COVID-19 Researcher Spotlight: Interview with Nathan Tanner

Hear how loop-mediated isothermal amplification from New England Biolabs is being used to develop COVID-19 detection methods and diagnostics.

Script

Lydia Morrison:
Welcome to the COVID-19 Researcher Spotlight Series. Today, we're speaking with Nathan Tanner, who's a senior scientist here at New England Biolabs. NEB's products are available for research use only. However, we've been supporting customers who are working with these reagents to develop diagnostic tools and vaccines for the SARS-CoV-2 virus. Nathan has been involved in many of these collaborations, in addition to the development of NEB products that have been used in COVID-19 related research applications.

Lydia Morrison:
Hey Nathan, thanks so much for taking time out of your schedule to be here today.

Nathan Tanner:
Sure, Lydia. No problem.

Lydia Morrison:
So I was wondering if you could tell our listeners and viewers a little bit about your recent publication, your preprint in MedRxiv.

Nathan Tanner:
Sure. So my lab at NEB focuses mostly on isothermal amplification methods and tools for simple diagnostics and things that people could do in the lab. And as the COVID crisis started up, we thought it was a good opportunity to just develop the potential for use of Colorimetric LAMP, one of our favorite of the simple tools for real diagnostics. So back in January sequence was available, we designed some primers, tested it out in the lab, just proof of principle. And then through a collaborator here at NEB, we had a connection to the Wuhan Institute of Virology, where they were obviously collecting lots of real samples at the time. So, we sent the LAMP information and some materials, they tried it out on just a few.

Nathan Tanner:
It's a small number of real samples, but performance was very good and it matched with qPCR. So we put it together and put it up as quickly as we could. So preprint services these days have been a great avenue for sharing information quickly. Peer review is excellent, but tends to take a while, so we wanted to share it as soon as we could. So we got our preprint up by late February. We weren't the only LAMP assay out, but a lot of people are doing the same thing as us and it was a great way to show off Colorimetric LAMP and really, hopefully show the power of a simple diagnostic to really be used for public health.

Lydia Morrison:
Yeah, absolutely. And what kind of samples was it originally tested on?

Nathan Tanner:
The very first ones, we had no samples at all, just RNA and DNA substrates, the lab in Wuhan was using extracted RNA from nasopharyngeal swabs, which were the standard at the time and are still the standard now. In the meantime, there have been an explosion of new sample types and test being used, but the original ones were just NP swab.

Lydia Morrison:
So, what makes LAMP so advantageous for a diagnostic assay?

Nathan Tanner:
Yeah. So the standard for molecular diagnostics has been and remains qPCR. Most of the tests being done every day, all around the world are RT-qPCR, and those are excellent. They tend to work very well, are very sensitive, but they require either sophisticated instrumentation, you have to have a qPCR machine to do the actual test and usually automated or sophisticated sample prep upfront. So these pipelines work and are great, but there's such a need for expanding testing right now. LAMP can help fill a need. It's a single temperature. You can use a very simple instrument. Our Colorimetric LAMP can be done in hot water. You don't need an instrument at all, but that's sort of a new paradigm for molecular diagnostics. We've talked a lot about democratizing diagnostics, taking things out of the lab and LAMP and other isothermal methods are a good way to do that. You can work at the very simple end, like I mentioned, with just hot water and eyeballs, or you can do high throughput automated things, if you want, still a much faster, easier way than the qPCR test.

Lydia Morrison:
Absolutely. And do you think LAMP is better suited for a research use, or do you think it's better suited for use in a clinical setting, or maybe even use in a home setting?

Nathan Tanner:
All of the above, I think. The research use is obviously where NEB is most comfortable and where most people get started. This is a new technique to most folks. So what we hope to support in the short term is getting the master mix and some primer sets in their hands, letting people try it out, compare performance, evaluate different sample types. Then move along the diagnostic approval path to EUAs or FDA approval. And several companies have already done that with LAMP, but like I mentioned, it's amenable to high throughput testing where you can take just a simple plate reader measurement very fast. You can put LAMP plates in the oven for 30 minutes at 65 degrees.

Nathan Tanner:
And there's a lot of simplicity advantage for really large scale testing. And at home test comes up a lot. There are several approved at home collection devices already, but the real power for at home testing would be rapid results, broad access. Everybody could do it. And this is a great idea. There's several companies working on doing it. And then isothermal method is a good way to do it because you could use simple battery power, hot water, like I mentioned. So as the tests come along and the regulatory environment shifts, I really do hope we get to an at home testing situation.

Lydia Morrison:
Yeah, me too. It certainly seems like that it's something that would give people a lot more peace of mind and really help facilitate return to office spaces, return to work, sort of more of a return to normal life.

Nathan Tanner:
Yep. Absolutely.

Lydia Morrison:
Have you seen a lot ... you've mentioned that there have been several studies using LAMP, other people using studies with different samples. Are there any publications that stand out in your mind that you want to share with us or any other collaborations that you've been involved with?

Nathan Tanner:
Sure. So like I said, our preprint was very simple and it was very early, so it showed the principal and got a lot of attention, but around the world there's been a lot of interest in taking what we did and making it better and we've been doing the same. So since ours came out, I'll tout our own preprint first, we just put one up on bioRxiv showing new and improved LAMP primer sets, as well as an additive quantity in chloride that you can add to the reaction to really boost the sensitivity. That was where the early reports fell short, was on sensitivity, so we've worked hard to improve that. And so have a lot of other groups, there have been a study we collaborated with from Massachusetts General Hospital, taking universal transport media samples and very simple, or almost no extraction of those and putting them right into Colorimetric LAMP. So, that's really good and it's a real clinical validation of the test.

Lydia Morrison:
And those would still be nasopharyngeal samples?

Nathan Tanner:
Yes. So those were nasopharyngeal swabs put into transport media, and then that media just used directly in LAMP and they showed that simple heat treatment step works or a very crude, silica bead treatment that came from a lab at Harvard. Brian Rabe another person you've talked to – that really improved the performance. So, that's when we liked a lot and like to point people to just for the clinical validity, there've been a couple of preprints showing more high throughput testing, one from Heidelberg and one from Washington University in St. Louis where they pick large numbers of samples and screen them with absorbance measurements in a pathway, very similar to Emergency Use Authorization approved tests, from Color Genomics, doing Colorimetric LAMP at the large scale. Another one that I think is good called EasyCOV, a company in France, put this out, it's a direct test from saliva. Spit in the tube and then do LAMP and they add a color indicator at the end. So, that one's pretty nice.

Nathan Tanner:
And then the others, I think are interesting are for extremely high throughput combining LAMP with sequencing. So there's one called LAMP-Seq. And then Oxford Nanopore has a method, LamPORE that could potentially pool thousands, tens of thousands, maybe hundreds of thousands of samples for really large scale testing by a combination of LAMP and next generation sequencing. So, that's just a few, there's dozens, different methods are being used, different kinds of detection, a lot of combination of LAMP and CASS enzymes, which I think is really interesting. So, there's a lot going on, NEB wants to be in a position to help it all. And hopefully some of these really make it to testing real people.

Lydia Morrison:
Yeah, I hope so. Do you think that there's a big difference between the viral loads and therefore the detectability of the virus in nasal pharyngeal swabs, compared to saliva or compared to like a more simple oral swab or nasal swab?

Nathan Tanner:
Yeah. That's a good question. A lot of labs have looked at saliva in particular just because it's so much easier to collect than a nasopharyngeal swab.

Lydia Morrison:
Yeah. I heard those are terrible.

Nathan Tanner:
I haven't had one myself, but they're supposed to be very unpleasant and if you don't do it right, you can get a false negative. So saliva could be much easier to get. It's a tougher matrix to process. You have to worry about RNases being present, the viscosity, pH for the Colorimetric LAMP matters. So it requires some treatment. There have been reports, like a good one from Yale came out showing that a viral load in saliva was higher than that from a nasopharyngeal swab. Other report suggested it's lower. So I won't claim to know for sure, but it definitely seems to be a usable matrix. And there's a couple at home collections now that use saliva and a few tests are using a swab from just the front of the nose. So much easier to collect than the one that goes all the way back. So some of that will make the testing much more simple and pleasant.

Lydia Morrison:
And what about sputum? Are people looking into using that too, or is that again a mucus that's a little bit harder to get to, like not everybody can bring that up on cue, so ...

Nathan Tanner:
Yeah. I think that's the limitation we've heard from clinical folks that it's a commonly used matrix. It's very challenging. So, you tend to validate your tests on the toughest sample you're going to use. And it's always been sputum because it's really viscous, you have to treat it and solubilize it a bit. So nobody likes it. But if your test works on that, it'll probably work on anything else. Early we were hearing that a lot of the COVID patients couldn't really produce much, sort of a dry cough and weren't really producing a lot of sputum. Some tests have indeed used it. So it's a matrix that will continue to get clinical attention, but probably not something for an at home or point of care test.

Lydia Morrison:
So is there anybody else that you're currently collaborating with?

Nathan Tanner:
I'd say we have tons of collaborators right now, which is really exciting. So once our preprint came out, people started asking from around the world. So we have conversations multiple times a day and not just me, other people at NEB, about how to do LAMP, how can they use our LAMP test, which we don't really have one, but we help them get theirs set up. So, I'd say hundreds of collaborating labs worldwide, but the really close relationships, we've had a good partnership with Massachusetts General Hospital. As I mentioned their preprint a little while ago, that's been very good. And Chris Mason's lab at Cornell, put out a nice preprint with a lot of sequencing data on COVID samples collected around New York and they've put together a global LAMP consortium that meets once a week and a hundred people or so trying to do LAMP from all around the world get together and share tips. People show data. So it's been really exciting to get that up and going.

Lydia Morrison:
That's amazing. Where do you see COVID research heading in the future?

Nathan Tanner:
I think there'll continue to be a big push for diagnostic tests, the NIH RADx program, for example, is putting a lot of money into novel diagnostic tools, so things that will enable field and point of care and hopefully at home testing. So, that'll really shift the paradigm of how diagnostic testing works. And I hope it leads to just more tests all the time. So if we end up testing more people for flu, wearing masks and things like that during flu season I think will help keep a lot of people safe and a ton will continue to go on, on the biology of the virus. I think we obviously don't know that much. It's so new. How do you get it? Super spreader phenomena and things like that. There'll be a ton of research continuing and diagnostic tools will be important to help keep that going.

Lydia Morrison:
Certainly, do you have any stories about something good that's happened during quarantine or have you been able to draw any silver linings from this crisis?

Nathan Tanner:
Yeah. Like everyone it's been very stressful and the news is terrible all the time. So, it's hard to feel positive sometimes, but being a scientist right now, there's been a lot of fulfillment in just contributing to public health. NEB makes enzymes, but our enzymes right now are being used to help people. And that's great. And just the worldwide scientific community has shifted overnight into supporting COVID testing and viral research. So a lot of the collaborators we're working with aren't diagnosticians, they could be cell biologists or genomics researchers, but they've shifted their labs into supporting COVID tests. And a lot of good has come out of that. So it's nice scientifically to all pitch in together, everybody used their brains to try to help. And I think it's been a real worldwide effort and it's great to be a part of that.

Lydia Morrison:
Yeah. I've certainly heard that sentiment echoed by others that I've spoken to. It's nice to see the free sharing of data. It's nice that the systems are in place now to allow the open access sharing and preprint sharing so that we can get some of this information out there faster. More great minds working on the same problems and working towards solutions that are going to benefit the globe.

Nathan Tanner:
Yeah. Absolutely.

Lydia Morrison:
And to that end, we certainly appreciate your efforts in the LAMP field, as well as in other molecular biology fields that have been applied to this. I know that you and your group at NEB have been working really, really hard on it, since the pandemic started affecting China. So thank goodness for the collaborations and thank you so much for all your efforts.

Nathan Tanner:
Sure. I'm more than happy to, our lab has pitched in a lot and many other labs at NEB also, we have information we think can help, we want to share it. So, people can reach out, anybody we see doing the work, we offer to help. We try to get reagents in their hands. People who need to scale up their testing, we do our best to support it. And I'm involved mostly in the LAMP and isothermal stuff, but we have a big team working on qPCR too. And our reagents and expertise there have been helpful for the more traditional testing pathways too, as just more and more of those tests are done every day. So we're always happy to help. Let us know if you have any questions.

Lydia Morrison:
Absolutely. Thanks so much for joining us today, Nathan.

Nathan Tanner:
You're welcome.

Lydia Morrison:
Thanks for joining us for this episode of the COVID-19 researcher spotlight series. We will continue this discussion in a future episode, when we speak with Greg Patton, a development scientist here at NEB. Greg is going to tell us about the new SARS-CoV-2 Rapid Colorimetric LAMP Assay kit, which was just released by NEB.


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