tetano
Editor, Senior Moderator
Microb Genom
. 2023 May;9(5).
doi: 10.1099/mgen.0.001013. Fast and cost-effective SARS-CoV-2 variant detection using Oxford Nanopore full-length spike gene sequencing
Cecilia Salazar[SUP] 1 2 [/SUP], Ignacio Ferrés[SUP] 1 2 [/SUP], Mercedes Paz[SUP] 2 3 4 [/SUP], Alicia Costábile[SUP] 2 3 4 5 [/SUP], Gonzalo Moratorio[SUP] 2 3 4 [/SUP], Pilar Moreno[SUP] 2 3 4 [/SUP], Gregorio Iraola[SUP] 1 2 6 7 [/SUP]
Affiliations
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.
Keywords: Oxford Nanopore Technologies; SARS-CoV-2; spike gene; surveillance.
. 2023 May;9(5).
doi: 10.1099/mgen.0.001013. Fast and cost-effective SARS-CoV-2 variant detection using Oxford Nanopore full-length spike gene sequencing
Cecilia Salazar[SUP] 1 2 [/SUP], Ignacio Ferrés[SUP] 1 2 [/SUP], Mercedes Paz[SUP] 2 3 4 [/SUP], Alicia Costábile[SUP] 2 3 4 5 [/SUP], Gonzalo Moratorio[SUP] 2 3 4 [/SUP], Pilar Moreno[SUP] 2 3 4 [/SUP], Gregorio Iraola[SUP] 1 2 6 7 [/SUP]
Affiliations
- PMID: 37200071
- DOI: 10.1099/mgen.0.001013
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.
Keywords: Oxford Nanopore Technologies; SARS-CoV-2; spike gene; surveillance.