Mark Moran [00:00:02] Hello and welcome to TGen Talks. I'm Mark Moran. Coronavirus, officially known as Corona Virus Disease 2019, or COVID-19 for short, is getting a lot of attention these days, both in the press and from health organizations in the U.S. and abroad. COVID-19 is a respiratory illness that spreads from person to person and its impact on daily life is making it public health enemy number one. Joining me to discuss COVID-19, is Dr. David Egnelthaler, co-director of TGen North. He joins Pathogen Microbiome Division in Flagstaff, Arizona, that just announced the launch of a genomic-based test for COVID-19, and their collaborative work with the Arizona Department of Health Services to test for and identify pockets of COVID-19 across the state. TGen testing uses RNA analysis to confirm the existence of the virus and if present, TGen scientists then sequenced the genome to identify the particular strain where it came from and how it's moving and mutating.
Mark Moran [00:01:11] Dr. Engelthaler, welcome.
Dr. Dave Engelthaler [00:01:12] Mark, it's great to be here.
Mark Moran [00:01:14] Let's start by placing this outbreak in perspective. There's been a lot of media coverage about COVID-19. Help us separate the fact from the fiction. What should we know? What should we be concerned about if we should be concerned? And if so, to what degree?
Dr. Dave Engelthaler [00:01:27] With this COVID-19 outbreak, what we call the novel Coronavirus, really starting to spread around the world. We certainly do have reason to be concerned. This is a highly infectious pathogen, spreads really easily between people and a has really significant effect on certain parts of the population, the elderly, those with other preexisting conditions like lung disease and heart disease. So it really is important, but it is important to keep it in perspective, too. If we think about this, this is almost like dropping in a brand new flu season on top of our existing flu season. If we didn't know about flu and all of a sudden it showed up the way that it normally does, and we see tens of millions of cases and tens of thousands of deaths, we think it's the worst thing ever. Hopefully that's not what we see here with coronavirus. It is what we'll see every year with flu. We may start to see coronavirus acting like another flu virus COVID-19.
Mark Moran [00:02:20] What do we know about it? What is it? Where did it start? How did it start?
Dr. Dave Engelthaler [00:02:23] COVID-19 is this new coronavirus disease that's really spread by the new novel coronavirus, which is also been called SAR-COV-2. It is essentially very similar to SARS, which is a type of a coronavirus. Coronaviruses are typically things that we know about that we spread as the common cold between humans. But these new viruses, the SARS virus in this new COVID-19 virus, these are animal viruses. And they when they get into humans, they act a little bit differently. They're not adjusted to us and we're not adjusted to them. So here we were thinking about a new virus coming into us. We're seeing a lot of fatalities because we're looking at the most severe cases, but it's more likely going to be spread a lot like the common cold and probably have a lot of disease like the common cold, mild respiratory disease or even mild pneumonia. So we don't know the full expanse of the disease. We do know that it is pretty significant and easily spread.
Mark Moran [00:03:21] TGen developed a test. Tell me about that. And tell me about how it works. Is this a simple saliva test or do you need a blood sample?
Dr. Dave Engelthaler [00:03:29] TGen quickly developed a test when the first genomic data was made available in about mid-January and by the end of the month we had developed several tests that actually look for very specific parts of the genome that give us a lot of accuracy. It's called a PCR test and that's where we amplify very specific pieces of the genome. Over and over. And then we could say whether or not that organism is there or it isn't. So it gives us a lot of specificity and a lot of accuracy. These types of tests are essentially what the CDC developed and what others are developing around the world. And they really look at respiratory samples. So thinking about the kind of the nasal swabs that people have been hearing about, that's the primary sample type we want to look at. And if the viruses present in that patient, it's usually picked up in that sample type and the TGen test can definitively determine whether or not the viruses in that sample taking a nasal swab or nasal pharyngeal swab is a very common thing that health care providers do to look for influenza or strep. And in this particular case, it's very useful for looking for coronavirus. It's a swab that goes really down deep into the past, the nasal cavity in and actually swabs the pharynx. You get a lot of respiratory material. That way we can actually take that swab, extract the genetic material out of that. That takes about half an hour to an hour to process. And then we get it into our PCR machines, which can give us results back in about 45 minutes. The whole process really takes less than an hour and a half. But when we're testing lots of samples, we're doing dozens to hundreds of samples at a time. We're talking about a 24 hour turnaround time.
Mark Moran [00:05:11] What's the timeline for launching the TGen test as of March 11th?
Dr. Dave Engelthaler [00:05:15] We have FDA allowance to use our test in a CLIA certified lab. So it is essentially FDA has been allowing for more tests to get out there quickly, quickly if they meet certain benchmarks. We have absolutely met all those benchmarks and proven the accuracy of the test, the analytical performance of the test. And now we can go ahead and use it for patient sampling in TGen's CLIA lab. Speaking of which, also as of March 11th, we have CLIA certification for the lab that is 100 percent dedicated to coronavirus testing. And we're using this now today to support the state's public health response here in Arizona. And in doing community screening, looking for the presence of virus circulating around in different communities in the state, as well as doing direct testing of patients that are high risk for possible coronavirus disease. CLIA testing has been talked about a lot recently in the media. It's essentially a certification that allows for a laboratory like ours to be able to handle patient specimens, carefully, analyze them, and then provide information back to a physician. These are federal regulations that essentially prevent just any lab from doing testing. You have to do it under very rigorous controls and quality maintenance. And we've been able to put that in place in the TGen lab.
Mark Moran [00:06:37] You're listening to TGen Talks I'm Mark Moran. We're discussing COVID-19 today, the Corona virus and we're joined by Dr. David Engelthaler, who is co-director of TGen North TGen's Pathogen and Microbiome Division in Flagstaff. Dr. Engelthaler, who's TGen testing? And is this test publicly available?
Dr. Dave Engelthaler [00:06:56] TGen is working directly with state, local public health officials, as well as the larger health care providers to make sure that the tests that we have can be used on the most likely patients in the patients that need to be tested. So we are don't have our shingle out saying send in your samples directly to us. We are working through the public health response. But we are making sure that the test gets to those who need it.
Mark Moran [00:07:22] What does that test look for? Is it different from other tests that are available?
Dr. Dave Engelthaler [00:07:26] The TGen test was designed very similar to the CDC tests, which has proven to be incredibly accurate and our test has shown the same. We've done side-by-side comparisons. We're very satisfied with that performance. The great thing about TGen is the -Gen, the genomics. As soon as we identify any presumptive positive samples, we can essentially put those samples straight into our genomic sequencing laboratory, sequence out the whole genome and better understand the virus. We can look to see where virus the virus strains are coming from, how they're moving around the community, which ones are more related to others and watch and understand this new pathogen as it evolves in front of us.
Mark Moran [00:08:08] Let's switch gears a little bit and talk about what TGen is doing with the state of Arizona. What sort of work you were involved in there for the past several weeks?
Dr. Dave Engelthaler [00:08:17] TGen has been working very closely with the Arizona Department Health Services and a couple of the large health care providers in the state to make sure that we can look for the virus circulating in our communities. So we devised a strategy of taking groups of samples that have already tested negative for influenza and for other respiratory pathogens and test those in the TGen lab using the TGen test to see if we can identify any virus circulating coronavirus in those samples. That'll give us an understanding if the virus is here where where it actually is. And is it expanding in certain regions?
Mark Moran [00:08:54] How many tests can you run a day? Is there a shortage of the TGen test?
Dr. Dave Engelthaler [00:08:58] This is a really important point that a lot of people have been hearing about the shortage of tests because it's really only been restricted to the CDC test run at the state laboratories. Recently, the FDA is has made allowances for some of these other tests that are definitely as accurate and as good to get out there and be used during this response, including the TGen test. We at TGen have been thinking about the shortage of not only of test kits but also of testing capacity. So we've had a two-pronged approach. Make sure that we have not only a great accurate test, but make sure that we have plenty of material to do testing moving forward so that we can test. Right now we have material to test 5000 samples were intending to grow that continuously during this overall response, but importantly to is how many can be tested a day. And we've developed a high throughput laboratory capacity that allows us to scale up. Now we can do hundreds of samples a day and we can move to thousands of samples a day and in pretty short order as the need evolves.
Mark Moran [00:10:02] It seems to me, is that we're playing defense against COVID-19, is that accurate and if so, how far are we from being able to play offense?
Dr. Dave Engelthaler [00:10:12] The interesting question is if we can play offense or defense, and I think we're we're doing both. Certainly the reactive testing, whenever there's a highly suspect patient and in the state Health Department's been working on that and we're backfilling and helping with overflow capacity, I think we're on offense now once we're doing this community-level screening. We're trying to find the virus where it's present before it's starting to cause the severe cases. So we better understand where it is and where to focus public health resources.
Mark Moran [00:10:42] You mentioned earlier that COVID-19 behaves similarly to the fl. Along that line, is this something that will be back again next year? Will it be seasonal? And next fall we'll be looking at some sort of coronavirus all over again?
Dr. Dave Engelthaler [00:10:56] Understanding this organism is critical. And as this virus continues to evolve, our understanding about the virus and the disease it's causing is continuing to evolve. We don't know all those answers yet. The more we learn, the more we see the spread where we're seeing it act like a seasonal respiratory virus, meaning that it is easily spread and it is acting like what we would see in during the winter. And so we think as it starts to warm up, the amount of disease spread will probably lessen. And it may shift to those parts of the world where they move into their winter, such as the southern hemisphere. That's exactly what happens with the flu virus and other respiratory viruses. This shift between the north and the south hemisphere, that's what gives us our seasonality. So we may likely see this come back around once it starts to cool down again in fall and winter. And that's also what we need to be preparing for.
Mark Moran [00:11:50] Who's at risk and what can people do to minimize that risk?
Dr. Dave Engelthaler [00:11:54] There's certainly been a lot of discussion in the media about who may be more risk for getting a serious disease. Think we're all at risk for potentially being infected just like we would be for flu or for the regular cold virus in this particular case. We see really the most devastating effects occurring in the elderly, and that's the significantly elderly, 80 and older. We're seeing much higher fatality rates than elsewhere. So that means that we really do need to focus our energy and efforts around protecting the most vulnerable. That doesn't mean that everybody else isn't at risk. In fact, we are. And we're at risk for exposing the elderly or people with other preexisting conditions. So it's really important for everyone to follow those public health guidances that are coming out. They sound trite or boring washing your hands, hand sanitizer, stay home when you're sick. They're absolutely critical for slowing down the spread and helping us reduce the possibility of exposing those that are most likely to be devastated by this particular virus.
Mark Moran [00:12:58] Dr. Engelthaler, lots of important research going on, a lot of interesting and important research going on, TGen North in Flagstaff. Thanks a lot for being here today.
Dr. Dave Engelthaler [00:13:06] Great to be here, Mark.
Mark Moran [00:13:07] Thank you Dr. David Engelthaler is co-director of TGenn North TGen's Pathogen and Microbiome Division in Flagstaff, Arizona. If you'd like to hear this or other episodes of TGen Talks, visit TGen.org/tgentalks. TGen is an affiliate of City of Hope. Thanks for listening to TGen Talks. I'm Mark Moran.