Fast and cost- effective SARS- CoV-2 variant detection using Oxford Nanopore full- length spike gene sequencing

Most biologically relevant and diagnostic mutations in the severe acute respiratory syndrome coronavirus- 2 (SARS- CoV- 2) genome have been identified in the S gene through global genomic surveillance efforts. However, large- scale whole- genome sequencing (WGS) is still challenging in developing countries due to higher costs, reagent delays and limited infrastructure. Consequently, only a small fraction of SARS- CoV- 2 samples are characterized through WGS in these regions. Here, we present a complete workflow consisting of a fast library preparation protocol based on tiled amplification of the S gene, followed by a PCR barcoding step and sequencing using Nanopore platforms. This protocol facilitates fast and cost- effective identification of main variants of concern and mutational surveillance of the S gene. By applying this protocol, report time and overall costs for SARS- CoV- 2 variant detection could be reduced, contributing to improved genomic surveillance programmes, particularly in low- income regions.

Automated summary

Most relevant mutations in the SARS-CoV-2 genome are found in the S gene, but large-scale whole-genome sequencing is challenging in developing countries due to cost and infrastructure limitations. To address this issue, a fast and cost-effective workflow is presented, which includes a library preparation protocol based on tiled amplification of the S gene and sequencing using Nanopore platforms. This protocol enables quick identification of key variants and mutational surveillance of the highly relevant S gene, reducing detection time and overall costs, particularly in low-income regions.