COVID-19 Researcher Spotlight: Interview with Chris Mason

In this video Chris Mason discusses COVID-19 research and collaboration efforts including global metagenomics studies and SARS-CoV-2 detection via LAMP. 

Script

Lydia Morrison:
Welcome to the COVID-19 Researcher Spotlight series. Today I'm joined by NEB Associate Director of Applications and Product Development, Eileen Dimalanta and her long time collaborator Dr. Chris Mason of Weill Cornell Medicine in New York City. Chris really hit the ground running when the coronavirus pandemic began its global spread, and he started with metagenomics studies in Grand Central and Times Square subway stations, but he didn't stop there. He's now receiving public transit samples from around the globe. Chris has also been instrumental in bringing loop-mediated isothermal amplification, or LAMP based SARS-CoV-2 detection methods to communities and he's giving new meaning to the word glamp. Chris, thanks so much for joining Eileen and I today.

Chris Mason:
Oh, thanks for having me. It's a pleasure to be here.

Eileen Dimalanta:
Thank you.

Lydia Morrison:
I was hoping that you could tell our listeners a bit about your COVID-related research.

Chris Mason:
Yeah, happy to, happy as well as exhausted to tell you about it. So I'd say it's been a really crazy few months ever since late February, when it was really clear that the wave was coming our way in New York City, we got hit as most people know, particularly hard. It really started with just ramping up RT-PCR and methods for diagnostics, basic diagnostics at our pathology core and then also at the hospital.

Chris Mason:
The big ramp up in the early days, was to get basic PCR methods up and running, but actually in discussions with NEB scientists like Eileen and others, Nathan Tanner, some the early discussions, even in February, were well are there other ways we could do fast diagnostics and testing. Some scientists from NEB and also researchers in China had a pre-print out using LAMP, which is a loop-mediated isothermal amplification method, that had showed that it worked on ... it was only the first seven patients tested on, but showed it that it was a possible way to detect SARS-CoV-2 in patient samples and looked really intriguing. So that launched, a whole flurry of activity for the past three months on thinking about LAMP for hospitals, looking at environmental sampling in subways, looking at patient samples, partnering with other academic groups, industry groups, nonprofits, all getting a variety of methods out for a rapid testing, which is LAMP, which we'll probably talk about a little bit more, but then also a more in-depth profiling of patient samples.

Chris Mason:
So for every one of the first patients that came through the hospital, the first 735, we did for almost all of them RT-PCR and then LAMP, and then also RNA sequencing with NEBNext kits for a ribodepletion and look at the total transcriptome, to see everything from the NP swabs, the nasal pharyngeal swabs, what's happening at the site of infection and what can we learn about the virus, the host response, and also the RNA biology, really what's happening of where the infection rate is occurring. So all that's happened, almost all of it with NEB reagents actually. So it's all really been powered by a lot of the supplies for rapid testing, as well as in-depth transcriptome profiling.

Lydia Morrison:
Well, that's great. So how does those different methods compare? How does does the LAMP method compare to the qPCR?

Chris Mason:
This is one of our first questions is, LAMP was first published by Japanese Group in 2000. So in some ways, it's decades old. It's not as old as say PCR methods in terms of development, but it's an amplification method that is a cousin of PCR in concept, except that as the name implies, it's isothermo, so you don't have to cycle through different temperatures. You can do it at the same temperature. There's even a Twitter post of someone who did it in his kitchen last week, who if you heat a certain ... seven deciliters of water to boiling and you add three deciliters of cold water, then you can actually run it on your stove top. So it's very portable and amenable to low resource settings. But, because it is in some sense simpler, there's been a question of, well, how would it compare?

Chris Mason:
So we did comparisons to RNA sequencing and RT-PCR, and found a correlation around .8 or 0.9, depending on which subsets we looked at. So it was very correlated in terms of a high viral abundance or medium or low, you could see pretty good correlation. We also observed that, obviously it's faster. The only difference was that you'd have to look at very low viral abundant samples, we'd start to see more variation, but that's true for any method. So if you look at RNA-Seq, or LAMP, or other diagnostic approaches, when you get low copies of any molecule, you get more noise as you get towards that sensitivity threshold.

Chris Mason:
But we put this online, worked again with multiple NEB scientists and some are on this call. So we put it online and actually eventually worked with Color Genomics. They also took early versions of the protocol and got it working at scale on Hamilton robots and it got FDA EUA approval, so now it's being used for diagnosing actually over 10,000 samples per day in San Francisco.

Lydia Morrison:
Oh, that's incredible. I didn't know they were up to that scale now.

Chris Mason:
Yeah, yeah, well allegedly, by text, up to 14,000 was the maximum per day. But that was actually why we really wanted to start to work with other groups and researchers, academic sites, commercial sites, is we've even started a consortium of LAMP researchers if anyone's interested because I kept ... My inbox was full of questions about our pre-print and ideas and so I said, "How about we just have a weekly call with everybody because I keep having lots of emails with the same questions?" And so now we have a Global LAMP Consortium or GLAMP, which is like glamor camping. It's kind of like that, but nothing like that it's very-

Chris Mason:
It's just the name, but it's been an extraordinary time because everyone, almost everyone, not everyone, but almost everyone is sharing protocols, methods, techniques, ideas, their failures, which are very important in this stage of a pandemic, okay, well what worked, what didn't work? Even on the call just last week, ways to do enrichments. We all know that SDS and other surfactants are bad for LAMP reaction, but someone was using Ficoll enrichment last week, which was kind of an ah-ha moment on the call and I was like, "Wow, never thought to even try Ficoll for ... " offer basically nucleating the reaction and increasing the stoichiometric density, so the reaction goes more efficiently, which is like, "Oh, that's a good idea." So it's been lots of long hours, but lots of fun collaborations.

Eileen Dimalanta:
Chris, you mentioned your pre-print and collaborations and we've had calls in the past few months, as you said. I think the pandemic's really forced global collaborations. Can you speak a bit about what you think the value of these pre-print services are, especially during the pandemic and how do you see them being used long-term in the future?

Chris Mason:
Yeah, it's been really interesting on Twitter, which is a major platform for presidential policy now as well as a great place for science exchange. It has been really extraordinary to watch the speed with which science has moved. It's an essential platform, as I think most pronounced in evidence of it is that Nature ... when we submitted the paper to Nature, you have to submit it to a pre-print server when you submit to Nature. I don't know how many other journals have had this policy, but one of the flagship journals of all science is requiring it now. So it's interesting that I had an email exchange with, I will just call an old school professor, in that he's over 60. I don't know, I'm getting close to old school, I'm like mid school.

Chris Mason:
He was actually insisting by email that he didn't want to put it on a pre-print server yet because he had this really big repository of NP swabs and other a clinical metadata. I said, "Well actually Nature requires you to," and he couldn't believe it, so it's really ... I think for anyone that's been thinking about science in the past two decades or even century, that idea is really, is new, at least in the biological sciences, but keep in mind for physics they've been using arXiv, the pre-print server actually since the late '80s. It's interesting and it really depends on the field you're in. The biological and medical science is a little bit more new to this idea, but in the physical sciences, they have been doing it for a long time.

Chris Mason:
But in the case of a pandemic, it's both good and bad because really sensational reports can come out and then people get distracted. But the better thing is within a matter of days usually, there's enough comments. It's pretty much clear the field has commented on something, whereas it's actually worse and slower for most journals. The chloroquine, hydroxychloroquine, trials that this random group called Surgisphere, they published a paper in The Lancet and then didn't release any of their data, any of their methods. It flew through peer review, it didn't really get peer reviewed because no one could look at the data. It is actually, if anything, it's further highlighted the challenges of the current publishing system that it's not ... I mean, no system is perfect, but in the case of pre-prints, the corrections are a matter of days where with papers, it can take weeks sometimes, or months, or even years. So I think it's been great, it's been essential. Mostly great.

Lydia Morrison:
So you mentioned that a lot of your work was on nasopharyngeal swabs, have you tested other sample types as well?

Chris Mason:
Yes. So since then, and even in the pre-print that we put online, there was some oropharyngeal, there is an ongoing debate about what is the best place of the body to trace the virus and even our fundamental knowledge of the tropism of the virus, or where's the density of the virus in the different parts of the body, the tropism just refers to the tissue specificity of where the virus goes and populates. We're still learning about that about SARS-CoV-2. But we know at least from ... there's a group, Anne Wyllie at Yale, published a paper saying that saliva is better than NP swabs. Other groups have said that NP swabs are better than any other collection site. They might both be right, because it might just depend on your state of infection and where you are on the trajectory of your infection.

Chris Mason:
So basically, the earlier time points have a lot more virus for almost all parts of the body, but the virus has been seen in stool as well. So we've begun looking at stool samples, including sewage and there, most of the virus does not seem to be infectious, but you can see it in people even weeks after they have no symptoms. So, we've seen in other parts of the body, but we're focusing almost exclusively on saliva. Actually, the slogan for our working group now is Saliva Is The Future, that's Ted David who said that that day, but we're hoping ... it's just so much easier to collect. So we know it can be useful and is either as good or maybe slightly worse than NP swabs. If you think about testing, people going back to college, elementary school kids, large employee populations from whole companies and municipalities, you can't jam a swab up people's nose, it's risk to the healthcare worker, it's uncomfortable. It's the equivalent of a cranial colonoscopy with no sedative, is what I like to call it, which is totally gross but I think illustrative of the process.

Eileen Dimalanta:
Colorful.

Lydia Morrison:
Yeah, it does sound illustrative of the process, yeah. I think everybody would really appreciate having to do that less in terms of testing.

Chris Mason:
For sure.

Lydia Morrison:
So you also tested samples from subways to look at the metagenomics data. How did you collect those samples?

Chris Mason:
Those were at Grand Central and Times Square and that was being done right at the beginning of the outbreak in early March. I have a penchant for subway sampling ever since 2013, when my daughter would put things in her mouth that she grabbed on the subway or lick subway poles, I became immensely curious. One of the best parts about science is just to be very curious about things, because it leads you to interesting places. So that's been part of an ongoing study to look at the genomics and also RNA viruses that are in different surfaces around the world, in public transit spaces. So there, we so far had tested negative. There was actually one LAMP reaction that turned slightly orange, but it didn't show up when we sequenced it. So we think it was maybe ... Really, even by LAMP or RNA sequencing, we don't really see much evidence of the virus in the early days.

Chris Mason:
However, we did just finish a big hospital study with NorthWell looking at patient rooms before and after they check out that are COVID positive and we're using LAMP right there to test it in the room and then also doing sequencing and RT-PCR, and we can for sure see some of it in the hospitals. It's not surprising, there are patients there, but the other thing we're putting on piloting out is getting it so you could work, so you can maybe do a really quick test in a room with LAMP to see, "Okay, is it here? Yes or no." We're working on that with NorthWell now, but the subway is a part of a broader project, it's called MetaSUB, which is the metagenomics and really ... it used to be called metagenomics, but now it's really meta-transcriptomics because we're looking at RNA.

Chris Mason:
So I think we have to recall consortium or rename it as metaomics of subways and urban biomes, is what it stands for, MetaSUB and then it links to ... within that group, there's a MetaMed, so looking at medical environments, MetaSew which is sewage, MetaCats, looking at how many cats are carrying coronavirus. We're launching that this week, so if people want to know what's in their cats, I think ... Well, I'm curious, we have two cats. I've looked at them suspiciously ever since we knew that cats can carry it. Although to be clear, there's no evidence of feline to human transmission yet, it's usually the other way around. Usually we're just spewing it onto our cats apparently, but there's very limited data. So anyway, yeah, we've done a little bit of subways that's in review as well and more work coming from the hospitals we use with the same protocols.

Eileen Dimalanta:
Do you think the subway study will go global?

Chris Mason:
Oh, it is. It will go viral. So it has already actually we have now 12 different hospitals repeating the MetaMed study and should be 51 cities who'll repeat the surface sampling. We just got some of the first plates back from Krakow in Poland and we're getting some from the UK tomorrow. So we're going to do a uniform extraction processing, actually that's also with the NEBNext ribodepletion RNA-Seq kit. So we're doing LAMP on them, basically aliquoting and doing LAMP and then RNA-Seq and we just got the first 300 samples back actually, that was a lot of .... Using the low input hospital samples. The only challenge with low input RNA is you have to do a little bit more PCR to actually ... there's not that much material. So we've been doing 18 cycles. So it increases the duplication rate when you do sequencing, this is a bit of technical, I don't know who's going to be in the audience for this podcast, but as a caveat, when you go to low amounts of RNA, the only challenge is you have to amplify more and then you get a little bit more duplication rate. But I just got a link last night from David Danko in the lab who's working on the data and you can very clearly see though the RNA-Seq picking up the SARS-CoV-2 from the hospital samples.

Eileen Dimalanta:
Wow.

Chris Mason:
So we'll get more from that global ... We'll probably finish all the extraction in the next few weeks and the next sequencing over the summer, but it'll be a really big global data set of what's on the surfaces during a once in a century pandemic.

Eileen Dimalanta:
Wow. Are you finding it in places that are unexpected, even in hospitals? Like, "Wow. I didn't think it would be there."

Chris Mason:
Yeah actually, interesting ... maybe at some point I have to give a talk with slides to show but interestingly, one of the more surprising places was ... we see it for example, the bedpans in the patient rooms and we had actually just got the updated draft of this paper. So again, this will probably be at least in a pre-print for ... depending on when this comes live, we could send a link to it, but we can see it, next to the bedpan, when the patients go to the bathroom, it's in their bathroom, when their COVID positive, it looks like it's ... it seems to be somewhat correlated with the CT threshold that was found in the patient but not always, sometimes people are super spreaders, but don't have as much, it seems in their NP swab.

Eileen Dimalanta:
Oh interesting.

Chris Mason:
But the surprising thing was really that in the bathroom, you'd think, where would it be? It's definitely there, but the place that had it the most was actually on the ceiling and we think it's because most of the toilets and hospitals are open, so when you flush it, you basically just aerosolize whatever's in the stool and I think it goes to the ceiling. So we actually swabbed the-

Chris Mason:
So yeah, you're making an appropriately gross face. I don't know what to call it for ... you know like nuclear fallout can happen. It's like fecal fallout is what I think... Yeah, so that was surprising and we're looking more into that, but we're sequencing those samples as well as the RT-PCR.

Lydia Morrison:
Yeah, that's disgusting.

Chris Mason:
There's is a big debate about should men close the toilet lid down or not, and men don't do it or who should do it? There's no ambiguity or everyone should just close the toilet, there's no-

Lydia Morrison:
Everyone shut the, yeah.

Chris Mason:
... anyone who doesn't do it is failing humanity. So just everyone put the lid down, please.

Lydia Morrison:
I couldn't agree more. So you mentioned briefly that you're involved in some COVID research consortiums you've gotten together some ... I mean, I know you have a lot of collaborations, so you mentioned GLAMP or is it glamping?

Chris Mason:
The GLAMP consortium I suppose, yeah and MetaSUB.

Lydia Morrison:
Could you tell us a little bit more about those groups that you're involved with?

Chris Mason:
Yes. So, the GLAMP consortium is a public private partnership, if you will. Anyone's welcome actually, explicitly defined as a pre-competitive space for people to share ideas. So people may take some of those ideas and commercialize them or optimize them, tweak them, that's great. It's similar to what actually ... NIST does this for some standards groups, the National Institute of Standards and Technology. They often define their work as a pre competitive space. So, get all the industry players together, the government groups, the academics, and say, "This is a place for exchange of ideas that is before you go out to try and commercialize something." That is the ethos and the structure behind the GLAMP group. It's open to anyone. It's just a call to share ideas. There's a Slack channel, a Google group and an exchange.

Chris Mason:
It really is meant to be an open forum for, for thinking about ways to address the pandemic, so that's been ... Again, it just started because I kept emailing people. So I just took everyone I was emailing with and made one big list and said, "Okay, let's all I'll talk once a week," but also we've been chatting a lot with Eileen and other NEB scientists also very frequently, sometimes daily depending on protocol iterations, to think about how we get saliva to work. It's been a really great collaboration within NEB and our lab, and then also with the whole consortium. There's one other group called Testing For America, which is a nonprofit I helped found a month ago during the pandemic to help also invest in more testing methods. So that's a philanthropic effort just to get more investment in, variations of LAMP for example, or another protocol called a LAMP-Seq, where you actually can do a quick LAMP reaction with a barcode or a swab seq, or even Nanopore methods we've been looking at, just came out, which we had some data about three weeks ago and then Oxford Nanopore had a LamPORE protocol that just got released.

Chris Mason:
I mean, I think in the early stages of this pandemic, we don't know what's going to be the best protocol, what's going to be the most scalable. So it's a lets launch as many ships as possible and support them all at launch and then we don't know which ones will make it the farthest in the ocean of uncertainty, I guess, is where this metaphor is going. But we want to have a exchange where everyone can at least launch their boats and then get as far as they can.

Lydia Morrison:
Absolutely. Thank you so much for, I think your efforts in that, certainly the coronavirus pandemic has brought to light the importance of global collaborations, I think.

Chris Mason:
Yeah, definitely.

Lydia Morrison:
Yeah, and a lot of the individual scientists wouldn't be able to make the great leaps and bounds, I think in discovery, without the immediate sharing of information from the pre-prints and without these global collaborations. And thank you for setting up consortiums to help answer everybody's questions and to help drive the research forward.

Chris Mason:
Yeah. Well, I feel like it's my duty as a human, I think, but it's also a sanity check. It's much more efficient to have a call with a hundred people interested rather than a hundred individual calls. So some of it was just for my own sanity I suppose. But also it's been really great to see people ... it's exactly, I think what when we were all kids thinking, "Oh, I want to be a scientist," and science is collaborative and you have ideas and there's no ego, and everyone's just hoping to make the world a better place. It's maybe the closest I've seen to that ideal scientist space that scientists have ever been, but there's still egos and still people trying to do the best of one thing, or get the fastest or best paper or method, or some people also trying to ... a lot of people are trying to pivot their business to somehow surviving COVID. So people that have companies, some of them are in this because they need to do something, whatever business model they had before may no longer be relevant, or it won't be relevant for another six months. So it's a really unusual time, but it has been the most selfless I've ever seen the entire global research community. It has been really inspiring.

Lydia Morrison:
Yeah. Some silver linings amid the crisis. Nice to see. Thank you so much for taking time out of your schedule to join us today, Chris.

Chris Mason:
Great. Well, thank you. It's a pleasure and thanks for making so many awesome reagents and putting them onto fountains that you can grab enzymes on. I've heard rumors that there's fountains of enzymes on campus that just shoot up and you can take a cup of and get your enzyme, is that true?

Eileen Dimalanta:
Yes, totally, yeah.

Chris Mason:
Okay, good. That's what I've heard, good.

Eileen Dimalanta:
There's another one about unicorns, that too.

Chris Mason:
Great.

Lydia Morrison:
You'll have to come see for yourself.

Chris Mason:
Yes. Yeah. I would love to come back. I've been there a few times, I guess, more than three times I think. So I'd love to come back, once we can start to see other humans again in person I'd love to go back, yes.

Lydia Morrison:
Well, we'd love to have you. Thanks again Chris.

Chris Mason:
Great. Thank you very much.

Lydia Morrison:
Hope you enjoyed this episode of the COVID-19 Researcher Spotlight Series. Catch our new episode in a couple of weeks when we switch back to podcast format and I interview Dr. Naama Geva-Zatorsky of Technion, the Israel Institute of Technology. Namaa's group developed a protocol for detection of SARS-CoV-2 RNA directly from nose and throat swabs, as well as self-collected saliva samples without the requirement for RNA purification. This method utilizes reverse transcription loop-mediated isothermal amplification, offering rapid results to enable successful community surveillance.


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