When one university’s COVID-19 testing task force began thinking about how to set up COVID-19 testing on campus in early 2020, they had two options: outsource testing, or set up a CLIA-certified CAP-accredited lab on campus. The team decided to set up a CLIA lab, began testing samples in August of 2020, and by May of 2022 had tested more than 1.5 million samples.
Speaking to attendees at ASM Microbe 2022, Prof. Jared Auclair, PhD, an Associate Dean of Professional Programs and Graduate Affairs, shared his lab’s experience ramping up testing, and eventually surveillance, on campus.
During the first year of the pandemic, Dr. Auclair’s lab tested students, faculty, and staff every three days, running up to 8,000 tests every eight hours. After several months of testing using Thermo Fisher Scientific’s multiplex TaqPath COVID-19 testing solutions* they started to notice the S-gene target failure, a signal a sample may contain a variant, in multiple samples. With new variants circulating on campus, the lab needed to evolve its testing strategy. For Dr. Auclair, the decision to use genotyping for virus surveillance was an easy one.
The lab considered whole genome sequencing, but the time to results was too long for their surveillance needs. Instead, they turned to Thermo Fisher’s TaqMan SARS-CoV-2 Mutation Panel**. “We decided we’d use the mutation panels to monitor variants for a couple of reasons,” said Dr. Auclair. “One, it’s much simpler and two, it’s much faster.”
Genotyping as a fast, cost-effective tool for SARS-CoV-2 surveillance
During his presentation, Dr. Auclair showcased genotyping with PCR as an easily implemented, cost effective and robust method for at-scale surveillance of SARS-CoV-2 variants of concern, especially in areas where sequencing capacity is limited.
To verify genotyping results, the lab ran a comparison study and found the TaqMan SARS-CoV-2 Mutation Panel was able to accurately assign lineage to all samples, as confirmed using next-generation sequencing on Thermo Fisher’s Ion Torrent Gene Studio S5 Plus System. In a sample set of 67 positives, the lab achieved 100% concordance between genotyping and sequencing.
Combining PCR for diagnostic testing and identifying variants of concern with targeted sequencing for positive samples helped keep the campus safe and provided valuable insights to guide the university’s evolving testing strategy. For example, the lab was able to identify when a variant was fading out and it was time to adopt a new set of primers to monitor the next variant.
Surveillance remains critical
“Disease surveillance is critical as the pandemic transitions toward an endemic phase,” Dr. Auclair told the audience. “Many of us, including the government, set up CLIA labs across the country to respond to the COVID pandemic and we should maintain those labs, or at least some portion of them, to be ready for the next pandemic.”
To watch Dr. Auclair’s presentation at ASM Microbe 2022, please click here.
To learn more about Thermo Fisher Scientific’s SARS-CoV-2 surveillance solutions, please visit thermofisher.com/mutationpanel.
* Intended use and regulatory statements of products vary. For specific intended use and regulatory statements, please refer to the Instructions for Use (IFU). Product availability by country varies. For product availability in your country, visit the product webpage.
**For Research Use Only. Not for use in diagnostic procedures.