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Optimer reagents detect all COVID-19 Variants of Concern

As SARS-CoV-2 continues to mutate we demonstrate the performance of Optimer reagents to the WHO Variants of Concern  

In the summer of 2020 we focused our rapid Optimer development platform on delivering reagents for the SARS-CoV-2 spike and nucleocapsid proteins to help beat COVID-19. As the pandemic has evolved, mutations in the virus have emerged. These new strains of SARS-CoV-2 are in some instances more virulent or more infectious and worries have arisen about their spread and accurate detection using reagents that were developed to the original SARS-CoV-2 wild type. 

Why do SARS-CoV-2 tests need to detect the new variants? 

Many countries are using rapid antigen tests to help track and prevent the spread of the coronavirus. To ensure proper detection and monitoring within communities it is important that all tests being used not only recognise the original wild type (WT) virus, but all subsequent strains too. If the affinity reagents used in these assays fail to detect the new variants, any tests that rely on these reagents could fail to recognise and accurately monitor COVID-19 cases. Equally, for researchers studying the disease they need to know that their reagents show comparable performance across the different SARS-CoV-2 mutants. 

Optimers recognize the SARS-CoV-2 WHO Variants of Concern

Throughout the pandemic, Aptamer Group has continuously monitored the performance of its SARS-CoV-2 Optimer binders to ensure researchers and diagnostic developers working with these Optimers can detect the major variants in the populations.   

The coronavirus S protein is divided into two domains: S1 and S2. The S1 domain mediates receptor binding and the S2 mediates downstream membrane fusion 

The SARS-CoV-2 spike protein is composed of two subunits: the S1 subunit that harbors the receptor binding domain (RBD) and the S2 subunit that anchors the spike to the viral envelope and following activation enables host cell fusion.

We have validated our SARS-CoV-2 Optimer binders to each of the World Health Organisation designated current and previous Variants of Concern:

  • SARS-CoV-2 Wild type
  • SARS-CoV-2 alpha variant, B.1.1.7 (first designated in December 2020)
  • SARS-CoV-2 beta variant, B.1.351 (first designated in December 2020)
  • SARS-CoV-2 gamma variant, P.1 (first designated in January 2021)
  • SARS-CoV-2 delta variant, B.1.617.2 (first designated in May 2021)
  • SARS-CoV-2 omicron variant, B.1.1.529 (first designated in November 2021)

In tests our SARS-CoV-2 S1 Optimers show the ability to bind to the spike (S) protein and the irradiated virus samples from each of the SARS-CoV-2 variants.  

Optimer binders show comparable binding to all SARS-CoV-2 variants

To examine the binding of the S1 Optimer to each of the SARS-CoV-2 variants we monitored the interaction with the specific mutant S1 protein subunit using the Octet Red384 biolayer interferometry system.  

The S1 Optimers were able to bind to all six of the SARS-CoV-2 variants. This suggests that the S1 Optimer is targeted to an epitope away from the site of major mutations within the S protein. Though there has been many fears of the potential for these novel mutations in SARS-CoV-2 S protein to allow the virus to evade detection by diagnostics and potentially reduce the efficacy of the vaccines, the S1 Optimer is not targeted to the current site undergoing mutations in the SARS-CoV-2 protein, and so should continue to recognise the variants of this virus, when used in various research and diagnostic assays.

Comparable performance for the Optimer binders with similar affinity was noted to all the tested SARS-CoV-2 variants. This comparable binding to all variants can simplify assay optimization with equivalent performance and maximise the likelihood of ongoing detection of COVID-19 infections.

VariantKD (nM)
WT10.7 ± 0.06
Alpha (B.1.1.7)7.16 ± 0.13
Beta (B.1.351)5.24 ± 0.09
Gamma (P.1)15.4 ± 0.14
Delta (1.617.2)5.68 ± 0.04
Omicron (B.1.529)10.85 ± 0.09

Affinity of the S1 Optimer to the SARS-CoV-2 variants shows similar binding kinetics to the WT and all five variant SARS-CoV-2 S proteins.

The data below shows example BLI traces to determine the binding kinetics for the SARS-CoV-2 Optimer binders to the different viral variants.

COVID-19 WT Optimer


Biosensor analysis of SARS-CoV-2 Optimer performance with comparable binding to S protein variants. BLI streptavidin probes were coated with 20 nM biotinylated Optimer, washed and the interaction measured in 80 μl of the target protein in buffer over the concentration range shown for (a) WT SARS-CoV-2 S1 (b) B. SARS-CoV-2 S1 and (c) B.1.529 SARS-CoV-2 S1.

In addition to the maintained performance of the S1 Optimer with regards to the SARS-CoV-2 variant forms, we have also developed a further Optimer to the S2 subunit of the S protein, that can be used as a sandwich pair for the detection of SARS-CoV-2.

There have been limited reports of mutations in the S2 protein, and these mutations have not been associated with significant changes in the infectivity or virulence of SARS-CoV-2. The extra specificity delivered through the use of the S2 Optimer within a sandwich pair, adds further reassurance regarding the detection of SARS-CoV-2 variants in experimental and diagnostic samples.

S1 and S2 Optimers bind SARS-CoV-2 variant virus particles

Irradiated virus samples are used in testing labs around the world, for basic research and analysis of diagnostic tests and in vaccine development. This is an inactivated form of the virus that can be safely used in standard laboratories without risk of infection. The analytical performance of SARS-CoV-2 antigen tests is initially verified using irradiated virus prior to clinical validation with patient samples.

When tested with irradiated virus within Aptamer Group laboratories, the SARS-CoV-2 S1 and S2 specific Optimers showed binding to the WT, the alpha and beta variant strains of the virus.

Biosensor analysis of SARS-CoV-2 variants and WT with S1- and S2-specific Optimers shows that each of the Optimers in the matched pair recognize the irradiated virus of the WT, B.1.1.7 and B.1.351 variant forms. BLI streptavidin probes were coated with 20 nM biotinylated Optimer, washed and the interaction measured in 80 μl of the target protein in buffer over the concentration range shown.

Clear binding was seen to all three of the irradiated virus samples of the SARS-CoV-2 variants by biolayer interferometry (BLI), showing that any assays and tests based on these Optimers will be able to detect whole virus particles of SARS-CoV-2 in research and diagnostic assays.

For more information regarding the performance of our SARS-CoV-2 Optimers to S1, S2 and nucleocapsid proteins in biosensor and ELISA formats download our application note or contact Aptamer Group below.

Download application note


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