Anne Wyllie: The Saliva Test

Harlan Krumholz: Welcome to Health & Veritas. I’m Harlan Krumholz.

Howard Forman: And I’m Howie Forman. We’re physicians and professors at Yale University, and we’re trying to get closer to the truth about health and healthcare.

Harlan Krumholz: Today, we’re going to be talking to one of our good friends here at Yale, Anne Wyllie, who has just been doing remarkable work in advancing testing for SARS-CoV-2 infection using saliva. And I know that’s going to be of great interest to everyone, but first, Howie, what’s something in the health news that has your attention?

Howard Forman: So, I think it was yesterday, the surgeon general released a toolkit to help individuals fight back against rampant misinformation. And this comes on the heels of a very well-regarded football player having deceived quite a large number of people regarding his own vaccination status, followed by spread of additional information. All of this occurring only because he actually became infected and developed COVID, and it turns out there’s very little legal recourse to health misinformation, and it makes it even more imperative then for each of us to do our part. Our country has some of the greatest free speech protections in the world, but this does come to some extent at a cost, but it comes with greater responsibilities for each and every one of us. And it’s one of the reasons why I’m really glad that we get to do this podcast every week.

Harlan Krumholz: Well, I just say, on that, I was really disappointed that Aaron Rodgers of the Green Bay Packers did that. Look, he’s someone who on the football field I’ve admired for a long time, and people really look to Aaron Rodgers. And then to come out like this, and again, it’s not about whether you wanted to take the vaccine or not, but it’s about whether you told the truth. And then to invoke a Martin Luther King quote—I mean the whole thing was just a debacle. But then to see that the NFL just came in with what really is a very light hand slap on the whole thing. So, the amount of misinformation is just enormous, and it is something that we have to work hard to try to clarify. And again, we need to be careful not to disparage those who have other beliefs but just work hard to make sure that good information is out there for people to access.

Howard Forman: By the way, to our listeners. If anyone wants to ask us questions, ask them by Twitter, ask them by email, we’ll happily incorporate them into the podcast because we really do want to be responsive to you about what you understand and how we can clarify it.

Harlan Krumholz: One of the things I wanted to talk about was actually a paper that I was involved in. One of the things that we did here at Yale was to look very carefully at people who had been coded for having a diagnosis of COVID-19. Now, within the medical record, we have official coders who will go through and assign labels to patients that will help us know what they actually had. And those labels are used by payers—for example, the insurance companies, or by others—but they’re also used by researchers to give us some sense of the healthcare hospitalization and utilization rates for various things. And we did a deep dive into the people who were labeled with these codes as having had COVID-19 and then went deeply into the chart and said, “How many of these people actually had positive testing?” And disappointingly, we found that for someone who had a label, only about two-thirds of them had any evidence that they actually had a COVID-19 diagnosis.

In addition, we also found that among people who had evidence of an infection, almost one in five had no label of having had it in these claims codes. So, there’s both a sort of misclassification, and we’re also missing some hospitalizations, and we’re over-calling others. And so, this is, I think, a problem that we need need to solve within our information systems in this country. If we really want to have a good idea of what the rates look like and how they’re progressing over time and what happens to people who have COVID-19 hospitalizations, then we really need to work harder on improving the fidelity of the information that’s flowing from our healthcare system so that we can track this in better ways. And here, we’re working on strategies around that, but I just want to say that it’s a disappointing part that sometimes we don’t have very much data, but also sometimes when we have data, we don’t know how well we can rely on it to really tell us what’s going on in the field.

So now, let’s move on Ann Wyllie. Howie, why don’t you go ahead and introduce her?

Howard Forman: So, it’s really a pleasure today to introduce Anne Wyllie, who is colloquially known and self-proclaimed the “spit queen of COVID,” and she comes to us though, through a really unique background. And so I’m going to let her just tell us the backstory, but to start off with, I’ll just prompt you with this. I learned what OE means from reading about you back in your native New Zealand, and you go to do this OE, which I now know what that stands for, but I think for our audience, it’s a great way to start.

Anne Wyllie: Yeah, thanks both, and thank you both so much for having me today. And indeed, I wrapped up my master’s in cancer immunology back in Auckland, New Zealand. And indeed, I set off on the very famous OE that pretty much every Australian, New Zealander considers doing at some stage in their life, and that does stand for “overseas experience.” Especially in New Zealand, we’re quite far away from the rest of the world. So that idea that we can get out, go overseas for a year or two and get overseas experience living, working abroad, traveling, Europe or the States. And that—

Harlan Krumholz: I thought that was a walkabout.

Anne Wyllie: That’s more the Australians. The Australians go walkabout. Yeah. Yeah, so I head off to London, but it was 2009. And I think coming straight out of study, as a New Zealander, I just didn’t actually really understand the recession. I didn’t really understand what was going on. But to move to London in 2009, it was incredibly hard to find a job. I ended up working in university administration for a year and a half and had a fabulous time there on my OE, working a normal working week, heading off over to Europe on weekends, traveling around. But in the end, I thought, it’s really time to get back to science. I’ve done this degree, need to get back into it, need to see what I can do with it. And rather, well, actually I tried to get a job again in London. Couldn’t do it. And so I moved to Amsterdam and decided to see where that would take me and yeah, got a job in Utrecht and ended up doing a PhD there.

Howard Forman: And tell us then, so you come to Yale, I believe in 2016, is it right? And—

Anne Wyllie: I don’t think so. Or 2017, yeah. April 2017.

Harlan Krumholz: Oh, I mean, why do you come here, first of all? How do you end up coming to Yale?

Anne Wyllie: Well, I just actually reached out to Dan Weinberger. Dan knew my PhD supervisor. They had worked together actually at Harvard, and I was a major fan of Dan’s work and the methods that he was doing with statistical modeling. I had done the majority of my analysis for my PhD in GraphPad or Excel and knew that there were probably much more robust ways of analyzing data. So I asked Dan if I could come and just do a short internship with him, if I could just come over for a couple of months, learn some of his methods. And he said, “Well, why don’t you come and do a postdoc?” And I thought, well, I’ve just been invited to do a postdoc at the Yale School of Public Health. I guess I should do that.

Howard Forman: Yeah, that’s cool. And so, let’s fast-forward now to January and February 2020, and the pandemic is now on our doorsteps, and a lot of the scientists across the university—Harlan and a group at the School of Public Health and others—are really pivoting hard turns to focus on this. How do you get drawn in from your research on, I think, pneumococcus into saliva testing for COVID?

Anne Wyllie: Twitter, actually. I reactivated my Twitter late 2019, having seen how many academics were on it, using it to share papers, get advice, even recruit people to join their teams. And I thought, that’s it. I’m going to rejoin Twitter. I’m going to use it purely professionally. Not going to follow just friends and family but follow those who are in my field. And late 2019, early 2020, the handful of people who I was following included Matt Lipsitch and Bill Hanage, who also come from a pneumococcal background. But very early on, these were two individuals at Harvard who had a lot to say on the unfolding pandemic. And so I almost had a stream of consciousness from their thoughts—very balanced, very wise takes on everything that was happening.

And while this really pulled me in, I didn’t know how I could possibly help other than give, pass on the information to friends and family until it was very early March, having one of our very last happy hours. And I was talking to Nate about the fact that I had tried out all of these different RNA extraction methods because he’d recommended using some of the cheaper brands, but I was working with saliva as a sample type. And I’d found that some of cheaper brands weren’t efficient enough for processing saliva and that I had to stick to the really expensive brand. And he reached out to me and just said, “Look, we’re having some problems with getting our RNA extraction up and running for SARS-CoV-2. Can we try some of these other methods that you have in your lab?”

So, it was Saturday night after dinner one night. We met in the lab and started running some of the very early samples just to see how they would compare against different methods. And I believe these were still swab-based methods, but even then, the method that I had been using just very fortunately performed much better than some of the other ones that the department was considering for SARS-CoV-2 testing. And so with that, I believe I was recruited and asked to help continue testing for SARS-CoV-2 as the pandemic sort of moved in on New Haven.

Harlan Krumholz: You really are one of the world’s experts on testing now. I mean, it’s interesting how you moved across and established yourself, and the collaboration with Nate just has been breathtaking and so productive and so important. But I was thinking for the listeners, maybe we could just go a quick primer on testing, because I think people still are a bit confused about all the options that are out there. So maybe you could, just for the lay audience, give a lay of the land in terms of what are the options. And people hear these words, antigen, PCR, they hear about “saliva versus swabs” and all these things, and maybe you could just give us a quick overview of how you think about the testing landscape right now.

Anne Wyllie: Yeah, sure. So, I think one of the best things to really clarify is that sample type and test type do still need to be considered separately. That we are considering talking about whether you’re going to take a nasal swab, saliva samples, or that sort of more traditional, but very uncomfortable, deep nasopharyngeal swab that goes all the way to the back of your throat, can sort of leave a burning sensation in the back of your throat for hours or the course of the day.

And so, once you’ve actually got your sample, and what we’re seeing is that a lot of these samples are actually performing very comparably when you’re using a sufficient method to test them. So, as you mentioned, we do have the PCR tests, and we do have the antigen tests. The PCR is still considered the gold standard. It is still recognized to be the most sensitive test that we have for SARS-CoV-2. There are a whole number of different ways of getting to this PCR test, and that can also affect how well or not they work. But pretty much with PCR testing, it is sensitive enough that you can detect very small levels of virus in an individual. And this is important if you want to stop the onward transmission. So you can detect very low levels of virus before someone is infectious or contagious, being a risk to passing on the virus to others. And if you’re very lucky to be able to capture them in that moment, you can stop those chains of transmission.

Harlan Krumholz: And just to say that in terms for people to be thinking about this, the test is actually amplifying the amount of material that we are trying to detect. So the reason that it’s so sensitive, and when we say “sensitive,” it means that if you’ve got it, it mostly will be positive. It can find very small amounts because the actual mechanism of the test is an amplification of whatever it finds.

Anne Wyllie: Yeah, that’s correct.

Harlan Krumholz: That’s the one side, the PCR test. And then by the way, are we trading off when it’s more sensitive? Any downside with regard to the PCR test? What’s the downside of it?

Anne Wyllie: There’s a couple of downsides. I mean, first of all, this relies on a sample getting to a lab, and it relies on that lab processing that sample and giving your result in a timely manner. Because we are only talking a matter of anywhere from sort of 24 to 48 hours of being in that sweet spot where you are not transmitting to other people, and you’re wanting to get that result back before you turn infectious, and before you’re out there spreading it on to other individuals.

And then, the only other downsides to it is that because it’s still so sensitive, as you actually clear your infection, you can still have little pieces of the virus genetic material, the RNA, present in your system, and this could also mean that you’re actually resolving your infection. You’re still testing positive and then trying to make those decisions about, should this individual actually be isolated or are they actually safe enough to return, to return to their places of work, to return to caring for their families because we know that they’re not going to be infectious.

And it’s that information that’s not properly being captured in a number of labs and properly returned to individuals, but at the stage where we’re still really trying to stop outbreaks, stop the pandemic as much as we can, it is sort of one of the trade-offs that we do have, but that’s where antigen testing can come in. So we do know that antigen testing can be less sensitive, but it’s really sensitive. It’s really great at detecting individuals who are infectious, who are contagious, and they can even have a smaller little window. There is a chance that some of them can detect someone just before they become infectious or contagious, but that window’s a lot smaller, but these are great for rapidly identifying individuals who could be posing a threat.

There’s cases where they’ll be using them at hospitals. So if people are coming into the hospital and you’re wanting to make sure, is this new patient, is this someone who we have to really isolate, keep away from others? Are they infectious? Can we determine that? They’re great if you’re at home and if you’re being one of the lucky few who can find these on the shelf somewhere, and you’re starting to develop sort of cold-like symptoms. You can take this and get an idea of, am I at risk of actually having SARS-CoV-2 and passing this off onto other people? And of course, a number of schools are using them. We’ve seen cases where people consider using them before going into concerts or sports games as well. So they can be used outside of the lab. They return a much faster result, so that’s one of the benefits of the antigen testing.

Harlan Krumholz: So what was the breakthrough with the use of saliva? I mean, what was it that you guys came up with that other people weren’t coming up with that suggest, because especially when you’ve introduced it, it was a time when most of the testing was that deep nasopharyngeal sort of collection that is so uncomfortable and difficult. So, what was the breakthrough thinking that led you to be able to take a different approach?

Anne Wyllie: So, I had been working with saliva as a sample type for about 10 years now, I think, as you mentioned, and it was just very, first of all, very early on seeing the supply chain disruptions around nasopharyngeal swabbing, of course, defaulted to the gold standard sample type all across the world based on what is used for the detection of other respiratory pathogens. And so, you suddenly have labs, hospitals right around the world, trying to source these nasopharyngeal swabs. They felt an incredibly short supply. Not to mention, one of the major suppliers of these is in Italy. And of course, Italy unfortunately experienced one of their very large outbreaks very early on when everyone was also trying to get these swabs.

And then, especially seeing it from the research point of view, I mean, we were trying to set up the Yale IMPACT biorepository, where we were trying to collect samples for research that researchers around the university, through the hospital, could better understand SARS-CoV-2 and COVID-19 disease progression. But this meant that we were trying to ask healthcare workers to take additional swabs from patients who are coming in. And of course, the healthcare workers were worried about getting up close and personal, even for an initial diagnostic sample type, let alone taking a second one for research. And as we’ve discussed, these swabs aren’t exactly a delight to have, and they can lead patients to sneeze or cough on an individual. Or of course, many patients were just very hesitant and not really wanting to go through that again, especially if they were feeling poorly or even feeling scared about what it meant if they were going to test positive for this virus.

So just seeing all of these challenges and having just worked with saliva, I mean, I didn’t... I mean, I had worked with saliva for one particular bacteria. I didn’t have a strong reason to suspect that it would work for SARS-CoV-2, but I thought, we needed to have other options and saliva being so easy to collect, you can self-collect it. It doesn’t need a really close interaction with the healthcare workers. People are much more willing to give daily saliva samples than have a daily swab. I thought, is there a way that we can look into this and see if there’s any potential for it? Because it could have just overcome a lot of the challenges that we were facing.

Howard Forman: So, from that, you now have a lab or a nonprofit entity, depending on what you want to call it, SalivaDirect. And you’ve got a 19-member group that functions in this way, and you have a wide distribution that is truly not for profit. I think it’s worth emphasizing that, and it’s open source, right? So you’re not trying to retain any type of licensing fees or anything from that. Why don’t you tell us a little about the operations of SalivaDirect and even maybe a little about the cases of the NBA and Broadway, for instance.

Anne Wyllie: Yeah, sure. So indeed, and so, I mean, I guess getting a little bit to Harlan’s previous questions as well is why and why saliva? And that’s also, as we started doing more and more of the testing, seeing that saliva would work, we just knew that there was going to be a need for frequent repeat testing. And again, saliva was going to be that, but we also wanted to make testing as cheap as possible. I mean, still to this day, so many tests out there are so expensive, which means that only those who can actually afford them can get tested. So, we wanted to make the test as cheap as possible. We wanted to make it as available to as many people as possible, hence the open-source nature of it, hence just trying to give it away.

The operation now, it’s just evolved from being more R&D on a test to rolling this test out and now working with community partners. So we continue to expand our test protocol in response to the laboratory needs. The test is deployed in 144 lab sites in 39 states across the country now, and if a lab has a new instrument that they want to see it because it can help them test the school down the road, we will just work with them to get this instrument incorporated onto our protocol so that they can use it.

We realized that with labs across the country, we were having schools reaching out to us. We were having sports teams, sports leagues, the NBA. I know that Yale Pathology here has also worked with the Women’s National Hockey League as well. And so we realized that people coming to us and then we could reach out to our laboratory network because the other thing that we wanted to really encourage was local testing. I mean, if you can have a local lab providing local community testing, you’re going to get much more actionable test results with faster test reporting. You’re supporting your local economy as well. You’re going to maybe get more better community buy-in to testing if you’ve got sort of maybe personal connections for the lab down the road.

And we also then realized that a lot of these labs were pivoting from that real traditional clinical diagnostic testing to ongoing screening, surveillance testing, testing schools, testing workplaces. And this is something that was also very new to them. So we’ve been working to help develop guidance for them. We’ve helped to develop guidance for schools, just to help whatever way we can to help inform communities about testing, to help support labs with being able to do their testing, and that’s just sort of, that’s where we’re at now. We’re just continuing to do what we can for the communities around here in the U.S., but we’re also now working with labs around the world as well. And trying to just outreach wherever we can. If there’s just anything that we can do to help, that’s what we’re trying to do.

Harlan Krumholz: Yeah. I just want to highlight the fact, from the very beginning, you guys exemplified, I just think, the very best of science. The degree to which you were committed to sharing information, to making this open-source, to not worrying about focusing perhaps on the profit side of it but rather on the public health side of it. You guys are in the School of Public Health. And I just think it was just remarkable. It was sort of, how do we get this information out and how do we enable as many people as possible to use the science that we’ve developed in order to get as many people as possible to benefit from the kind of testing that’s out there?

Why isn’t it more ubiquitous? I mean, why hasn’t it emerged as the dominant testing platform where everyone’s using it? You’re talking about groups that have embraced it, but I still feel that we aren’t at a point where saliva testing is the way to do testing, and what’s holding us back? Why isn’t it spreading more avidly, especially given all the good work that you’ve done and the degree to which there’s no financial barrier to people adopting this and putting this into practice? What is it that’s keeping it from even getting more use?

Anne Wyllie: I think, unfortunately, that it’s just still such a relatively new sample type for most infectious diseases. I mean, until recently, I mean, there’s been some amazing testing to be done for HIV with saliva, and it’s being used for other testings of sort of genetic diseases or even sort of drug testing in organizations. So, it’s not completely unknown as a sample type, but for especially respiratory infectious diseases, it is. And I think, unfortunately, while there are a number of us around the world even who have published on how to take a saliva sample, how to process it as robustly as possible to get very sensitive results from it, and show how well it can work, there’s also been a lot of labs who have thought, “Well, let’s just take our existing methods that we use for swabs, try testing the saliva in these existing methods and see what happens.”

And unfortunately, I mean, when you take a swab, you put it into a buffer that is very similar, almost consistency, almost to water. And now if you think about your saliva sample, it’s not quite this consistency of water. It is more, thicker, little bit, can be more difficult to work with, very variable between individuals. And so, some of these methods that, well, actually a lot of the methods that work for swabs just aren’t enough to process a saliva sample. And so there are a lot of studies that came out when people took the saliva sample, they processed it by this existing method, and it didn’t work. And they blamed saliva instead of saying, “Well, hang on. We wouldn’t have taken a blood sample and done it the same way. We wouldn’t have taken a urine sample, done it the same way and then sort of blamed the sample type. We would’ve gone, this probably wasn’t the best way of actually processing the sample.”

And unfortunately, this is what’s happened with saliva. There are just so many papers that are out there that found that saliva didn’t work for them in their hands because they used the wrong method. But instead of clearly expressing, “Hey, this wasn’t the best method to do this. We should probably go back and look at those ones that did work, build off those, optimize those.” They just went, “No, sorry, saliva doesn’t work.” And unfortunately, a lot of that has gained a lot of traction in the media, and that’s what we’ve also been trying really hard to rectify. I mean, we’ve put together a lot of resources, compiling this, getting a lot of messaging out there, and just showing that there are really some great studies, some great methods that can do this well. And I think, I really hope to think that we can continue working with saliva. However, I mean, again, we’ve seen how easy it is to collect. We’ve seen how supportive healthcare workers can be for it, how willing everyone has to give a sample, that there’s a lot more potential for it. Can we be doing more of our respiratory diseases, doing flu testing, going into schools, getting more regular testing with such an easier sample type? So I do hope it is just a start for it and that we will get there and see a lot more development coming out of it.

Harlan Krumholz: So in a year, in two years, what’s it going to be like? Will saliva be more of a common test for SARS-CoV-2? Will it?

Anne Wyllie: I’m confident. I mean, I was going to say, I would be hopeful, but I also know how much my team has been working on this, how many other people are really excited about it, about its potential, how many people out there in the community are just getting used to it, that I really do think that this has the potential to really transform how infectious disease diagnostics is conducted.

Harlan Krumholz: That’s amazing. I just, I want to thank you. Look, you are one of the heroes of what’s been a remarkable response at Yale and throughout the world, and I just have such great admiration for the work you’ve done.

Howard Forman: No, I just think that among the silver linings that have come from a dreadful time has been having you both doing the great work that you’re doing but also promoting so many others at the same time. You’ve become a mentor to many people, a support of many people. And as you point out, if Twitter did draw you in, you have been very effective on Twitter as well, and I appreciate you very much.

Anne Wyllie: Oh, thank you both for having me. I mean, it’s just, again, the amount of collaboration that we’ve seen over the past year and a half, two years, two years almost, we would not have been anywhere where we are without just so many people throwing themselves into this and just being so open and willing to work together. And it’s brought so many of us together that I’m just really glad that I’ve had the opportunity to work with you both as well.

Howard Forman: Well, that was a really great conversation with Anne. Harlan, what’s one thing that either keeps you up at night or has your interest right now?

Harlan Krumholz: Yeah, I just want to pick up on one thing that Anne said, because actually, that caught my attention and is on my mind too, which is the role of social media in science these days. And of course, social media gets a bad name, and justifiably so, for so many things that are happening around it that are threatening our society. But actually, in science, what I’ve been seeing over the past couple years is communities of scientists rapidly exchanging information, contacts, networking, and helping to accelerate the field through the use of social media. And you know, Anne said, that’s what actually drew her into working on saliva for the pandemic, and I’ve heard this story in so many different ways. And so it’s actually a bright light for the use of it. I’m an avid user of Twitter, and I have found that I’ve learned so much from other people, I’ve connected with people I might not have met otherwise, and it’s fostered a lot of collaborations and idea generations. So anyway, how about you?

Howard Forman: Yeah. So for me, I’m going to pivot to something completely unrelated, and it’s the infrastructure bill, and it too in some ways relates to Twitter for me, because I do use Twitter both for my professional position but also to follow what’s going on in the world. And the infrastructure bill to me is a great example of the glass being at least half-full. It may not be truly inspirational, but this turned out to be a truly bipartisan bill in every sense of that word. It passed through the usual workings of our legislative branch rather than being pulled together in the middle of the night. It provides incredibly important and necessary investments in our country, including broadband to rural areas, trains, bridges, and more traditional infrastructure which has been sorely lacking for decades. And in a time when the workings of government often seem to be lacking, this gives me hope that there are paths that exist for important legislation to pass.

Harlan Krumholz: I’m just glad you’re such a glass-half-full guy. I mean, I feel a bit the same way, but look, this infrastructure bill started with the last administration. By all rights, they all should have come together, and yet only 16 Republicans in the House vote for it, and they’re getting ostracized and targeted, and I just don’t get it. It’s almost like if one side doesn’t want the other side to get credit for something, but look, hey, I’ll go glass-half-full with you today and say, “Hey, it was nice to see it passed, and the country needs it, and that’s great.” So, let’s keep going for it, right?

Howard Forman: Raise a toast with me, yep.

Harlan Krumholz: A half-full, yeah, toast.

Howard Forman: Yes.

Harlan Krumholz: You’ve been listening to Health & Veritas with Harlan Krumholz and Howie Forman.

Howard Forman: So how did we do? To give us your feedback or to keep the conversation going, you can find us on Twitter.

Harlan Krumholz: I’m at @HMKYale, H-M-K-Y-A-L-E.

Howard Forman: And I’m @thehowie. That’s @thehowie, H-O-W-I-E.

Harlan Krumholz: Health & Veritas is produced with the Yale School of Management. Thanks to our researcher, Sherrie Wang, and to our producer, Blake Eskin of Noun & Verb Rodeo. Talk to you soon, Howie.

Howard Forman: Thanks very much, Harlan. Talk to you soon.