To catch and contain COVID, step two is to process samples

The second in a series on the steps the health care community takes to quelling the spread of the virus, a look at the 24-hour cycle of testing.

It’s 5:30 a.m.

Jessica, a lab technician of pathology at Penn Medicine, is prepping COVID-19 samples to test. Her first batch of the day includes almost 400 samples left from the night before when the lab closed at around 1:30 a.m., a handful of COVID-19 samples that need to be run again and a plate of 100 new specimens that have started arriving this morning.

Three medical personnel in full PPE working at a drive-up COVID testing site.
Medical personnel gather nasal swabs at a drive-through COVID testing site in West Philadelphia in March 2020

“One of those plates of 100 samples is about three hours of work,” Jessica says. “I don’t even know what normal is anymore.”

Penn Medicine’s labs are constantly busy. When it comes to testing for COVID-19, they continue to turn around results within 24 hours for the thousands of patients Penn tests every day. 

When technologists arrive first thing in the morning, often they start with collecting results from samples that were run overnight and then triaging to make sure that racks of samples set up the night before to be run on the testing assays are ready to go. They unbag new specimens, make sure nothing needs to be maneuvered around, and put them into batches to be run. There are five different assays in the Molecular Pathology lab and two in the Microbiology lab, and lab staff choose which assay to use based on the particular need for that sample as well as available supplies, like of reagents or kits needed to run assays. Due to pandemic shortages, there are availability limits of different items at different times.

“That’s why we have multiple platforms to meet capacity,” Jessica says.

At 9 a.m., Faye and Natalie, both lab technologists, have joined her on the morning crew and hit the ground running the moment they walk in the door.

They are almost ready to load the first multiplex real-time RT-PCR diagnostic assay—a technique designed to rapidly detect RNA (genetic material) from the SARS-CoV-2 virus if it’s present. They can run 94 tests every three hours on this particular testing platform and the lab has multiple of these platforms. These days, they never stop running.

The spread of the novel coronavirus happened fast. As the state of Pennsylvania and many others across the United States shut down, the faculty and staff at the Molecular and Microbiology labs at Penn went into overdrive. Those two labs between them had set up multiple assays to test for the coronavirus by the end of March. Subsequently, capacity was expanded in these labs and equivalent labs at each of the health system hospital entities across the region. Now, across all the labs nine assays are running to test about 2,700 COVID-19 samples a day across Penn Medicine, with the majority of tests happening at the Hospital of the University of Pennsylvania. That’s in addition to the many other different kinds of tests the labs need to perform on a daily and weekly basis.

Read more at Penn Medicine News.

Read the first story in the series.