In late November of 2020, the University of Birmingham’s COVID-19 testing lab first noticed a significant change in its COVID-19 test results. Suddenly, a number of tests were coming back positive for only two of three gene targets. When the lab analyzed the data, they noticed that the same gene, the S gene, was failing to amplify every time. They started referring to the dropout as the “S gene target failure.”
The lab had specifically selected Thermo Fisher Scientific’s Applied BioSystems TaqPath COVID-19 CE-IVD RT-PCR Kit because it is a multiplex test designed to target three distinct regions of the SARS-CoV-2 genome. By definition, if a sample reacts with at least two of the targets, it is deemed positive. Before November, the team had not observed gene dropouts as a recurring trend. But over the next several weeks, the lab found S gene target failures accounted for about 90 percent of their positive cases. As it turns out, they were witnessing early evidence of the emergence of the B.1.1.7 variant – a new SARS-CoV-2 mutation that was rapidly spreading across the United Kingdom and would soon start making its way around the world.
In a recent webinar with GenomeWeb, Manoj Gandhi, M.D., Ph.D., Thermo Fisher’s senior director of medical affairs, Genetic Sciences, spoke with Alan McNally, Ph.D., a professor in microbial genomics at the University of Birmingham, and Emmanuel André, M.D., Ph.D., co-director of the Infectious Disease Laboratory at the University Hospital of Leuven, on the importance of identifying emerging variants.
During the webinar, Dr. Gandhi explained how the S gene dropout may be used as a signal to detect the presence of the B.1.1.7 variant. He also described, as both the European Centre for Disease Prevention and Control (ECDC) and U.S. Food and Drug Administration (FDA) have recognized, how Thermo Fisher’s TaqPath COVID-19 test may be used for early identification of the B.1.1.7 variant. Importantly, the S gene dropout does not cause a false negative, due to the built-in redundancy of the multiplex assay. “It only means that the S gene could not be detected,” said Dr. Gandhi. He described how Thermo Fisher regularly monitors assay performance, understanding that with selective pressure on the virus new mutations will arise. “Overall, sensitivity of our tests has not been impacted by any of the variants,” he said.
Thermo Fisher’s New Rapid Genotyping Solution
Dr. Gandhi then described how Thermo Fisher’s new TaqMan SARS-CoV-2 Mutation Panel* offers a broadly deployable solution for rapid detection of known variants. “We certainly have a lot of different tools in our toolbox,” said Dr. Gandhi. While next-generation sequencing (NGS) and Sanger sequencing are also available for variant surveillance, the mutation panel offers a quick option to look for specific mutations and variants of concern. “We have about 22 verified assays already and we are constantly building on this menu,” said Dr. Gandhi. He continued, “this uses the same real-time PCR instrument that is used for TaqPath assays and you can run one or a few hundred samples, depending on the type of format or the setup that you have.”
To hear how rapid genotyping assays can support widespread surveillance efforts and how Dr. Emmanuel André implemented this approach in his own lab, watch the on-demand webinar.
To learn more about Thermo Fisher Scientific’s COVID-19 Testing Solutions, please visit thermofisher.com/covid19.