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

Abstract Since December 2019, a novel coronavirus responsible for a severe acute respiratory syndrome (SARS-CoV-2) is accountable for a major pandemic situation. The emergence of the B.1.1.7 strain, as a highly transmissible variant has accelerated the world-wide interest in tracking SARS-CoV-2 vari...

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Autores principales:	François Stüder, Jean-Louis Petit, Stefan Engelen, Marco Antonio Mendoza-Parra
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/aae11a66f3d94b1294c5335129e11b77
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spelling	oai:doaj.org-article:aae11a66f3d94b1294c5335129e11b772021-12-02T18:49:36ZReal-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing10.1038/s41598-021-95563-w2045-2322https://doaj.org/article/aae11a66f3d94b1294c5335129e11b772021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-95563-whttps://doaj.org/toc/2045-2322Abstract Since December 2019, a novel coronavirus responsible for a severe acute respiratory syndrome (SARS-CoV-2) is accountable for a major pandemic situation. The emergence of the B.1.1.7 strain, as a highly transmissible variant has accelerated the world-wide interest in tracking SARS-CoV-2 variants’ occurrence. Similarly, other extremely infectious variants, were described and further others are expected to be discovered due to the long period of time on which the pandemic situation is lasting. All described SARS-CoV-2 variants present 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, herein we propose to focus on the SPIKE region to increase the number of candidate samples to screen at once; an essential aspect to accelerate diagnostics, but also variants’ emergence/progression surveillance. This proof of concept study accomplishes both at once, population-scale diagnostics and variants' tracking. This strategy relies on (1) the use of the portable MinION DNA sequencer; (2) a DNA barcoding and a SPIKE gene-centered variant’s tracking, increasing the number of candidates per assay; and (3) a real-time diagnostics and variant’s tracking monitoring thanks to our software RETIVAD. 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.François StüderJean-Louis PetitStefan EngelenMarco Antonio Mendoza-ParraNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q François Stüder Jean-Louis Petit Stefan Engelen Marco Antonio Mendoza-Parra Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing
description	Abstract Since December 2019, a novel coronavirus responsible for a severe acute respiratory syndrome (SARS-CoV-2) is accountable for a major pandemic situation. The emergence of the B.1.1.7 strain, as a highly transmissible variant has accelerated the world-wide interest in tracking SARS-CoV-2 variants’ occurrence. Similarly, other extremely infectious variants, were described and further others are expected to be discovered due to the long period of time on which the pandemic situation is lasting. All described SARS-CoV-2 variants present 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, herein we propose to focus on the SPIKE region to increase the number of candidate samples to screen at once; an essential aspect to accelerate diagnostics, but also variants’ emergence/progression surveillance. This proof of concept study accomplishes both at once, population-scale diagnostics and variants' tracking. This strategy relies on (1) the use of the portable MinION DNA sequencer; (2) a DNA barcoding and a SPIKE gene-centered variant’s tracking, increasing the number of candidates per assay; and (3) a real-time diagnostics and variant’s tracking monitoring thanks to our software RETIVAD. 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.
format	article
author	François Stüder Jean-Louis Petit Stefan Engelen Marco Antonio Mendoza-Parra
author_facet	François Stüder Jean-Louis Petit Stefan Engelen Marco Antonio Mendoza-Parra
author_sort	François Stüder
title	Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing
title_short	Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing
title_full	Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing
title_fullStr	Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing
title_full_unstemmed	Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing
title_sort	real-time sars-cov-2 diagnostic and variants tracking over multiple candidates using nanopore dna sequencing
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/aae11a66f3d94b1294c5335129e11b77
work_keys_str_mv	AT francoisstuder realtimesarscov2diagnosticandvariantstrackingovermultiplecandidatesusingnanoporednasequencing AT jeanlouispetit realtimesarscov2diagnosticandvariantstrackingovermultiplecandidatesusingnanoporednasequencing AT stefanengelen realtimesarscov2diagnosticandvariantstrackingovermultiplecandidatesusingnanoporednasequencing AT marcoantoniomendozaparra realtimesarscov2diagnosticandvariantstrackingovermultiplecandidatesusingnanoporednasequencing
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Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing

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