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72 Hours to Catch and Contain COVID-19 | Step 2: Processing Samples

Step Two

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.

“One of those plates of 100 samples is about 3 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. In the first part of this series on the Penn Medicine News Blog earlier this week, Lauren Ingeno walked through her own process of getting tested for COVID-19 and shared information about how testing at Penn Medicine works. Today, we’ll spend 24 hours in the lab while these tests are processed and results delivered.

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.

Nasal Swab Testing at Penn Medicine

If you’ve had a COVID-19 test, or a nasopharyngeal swab for another respiratory illness, the sample they’re about to run through the assay comes from the very long Q-tip the clinician stuck up your nose that felt like it might touch your brain (or swabbed gently around just inside your nostrils). Once the Q-tip is placed in the vial — whether you were collected as a patient at the Hospital of the University of Pennsylvania, a community member at the West Philly drive-thru testing site, or at Penn Medicine Radnor — they’re bagged for a courier to pick up. All test samples taken throughout the University of Pennsylvania Health System and at community testing sites operated by Penn Medicine are delivered by courier first to Central Receiving, where lab assistants then route them to the appropriate Pathology and Laboratory Medicine lab. For COVID-19 samples, that is the Molecular and Microbiology labs.

Dealing with the Fast Spread of Coronavirus

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. Today, 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.

Statewide Molecular Diagnostic Testing

The Molecular Pathology lab regularly performs numerous types of molecular diagnostic testing, including detection of biomarkers for cancers, and identifying disease susceptibility, like for Huntington Disease. The lab was established in 1985, one of the first of its kind at a university hospital in the country. Penn was also among the first Molecular Pathology training programs in the country in the early 1990s. The Microbiology lab performs diagnostic testing specifically for infectious diseases caused by bacteria, mycobacteria, fungi, viruses, and parasites. It is arguably the most comprehensive diagnostic microbiology laboratory in the region.

Together a team of staff and faculty have pulled together one of the largest COVID-19 testing apparatuses in Pennsylvania, at one time performing 20 percent of all COVID-19 testing statewide and now running at about nine percent.

“It’s a little comparing apples to oranges,” says Caren, a lab specialist. “But in ‘normal’ times, we usually run about 1,500 tests per week. Now we’ve almost doubled that, and on a daily basis, with just COVID-19 tests.”

Sarah, a research coordinator, chimes in, “Right now, you pitch in where you can to make sure everything gets done and no one person or team gets overwhelmed.”

The lab uses a spectrum of molecular techniques and platforms to evaluate patient samples, including PCR, which is used for all COVID-19 testing at Penn.

In PCR analyses, the machines amplify RNA, a type of genetic material found in every cell and many viruses, including SARS-CoV-2. The COVID-19 assays are designed to detect between one and three different unique parts of the SARS-CoV-2 genome. If the viral RNA is detected above a specified level for that test, the assay delivers a positive test result.

Some assays take an hour and a half to give results, while others might take six or seven. But as Lauren was told when she got her test at the West Philly community testing site in part one of this blog series, anyone who gets a test through Penn Medicine will have their results in 24 hours.

Now, it’s nearly 2 p.m. and Sondermann is checking in with Zhen, a research associate. Zhen devotes most of her time in the lab to COVID-19 tests and is responsible for setting up the next batches of samples to run through the machinery. Jessica says, “she’s one of the fastest in the lab.”

“Not quite as fast as I was,” Zhen replies. “Now I use my left hand to pipette and my right.”

With so many racks of samples coming in, Zhen taught herself to use her left hand to pipette samples so she could switch back and forth.

“That’s crazy,” Jessica replies. “That’s awesome, just pure awesomeness.”

Working Overtime to Meet COVID Testing Demand

Central Receiving and the Microbiology lab are operating 24 hours a day seven days a week, and the Molecular Pathology lab is operating 20 hours a day seven days a week. Members of the Molecular and Microbiology labs are performing COVID-19 tests on an almost constant basis and, often, or really always, working overtime to try to meet the demand, particularly as cases continue to rise. 

Meanwhile, around the clock, the labs keep turning out test results. In thousands of online medical records every day, eager patients are logging in to find out their status. Some, like Lauren, who shared her story earlier in part 1 of this blog series, find out they have a negative COVID test (but are still advised to stay home and avoid infecting others while they have symptoms of potentially some other illness). Those who test positive still have an important role to play in helping to stop the spread of COVID-19. Read more in Part 3, the final part of this series.


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Views expressed are those of the author or other attributed individual and do not necessarily represent the official opinion of the related Department(s), University of Pennsylvania Health System (Penn Medicine), or the University of Pennsylvania, unless explicitly stated with the authority to do so.

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