• April 2021

    Pathology preparedness and a scalable pandemic response

The 2020 COVID-19 pandemic associated with the novel SARS-CoV-2 virus has required an unprecedented mobilization of resources worldwide. One of the cornerstones to pandemic response is rapid initiation of widespread testing. To meet this need, physicians and researchers at Baylor Scott & White Research Institute were quick to establish reliable testing for SARS-CoV-2 virus, and their experience can serve as a guide for the response to future novel infectious diseases.

Arundhati Rao, MD, PhD, chair of pathology at Baylor Scott & White Medical Center – Temple, is a physician researcher who combines general pathology and molecular genetics to study the etiology of a wide range of diseases. According to Dr. Rao, “Testing for infectious disease has been revolutionized by the advent of molecular techniques including polymerase chain reaction (PCR) and other nucleic acid amplification tests (NAATs), as well as rapid antibody and antigen tests. We have been on the frontline of this technology for many years and offer molecular techniques for many infectious pathogens including influenza and other respiratory viruses. So, when we saw the SARS-CoV-2 virus emerging in China, we knew we had the experience necessary to join the fight.”

Developing a SARS-CoV-2 Testing Program for North and Central Texas

On March 10, 2020, in collaboration with Luminex Corporation, Dr. Rao’s pathology team submitted an FDA emergency use authorization application for an internally validated SARS-CoV-2 real-time reverse transcriptase PCR (rRT-PCR) test, allowing them to trace the early community spread of the virus in North and Central Texas. As a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory for high-complexity testing, the Baylor Scott & White laboratory was permitted to start testing immediately.

According to Dr. Rao, “We were thankful to already have the instrumentation and reagents in house and to be well integrated with local public health agencies for rapid reporting of results. This allowed us to get started very quickly.”

On March 11, laboratory staff began testing nasopharyngeal swab specimens collected at drive-up testing sites or inpatient centers. Testing eligibility was determined according to the World Health Organization guidelines.

In the May 15 issue of the Journal of Medical Virology, Dr. Rao’s team reported their findings between March 11, a time when there were 1,267 reported cases and 38 deaths nationwide, to March 23, when the numbers had jumped to more than 33,000 cases and 400 deaths in the US.

Of the 3571 specimens collected by the Baylor Scott & White Research Institute group, 6.9% were positive, meaning that they identified nearly 250 infectious people in the community. The highest percentage of positive tests was among 25-to-34-year-olds (7.4%). Their work demonstrates that well-established private laboratories, in collaboration with equipment manufacturers and state and federal agencies, can provide important early information for pandemic response.

Next Steps – Antibody and Antigen Testing

As the pandemic continues, interest has turned to antibody and antigen tests, which offer the potential for rapid, low-cost testing at the point of care. The antigen tests, similar to those available for influenza, offer the promise of rapid screening for proteins that indicate active infection, whereas the antibody tests evaluate levels of circulating antibodies, which could indicate past exposure. In collaboration with a variety of manufacturers, chemists with the Baylor Scott & White pathology team have been vetting available tests for sensitivity, specificity, and ease of use, and antibody tests are available at the Temple and Dallas sites.

The Baylor Scott & White team continues to offer the RT-PCR-based test and other NAATs, which can deliver same-day results. According to Dr. Rao, “Our experience and capabilities have put us in a position to have enough capacity to support the needs of the entire Baylor Scott & White system.” These tests are now offered at laboratories throughout the Baylor Scott & White service area.

Importance of Flexible Teamwork for a Robust Pandemic Response

For establishing their robust SARS-CoV-2 testing program, Dr. Rao describes the need for flexibility. “We have learned how to be very agile and keep multiple platforms going to maintain a testing pipeline in the face of reagent shortages,” she said. For this, systemwide teamwork is essential. “Our experienced laboratory staff was able to rapidly set up the testing protocols, and the supply chain services staff were willing to search the marketplace to rapidly find new providers if reagents became unavailable. Each group had to respond quickly to new concerns.”

She also highlights the importance of strong collaborations with the emergency department, surgical team and others, who dynamically incorporated testing into the patient flow and adapted to the changing needs of the testing laboratory. “Overall, we have found that our strength comes from operating as an integrated healthcare system. This model has helped us build strong relationships through years of related experience with a variety of infectious diseases, and it continues to allow us to jump very quickly on a new disease and rapidly offer a solution for our patients.”

The Baylor Scott & White lab in Temple, in coordination with Baylor Scott & White Research Institute and under the leadership of the principal investigator (PI), Dr. Manju Gaglani (Endowed Chair in Pediatrics), has been involved in a CDC-sponsored influenza vaccine effectiveness trial for several years. This involves testing samples from enrolled participants during the season. This year, the longitudinal study protocol was updated to include SARS-CoV-2. To build upon the group’s long-standing history of involvement in infectious disease research and surveillance, Baylor Scott & White Research Institute is working to establish a formal viral bank program in Temple. The purpose of the viral bank will be to collect, process, store, and distribute high quality tissue (including normal tissue, tumor tissue and certain bodily fluids), swab samples, and clinical data with the purpose of enhancing resources available for research. The research team believes that the development and maintenance of an institutional tissue procurement and repository facility with an informatics infrastructure is vital to current and future intramural and extramural clinical, translational, and basic research efforts. Access to samples and specimens in the bank will allow the team to conduct validation assessments to know what viruses are detected or not detected by a given test. It will also allow the team to complete calculations of sensitivity and specificity before a test is put into clinical use.

“A viral bank to store all these isolates is a great value as it would accelerate our ability to efficiently screen for new pathogens and monitor any mutations or changes that could evolve as the viruses circulate within the community,” said Dr. Rao.

Projects like the viral bank have been brought to life through contributions from our generous donors and other supporters of the Baylor Scott & White Central Texas Foundation who are committed to helping advance medical research.