collecting swabs, you know, from all of the major hospitals throughout that period and testing them, you know, not only for flu, but also for 25 other respiratory pathogens. And it was this really marked trend in the data where you could see that the fact of everyone staying home for a week or two really kind of seriously interrupted the transmission of any of these pathogens, and the extent to which they were they were spreading.

Rob Piercy

That’s Jay Shendure, a genomics researcher from the Allen Discovery Center at UW Medicine and scientific director of the Brotman Baty Institute for Precision Medicine. He also leads the Seattle Flu Study, which has been kind of rebranded this year, as we’ll get to later. The Seattle Flu Study was an epidemiological study to trace how influenza virus spreads in a large community — Seattle. The researchers would take nasal swabs from study volunteers and analyze the genome sequences of flu and other respiratory viruses in that swab sample. The researchers can figure out how viruses are transmitting based on their genetic sequence.   

Rachel Tompa

This is a concept you might have heard about recently. It’s been done a lot with the novel coronavirus. But scientists have been using genetic sequences to trace the spread of other viruses for a while now. 

The Flu Study started a few months before the snowpocalypse. And they made this interesting observation. Let me just read you the title of the scientific article the Flu Study team wrote on this subject, it’s fascinating in light of where we are today. The title is “Effects of weather-related social distancing on city-scale transmission of respiratory viruses.” 

Rob Piercy

Like Jay said, they got this first hint that staying in our houses, even for just a week or two, dramatically slowed the spread of flu and other respiratory viruses, at a time that should have been the peak of flu season. This hadn’t really been shown on such a large scale before. It was a weather-induced experiment in social distancing. That was the 2018-2019 flu season, and the study team felt well-prepared coming into this season.

Rachel Tompa  

If we could go back to the beginning of the 2019/2020 flu season. How did things start out this year?

Jay Shendure

So, they started out great. *laugh* You know, I think we learned a lot from the first year of the flu study, it turned out it was good that we were prepared early and up and running because it was an early flu season. We were seeing a lot of flu cases early on. And I think largely, the study was on track. And we were already starting to see, you know, looking back at the year one data that even feeding into year two how the genome sequences of influenza could be leveraged to see patterns of transmission within Seattle. And I think we were really digging into them. At the time that things kind of took it took a turn.

Rob Piercy

When was it that there was this pivot? When was the first red flag about this thing that was not flu?

Jay Shendure

I think that the moment that at least this really came onto my radar in a kind of -in-your-face way was we had a PI meeting. I think it was in early January, where Trevor Bedford, who's one of the other principal investigators of the of the Flu study, brought this up as an agenda item. And he'd been carefully reviewing all the available information. And I remember him saying this could be 1918. It might not be, but it could be and I'm worried. And he's the kind of person I think when he said something like that you pay a lot of attention. And that really started us pivoting.

Rob Piercy

Trevor Bedford is a researcher at Fred Hutchinson Cancer Research Center, also here in Seattle. He’s an expert on viral evolution and how viruses move around the world. 

Rachel Tompa

The 1918 flu pandemic was the most severe pandemic in recent history – until this year. 

Rob Piercy

These days, we’re able to test for the genetic material in viruses, in a widespread way. That’s the basis for what the Seattle Flu Study was doing. They use a lab test called PCR to look for a piece of the flu genome, and for other respiratory viruses.  

Rachel Tompa

After that meeting, the Flu Study team put together a PCR test for SARS-CoV-2, the novel coronavirus. They had that ready by late February. Any swab that came in as part of the Flu Study, they started testing for the coronavirus too.

Jay Shendure

Nothing on the first day, you know, nothing on the second day, then on the third day, we picked up a positive test.

Rachel Tompa

Did you guys think that it would be that fast that you’d get a positive result?

Jay Shendure

I don't think we knew, honestly, it was an honest to goodness research question. No one else was testing and they should be right. We had all these samples that were coming in, you know, and were in a position to test on them and none of that testing was happening. We were genuinely surprised, I think, but at the same time, I think we wouldn't have been doing it if we didn't have some feeling that it might have been a possibility.

Rob Piercy

The first known positive case in the U.S. had been in mid-January near Seattle. There were no other positives for weeks after that, but nobody had really been looking for them. The testing criteria from the CDC at that time were really stringent. 

Rachel Tompa

Once they got that positive result of SARS-CoV-2 in the community, that set off a lot of other events. 

Jay Shendure

I remember, I think I just took five minutes, I think, to kind of absorb information and then and then kind of kicked into gear, there's obviously a lot of things that needed to get sorted out. We confirmed the result later that night, we sequenced the genome as quickly as we could, which Trevor then analyzed and suggested that community transmission had been going on for some time. I look back on my calendar for around then and I had a calendar item that says go to Costco. Right. So, you know, think clearly, at least some bug in my head was telling me that this could take a certain turn, it still was a big leap to imagine that things could go from where they were at that moment, with really just a second case to how quickly they would spiral into what happened.

Rachel Tompa

The Seattle Flu Study soon shifted its focus entirely to SARS-CoV-2. Jay and the other researchers partnered with the King County Public Health Department and relaunched as the Seattle Coronavirus Assessment Network, or SCAN, on March 23.

Rob Piercy

The SCAN program is a really simple but brilliant concept where people out in the community become “citizen scientists.” How it works is you go to the SCAN website, enter your zip code and if you meet all of the requirements, they’ll send you a test kit where you can collect a nasal swab at home.

Rachel Tompa

I remember when the study launched, I read about it in the Seattle Times and I was like “Oh, this is cool.” I tried to sign-up, but couldn’t. The site was just full.

Rob Piercy

Same. The first several times that I tried to go to the website, the test kits were already gone by the time I got through. There was just a lot of interest out there in the community who wanted to be a part of this project. What happens though if you do get through, is that a courier delivers a test kit right to your front doorstep. And then you get the distinct pleasure of sticking something up your nose for science. 

Jay Shendure 

Yeah, so let's start with the kit landing on your doorstep, you get it from your doorstep, there are pretty clear instructions in there. And you know, it's pretty simple. You're taking out a swab, which we provide, you're following instructions that are provided and there are videos and other resources to make it as clear as possible for you to swab yourself or your child.

Rob Piercy

So, I am I'm going to share my screen here. And my question is, am I doing this right?

Jay Shendure

Ah, hahaha… Looks to me like you are I think maybe you could go a little deeper, but I think you're doing pretty well.

Rachel Tompa

At this point in the interview, you were showing Jay a photo of yourself taking the test. To describe this photo a bit for our listeners, Rob has his ring-light and tripod set up on his dining table to get that beauty shot of him with a swab up his nose. And you are kind of wincing there, it’s great.

Rob Piercy

Yep… spoiler alert, everyone, Rachel and I both got through on the website and got test kits and then we documented the whole process.

Rachel Tompa  

So, I just opened my package, and there's just a little blue box.

Rob Piercy  

I'm actually pretty excited to do this. I've never been part of any kind of public health study or really any study, at least not that I know of.

Rachel Tompa  

It has a quick start guide like it's an iPhone or something like that.

Rob Piercy  

This is the test tube that you have to put the sample in.

Rachel Tompa  

Remove this swab from packaging. This is the nasal swab right here. Alright, I need to blow my nose. I cannot believe I'm recording this.

Rob Piercy  

Alright, here we go. 

Rachel Tompa  

Ooh, ow.

Rob Piercy  

That's really unpleasant.

Rachel Tompa  

Okay, I had to pause because that was very uncomfortable.

Rob Piercy  

Not quite touching the brain but close. I just really want to sneeze right now.

Rachel Tompa  

Please place the swab into the solution in the provided tube.

Rob Piercy  

Alright, and now we just seal it up.

Rachel Tompa  

That's it. Screw the cap on. And I'm done.

Rob Piercy  

I am curious to know what the result is.

Rob Piercy

So, I send my test back. And I was actually surprised at just how quickly the courier came and picked it up. And within a day or two. I got the results back and... negative.

Rachel Tompa  

Yay! Right. So yeah, I took the test to I think I managed to get into the site maybe a week or two after you did that. And I didn't quite have the same citizen science excitement. It more reminded me of my grad school days, I guess because I used to do a lot of PCR tests.

Rob Piercy

Yeah, important to point out for our listeners here there's only one Ph.D. biologist for whom this wasn't their first rodeo.

Rachel Tompa  

Yeah, that's me. I'm a former lab scientist, I suppose. But yeah, I stuck this while all the way up my nose and mailed it off and then got the results back and… womp, womp -- sad horns.

Inconclusive.

Rob Piercy

Which can happen with these sorts of tests if you don't have enough genetic material on the swab.

Rob Piercy  

You know, for me, being a part of the scan project felt important. Like maybe I could make a difference in some small way and help scientists to learn something about this virus that could ultimately help them fight it. Have you gotten that sort of feedback from folks, Jay?

Jay Shendure 

Yeah, we've definitely got that sentiment in a few different directions. One is just emails or things like that, that are sent to the scan program to the sale through study. And other sometimes we'll you know, we'll get a note clip, like a short, written message or something like that, that comes back with the kit, and will often you know, we'll just post those where people can see them. It is a real big team of people working hard here and putting in, you know, putting in some real hours, including all the techs and the staff who really are critical for making this happen. And so yeah, that feedback has been great.

Rob Piercy

In the six months since the study began, what have the SCAN researchers learned?

Jay Shendure

One of the big questions early on was whether there was some massive reservoir of cases in the community that was going completely undetected. Our testing, early testing so that those early months I think, clearly painted a picture that that was not the case. The overwhelming majority of individuals that we test, who test positive, either have some symptoms, or, you know, know someone who had symptoms, or are a household member of someone you know, with someone who has symptoms or tested positive.

Rachel Tompa

They’re also measuring the prevalence of SARS-CoV-2, or the percent of people who are infected. Their results match what other groups tracking coronavirus prevalence in Seattle are seeing. All these different data-streams eventually feed into the county’s public health decisions around opening or closing parts of our community.

Rob Piercy

In the last few months, SCAN also started tracking behavior through simple questionnaires. In Washington state, we had a mask mandate for the general public put in place at the end of June. 

Jay Shendure

Just in the last several weeks, you know, as kind of the messaging has changed, we've definitely seen that mask usage has increased. But at the same time, we've also seen that social distancing has decreased. And in particular, that decreasing trend has been pronounced amongst individuals in their 20s and 30s, which is exactly the group that we're also seeing an increase in cases.

I think testing is important. And I think testing is a critical part of all of this, to understand what's going on and how things are getting transmitted through the community. But at the end of the day, the most important thing we can do right now is to really get people to adhere to the behaviors that are being recommended by public health. That's the most important thing. 

Rob Piercy

This is just a general stumbling block about public health and population behavior, right? How do scientists and public health experts get people to adopt behaviors that are good for their health?  

Rachel Tompa

It might help if we weren’t all getting mixed messages on the subject.

Jay Shendure

I think that public health officials here in Washington and in King County have been doing an outstanding job, the research community, the medical community, the testing community, you know, a lot of things have come together to work. And so, I think, here, I think we're doing okay, relatively speaking, but obviously, you can't let your eyes off the road. And I think maintaining that it will be important to continue to keep doing all the things that we're doing as well as to keep paying attention to what public health is recommending. And to follow that guidance very closely. You know, nationally, I think the picture is more dire, I think, with a lot of conflicting guidance coming from a lot of different levels. And we need a coherent national plan.

Rob Piercy

So, where does Jay see us six months from now – a year from now?

Jay Shendure

So, I think there's two very different futures six months from now, there's one future in which we have this under control. There's another scenario in which we're still struggling with this exactly the way that we are right now. You know, things bouncing back and forth in terms of opening and cases going up and down in different parts of the country. And so, I think that's very much a choice which of those roads we choose, and I'm hoping as soon as we can, we choose the road that leads us to that first possibility. You know, in a year, I'm reasonably optimistic that some of these vaccines, you know, for which there's encouraging data are going to pan out. And so that's really what I'm, I'm hoping for, and you know, that a year from now I'm getting my kids ready for school and, you know, not having to think about a lot of the things that we're all thinking about right now with respect to whether that's going to happen or not. 

Rob Piercy

Looking farther out — Jay hopes the lessons learned about social distancing during those snow-bound days of 2019, as well as everything they have learned and will learn from the SCAN study, will influence better decisions down the road.

Jay Shendure

And then in five years, this is all a memory and our kids are called the “Zoomer generation” or something like that and also things have flipped on how we view science and public health, in terms of the trust being restored and if anything enhance, and that points us to a brighter future for the next time this happens… which it inevitably will.

Rob Piercy

I’m Rob Piercy.

Rachel Tompa

I’m Rachel Tompa. For more Lab Notes episodes and science research news, visit our website alleninstitute.org.

Rob Piercy

Thanks for listening.