Xfree™ COVID-19 DIRECT RT-PCR
Is the Xfree™ COVID-19 Direct RT-PCR test affected by the new mutations in the SARS-CoV-2 genome initially identified in the UK and South Africa?
No. There are 17 non-synonymous mutations and deletions identified to date within the B.1.1.7 lineage, with 15 of those being located in the ORF1ab, ORF8, and Spike Protein genes. None of these mutations affect viral detection ability by any of the BioGX assays which target the N gene. Moreover, out of the 17 identified mutations only 2 are located in the N gene region, but are located outside of the region targeted by BioGX assays. The BioGX assays target a unique region of the N gene which is unaffected by the N gene mutations in the B.1.1.7 lineage or the 501Y.V2 variants.
BioGX utilizes primers and probes for detection of SARS-CoV-2, targeting the viral nucleocapsid gene (N gene region), human RNaseP gene as an endogenous control, and a non-naturally occurring internal amplification control (IAC). Both the SARS-CoV-2 N1/N2, and RNase P primer/probe sets are based upon those designed and recommended by the US Centers for Disease Control and Prevention. The following four BioGX SARS-CoV-2 testing products utilize the US Centers for Disease Control and Prevention primer/probe set designs for N-gene region(s):
- BioGX Xfree™ COVID-19 Direct RT-PCR
- BD BioGX SARS-CoV-2 Reagents for BD MAX™ System
- BioGX SARS-CoV-2 HMP – N1, N2 & RNase P Multiplex
- BioGX COVID-19, Flu A, Flu B, RSV RT-PCR for BD MAX™
BioGX performed exhaustive genomic sequence database (GISAID & NIH) analysis in order to determine if any of the genomic sequences from the potentially more infectious B.1.1.7 lineage or 501Y.V2 variant possess any mutations in the N region targeted by the BioGX test might affect detection of the virus. Our in silico analysis utilized over 4,200 SARS-CoV-2 B.1.1.7 lineage genomes available from the GISAID and NIH databases (as of January 4, 2021).The predicted detection of 99.9% of the SARS-CoV-2 B.1.1.7 lineage remains unchanged with the BioGX tests. In silico analysis of the 320 sequences available in the GISAID database (as of January 4, 2021) belonging to the 501Y.V2 variant (within B.1.351 lineage) predicted no change in PCR detection with the BioGX tests.
In summary, as of January 4, 2021, in silico analysis of the N gene regions targeted by the BioGX tests predicts strains within the potentially more infectious B.1.1.7 lineage and 501Y.V2 variants (within B.1.351 lineage) of SARS-CoV-2 circulating in the United Kingdom, South Africa, and other countries will be detected.
I am currently utilizing SARS-CoV-2 diagnostic tests that identify SARS-CoV-2 via two or three diagnostics targets. Since the BioGX Xfree™ COVID-19 Direct RT-PCR test uses only one SARS-CoV-2 diagnostic target (N1 gene region), is this a limitation in virus identification? If not, what is the status of the BioGX Xfree™ COVID-19 Direct RT-PCR EUA review?
The FDA guidelines provided in June 2020 supported the use of single target SARS-CoV-2 identification as an acceptable approach for clinically validated tests. The FDA has received the BioGX Xfree™ COVID-19 Direct RT-PCR application and validation data for EUA review.
The FDA lists the BioGX Xfree™ COVID-19 Direct RT-PCR product under the Question: What commercial manufacturers are distributing diagnostic test kits under the policy outlined in Section IV.C of the Policy for Coronavirus Disease-2019 Tests? (Updated 12/14/20). (https://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/notifications-and-emergency-use-authorizations-faqs-testing-sars-cov-2).