Interviewers: Lydia Morrison, Marketing Communications Writer & Podcast Host, New England Biolabs, Inc.
Interviewee: Naama Geva-Zatorsky, Principal Investigator, Technion - Israel Institute of Technology.
Welcome to the COVID-19 Researcher Spotlight series. Today, I'm joined by Naama Geva-Zatorsky of Technion, the Israel Institute of Technology. Naama's group developed a protocol for detection of SARS-CoV-2 RNA directly from nose and throat swabs without the requirement for RNA purification. Her group has also applied this protocol to saliva samples. The method utilizes reverse transcription loop-mediated isothermal amplification, or LAMP, offering rapid results that Naama and her team hope will enable successful community surveillance.
Lydia Morrison: Hi, Naama. Thanks so much for joining us today.
Naama Geva-Zatorsky: Sure. Thank you.
Lydia Morrison: I was wondering if you could tell our listeners a little bit about your latest COVID-related research.
Naama Geva-Zatorsky: Yes. Happy to. We performed the collaborative research at the Technion together with the Rambam Hospital, in which we tested whether we can apply the NEB LAMP method directly on human samples. We tested nasopharyngeal and throat, throat and nose swabs, and then also some saliva samples.
Naama Geva-Zatorsky: So our first set was on the swabs that are usually taken and submerged in the media that they are submerged in. We directly took this sample and tested whether we can detect the virus there. The next set was on saliva samples, directly on saliva samples. The throat and nose swabs are submerged in Universal Transport Medium, UTM, and usually are taken to the standard lab qRT-PCR machine.
Lydia Morrison: So Naama goes on to explain that the detection of RNA in RT-qPCR begins with the RNA being transcribed to cDNA. cDNA amplification is then measured in multiple cycles with each cycle producing more DNA, until it reaches some detectable level of the target. The number of cycles required to reach this detection threshold is inversely proportional to the amount of target RNA in your starting material, in this case, SARS-CoV-2 RNA. So, more virus in a sample results in fewer cycles to detection.
Naama Geva-Zatorsky: This is the standard method. We took the same samples and applied the NEB LAMP method on them and compared it to the cycle number of the standard technique.
Lydia Morrison: How do the sensitivity of these assays, of the LAMP assay, compare to the sensitivity of an RT-qPCR assay?
Naama Geva-Zatorsky: So we adjusted the protocol and in the adjusted protocol, we found out we can detect viral load at cycle 28 and lower meaning viral load that is equivalent to cycle 28 or a higher viral load. Very few false negatives and on the false positive end, we see that we didn't have any false positives, only one. Even that false positive was because we were very cautious. So in the NEB LAMP method, the color change it's isothermic and colorimetric, so we can see the change in color when the virus is present.
Naama Geva-Zatorsky: So we first looked at the sample by eye and then also took a picture with a phone because we were very limited. We worked in the corona lab, which it's BSL2+ and we had to be very careful with machines that we bring there. So we didn't have a very sophisticated camera, but I think it's cool because the idea was to see whether we can apply the LAMP to the population, just with no equipment, no professional experience. So regarding this false positive sample, by eye it didn't look false positive, but when we took the picture and gave it to several people, some thought it's positive. So that's why we mentioned this is false positive, but in general, we were confident that the false positive rate is very low.
Lydia Morrison: Is it very easy to identify a negative result versus a positive result by eye?
Naama Geva-Zatorsky: Yes. It's very easy. It's important to look at the sample at the very beginning. Especially if we use saliva, but also with the UTM. It's important to compare time equals zero, at the very beginning, and 40 minutes after the reaction has started. But in any case when it's positive, it's clear yellow and there is no problem to identify it.
Lydia Morrison: That's great. So you mentioned that this might be something that people could perform on their own. Do you envision this assay being something that is a test that someone could do by themselves in their home?
Naama Geva-Zatorsky: Yes, I think so. It can be done at home. I would like to mention that Rich Roberts and Nathan Tanner were very helpful throughout, really supporting us and it was extremely helpful, gave us tips and etcetera and it was fun also to interact with them.
Lydia Morrison: Yeah, they're great.
Naama Geva-Zatorsky: Okay. I would say it's possible to do this at home. It's important to have something that can either boil water or keep hot water. We think that the thermal cup is the best, a Thermos. Important to have a thermometer, it doesn't have to be too precise. So the reaction is performed at 65 degrees, but it's okay if it's plus, minus several degrees. However, we still need to perform a larger experiment and to get the regulation and in order to approve that you can do this at home and then when you get a yellow result, you are for sure positive.
Naama Geva-Zatorsky: It's important to note that at this point with the conditions that we performed the reaction, if you are negative, it's not 100% that you're negative. It's more to find out if you are positive, but it not yet will clear you if you're negative because we could not detect viral loads that are above cycle 28. So lower viral loads that are still considered positive in the hospital we could not detect at this point.
Naama Geva-Zatorsky: So if you're negative, it's not sure you're negative. If you're positive, we are confident that you're positive. Of course, it's not bad to go and do the normal test as well, but it's another surveyance. We see this as a surveyance test that can come in addition to the standard tests because it's fast, it's easy, it's cheap. You can do it at home. You can do it whenever you're worried. You don't need to go and convince anyone to perform at a test on you, all these advantages.
Lydia Morrison: Yeah. And so in terms of putting together the sample into the test components, I assume that you're pipetting some very small quantity of the Universal Transport Media or the saliva into the assay itself. So have we thought at all about how that might be accomplished at home?
Naama Geva-Zatorsky: Yes. There are loops. It really looks like a loop at the end of the circle and a stick. We use it a lot in lab. So it's a stick and at the end you have just a circle. It reminds me of the loops that kids use to blow bubbles. Soap Bubbles.
Lydia Morrison: Sure.
Naama Geva-Zatorsky: So we have those and companies create those in quite precise quantities. So quantities of volume of microliters. So you can perform this reaction at home with such a loop that picks up two microliters, five microliters, one microliter, whichever. We're still trying to understand, which is better, but it's truly possible to use a loop of two microliters and then perform all the steps only with such loops, not difficult. So the reaction would be spit into a tube, leave the tube at room temperature for 15 minutes, then take this tube into a thermal cup with boiled water.
Naama Geva-Zatorsky: Even the boiled water, it doesn't have to be at a hundred degrees. It does not have to be boiling, but it can be from just a bar, like we have at home and at work. When you press the hot button, we did that as well and it worked. It's better to have a small floating piece in which you can stick the tube. The tube sits in this 95 degrees plus, minus for five minutes. Then you add cold water until you get to the 65 degrees. That's the degree where the reaction is performed, wait for 40 minutes, and watch the color change. So after 40 minutes, you take the tube out and you compare this to the color you had at the very beginning. So it's not a bad idea to take a picture at the beginning and at the end, but it's also fine. If it's positive, you really can see the yellow color so it's very convenient.
Lydia Morrison: Yeah. That's really interesting and exciting to hear. I'm sure that there's a very high demand for people to be able to do some self-monitoring at home. This sounds like it could really enable that in a pretty simple way with items that people probably already have in their home. I certainly have a teapot and a thermos. So it sounds like all I'm missing is a LAMP reaction and a loop.
Naama Geva-Zatorsky: Yeah and then, we need the regulation. So I cannot say that you can do it right now at home. We are starting a big experiment at the end of this experiment, I hope we'll get an approval to let the population work with this reaction and decide whether they are positive or negative. So at this point I can not say "Try it at home and for sure, if you're positive, you're positive." We need to perform a much larger experiment in order to get the approval.
Lydia Morrison: That's really interesting. I look forward to that night. I hope that you receive approval for that test soon. Could you tell us a little bit about how you got involved in this project?
Naama Geva-Zatorsky: Two friends of mine. With one of them, I performed my PhD side-by-side in the same lab, Shai Kaplan. The other friend, Assaf Rotem, with whom side-by-side we performed our post-docs in very different labs, but all three of us are very good friends. So they read the paper by Zhang and Tanner from NEB showing that LAMP can detect the nucleic acid of SARS-CoV-2. We talked over the phone, they asked me whether I would be interested to see whether this can work in my lab, in the settings on the Faculty of Medicine here at the Technion, and adjacent to the Rambam Hospital, we are in close contact so they felt if I'm interested, they thought it should be important to show the world if this works or not.
Naama Geva-Zatorsky: So it took me several days to absorb this and understand whether this is a good idea, but quite quickly, I was happy with it and very enthusiastic. We also called Rich Roberts as we know each other from another collaboration that we're performing for several years now on a very different topic. And after talking with Shai and Assaf, talking with Rich, thinking, and quite quickly, all the lab was very enthusiastic about it. So quite a few students and myself, my lab manager as well, came to lab and almost didn't go home for about two weeks and very, very few hours of sleep.
Naama Geva-Zatorsky: I would say that the Rambam Hospital was crucial here as well, because very fast, they were also very enthusiastic and did everything they could to enable this experiment, these tests. Also Technion, we had to get approval because it was during the lockdown phase of the labs. So every experiment or every project had to get approval. So the response I got was, wow, it wasn't the word crazy, but this sounds wild, but wild can make big leaps in science, so just go for it. That's how it started and with all this enthusiasm, we worked very hard, but also very happy to do this type of work because we really felt it can help the world. After two weeks, we got this paper written with over 200 different samples.
Naama Geva-Zatorsky: I have to say the saliva test was also quite an adventure because we got approval for a few saliva tests. We had to find someone that will agree to give us his or her saliva test because it wasn't the standard. So it was also a mission. I put Inspector Gadget on our group icon.
Lydia Morrison: Yeah. It sounds like a very exciting time for your lab and we really appreciate all the hard work that you and your team have been putting into developing new diagnostics, new tests for COVID to really help the world recover from this pandemic. So, thank you so much for your efforts.
Naama Geva-Zatorsky: Thank you and thanks NEB for this LAMP reaction. It really has a lot of potential. I can also elaborate that we also tested different viruses with this method and the method only picked the SARS-CoV-2. Even other RNA viruses, DNA viruses, we didn't get a positive result on them.
Lydia Morrison: Awesome. I know our scientists are really proud of it and happy to have all these collaborations and to see all these different applications of the method really, hopefully, help the world move on from this pandemic, move forward in a safe and healthy way.
Lydia Morrison: Well, thank you so much for joining me today Naama. It's been really interesting to hear about your application of the LAMP assay and I look forward to hearing more about it in the future and hopefully hearing about an authorization for diagnostic use.
Naama Geva-Zatorsky: Yes, yes. We're waiting for the authorization but I'm optimistic.
Lydia Morrison: Excellent. Well, good luck.
Naama Geva-Zatorsky: Thank you.
Lydia Morrison: Thanks for joining us for this episode of the COVID-19 Researcher Spotlight series. At the time of this podcast release, New England Biolabs currently has made available a research use only SARS-CoV-2 Rapid Colorimetric LAMP Assay Kit and is focused on supplying research use only reagents to companies developing diagnostics and vaccines.
Join us next time when I interview Dr. Josh Quick, a Post-Doc at the University of Birmingham in the U.K. Josh's work focuses on using genomics to inform diagnosis and surveillance of infectious diseases. Josh's experience began with the West African Ebola outbreak in 2015 and continued with the Zika outbreak in Brazil the following year. During the current COVID-19 pandemic, Josh has been an important part of the Arctic Network, which early on, made available information like primer sets, protocols, and data sets to assist researchers in sequencing this virus.
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