With COVID-19 cases resurging around the globe, experts warn that vaccination does not offer complete protection against infection. A special envoy to the World Health Organization recently cautioned in an interview with Bloomberg TV, “Variants that can beat the protection offered by vaccines are bound to emerge all over the world in the coming months and years.”
The European Congress of Clinical Microbiology & Infectious Diseases (ECCMID) is one of the most comprehensive and influential congresses in the field of infection. This year, infectious disease researchers, test developers, and heads of global laboratories met at a symposium at ECCMID to discuss emerging mutation surveillance and the best approaches available to rapidly identify SARS-CoV-2 variants. Despite increasing concerns about highly transmissible new strains, the presenters highlighted how testing is evolving to stay ahead of the virus.
Staying Ahead of SARS-CoV-2 Mutations
“Over the course of the pandemic, there has been a growing interest in test features which could improve sample analysis,” Jelena Feenstra, senior manager for global scientific communications, shared during her talk at the conference. In the face of emerging variants, Feenstra highlighted the need for tests that analyze multiple targets and have increased redundancy to minimize the potential impact of mutations on assay performance. Thermo Fisher designed the TaqPath SARS-CoV-2 2.0 assay menu to compensate for current and future SARS-CoV-2 mutations.
Both assays in the menu look at three genomic regions and eight total targets not including the S gene, which has been shown to have a high risk of mutation. The menu includes the TaqPath SARS-CoV-2 Fast PCR Combo Kit 2.0*, a fast, direct-to-PCR raw saliva solution for widespread, high-frequency testing. Not only is saliva sample collection easy and non-invasive, it can be performed without the need for a trained healthcare professional, limiting risk of infection. The menu also includes the TaqPath SARS-CoV-2 RNase P Assay 2.0*, featuring an updated assay design using RNase P as an internal control to both confirm a human specimen and ensure nucleic acids in the sample are preserved during transport.
Identifying New and Emerging Variants
For many laboratories, the goal is not just to stay ahead of SARS-CoV-2 mutations, but also to aid global efforts to detect new and emerging variants of concern. At ECCMID, Simone Vanoni, Ph.D., a molecular biologist at PharmGenetix GmbH based in Austria, shared results from a recent study evaluating a dual workflow for identifying variants using whole genome sequencing (WGS) and Thermo Fisher’s TaqMan SARS-CoV-2 Mutation Panel.**
With WGS, Dr. Vanoni’s lab was able to determine if a sample contained a variant of concern, but the results were not available for three days or more – a turnaround time that is less than optimal when rapid insights are needed to curb new outbreaks before they spread. In addition, as Dr. Vanoni shared during his talk, WGS requires significant resources and is not easily scalable.
Dr. Vanoni´s lab tested a workflow where all samples positive for SARS-CoV-2 as determined by the TaqPath COVID-19 CE-IVD RT-PCR kit were sequenced with the standard WGS protocol and also analyzed with a custom mutation panel covering seven mutations of interest. In an analysis of 99 samples, his team found 100% agreement between the mutation panel screening and parallel WGS. While WGS remains an important tool for continuous monitoring for novel and undetermined strains, Dr. Vanoni’s data show that the TaqMan SARS-CoV-2 Mutation Panel can enable reliable detection of lineages that impose the highest threat to the public health in less than 24 hours, making the panel an ideal solution to aid surveillance efforts in areas where variants of concern or interest are circulating.
To watch the on-demand talks, as well as additional ECCMID presentations, please visit https://www.thermofisher.com/eccmid2021.
To learn more about Thermo Fisher Scientific’s COVID-19 Testing Solutions, please visit thermofisher.com/covid19.
*CE-IVD for in vitro diagnostic use.
For Emergency Use Authorization (EUA) only. For prescription use only. For in vitro diagnostic use.
**For research use only. Not for use in diagnostic procedures.