Contamination Source Identification (CSI®), a company located in Huntingdon, has recently pivoted its one-of-a-kind infectious disease testing facility to tackle the COVID-19 pandemic.
According to Dr. Regina Lamendella, co-owner of CSI and a professor at Juniata College specializing in molecular biology, their test system is able to capture the entire genome of a virus whereas other tests can only capture pieces of one.
“A publication recently came out that looked at the accuracy of the current (COVID-19) tests that big labs are doing like Labcorp and Quest, which is a PCR-based test. In that study they were showing the sensitivity was as low as 66%. Right now our analytical validation and clinical validation of samples that we know are true positives is 100%. We’re hoping we can keep it there, but in our hands our test system is nearly flawless,” she said.
When asked whether there was any other testing facility producing anything near that level of validation, Lamendella replied, “To my knowledge, no.”
She also noted that due to the backlog of samples at big laboratories, there has between a 7-12 day turnaround time to receive results.
“That’s just not serving clinicians well,” she said. “How do you know whether to quarantine someone or not? And how do you wait that long to hear back about the results? We want to give people a 24-hour turnaround time.”
CSI processes DNA and RNA sequences through the genomics database of their supercomputer to assign the correct identification of those sequences, providing a diagnosis in a matter of hours, not days.
Dr. Alexander Shope, chief medical officer at CSI, explained that the RT-PCR tests in widespread use throughout the country work well for screening, but produce a large number of false positives.
He used a striking analogy to highlight the difference between the two methodologies.
“Usually screening tests need to be followed up with an additional test, a confirmatory one that absolutely defines, ‘yes, this person does in fact have this disease or does not have this type of disease.’ That type of test is more our bread and butter. We call it our CSI-Dx™ test. That test does not use specific segments of DNA or RNA. We sequence everything in the sample so we don’t miss anything. We liken it to fishing with dynamite versus fishing with hooks and bait.
“We have done internal validation studies according to FDA guidelines that have shown we have 100% accuracy in detecting the COVID-19 viruses in samples we were running,” he continued.
Shope noted that the World Health Organization originally set out guidelines for RT-PCR tests to be followed up with confirmatory tests, but due to limited number of labs capable of carrying this out within the U.S., those guidelines were not incorporated in the country.
“They do go through a confirmatory process initially when a lab comes online in order to run some of these assays (analyses). They have to send a certain number of their first positive and negative samples to a lab already established in order to make sure their labs all line up. But that’s not necessarily confirming the entire genome of that virus is there,” he said.
All this is going on against the backdrop of a recently reported investigation by The New York Times which revealed that careless laboratory practices at the Centers for Disease Control and Prevention contaminated the nation’s first batch of tests back in February, making them ineffective.
CSI’s 11 employees have been working round the clock since the pandemic hit the U.S., but Lamendella said the company is concentrating on the local situation for now.
“We’re trying to keep this as locally and regionally focused as we can. We just want to do our part. And help protect our communities, especially our at-risk communities like the Amish and Mennonites,” she said.
CSI approached Dr. Holmes Morton, who has decades of clinical experience working with the Amish and Mennonite communities, to be the company’s lab director.
Morton runs a medical facility, the Central Pennsylvania Clinic, in Belleville, where he is currently collecting samples from these communities and sending them to the CSI labs for analysis.
“I am told by friends who are within the Amish community that they are doing a lot of self-isolation. Families are limiting gatherings,” he said, noting though that the Amish are particularly reluctant to suspend worship services.
“There should be more testing,” Morton told The Daily News. “We’ve had very little testing going on, we’ve made it available will schedule appointments for testing to be done. We’re hoping to pick up on asymptomatic patients which would mean something in terms of them not going out to church.”
With new equipment shortly arriving, CSI will be able to do 92 RT-PCR tests per shift, and can currently process 48 CSI-Dx tests per day.
Lamendella believes COVID-19 will likely be a yearly occurrence, and said CSI is well-positioned to provide essential data.
“I think COVID-19 isn’t going away. There’s the thought it could be circulating like the flu every year. If that happens to turn out to be true, we can more thoughtfully come up with a strategic plan of how we can offer this beyond regional testing. What’s beautiful about that is we’re able to keep up with the evolution of the virus. The virus is changing as it circulates through the population and since our test is non-targeted, we’re able to keep up real time with its evolution, which is really important when you think about it. The database we’ll be able to accrue from positive individuals will be really helpful for pharmaceutical companies that are looking into vaccine development, because that target of the vaccine may need to change over time,” she said.
The fact that such a cutting edge testing facility is located in Huntingdon is hard to fathom.
“It’s almost miraculous that this happened here in Huntington. You have the right set of talent coming together. It’s team science at its best. You have the molecular knowledge of how to do the laboratory work, you have the brilliant Juniata grads who work for the company that have all this computational biology and computer science experience to do the bioinformatics, we have Dr. Morton on board who is an incredible clinician,” said Lamendella.
The company isn’t considering COVID-19 testing as a long-term strategy, but as a response to a public health crisis. Within 2020, they expect to refocus on their testing for tick borne illnesses, such as Lyme disease, and beyond that to life threatening illnesses such as C. Diff., colitis and sepsis.
CSI’s CEO Gary Shope, a Huntingdon native and father of Alexander Shope, is committed to growing the company in Huntingdon.
“We jokingly say we’re going to make Huntingdon the meta-genomics capital of the world. And because we are unique and two generations ahead of everybody else, our goal is to try to attract additional research. Huntingdon itself is our primary focus in regards to creating a tax base for a business. The real outcome of this would be Google Health or a pharmaceutical company will buy CSI. Whether it stays here or not is hard to predict, but I’ll be doing everything I can to make sure it does stay in Huntingdon,” he said.
Nathan can be reached at email@example.com.