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May 2020

Put to the Test: URMC's Clinical Microbiology Team Shines in Pandemic


Microbiology Med TechsNecessity is the mother of invention, and in the case COVID-19, grit and innovation. One great necessity in this fight has been the push to make more testing available. Like clinical laboratories across the nation, UR Medicine’s Clinical Microbiology Laboratory has overcome a series of setbacks to establish testing for SARS-CoV-2, the virus that causes COVID-19.

Thanks to a dedicated team of scientists and collaborators, the lab successfully went from having zero testing in place to providing results for 1,000 people a day in just two months.  

Answering the Call

Flu season is one of the busiest for the lab, and it was just beginning to wind down in early March. But then, “COVID-19 didn’t give us much warning or time to prepare,” said Dwight Hardy, Ph.D., director of Clinical Microbiology (right).

At the onset of the pandemic, the Micro team was asked to develop a molecular test for detecting the virus. The effort was led by Nicole Pecora, M.D., Ph.D., the lab’s associate director, along with postdoctoral fellows, Andrew Cameron, Ph.D. and Jessica Bohrhunter, Ph.D., Hardy, and a group of medical technologists.

The team faced some immediate obstacles, like shortages in chemical reagents needed for testing, and lack of equipment. But after many days of long hours, they created a manual laboratory developed test (LDT) modeled after the CDC’s emergency use authorization (EUA). On March 16, the lab started testing and reporting its first patient results.

Due to instrument and reagent shortages and the manual nature of the LDT, the lab was only able to provide results for about 200 patient specimens per day. This limited testing capacity presented a stark dilemma: Who would get a test?

To address that challenge, URMC leadership brought together the Micro team and a host of other groups including Infection Prevention, Intensive Care, Emergency Medicine and others to develop testing criteria. They decided that testing would be prioritized for symptomatic inpatients and health care workers (whether or not they showed symptoms).

The goal? To help stop the spread of the disease a by identifying the COVID status of patients at the hospital for care, as well as any workers who were potentially exposed.

In about two weeks, the lab gradually increased the number of specimens it could test. Then good news came in the first week of April as the FDA gave approval to have SARS-CoV-2 testing run on an automated instrument, Roche Cobas 8800. “The Roche” is a state-of-the-art machine that was already being used to test for other infectious diseases. Because of its ability to run batches of tests at a time, this proved to be a game changer.

Instead of being forced to send specimens to commercial reference labs, all testing for SMH and its affiliates could now be performed in-house within 24 hours. This meant more patients could be tested to determine whether they were positive for COVID-19.

Compassion Behind the Scenes

The lab now performs over 1,000 tests per day and hopes to more than double that number. Shortages of test kits, reagents and specimen collection kits continue to limit the lab’s ability to increase testing volumes.

While each day is a new day when it comes to availability of resources, Hardy said supply chains appear to be slowly stabilizing. He added that in spite of the ongoing hurdles his team has faced so far, and potentially more on the horizon, he’s extremely proud of the Micro team for coming together to meet the challenges head on.

“All of us in the laboratory feel compassion for patients, their families and their loved ones and want to do the best we can as quickly as we can, to do our part in either the diagnosis or management of this particular disease,” he said. “I think that’s why people were so willing to step up to the plate, to be flexible and work long hours without being asked. They were dedicated to patient care and wanted to do their part in this unusual circumstance.”

What’s Next?

Strong Memorial Hospital now requires all asymptomatic inpatients to be tested for COVID-19. It’s one thing to keep up with heavy clinical volumes as specimens for testing continue to increase. Lab teams are accustomed to this, even in non-pandemic times. But it’s another thing to do this work while under pressure to develop new and effective testing for the general public.

Since April, the Micro team has undertaken a second wave of test development – this time for a serological blood test to detect SARS-CoV-2 antibody, which would determine whether someone has had COVID-19 in the past.

Much like earlier discussions about who should be tested for the virus, Medical Center leaders are now finalizing the logistics of a what widespread serological testing would look like. Meanwhile, the Microbiology team is working hard to validate the test so it is more than 99 percent accurate.

While health leaders and scientists are eager to provide antibody testing as quickly as possible, they want to get it right. And since the virus is so new, it’s not yet possible to know from an antibody test whether a patient is immune to COVID-19 or how long immunity might last.

Antibody tests will be very useful in determining past infections in our community. The next chapter of the pandemic remains unknown, but Hardy says the lab is equipped and ready for what’s ahead.

“Our team has risen to unprecedented challenges that were un-predicted just a few months ago,” he said. “We realize that the challenges are not over, but we continue to do our part day-by-day to provide the best diagnostic testing possible for our patients and community.”

Testing Timeline

March 12:  First positive COVID-19 case confirmed in Rochester

March 16: UR Medicine’s Clinical Microbiology Lab issues first patient test results. Due to manual nature of the test and limited testing resources, strict criteria is put in place for who can be tested.

April 3:  Following FDA approval, UR Medicine Labs starts running automated testing on Roche 8800, which greatly increases test volume.

Mid-April: Testing becomes available for some asymptomatic patients, including nursing home residents, those with respiratory symptoms, and those coming for elective procedures.

May 13: Strong Memorial Hospital requires universal testing for patients that are admitted.

June 1: UR Medicine to begin antibody testing.

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