RT-LAMP Duo and Direct Kits’ reliability in recognition of identified SARS-CoV-2 significant variants, among them the Breton that has the potential to escape standard RT-PCR testing analysis from swab-based samples, has been fully confirmed. Recognition of multiple variants by the RT-LAMP Duo and Direct Kit is important to ensure public health safety where accurate testing against multiple types of SARS-CoV-2 variants of concern is absolutely crucial in sustaining efforts against pandemic surviliance.
Methodology:
The in-silico analysis was performed by analyzing the NCBI reference sequence of SARS-CoV-2 (NC_045512.2) together with below mentioned whole genome sequences of specific strains deposited in GISAID database EpiCoV:
| Accession number | Variant | WHO classification |
|---|---|---|
| EPI_ISL_723044 | B.1.1.7 | Alfa |
| EPI_ISL_825139 | B.1.351 | Beta |
| EPI_ISL_792680 | P.1 | Gamma |
| EPI_ISL_2650470 | B.1.617.2 | Delta |
| EPI_ISL_2631197 | B.1.427/B.1.429 | Epsilon |
| EPI_ISL_2614193 | P.2 | Zeta |
| EPI_ISL_1563854 | B.1.525 | Eta |
| EPI_ISL_1122452 | P.3 (version: 2021-04-01) | Theta |
| EPI_ISL_2647531 | B.1.526 | Iota |
| EPI_ISL_1415353 | B.1.617.1 | Kappa |
| EPI_ISL_2536799 | C.37 | Lambda |
| EPI_ISL_1259297 | Breton (hCoV-19/France/BRE-IPP04233/2021) | N/A |
Sequence alignment was performed by utilizing multiple sequence alignment program Clustal Omega (EMBL-EBI) that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more genomic sequences. Further visualization of the alignment was performed by using MView (EMBL-EBI).
For further wet-lab analysis fragment-specific sequences different from the reference genomic sequences were utilized, as several of the abovementioned new variants exhibit mutations’ similarities in the S and N genes. For this purpose, cDNA for S and N genes specific-fragments where synthetized and after dilution to 1000 copies / µl utilized as a template when setting-up reactions with primer sets utilized in RT-LAMP Duo and Direct Kits.
The above-mentioned steps show that Genomtec® SARS-CoV-2 EvaGreen® RT-LAMP CE-IVD Duo Kit and oraz Genomtec® SARS-CoV-2 EvaGreen® Direct-RT-LAMP CE-IVD Kit successfully detects all of the abovementioned SARS-CoV-2 variants.
Genomtec constantly evaluates how newly emerged SARS-CoV-2 variants might impact assay performance by utilizing both in-silico as well as wet-lab approach in order to assure customers of the high inclusivity of Genomtec® SARS-CoV-2 EvaGreen® RT-LAMP CE-IVD Duo Kit and Genomtec® SARS-CoV-2 EvaGreen® Direct-RT-LAMP CE-IVD Kit among SARS-CoV-2 variants of concern.
Report has been prepared by: Miron Tokarski, CEO, Genomtec SA
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