A straightforward molecular strategy to retrospectively investigate the spread of SARS-CoV-2 VOC202012/01 B.1.1.7 variant

Abstract

The spread of new SARS-CoV-2 variants represents a serious threat worldwide, thus rapid and cost-effective methods are required for their identification. Since November 2020, the TaqPath COVID-19 assay (Thermo Fisher Scientific) has been used to identify viral strains of the new lineage B.1.1.7, since it fails to detect the S-gene with the ∆69/70 deletion. Here, we proposed S-gene mutations screening with the Allplex SARS-CoV-2 assay (Seegene), another widely used RT-PCR test that targets Sarbecovirus E, SARS-CoV-2 N, and RdRp/S genes. Accordingly, we evaluated the S gene amplification curve pattern compared to those of the other genes. Exploiting an Allplex assay-generated dataset, we screened 663 RT-PCR digital records, including all SARS-CoV-2 respiratory samples tested in our laboratory with the Allplex assay between January 1st and February 25th, 2021. This approach enabled us to detect 64 samples with peculiar non-sigmoidal amplification curves. Sequencing a selected group of 4 RNA viral genomes demonstrated that those curves were associated with B.1.1.7 variant strains. Our results strongly suggest that B.1.1.7 variant spread has begun in this area at least since January and imply the potential of these analytical methods to track and characterize the spread of B.1.1.7 strains in those areas where Allplex SARS-CoV-2 datasets have been previously recorded.

Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection

“…In the Allplex assay, mutations in the VOC B.1.1.7 variant in the S- and RdRP- gene targets did not affect the amplification curve pattern compared with the N gene. A study comparing amplification curve patterns of the envelope (E), N, and RdRP/S genes of the Allplex SARS-CoV-2 assay (Seegene) found peculiar, non-sigmoidal amplification curves in the RdRP/S genes that were associated with B.1.1.7 variant strains ( Ibba et al, 2021 ). Although the Allplex assay used the S-gene target, the Allplex SARS-CoV-2 assay used a combination of two gene targets: RdRP and the S gene.…”

Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia

“…In this study, we showed that the B.1.1.7 lineage rapidly spread becoming the prevalent lineage from January to March 2021. Indeed, a progressive increase in positive cases of SARS-CoV-2 infections and the concomitant emergence of the Alpha variant were reported in diverse regions of Italy [ 6 , 7 , 15 , 16 ]. Lai and colleagues reported that the B.1.1.7 lineage significantly increased from 3.5% in December 2020 to 86.7% in March 2021, replacing the previously circulating variant B.1.177 [ 7 ].…”

Physicochemical effect of the N501Y, E484K/Q, K417N/T, L452R and T478K mutations on the SARS-CoV-2 spike protein RBD and its influence on agent fitness and on attributes developed by emerging variants of concern

“…Mutation identified so far only in the SARS-CoV-2 variant that emerged in the UK (lineage B.1.1.7). Consequence of deletion of 21,765–21770 genome region, it is characterized by the two amino acids deletion at positions 69/70 (del69-70/(ΔH69/V70), and appears to have arisen in multiple genetic backgrounds of SARS-CoV-2, accordingly with some studies ( Ibba et al, 2021 ; Borges et al, 2021 ).…”