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Dryad

Raw signals of nucleotides in the S gene of 12 SARS-COV-2 strains

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Aug 01, 2023 version files 241.27 MB

Abstract

The surveillance of the SARS-CoV-2 genome has become one of the crucial techniques in the management of COVID-19, aiding the pandemic response and supporting effective public health interventions. Typically, whole genomic sequencing is used along with PCR-based target enrichment techniques to identify SARS-CoV-2 variants, which is a complicated and time-consuming process that requires central laboratory facilities. Thus, there is an urgent requirement for developing rapid and cost-effective tools that can precisely detect and identify SARS-CoV-2 strains on-site. In this study, we demonstrate the diagnosis of COVID-19 patients and rapid identification of SARS-CoV-2 variants by amplifying and sequencing the entire length of the SARS-CoV-2 S gene using an isothermal enzymatic recombinase amplification combined with the most advanced Oxford nanopore sequencing. The entire procedure, from sampling to sequencing, takes less than 8 hours and can be performed with limited resources. The newly developed method has noteworthy implications for examining the transmission dynamics of the virus, detecting novel genetic variants, and assessing how mutations affect the efficiency of diagnostic approaches, antiviral treatments, and vaccines.