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Article: Agena Bioscience’s SARS-CoV-2 Tests: Providing Resilience Against the Emergence of New Variants

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Robin Everts PhDRobin Everts, PhD, PGx expert and former Agena Bioscience Scientist
January 5, 2021

The 2019 outbreak of the novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), quickly escalated to a worldwide public health emergency. Throughout the course of the pandemic the virus has mutated, resulting in multiple SARS-CoV-2 variants circulating around the globe. Laboratories are concerned about how these emerging strains may impact their ability to accurately detect SARS-CoV-2. As described below, Agena Bioscience’s MassARRAY® SARS-CoV-2 Panel was designed with five unique assays targeting three different regions of the viral genome, making it robust against the emergence of new variants, including the recent United Kingdom and South African mutations.

New SARS-CoV-2 variants with mutations in the S gene discovered in the United Kingdom and South Africa

Two independent new coronavirus variants have emerged, one in the United Kingdom (UK) and one in South Africa. The strain in the UK is known as B.1.1.7 (also known as SARS-CoV-2 20B/501Y.V1 or VOC 202012/01 for the first Variant of Concern from December 2020) and the strain in South Africa is known as 20C/501Y.V2 or B.1.351. These new strains have an unusually large number of mutations and appear to spread more quickly and easily than other variants1,5, reportedly accounting for a majority of new infections in the UK and South Africa.  The UK variant was first detected in September 2020 and has since been detected in other countries around the world, including the United States and Canada. The South African variant emerged in December and has already been detected in several other countries around the globe. There is currently no evidence that these variants cause more severe illness or increased risk of death, but health officials continue to monitor them.

Due to selective pressures (therapeutics, immune response, environmental factors) viruses are constantly changing. SARS-CoV-2 mutates regularly, at a rate of one new mutation about every 2 weeks2.  Many mutations do not lead to changes in the structure or the function of the proteins for which the genome encodes. However, some mutations can have a more significant impact, such as the increased transmissibility observed with the B.1.1.7 and 501Y.V2 variants. The mutations in these two variants occur mostly within the receptor binding domain of the spike protein (S protein). In particular, both variant strains include the N501Y mutation, which may allow the virus to attach and enter human cells more effectively.

SARS-CoV-2 Testing PanelMultiple-target assay design provides resilience against mutations

Many of the FDA EUA3 and CE-IVD tests on the market have fewer than 3 gene targets and less than 5 assays, making them potentially more susceptible to giving false results in the case of viral mutations. If the mutation occurs at the location of the assay-specific primers or probes, it could lead to a loss of the ability to detect the target (e.g., assay dropout)6,7,8.

Knowing the frequency and likelihood of mutations within viruses, particularly RNA viruses like SARS-CoV-2, the MassARRAY SARS-CoV-2 Panel was designed to target three independent highly conserved regions of the viral genome, based on 18,772 complete genomes available9. These regions are less likely to be impacted by mutations. Should a mutation occur in one of the target regions, the panel has the built-in redundancy of 5 unique assays targeting these three areas of the viral genome (Table 1). For a positive test result, only 2 of the 5 assays need to be detected. This assay design makes the MassARRAY SARS-CoV-2 Panel robust against the emergence of new variants. In the unlikely scenario that a mutation arises and one of the 5 assays is not able to detect its target, the panel will still provide an accurate result.

Table 1: MassARRAY SARS-CoV-2 Panel Assay Targets

SARS-CoV-2 Panel Assay Targets

The MassARRAY SARS-CoV-2 Panel is not impacted by the B.1.1.7 or B.1.351 variants

Some of the FDA Emergency Use Authorization and CE-IVD tests on the market do target the S gene, they may be impacted by the B.1.1.7 or B.1.351 variants. This causes labs to question whether their testing method is impacted by these new strains and the potential for producing false negative results. For this reason, labs utilizing tests targeting the S gene have been advised to review their PCR performance and dropout of the S gene4. These developments highlight the importance of assay design in providing laboratories with confidence in their test results.

Because the MassARRAY SARS-CoV-2 Panel targets the nucleocapsid (N) gene and ORF1ab, but not the spike (S) gene, the panel’s test results are not affected by the B.1.1.7 or B.1.351 variants.

The MassARRAY SARS-CoV-2 Panel provides confidence in detecting COVID-19 positive patients in a high throughput capacity

With its multi-target, multi-assay design Agena Bioscience’s MassARRAY SARS-CoV-2 Panel ensures detection resilience against the emergence of new SNPs should the SARS-CoV-2 virus continue to mutate. With the ability to run thousands of samples per day on the high-throughput MassARRAY System, as well as a reliable supply of reagents to help resolve supply chain constraints, Agena Bioscience is committed to supporting our global customers during these unprecedented times.