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Volume 9, Issue 5

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

Abstract

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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Oxford Nanopore Technologies , SARS-CoV-2 , spike gene and surveillance
Funding
This study was supported by the:
  • FOCEM (MERCOSUR Structural Convergence Fund) (Award COF03/11)
    • Principle Award Recipient: NotApplicable
  • Fondo de Solidaridad para Proyectos Innovadores, Sociedad Civil, Francofonía y Desarrollo Humano (FSPI), Ambassade de France
    • Principle Award Recipient: NotApplicable
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2023-05-18
2024-05-16
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Fast and cost-effective SARS-CoV-2 variant detection using Oxford Nanopore full-length spike gene sequencing
M Gen 9, 001013 (2023); https://doi.org/10.1099/mgen.0.001013
/content/journal/mgen/10.1099/mgen.0.001013
/content/journal/mgen/10.1099/mgen.0.001013
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