By Kristen Mitchell
Have you ever thought about what happens to your Testing for COVID-19 after submitting your nasal swab at one of George Washington University’s testing centers? Since beginning operations in August 2020, the GW Public Health Lab has processed nearly 400,000 PCR tests to keep the university community safe.
The GW Public Health Laboratory, which operates on the first floor of Science and Engineering Hall, is processing COVID-19 testing for approximately 25,252 community members on campus – people who must participate in the regular testing protocol as a condition of the access to the campus. This testing protocol allowed the university to bring students, faculty, and staff back to campus for in-person activities at the start of this academic year.
From test processing and sample extraction to molecular PCR testing and data analysis, a team of laboratory professionals work behind the scenes to keep the GW community safe. Over the past year and a half, the team has increased the use of automation, improved workflow procedures and managed supply chain challenges to ultimately develop a system that enables day-to-day processing of more than 3,000 samples.
“People might think you put the swab in your nose and then maybe it’s put in an instrument and the results come up, but there are so many steps between when the swab arrives at the lab and the time the results are released,” said Praveena Tummala, technical director of laboratory operations. “We are constantly working on the workflow, making it leaner. It used to be mostly manual, but automation has helped us increase accuracy and improve turnaround time. »
The laboratory is managed by Tummala, laboratory manager Jack Villani and Medical Director Jorge Sepulveda, a professor in the SMHS Department of Pathology. The lab is the result of a joint effort between the Milken Institute School of Public Health, GW Medical Faculty Associates, and the GW School of Medicine and Health Sciences.
Here’s what happens to your nasal swab after you collect your sample and drop it off:
Bagged tests are packaged in refrigerated biohazard containers for safe transport to the GW Public Health Laboratory. The lab receives new specimens from asymptomatic and symptomatic Foggy Bottom testing sites several times a day. The lab also receives samples from the Virginia Science and Technology campus and GW testing sites in Arlington, Alexandria and Rockville several times a week. Laboratory staff prioritize processing symptomatic tests first to ensure results are available to patients as quickly as possible.
Once the bagged samples are ready for processing, laboratory staff remove them from the biohazard containers and begin the intake process – a visual inspection to ensure that each sample includes a nasal swab and is correctly identified and sealed. From this point, it will take approximately six hours of procedure for the PCR test to be completed.
Once the samples are verified, they are transferred to the laboratory processing room, which has enhanced biosecurity procedures for the protection of laboratory personnel. Inside this room, staff prepare samples for batch processing, in order to process a larger volume of samples simultaneously. Staff remove samples from bags and dispose of swabs as biohazardous waste before transferring the liquid contents of the tube into 96-well plates, each containing 91 samples and 5 extraction controls, for testing – systematically correlating which samples go where to ensure results are reported accurately.
In the processing room, samples are also combined with a chemical inactivation buffer that inactivates many viruses, ensuring that nothing leaving the room poses a threat to laboratory staff. Sample tubes are heat inactivated, stored for up to a week in case retesting is needed, and then discarded as biological waste.
Then, the plates are taken out of the processing room to be extracted. Before samples can be tested for COVID-19, the laboratory must purify any human or viral RNA present. RNA plays an important role in transmitting information about the structure of proteins between cells. To do this, the lab uses liquid-handling robots to break down the cells and virus particles present in the sample. The extraction procedure on the robots preserves the RNA needed for the test and removes anything that could contaminate the sample, leaving only purified RNA.
Members of GW Public Health Laboratory team. (William Atkins/GW Today)
To perform the analysis, the lab uses PCR (polymerase chain reaction) technology to amplify small amounts of RNA from samples into deoxyribonucleic acid (DNA), which is replicated until SARS- CoV-2 is detectable if present. Using a machine, the purified RNA samples are combined with a pre-prepared “master mix”, which includes everything needed to trigger a PCR reaction, except for the sample itself. Lab staff create a batch of this mixture approximately every three hours, as needed. From there, the samples are ready for PCR testing.
The PCR test instrument is programmed to test two SARS-CoV-2 viral gene targets and one human gene target. The human gene target acts as an internal control to ensure that there are sufficient samples present; if not, the laboratory team has little confidence in the validity of a result. During testing, the instrument amplifies genetic targets using 40 cycles of heating and cooling and shines a laser into each sample on the well plate each cycle. Samples fluoresce or light up when enough COVID-19 RNA has been amplified. The instrument measures the brightness and at what amplification cycle individual samples light up, forming the basis for determining whether a viral test is positive or negative. If only one of the viral targets is amplified, the result is labeled as inconclusive – however, for practical purposes, the lab team assumes that viral COVID-19 RNA is present and individuals should behave as s they were positive. Invalid results mean that no sufficient amount of human RNA was detected and samples are flagged for reprocessing or to advise individuals to request retesting.
Once the PCR tests are complete, the data is reviewed by the lab team to assess any discrepancies and approve the results for release on the medical portal. This usually happens within 24-36 hours of the initial nasal swab arriving at the lab
The lab has a sophisticated lab information management system that makes it easy to manage workflows but also get results to those who need them. All results are forwarded to relevant clinicians at GW Student or Employee Health Services for any necessary medical follow-up, as well as as the Campus COVID Support Team (CCST) for support, including collecting campus contact information.
No later than 48 hours after the results are produced, the CCST forwards all positive and negative results to GW’s Business Intelligence group for inclusion in the next update of the GW coronavirus dashboard. As required by law, all results are also provided to the Washington, DC, or Virginia health departments, which in turn report the results to the Centers for Disease Control and Prevention.