Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing

Studer, F.; Petit, J.-L.; Engelen, S.; Mendoza-Parra, M. A.

Since December 2019, the emergence of a novel coronavirus responsible for a severe acute respiratory syndrome (SARS-CoV-2) is accountable for a major pandemic situation. As consequence, a major effort worldwide has been performed for the development of viral diagnostics strategies aiming at (i) reducing the diagnostics time, (ii) decrease the costs per assay, and (iii) providing population-scale solutions. Beyond the diagnostics requirements, the description of the B.1.1.7 strain, originated in the south of England, as a highly transmissible variant has strongly accelerated the worldwide interest in tracking SARS-CoV-2 variants occurrence. Since then, other extremely infectious variants were described and unsurprisingly further others are expected to be discovered, notably due to the long period of time on which the pandemic situation is lasting. Interestingly, all currently described SARS-CoV-2 variants present systematically several mutations within the gene encoding the Spike protein, involved in host receptor recognition and entry into the cell. Hence, instead of sequencing the whole viral genome for variants tracking, our proposed strategy focuses on the SPIKE region, as a way to increase the number of candidate samples to screen at once; an essential aspect to accelerate SARS-CoV-2 diagnostics, but also improve variants emergence and progression surveillance. Herein we present a proof of concept study, for performing both at once, population-scale SARS-CoV-2 diagnostics and variants tracking. This strategy relies on (i) the use of the portable and affordable MinION DNA sequencer; (ii) a DNA barcoding strategy and a SPIKE gene-centered variants tracking, for largely increasing the number of candidates per assay; and (iii) a real-time diagnostics and variants tracking monitoring thanks to our software RETIVAD. As a whole, this strategy represents an optimal solution for addressing the current needs on SARS-CoV-2 progression surveillance, notably due to its affordable implementation, allowing its implantation even in remote places over the world.