NEB Podcast #29 -
COVID-19 Researcher Spotlight: Interview with Chan Zuckerberg Biohub Scientists

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Transcript

Interviewers: Lydia Morrison, Marketing Communications Writer & Podcast Host, New England Biolabs, Inc.
Interviewees: Amy Kistler, Group Leader of Infectious Disease, Chan Zuckerberg Biohub; Eric Chow, Asst. Adjunct Professor, Department of Biochemistry and Biophysics, University of California San Francisco; Emily Crawford, Asst. Adjunct Professor, Department of Microbiology and Immunology, University of California San Francisco



Lydia Morrison:
Welcome to the COVID-19 Researcher Spotlight Series. I'm your host, Lydia Morrison, and today we're sharing an interview with three scientists from the San Francisco Bay Area who worked to establish COVID-19 testing for Californians as a collaborative effort between UCSF and the Chan Zuckerberg Biohub. Eric Chow, Amy Kistler, and Emily Crawford have helped to provide reliable COVID-19 testing, as well as genomic sequencing of SARS-CoV-2 to better understand and diagnose the spread of the coronavirus in California.

Lydia Morrison:
Hi, Eric, Amy, and Emily. Thanks so much for joining me today.

Amy Kistler:
Thanks for having us.

Emily Crawford:
Yeah, thanks for having us.

Lydia Morrison:
I was wondering if we could sort of circle up with each of you and have each of you tell us a little bit about your COVID related research.

Emily Crawford:
Yeah, I can go ahead and start. This is Emily. My background is as a protein biochemist, but in the past five years or so, I've been focused on development of novel diagnostic methods for infectious diseases. It was a relatively easy transition for me to start focusing entirely on COVID-19 when the pandemic began, and I am now running a clinical diagnostic testing facility hosted by UCSF and the Chan Zuckerberg Biohub where we take samples from public health departments around the State of California, and we return clinically reportable PCR results showing presence or absence of SARS-CoV-2.

Emily Crawford:
Eric has been helping out setting up the lab as well over the last few months.

Eric Chow:
This is Eric. My background is in genomics around next generation sequencing, as well as automation. And a lot of the focus of my previous research before COVID is on improving ways of using technology to do genomic research, such as new ways of doing NGS library prep, different ways of using automation to enable higher throughput sample processing. Some of these skills definitely applied well to the current situation where we need to do a lot of nucleic acid-based tests to detect SARS-CoV-2.

Eric Chow:
And over the past couple of months, I've been really involved in the UCSF, Chan Zuckerberg Biohub efforts to get a testing lab booted up and to scale up operations.

Amy Kistler:
My name is Amy Kistler, and I've been focusing on sequencing efforts, the genome sequencing efforts, of SARS-CoV-2 that are circulating in California. My background is in viral genomics and virology, and it was a very natural transition for me to shift gears with the established metagenomic sequencing efforts that we've developed here at the Biohub, a number of them that Emily has been significantly involved in developing to pivot to begin looking at those strategies for mapping the distribution of SARS-CoV-2, to understand its transmission and circulation in California.

Lydia Morrison:
And Amy, just to stay on that topic, how is your work in sequencing the genome of SARS-CoV-2 going to inform our understanding of the virus and inform our understanding of how it's moving through the State of California?

Amy Kistler:
Yeah. SARS-CoV-2 accumulates mutations at a rate of about one per every two weeks. Mutations can arise over the course of transmission events. And what this allows us to do is understand when we see cases rising, how closely related they are in space and time, as well as in genetic sequence. And that helps us with collaborative information from epidemiologists at Departments of Public Health, where a number of the samples are coming from, to really get a much higher resolution picture of how the virus is actually moving around.

Amy Kistler:
Each mutation or the sequences of the virus, you could think of them as kind of like a barcode for the virus. And so we can be following the viruses based on their barcodes as they move around the state.

Lydia Morrison:
That's really interesting. Emily, just to follow up on specifically the research that you're doing, could you talk us through the workflow for detecting SARS-CoV-2 in patient samples that you're receiving?

Emily Crawford:
Yeah, sure. I'll start by giving a little bit of background on how our testing facility got started, if that's okay. I've been a researcher, a research scientist, for my whole career, and so have Eric and Amy and most of the people that we're working with now. But back in March, the Governor of California made a few small tweaks to regulations around who can do clinically reportable diagnostic testing in the state.

Emily Crawford:
And as a response to that, UCSF realized that they were sort of sitting on a great resource to help out the community, which was a large number of graduate students and postdocs, a lot of equipment, a lot of expertise in doing the thing that's most needed by the state and by the world right now, which is testing people for SARS-CoV-2. In early to mid-March, we transitioned our research labs space into a clinical diagnostic space where we now take samples in and results out presence or absence of SARS-CoV-2. And the process, it's interesting.

Emily Crawford:
It's been an interesting experience to understand what the different challenges are with doing clinical diagnostic, as opposed to doing a research test. The most notable is that the difficulties and the hard work all happens upstream of the analytical steps. We receive from our public health department partners hundreds, and thousands per day actually, of tubes with samples in them. These are collection tubes containing the nasopharyngeal swabs that everyone is familiar with.

Emily Crawford:
We need to enter the patient information from that tube into our database, and we need to transfer the material in the tube into a 96 well plate format so that we can process it in high throughput and then actually proceed with the PCR. One of the biggest challenges there is just how do you take samples in tubes and transition them into plates? And actually, Eric has been sort of spearheaded the efforts to figure out how to do that early on. We have a couple of different robotics solutions for making that transition happen.

Emily Crawford:
But it's something that as a researcher, you don't necessarily think about that step as being the biggest challenge. But when you're actually trying to do this work at scale, that becomes potentially a big bottleneck. So after the samples are in plates, we do RNA extraction, just the way you would do in any kind of typical research setting. And we do that, again, in 96 well format on a liquid handling robot. And then we transfer the RNA into a 384 well plate to do a PCR reaction.

Emily Crawford:
And early on, we played around with a few different sets of PCR probes and made the decision to use one N gene probe and one E gene probe, which we thought performed best in our hands. That's how we developed our EUA assay based on those two. And then the final step that's really important to think about is the data processing. And another key aspect of setting up the lab was creating a LIM system, a laboratory information management system, where we were able to keep track of all of the information that sort of came with the tube to begin with, and then connect that to the results in the end.

Emily Crawford:
The actual resulting where the positive or negative result goes out to the clinician or the public health department, that is taken care of by our clinical lab partners over at UCSF.

Amy Kistler:
I just wanted to highlight just how Emily's workflows, the sequencing workflow is kind of an outgrowth of Emily's workflow. Early on during the outbreak, the huge priority for us here was to develop surge capacity for testing as we were seeing the pandemic unfold. What Emily described got spun up in an amazingly rapid time on the order of about a week from ground zero to the first testing. Am I correct, Emily, for the CLIAHUB, eight days? What she described happened and tremendously rapidly.

Amy Kistler:
And in terms of the sequencing workflow, that was something that has been a secondary follow on work in terms of the public health need and urgency and the work that Emily and Eric did to pull all this together. Actually, we were on the sequencing side, we had established metagenomic sequencing flows, et cetera, for basic research.

Amy Kistler:
And so there was less development there that needed to be done from the ground up, but a follow on workflow needed to be developed in order to be able to, A, process the samples that people were sending directly to us, as well as samples that we had clearance to carry out sequencing analysis that were coming through the CLIAHUB testing lab. All the work that they did and the groundwork they laid was a great model for us as we built additional tools to enable both metagenomic and amplicon sequencing of SARS-CoV-2.

Amy Kistler:
Even at the level of, a lot of build labs were sending us tubes and we needed to move things from tubes to plates to automate it much in the same way that they did downstairs, and all the groundwork that Eric laid for processing clinical samples also worked with processing RNA samples that were sent to us from different labs around the state.

Lydia Morrison:
Really phenomenal that you were able to implement those new systems. And I'm sure there's lots of new regulatory requirements that you needed to meet. Eight days seems like a phenomenally short amount of time to be able to accomplish that in. Eric, do you want to speak a little bit to what it took to be able to implement those robotics to allow for this magnitude of samples to be tested?

Eric Chow:
Yeah, definitely. I would say that everything that we're describing here is the work done by dozens and dozens of people at UCSF and Biohub to get this together. As you mentioned, getting a lab booted up in eight days to do CLIA testing is no small feat. And a lot of this is really due to the really close cooperation and really tight teamwork between the groups here. I'd say especially with the uses of clinical labs, that provided a lot of guidance. As Emily and Amy both mentioned, we're all research scientists.

Eric Chow:
We don't do CLIA testing as our professional lives, and so we really depended on the expertise from those groups to guide us on how to file the FDA EUAs for our laboratory developed tests. And without their help, it just wouldn't have happened. But in terms of the robotics, a lot of this is working with different vendors for us to see which vendors could deliver equipment in a rapid manner. As you imagine, you've heard about supply shortages for reagents for doing COVID testing. The same thing is happening with equipment as well.

Eric Chow:
The first thing was finding automation vendors that we could find that could provide the supplies and equipment in a timely manner and we were able to do that, and to also work closely with those automation vendors just to get the programs developed. We had ideas of how we wanted the workflows to operate and work really closely with some of the application specialists at these automation companies to enable those workflows to happen.

Lydia Morrison:
Well, it's a good thing you had such strong relationships built with them already.

Eric Chow:
Yeah, definitely. I think we've all used quite a bit of automation at Biohub and over at UCSF, and so we're definitely able to leverage those existing relationships.

Lydia Morrison:
I'm curious now that you're up and running and I know that California is experiencing a surge in cases again right now. We're recording this on July 17th and California is sort of in the middle of a new wave or maybe the second half of the first wave. How many samples are you able to process in a day, and what does that look like in terms of sample turnaround time?

Emily Crawford:
Yeah, I can speak to that. I think our average number of samples per day that we process hovers around a thousand per day. Our record, which we set just this past Sunday actually, was 1,932 samples processed in one day. There has been a trend upward in how many samples we're receiving, and we are doing our best to accommodate that, again, working with just a phenomenal group of people in the lab.

Emily Crawford:
We're mostly staffed by volunteers, UCSF PhD students and graduate students and actually MD students as well who come in and give us their time after they're done with their normal research days or classes or whatever it be. They really have been phenomenal in stepping up and coming into help and donate their time. We really appreciate that so much. But we are also working on ways to improve our capacity because we know that it's very badly needed.

Emily Crawford:
And we're trying to do that while also keeping an eye on our turnaround time, because we know that the value that we provide to the public health department partners is really in how rapid we are when they send samples right now to Quest or LabCorp. Unfortunately, most of the time they have a several day turnaround time, and that can be really detrimental to trying to control an outbreak. We know that we have to keep our sample numbers relatively low in order to not build up a backlog. That's kind of something that we think about regularly.

Emily Crawford:
And we work closely again with our UCSF partners and we also work closely with the public health departments to communicate with them about what their needs are and how we can best meet them.

Lydia Morrison:
Well, that's really important. It sounds like the collaborations and the communication that you've been able to establish are really key to a lot of the success of the turnaround time and the system that you have set up there to support the community in the State's testing efforts. I'm curious, Amy, why is this work important to you?

Amy Kistler:
One piece about the work that's important to me is just being able to apply modern 21st century approaches to this question, that's really where technology can make a big contribution. A lot of the tools that epidemiologists in the public health sector have available to them are not really that different. Boots on the ground, epidemiology is not that different from what was done during the pandemic of influenza in 1918. I mean, certainly we have some more sophisticated tools on that front, but it does boil down to kind of tracking down leads and digging through paperwork, et cetera.

Amy Kistler:
And if there's a way that we can contribute to helping them solidify the data that they have, that's important to make potentially really challenging public health interventions, such as understanding if it's an outbreak in a congregate setting, like a skilled nursing facility or some kind of a workplace where there's a question about whether that workplace needs to shut down.

Amy Kistler:
Really being able to have sequence data that is hard data that can help you clarify the inferences you have about whether something's an outbreak from a single introduction versus potentially multiple sources feeding into cases that are occurring around the same time can be incredibly helpful for public health. And just to be able to help them do that in a rapid way with these new technologies that may not be readily available in all the public health labs I think has been really important to me.

Lydia Morrison:
Certainly an advantage for Californians.

Amy Kistler:
We have Silicon Valley as one of our neighbors. And I think people generally think about California as the center of high technology. The idea of being able to, whether it's testing or sequencing, deploy all the technology and expertise that we have available in the State to help address the pandemic and maybe control or mitigate the outcomes associated with the pandemic, that's really important to me, to be a part of that and to be driving that forward.

Lydia Morrison:
I know that all of you are involved in a lot of collaborations regarding COVID-19 research. Could you tell us about some of them?

Emily Crawford:
Sure. I can just talk briefly about some of the clinical research studies that we've been able to be involved in. Another value to having this testing capacity has been not only to be able to help with fulfilling public health needs, but also to support research studies that have gone on in the community. The most notable one that we participated in back in...

Emily Crawford:
Gosh, I guess it was back in April now, or maybe May, was a study in the Mission District of San Francisco where a UCSF group was able to partner with some local community groups in the Mission District to set up a very comprehensive testing campaign over the course of a couple of days where they tested about 4,500 people from one small census tract in the Mission District. We were able to process the samples there and deliver results. There are a number of people who tested positive, many of whom were asymptomatic.

Emily Crawford:
That was a valuable information on an individual level, as well as valuable to understand the extent of asymptomatic infection in our community. And what was really valuable about that study is that it was done by Diane Havlir's group at UCSF, and they put a lot of thought into designing it in a way that we would get useful information out of it.

Emily Crawford:
And kind of the really key take home from the results was that there was a very strong increased risk of testing positive among people who were unable to work from home, so people whose jobs required them to be out of the home and be out in the community. This is what we refer to as essential workers. Those are really the people that were being hardest hit. It really highlighted for us as a city and as a community, I guess, how big the disparities are with this disease already, where we're seeing certain groups of people hit really harder than others.

Emily Crawford:
And I think that that has helped us all to kind of refocus our efforts both in testing, as well as in public policy to try to support the people who need it most.

Amy Kistler:
I can speak to the sequencing aspects that are both linked to the work that Emily has been doing, as well as independent basic research that we're doing here on SARS-CoV-2 as outbreak unfolds. The Mission study that Emily described was a really, really great collaboration and example of the synergy that we can have between the testing that's going on in the CLIAHUB and the sequencing that we're carrying out at the Biohub for research purposes. So among the samples from the Mission District study that Emily described, we identified and cherry picked through the automation practices that have been developed downstairs and upstairs.

Amy Kistler:
We were able to through the LIM system that was developed rapidly identify all the positive samples from the Mission District study, cherry picked them for sequencing upstairs, performed sequencing, and then begin to analyze how any patterns that we were seeing of the types of clusters that were identified epidemiologically in the really careful high-touch epidemiologic work that Diane Havlir's group was doing in terms of the data that was going on and households or contacts among the people in the community that participated in this study, and the actual sequences of the viruses that we were seeing arising within the positives.

Amy Kistler:
That was a really beautiful... I feel like a really beautiful illustration of how the testing through to sequencing can help us to really understand how the virus is moving within a community. And what was really gratifying I think I can speak for myself and probably for Emily to say that Diane Havlir's group was also going back and returning to the community to follow up with the families and the patients and the positives for treatment and further clinical follow-up. That was a great experience to be involved in that.

Amy Kistler:
I guess aside from that study, there are sort of three categories of sequencing research that we're doing around the SARS-CoV-2 during the pandemic. One is also somewhat tied with Emily's work. Through the connections that Emily forge with departments of public health, we extended those to invite departments of public health to provide us samples for sequencing, for epidemiologic analysis. We did that in small scale, and now that turned into a bigger project where we've opened the doors for free sequencing to all county public health labs, as well as the state public health lab.

Amy Kistler:
And that's a project we're calling internally here at the Biohub COVID Tracker, but there have been some continued discussions with the Department of Public Health of California, and they're expanding and kind of connecting a more statewide effort to... They're calling COVID-Net. That includes not just the Biohub, but other academic and potentially commercial labs that can facilitate sequencing of islets across California to get a better understanding of the phylogenetic tree of SARS-CoV-2 circulating in California, as well as to help public health labs with epidemiologic tracing.

Amy Kistler:
That's one big project and that's really been spearheaded by actually a data scientists at Biohub Joshua Batson, David Dynerman, and also our bio-security fellow Patrick Ayscue.

Lydia Morrison:
I'll certainly be interested to hear how those studies play out. I think it's really important information not just for the community of California, but really for the United States, as well as for the rest of the world right now. I just wanted to thank you all for your collaborative spirit and your ingenuity in bringing this fast, reliable testing and genomic sequencing to further the understanding of the spread to the State of California. Emily, Amy, and Eric, thank you so much for taking time out of your research schedules to talk to me today.

Eric Chow:
Thank you.

Emily Crawford:
Thanks for having us.

Lydia Morrison:
This interview was recorded prior to the CLIAHUB COVID-19 testing facility being closed in October, as testing capacity improved in California. Testing for the public health departments is now being conducted at UCSF among other locations. Overall, the group completed more than 160,000 tests. Amy is continuing her work at the Chan Zuckerberg Biohub. With the recent surge in COVID-19 cases in California, her group has received a deluge of COVID-19 positive samples for SARS-CoV-2 genome sequencing.

Lydia Morrison:
This COVID tracker genomic epidemiology project with California county departments of public health and the State DPH will continue into 2021 with an added emphasis on capacity building. Emily has returned to her research at UCSF, and she continues to support the project as an independent consultant. Eric is currently back to running the technology team at the Laboratory for Genomic Research, a functional genomics collaboration between UC San Francisco, UC Berkeley, and GlaxoSmithKline. The goal of this collaboration is to develop and deploy new CRISPR CAS-based screening tools to better understand the genetic causes of diseases.

Lydia Morrison:
Thanks for listening to this episode of the COVID-19 Researcher Spotlight Series. Join us next time when I interview senior scientists Bijoyita Roy, who leads a lab in the RNA research department here at New England Biolabs. Bijoyita walk us through the process of COVID-19 vaccine development, with a focus on mRNA vaccines and the promising candidates awaiting FDA approval. She'll also discuss with us how NAB research scientists are working to improve and streamline mRNA synthesis workflows.

 

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