ITHACA, NY -- You’ve spit in a tube, undergone a nasal swab — now what? To learn more about how the COVID-19 testing process works, we spoke with Rheonix, a local biotechnology company whose diagnostic instruments process the majority of COVID-19 tests at Cayuga Medical Center.
One of the major differences for how people get a test is whether they receive a nasopharyngeal test, where a swab is placed up the nose, or a saliva test, where patients spit in a sample tube. While nasopharyngeal tests were more common in the beginning of the pandemic, more organizations are starting to receive emergency FDA authorization to use saliva testing. Rheonix just received expanded emergency use authorization on its COVID-19 MDx assay to include saliva as a sample type this past week.
“Saliva testing is much more comfortable and easier for patients, and healthcare professionals can stand six feet away, so they are not being exposed as directly if they were inserting a swab in someone’s nose,” said Brooke Schwartz, Rheonix’s vice president of strategy and marketing. Logistically, she also pointed out how saliva samples are easier to handle and store, and less expensive to collect. Where the materials for nasopharyngeal sample collection can cost a few dollars per sample, saliva collection materials cost only around 15 cents.
After the sample is collected, by either method, it is processed. But the sample contains your own DNA, the virus’ genetic material, which is RNA, and potentially other genetic material. It’s like trying to find a few strands of hair on the top of your head. So how do you find the genetic material for just the coronavirus? As with most COVID-19 diagnostic tests, Rheonix’s assay uses something called reverse transcription polymerase chain reaction (RT-PCR).
“PCR is a molecular method for copying [the] segments of DNA of interest,” said Hazel Higgins, PhD, a product application scientist at Rheonix. “More specifically, the reverse transcription part of the reaction converts the virus’s RNA to DNA, to enable the polymerase chain reaction.”
The polymerase chain reaction uses primers, short sequences of DNA, that align with the start and end of the targeted DNA sequence. The reaction then copies the targeted DNA between these primers, in this case a specific part of the virus’s genetic material, over and over again. The logic is similar to if you copied the strand of hair over and over again, it will be easier to find and detect. After the reaction is complete, Rheonix’s instrument uses end-point detection to differentiate between a positive and negative sample.
The process for the machine is almost entirely automated, so laboratory technicians just have to prepare the samples, load them on the instrument, and wait for the results. “The instrument uses microfluidic and robotic liquid handling to replicate what lab bench equipment and highly trained scientists would be doing,” Schwartz explained.
Processing time for a COVID-19 sample on a Rheonix instrument takes around 5 hours, and each instrument processes 22 samples and two controls. To be able to process more tests in a shorter amount of time, Cayuga Medical Center has also used something called pooling. Essentially, you put a few samples together and test all of those together as one sample. If the pooled sample comes back as positive, then you check each sample individually to isolate which was positive. Otherwise, you can conclude that if the pooled sample is negative, all the tests were negative.
As of Dec. 15, Cayuga Health has processed over 700,000 COVID-19 tests and currently has 14 Rheonix instruments. In a video posted by Cayuga Health, Dr. Elizabeth Plocharczyk, medical director of the Cayuga Health Laboratories, states how crucial the partnership with Rheonix has been to be able to process potentially thousands of samples each day.
“We actually have three other types of analyzers in our laboratory that are capable of performing COVID-19 testing that we use for other diseases,” said Plocharczyk in the video. “To this date we've not been able to get enough reagents for any of those analyzers to be able to perform testing.”
Schwartz said that Rheonix has also had to overcome major challenges accessing materials in the face of supply chain shortages, as well as scaling up manufacturing to meet the needs of the pandemic. The partnerships with New York State laboratories and companies have been very important to Rheonix. When one of their previous suppliers was experiencing shortages, they decided to switch to a New York-based company that has consistently delivered critical consumables to Rheonix.
Despite these challenges, Schwartz said that it has been “incredibly invigorating and motivating” to work on the testing.
“That was the dominating sentiment as we went into developing, seeking authorization, and launching this assay,” said Schwartz. “It was the drive to contribute to our community, to help Ithaca and Central New York, and eventually the broader U.S. get tested. This was the way we could contribute to fighting the pandemic.”