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2nd July 2021  Editorial by: Paul Carton

A Faster Alternative to NGS for Detecting Delta and more COVID-19 Variants of Concern

There are mutations happening within the SARS-CoV-2 genome, that for reasons yet to be fully understood, make the virus more transmissible and, in the case of variants of concern (VOC), potentially more virulent.

Up until now, public health laboratories have been relying on RT-qPCR tests showing S-gene failure to indicate a variant is present and NGS to identify the exact one such as Alpha, Beta, Gamma, Delta or Delta Plus. However, NGS can mean extra cost and a longer time to result. With concerns of the virus becoming endemic within the world's population and uncertainty around the efficacy of current vaccines against future variants, is there a strong argument for routine labs to be equipped with assays to detect new and emerging variants? In this interview with Seden Grippon, Respiratory Product Manager at Novacyt, Seden tells rapidvirology.com how labs and public health agencies will benefit from using its recently launched SNPsig® EscapePLEX SARS-CoV-2, a faster, less-expensive method in detecting SARS-CoV-2 variants than the current NGS route and explains how the test works.

Q. Novacyt recently launched the SNPsig® EscapePLEX SARS-CoV-2 genotyping assay detects 4 important mutations (E484K, K417N, K417T, and P681R). Can you explain the significance of these mutations?
Seden: These four mutations have been identified in several VOCs and variants under investigation (VOI), including Beta, Gamma, Delta, and Delta Plus. They have been demonstrated to increase transmission rates and provide the virus with the ability to evade antibodies, decreasing the efficacy of currently available vaccines and posing a great risk to public health. Being able to identify these mutations in the COVID-19 positive samples as soon as possible will have a considerable positive impact on the containment of the spread of the virus.

Q. With other options such as multiplex PCR and NGS – what advantages does the Novacyt genotyping method offer?
EscapePLEX has been developed as a reflex test that can be run with the same sample used for the primary detection of the presence of the virus. This approach eliminates the need for an additional extraction and improves the time to result, yielding results in less than 90 minutes, while NGS results can take days to arrive. In some countries, NGS is not even available.

Q. Your COVID-19 genotyping assay for detecting variants (including the delta variant) is based on 5 Single Nucleotide Polymorphisms (SNPs) common to these variants. What controls are used for such a complicated assay to avoid any false negatives/positives?
Seden: Novacyt’s bioinformatics surveillance group has worked with a global network of virologists tracking variants to identify the mutations, or Single Nucleotide Polymorphisms (SNPs), including these four clinically significant variants. The targets on EscapePLEX have been designed to allow the detection of the specific mutations of interest-based on the use of specific primers designed to only recognize the mutated version of the DNA strain, not recognizing any other sequences. A second tube included in the assay can detect different SARS-CoV-2 targets to confirm that the sample is positive in the case of having negative results for the four mutations on the first tube, as well as an internal control. The assay also comes with a positive control for all the targets to ensure the correct performance of the assay.

Q What sort of laboratories will benefit from this assay? And how will public health laboratories, in particular, benefit from knowing the exact lineage/variant of the virus a single person is infected with?
Both public and private sector testing globally will benefit from using this assay to monitor and detect the presence of those variants carrying the clinically significant mutations. Early detection will allow for a suitable response to be initiated in a timely manner to handle any potential spreads.

Q. Can this assay be run on any PCR thermocycler, or does it require special instrumentation?
These assays are compatible with most Real-Time PCR instruments that can detect fluorescence in the FAM, HEX/VIC, ROX, and Cy5 and are validated for a wide variety of them as part of our validation protocols. Compatible instruments also include Novacyt’s very own genesig® family of thermocyclers.

Q. What is the current approval status of the Novacyt genotyping kit?
 Currently, this assay is for Research Use Only (RUO), but we are planning to extend its use for clinical diagnostics for the greater benefits to public health. EscapePLEX will be CE-marked.


Seden Grippon is currently the Respiratory Product Manager at Novacyt Group. She holds a Ph.D. in Molecular Biosciences from Imperial College London and has numerous publications under her belt.  Her years of experience and achievements as an accomplished scientist helped Novacyt Group launch over ten highly innovative COVID-19 products

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Date Published: 2nd July 2021

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