New Strains. No Problem.

Californian L452R mutation.

As new strains of SARS-CoV-2 are identified across the globe, we will supply an update related to the coverage of BioGX COVID-19 assays.

On January 18, 2021, BioGX performed in silico analysis of the primer and probes used for SARS-CoV-2 diagnostics using the N1- and N2-gene regions.  A total of 793 SARS-CoV-2 genome sequences possessing the S-gene L452R mutation, (California) available in the GISAID database were analyzed for the presence of additional mutations within the N1- and N2-gene regions targeted by BioGX SARS-CoV-2 tests. 

N1-gene region

22 of the 793 SARS-CoV-2 sequences with the L452R mutation were analyzed and found to contain a single base pair mismatch.  None of the 22 SARS-CoV-2 sequences contained the mismatch in an area that may affect amplification efficiency. 

N2-gene region

29 of the 793 SARS-CoV-2 sequences analyzed have a single nucleotide mismatch in the N2 region. None of the single base pair mismatches are located in areas that would be predicted to negatively affect amplification or reporting of the BioGX assays.

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).  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):

 

  1. BioGX Xfree™ COVID-19 Direct RT-PCR
  2. BD BioGX SARS-CoV-2 Reagents for BD MAX™ System 
  3. BioGX SARS-CoV-2 HMP – N1, N2 & RNase P Multiplex 
  4. BioGX COVID-19, Flu A, Flu B, RSV RT-PCR for BD MAX™

Learn More about the UK, B.1.1.7 and South African, 501Y.V2 strains

All BioGX COVID-19 tests have coverage for new strains of SARS-CoV-2

During the course of the SARS-CoV-2 pandemic the virus has accumulated a number of mutations in its genome, causing concern not only for whether the mutations might affect vaccine effectiveness, but also for diagnostic test detection of emerging strain variants.  Most recently, a number of reports have hypothesized that strains from the B.1.1.7 lineage of SARS-CoV-2 possess a higher infectivity rate compared to the other SARS-CoV-2 lineages. The strains from this lineage are the predominant strains currently circulating in the United Kingdom and have been recently identified in other countries. In addition to this lineage, a strain variant designated 501Y.V2 (within B.1.351 lineage) has been associated with increased infectivity and is currently circulating in South Africa.  

 

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):

 

  1. BioGX Xfree™ COVID-19 Direct RT-PCR
  2. BD BioGX SARS-CoV-2 Reagents for BD MAX™ System 
  3. BioGX SARS-CoV-2 HMP – N1, N2 & RNase P Multiplex 
  4. 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.