Anyone who has done a COVID-19 PCR test knows this exercise—wipe the nose with a swab, then the tester puts the swab in a plastic bag and takes it out. That was the beginning of the hard work to determine whether the sample was infected with the SARS-CoV-2 virus.

After leaving the patient's nostrils, thousands of samples are sent to the patient selection laboratory on the northwest side each week. At the beginning of the pandemic, the laboratory opened in 2013, and when the supplier needed to know what microorganisms were on the swab, they turned to be one of the places the supplier asked for help.                      

Before COVID, the laboratory was one of the largest in the Midwest, focusing on urinary tract infections, sexually transmitted diseases, wounds, and highly contagious nail fungal infections, which could pose major challenges for long-term care facilities.

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CEO Brad Moss said that when COVID hits, many laboratories turned to focus on the new virus in town. PCL has just added COVID to its test list and has not given up any customers, because realizing that the arrival of COVID does not mean people stop developing UTI and other diseases, and testing is the key to determining treatment.  

"We are a very loyal group of people," Moss said. "We have been here for a long time."         

Chief Operating Officer Thomas Payne (Thomas Payne) said that the laboratory doubled its staff and purchased additional equipment to enable it to continue the tests it had done before COVID, while also testing for new viruses. The pandemic has brought additional work beyond testing for the new coronavirus; as drug use and overdose have increased in the past year and a half, the demand for drug testing has also increased.

Currently, laboratories conduct about 2,000 to 3,000 COVID tests in a week, but there was a time when they did as many tests as they did in a day. The laboratory can process as many as 10,000 to 15,000 per day.

The laboratory runs from 6 am to midnight 7 days a week. The goal is to send out all samples that come in before midnight that day.

Patients choose laboratories to test various entities, from nursing homes to medical clinics to drive-through stations. The samples came from many different states, including Indiana, Oklahoma, Kentucky, Florida, and West Virginia.

Samples usually arrive by express, but some local customers (such as nursing homes) may deliver them themselves. Once the vial arrived, one laboratory worker entered the data into the computer, while the other removed the red cap of the vial, which was a sign that it contained a COVID test sample.

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Then the machine will automatically drop the droplets in the sample into the liquid solution to prepare for the next step-extraction. Laboratory operations director Jerome Nypaver (Jerome Nypaver) said that at the same time, the remaining samples will be resealed and frozen. The rest of the sample is stored; if the test result is negative, it will be discarded later.

The sample then enters the machine to extract genetic material in the form of RNA from the sample and convert it into more stable complementary DNA, which is mixed with primers and probes, which will help determine whether the virus is present.

Payne said that other laboratories omitted this extraction step to speed up the process, but this would result in more false negatives.

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After the DNA is extracted, the sample is transferred to another machine, the PCR system machine, which analyzes the sample to detect COVID. Payne said these machines can run up to 384 samples at a time.

"We want to have a good automated process to eliminate human error," Payne said. "We invested energy, time and resources and ensured that we basically automate every process to reduce human error and increase efficiency."

The screen next to the PCR system machine can distinguish between positive and negative samples. The screen displays each sample as a line on the chart. The y-axis shows the viral load, and the x-axis shows the number of cycles that have been run.

"Basically, the more you have, the fewer loops you need because the primers can find their target faster," Nypaver said.

Nypaver says this is different from magnetism. If there is a large amount of COVID, the sample is like a large magnet, quickly pulling the primer towards it. If there is not too much COVID, it will take longer to attract primers. If there is no COVID, there is no attraction.

On the reading, a flat line indicates that the sample is negative. The rising curve indicates that the sample came from an infected person.

After analyzing the sample, the staff will immediately view the data and check out the case, and then send the information back to the provider.

When the sample tests positive, the laboratory will conduct further tests to carefully observe the virus. Through this step, the laboratory tested about ten common variants, and the most common one is the delta variant.

"I think we are doing more PCR mutation tests than any laboratory," Payne said. "We are pushing the limits of PCR, which is really cool."

If the sample does not appear to be any known variant, the laboratory will send it to Eli Lilly or the state laboratory for further, more complex analysis. Nypaver said that in the first few months of the pandemic, Patients Choice sent many samples to the Centers for Disease Control and Prevention to help federal scientists study the new virus.

Labs like Patients Choice can be the early canaries that come as new variants. Nypaver said, for example, last year they sent samples to the federal government that represent re-infections in patients who have already tested positive once.

Scientists at the patient's choice laboratory are also trying to predict potential obstacles that may arise. Although the laboratory has not encountered any supply chain issues, its scientists are now testing new reagents and substances used in the tests to ensure they have a backup plan in the event of shortages.

"This is one way we try to take proactive measures and ensure that we are here to serve the community," Payne said.  

Although most of the laboratory's work has been done behind the scenes so far, last week, Patients Choice began to provide two hours of PCR test turnaround time directly to consumers on the roadside outside the office.

Moss said that the cost of this rapid turnaround test is about $200, which may attract passengers who need a negative test before boarding or other people who need to quickly know if they are infected.

For more information or to schedule an appointment, please call (317) 299-5227.

Contact IndyStar reporter Shari Rudavsky at shari.rudavsky@indystar.com. Follow her on Facebook and Twitter: @srudavsky.