During the COVID-19 pandemic, new genetic variants of the etiologic agent, SARS-CoV-2, have been identified in different geographical regions. These variants have spread rapidly across the globe creating concern as to their transmissibility and impact on current vaccines or available immunotherapy.1
Genetic changes in SARS-CoV-2 are associated with mutability of its genome during viral replication. SARS-CoV-2 genomic replication requires the RNA-dependent RNA polymerase or non-structural protein 12 (NSP12) and the exoribonuclease (NSP14), a proofreading system responsible for the high fidelity of SARS-CoV-2 replication.2 As a result, coronaviruses, including SARS-CoV-2, generate fewer mutations over time than other RNA viruses.
However, despite this error correcting genomic feature in coronaviruses, several genetic variants of concern have been identified that give the altered SARS-CoV-2 genetic variants a competitive advantage. These advantages include enhanced transmissibility due to stronger binding to viral receptors (e.g. the ACE2 protein3) on the surface of respiratory tract cells allowing enhanced entry into the target cell, overproduction of spike protein within infected cells, conformational changes in the virus spike protein allowing evasion of immune responses and mutations in the furin cleavage site of the spike protein that modulate its pathogenicity.3,4,5,6
The DiaSorin Molecular Simplexa® SARS-CoV-2 Variants Direct kit is a Research Use Only (RUO) assay intended for the in vitro qualitative detection and differentiation of the mutations N501Y, E484K, E484Q and L452R present in the genome of SARS-CoV-2 in nasal and nasopharyngeal swab specimens from patients with known SARS-CoV-2 infection.
To learn more about DiaSorin’s response to the COVID-19 outbreak, visit https://diasoringroup.com/.
2. Romano M, Ruggiero A, Squeglia F, Maga G, Berisio R. A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping. Cells. 2020;9 (5):1267. Published 2020 May 20. doi:10.3390/cells9051267
3. Becares M, Pascual-Iglesias A, Nogales A, Sola I, Enjuanes L, Zuniga S. 2016. Mutagenesis of coronavirus nsp14 reveals its potential role in modulation of the innate immune response. J Virol 90:5399–5414. doi:10.1128/JVI.03259-15
4. Ou J, Zhou Z, Dai R, et al. Emergence of SARS-CoV-2 spike RBD mutants that enhance viral infectivity through increased human ACE2 receptor binding affinity. bioRxiv. 2020:2020.03.15.991844. doi:10.1101/2020.03.15.991844
5. Zhang, L., Jackson, C.B., Mou, H. et al. SARS-CoV-2 spike protein D614G mutation increases virion spike density and infectivity. Nat Commun 11, 6013 (2020). https://doi.org/10.1038/s41467-020-19808-4. Xie, X., Liu, Y., Liu, J. et al. Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K and N501Y variants by BNT162b2 vaccine-elicited sera. Nat Med (2021). https://doi.org/10.1038/s41591-021-01270-4
6. Johnson, B.A., Xie, X., Bailey, A.L. et al. Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis. Nature 591, 293–299 (2021).
Why to choose it
RT-PCR assay direct from nasopharyngeal and nasal swab specimens without RNA extraction that allows in vitro qualitative and differential detection of the SARS-CoV-2 variant mutations N501Y, E484K, E484Q, and L452R. These mutations are present in potential variants of interest including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), Epsilon (B.1.427/B.1.429), Zeta (P.2), Eta (B.1.525), Iota (B.1.526) and Kappa (B.1.617.1).
In vitro qualitative differential detection of the mutations N501Y, E484K, E484Q, and L452R
*Phylogenetic Assignment of Named Global Outbreak Lineages
**Mutation has been described in some but not all strains sequenced
Leveraging the Unique Fluorescence Melting-Curve Analysis Feature of the LIAISON® MDX
In the Simplexa® SARS-CoV-2 Variants Direct (RUO) assay, forward and reverse primers are used to amplify the SARS-CoV-2 S gene region containing the sites of mutations. Fluorescent probes specific for each mutation are used to perform a post-amplification melting analysis to identify the presence of mutant or wildtype nucleotides at specific locations. RNA internal control amplification is used to detect RT-PCR failure and/or inhibition.
Identification of N501Y Mutation Using Melting-Curve Analysis
Simplexa® SARS-CoV-2 Variants Direct (RUO)
|Code MOL4350||Reactions 24|
Simplexa® SARS-CoV-2 Variants Positive Control Pack (RUO)
|Code MOL4360||Reactions 10|