Since the first emergence of highly transmissible SARS-CoV-2 variants last fall, there have been increasing reports of new mutations across the globe. The emerging strains have not only raised concerns about increased transmissibility and disease severity, but researchers also believe  they may be able to evade the antibodies generated in response to existing vaccines.
Governments, pharmaceutical and diagnostics companies, and other organizations have all risen to the challenge to contain the pandemic as the virus continues to evolve by introducing large-scale testing, test and trace plans, and surveillance of genetic variants. At the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) Global Conference on COVID-19, leaders in laboratory medicine discussed the cutting edge technology and vital research happening in clinical laboratories today to support these efforts. Manohar Furtado, Ph.D., Director R&D, Genetic Testing Solutions at Thermo Fisher Scientific, spoke during one of the plenary sessions to discuss Molecular Testing for the Detection and Strain Identification of SARS-CoV-2.
The following offers highlights from Dr. Furtado’s presentation:
Superior targeting for specificity to SARS-CoV-2
Dr. Manohar Furtado: At the start of the pandemic, we did not have much sequencing data available on the virus. Therefore, when we developed our PCR test we decided to target three regions of the SARS-CoV-2 genome—the ORF1ab, the N gene and the S gene—as an added precaution so that even if the virus mutates the test would be able to identify positive cases.
The Applied Biosystems TaqPath COVID-19 Combo Kit target these regions specifically as they are unique to the SARS-CoV-2 virus and allow us to reduce detection of other coronaviruses. Targeting three regions also provides redundancy in terms of “mutation proofing” the assay, meaning variations in any one region will not impact the accuracy of the assay, providing extensive strain coverage.
Furthermore, the workflow for detection is relatively simple. First, RNA is extracted using magnetic bead-based technology using chaotropic buffers. Isolated RNA is then used to set up a PCR reaction on our systems. Following this process, one step reverse transcriptase-PCR is performed to convert RNA to cDNA and then the DNA is amplified with data collection in real-time.
From there we have Research Use Only tools to confirm variants using Sanger sequencing and next-generation sequencing (NGS).
Monitoring the emerging variants of SARS-CoV-2
Dr. Manohar Furtado: Emerging SARS-CoV-2 mutations have led to several new variant strains which appear to be associated with increased virus transmissibility. Global epidemiological surveillance is critical to understanding the evolution of viral pathogens and in turn monitoring for changes in transmissibility, virulence and disease pathology.
At Thermo Fisher, we are closely monitoring the variants to understand the location of the mutations and potential interaction with our coronavirus related assays. Perhaps what is most intriguing about the virus is that the same mutations appear in different variants. For example, the E484K mutation first seen in the South African strain has now shown up in the in the B.1.1.7 variant, where it was not initially found. As the virus evolves, data around these strains will be of increasing value. We are also actively launching genotyping assays to detect specific mutations and variants of concern using our qPCR systems in addition to enabling sequencing on our Sanger sequencing and NGS platforms.
Detection, surveillance and strain identification in 2021
Dr. Manohar Furtado: The United States is behind on its surveillance efforts right now, but I have hope that we will catch up in the next few months. To help prepare for emerging mutations and ensure vaccine efficacy, Thermo Fisher has introduced new testing solutions, including antibody testing, and continues to work to enable sample collection and vaccine production efforts. We are committed to continuing to drive rapid, proactive product modifications and communications to ensure we are doing our part to meet the evolving needs of our global community.
Watch the on-demand webinar and learn more from Dr. Furtado’s presentation.
To learn more about Thermo Fisher Scientific’s COVID-19 Testing Solutions, please visit thermofisher.com/covid19.