Combining next-generation sequencing with PCR provided timely, accurate information about SARS-CoV-2 variants.
In a study published in the journal Viruses, researchers at the University of Miami Miller School of Medicine showed that a combination of next-generation sequencing (NGS) and reverse-transcriptase quantitative polymerase chain reaction (PCR) provided the speed and the low-cost and unbiased information researchers and clinicians needed to continuously track COVID variants.
“While sequencing is the gold standard to identify variants, we make a really strong case that selectively designed PCR assays can be equally effective,” said David Andrews, M.D., clinical associate professor at the Miller School, vice chief of pathology and laboratory medicine at Jackson Health System, and senior author on the study. “Combining both techniques helps us react quickly to variants and continuously validate those findings.”
NGS provides detailed information about viral variants, but it comes at a price: The technique can be slow, complicated, and expensive. While PCR does not provide as much information as NGS, it does deliver faster turnaround times at a fraction of the cost.
Early efforts to understand the SARS-CoV-2 Alpha variant showed PCR could provide an effective alternative to NGS. To build on that success, the Miller School team adopted commercially available PCR assays, as well as designing new ones in-house to track the Delta and Omicron variants.
‘Rolling Validation’ of NGS, PCR Testing
Over 18 months, the group used PCR on 8,000 clinical samples and NGS on 1,600. The samples came from routine tests at UHealth and Jackson, and from students and faculty.
“We created a panel of simple PCR reactions, which cost just a few bucks each, that we could run in real time,” said Dr. Andrews. “We would get snapshots of where we were in the progression from Delta to Omicron, as well as Omicron subvariants. We hit on some good PCR assays, and our data was generally a couple of weeks ahead of the national trend.”
While the PCR tests provided rapid information on variants in the community, the NGS data offered more detailed information about viral evolution and helped validate PCR results.
“We called it a rolling validation,” said Dr. Andrews. “If we relied exclusively on PCR, we might miss something. Every time we conducted a new sequencing run, we made sure none of the variants had changed. In addition, we were constantly checking global databases to ensure our PCR tests remained accurate.”
While this was exclusively a research project, with limited clinical impact, these results did help inform care in real time. As Omicron became the dominant variant, monoclonal antibodies that had been effective against Alpha and Delta stopped working. Knowing which variants were prevalent in the community helped inform how ICU clinicians provided care. These findings also supported administrative decision-making: A new variant might mean it’s a good idea to reduce family hospital visits.
This approach could have a significant impact on hospitals worldwide. Most facilities do not have easy access to NGS, and PCR offers a less expensive and more available alternative.
“We can envision deploying PCR-based methods more widely, especially in the developing world,” said Dr. Andrews. “If we should face another pandemic, I think it would benefit us to develop parallel PCR tests to complement sequencing.”