The UK SARS-CoV-2 variant under investigation (VUI) called VUI 202012/01 (B.1.1.7 lineage) has multiple mutations in the spike glycoprotein’s gene S. Five are amino acid replacements (D614G, A222V, N439K, Y453F and N501Y), and one deletion (del) . The South African variant called 501.V2 (B.1.351 lineage) also has mutations in the spike protein: D80A, D215G, E484K, N501Y and A701V. The VUI202012/01 (B.1.1.7 lineage) variant has 23 mutations with 14 amino acid replacements and 3 in-frame deletions. Two of these mutations have already been described to alter SARS-CoV-2 biology: N501Y sits in the receptor binding motif (RBM) of the Spike protein, and has been described to increase binding affinity to the human ACE-2 receptor; 69-70del has been identified in variants associated with immune escape in immunocompromised patients and is responsible for a “dropout” in the S gene PCR target in certain diagnostic tests.
Reference: “Emerging SARS-CoV-2 Variants”. Centers for Disease Control and Prevention. 3 January 2021.
Do These Mutations Affect PerkinElmer’s Diagnostic Coronavirus RT-PCR Assays?
PerkinElmer’s SARS-CoV-2 RT-PCR assays are designed to identify SARS-CoV-2 ORF1ab and N genes, therefore the mutations in the above variants do not affect the detection of SARS-CoV-2 by PerkinElmer RT-PCR assays. As described in the kit insert, PerkinElmer’s RT-PCR assays target two specific genomic regions of SARS-CoV-2: nucleocapsid (N) gene and ORF1ab. Thus, the mutations in spike protein do not impact the safety and effectiveness of PerkinElmer’s assays.
PerkinElmer’s Proactive Risk Management Plan:
PerkinElmer monitors SARS-CoV-2 variants database in NCBI, GISAID and SARS-CoV-2 publications (PubMed) and works closely with our government and commercial testing partners. The information is used to perform thorough bioinformatics analysis routinely. Based on in silico analysis, the performance of the kit is not impacted by the mutations.
What Should Laboratories Watch For?
On January 8, 2021, the U.S. FDA issued an alert about potential false negative results associated with commonly used COVID-19 tests due to mutations in the novel coronavirus’s genetic code. U.S. FDA’s analysis identified three molecular assays whose performance could be impacted by these SARS-CoV-2 variants. They requested and received reports from test developers that showed reduced analytical sensitivity associated with these SARS-CoV-2 molecular tests. Labs that use one of these assays should proceed with extreme caution – the extent, breath or depth of false negative outcome is completely unknown, therefore utilizing these tests to track the new variant is unwise and unauthorized. The FDA recommends repeating the tests performed with any of these affected assays using an unaffected assay, when there is suspicion of a false negative result.
How Can PerkinElmer Help?
PerkinElmer has received several inquiries about the availability of our kits from concerned labs currently using assays that have been flagged due to potential false negative results. PerkinElmer can assist by ensuring a steady supply of the most-sensitive commercially available RT-PCR kit for SARS-CoV-2 detection* as established by the U.S. FDA’s Reference Panel Study wherein the FDA developed an experiment to precisely compare the performance of the nucleic acid-based SARS-CoV-2 assays which have received Emergency use Authorization and published a comparative performance analysis. The PerkinElmer New Coronavirus Nucleic Acid Detection Kit has the lowest Limit of Detection among all the commercially available kits tested – this means a significant reduction in false negative rate even in a world without new variants. As PerkinElmer’s assays are unaffected by the variants described above, the team continues to leverage its strong position to help.
* FDA Reference Panel Comparative Data. Jan. 12, 2021.