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.
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_1122452||P.3 (version: 2021-04-01)||Theta|
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
Additional information available at: