- 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.
Hey, Nathan,
thanks so much for taking time out of your schedule
to be here today.
- Sure, Lydia, no problem.
- So I was wondering if you could tell our listeners
and viewers a little bit about your recent publication,
your pre-print in MedRxiv.
- 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.
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, pre-print 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 pre-print up 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.
- Yeah, absolutely.
And what kind of samples was it originally tested on?
- 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.
- So, what makes LAMP so advantageous
for a diagnostic assay?
- 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.
- Absolutely.
And do you think LAMP is better suited for a research use,
or do you think it's better suited for, like, use
in a clinical setting, or maybe even use in a home setting?
- 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.
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. - Yeah.
- 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.
- 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.
- Yep, absolutely.
- Have you seen a lot-
You've mentioned that there have been, sort of,
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?
- Sure.
So, like I said, our pre-print was very simple
and it was very early,
so it showed the principle 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 pre-print first,
we just put one up on bioRxiv,
showing new and improved LAMP primer sets,
as well as an additive guanidine chloride that you can add
to the reaction to really boost the sensitivity.
That was where the early reports, sort of 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 one,
and it's a real clinical validation of the test.
- And those would still be nasopharyngeal samples?
- 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 worked
or a very crude, silica bead treatment
that came from a lab at Harvard.
Brian Rabe another person we'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 pre-prints
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 pretty 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.
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 Cas 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.
- 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, like, oral swab
or nasal swab?
- 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.
- Yeah, I heard those are terrible.
- I never,
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,
a good one from Yale came out,
showing that a viral load in saliva was higher
than that from a nasopharyngeal swab.
- Wow
- 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.
- Yeah. - So some of that
will make the testing much more simple and pleasant.
- And what about sputum?
Are people looking into using that too,
or is that, like, again, sort of like a mucus
that's a little bit harder to get to,
like not everybody can bring that up on cue, so.
- 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. - Okay.
- 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. - Okay.
- But 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.
- So is there anybody else
that you're currently collaborating with?
- I'd say we have tons of collaborators right now,
which is really exciting.
So, once our pre-print came out,
people started asking from around the world.
So, we have conversations multiple times a day
and not just me, the 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 pre-print a little while ago,
that's been very good.
And Chris Mason's lab at Cornell.
- Okay.
- Put out a nice pre-print with a lot of sequencing data
on COVID samples collected around New York
and they've put together, sort of 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.
- That's amazing.
Where do you see COVID research heading in the future?
- 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.
- Certainly.
Do you have any stories about something good
that's happened during quarantine
or, sort of like,
have you been able to draw any silver linings, you know,
from this crisis?
- 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.
You know, 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.
- Yeah.
I've certainly heard that sentiment echoed by others
that I've spoken to.
You know, 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 pre-print sharing
so that we can get some of this information
out there faster.
You know, more great minds working on the same problems
and working towards solutions
that are going to benefit the globe.
- Yeah, absolutely. - 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.
You know, I know that you and your group at NEB
have been working really, really hard on it,
since, you know, really since the pandemic
started affecting China.
So, thank goodness for the collaborations
and thank you so much for all your efforts.
- Sure.
I'm more than happy to.
Our lab has pitched in a lot
and many other labs at NEB also,
you know, we have information we think can help,
we wanna 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, you know, 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.
- Absolutely.
Thanks so much for joining us today, Nathan.
- You're welcome.
- [Lydia] 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.