Skip to Main content Skip to Navigation
Journal articles

Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100TM System

Abstract : Global human health is increasingly challenged by emerging viral threats, especially those observed over the last 20 years with coronavirus-related human diseases, such as the Severe Acute Respiratory Syndrome (SARS) and the Middle East Respiratory Syndrome (MERS). Recently, in late December 2019, a novel Betacoronavirus, SARS-CoV-2, originating from the Chinese city of Wuhan, emerged and was then identified as the causative agent of a new severe form of pneumonia, COVID-19. Real-time genome sequencing in such viral outbreaks is a key issue to confirm identification and characterization of the involved pathogen and to help establish public health measures. Here, we implemented an amplicon-based sequencing approach combined with easily deployable next-generation sequencers, the small and hand-held MinION sequencer and the latest most compact Illumina sequencer, the iSeq100TM system. Our results highlighted the great potential of the amplicon-based approach to obtain consensus genomes of SARS-CoV-2 from clinical samples in just a few hours. Both these mobile next-generation sequencers are proven to be efficient to obtain viral sequences and easy to implement, with a minimal laboratory environment requirement, providing useful opportunities in the field and in remote areas.
Complete list of metadatas

Cited literature [19 references]  Display  Hide  Download

https://hal-pasteur.archives-ouvertes.fr/pasteur-02976015
Contributor : Charlotte Guy <>
Submitted on : Friday, October 23, 2020 - 10:51:00 AM
Last modification on : Monday, November 16, 2020 - 5:56:03 PM

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

Collections

Citation

Véronique Hourdel, Aurelia Kwasiborski, Charlotte Balière, Séverine Matheus, Christophe Frédéric Batéjat, et al.. Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100TM System. Frontiers in Microbiology, Frontiers Media, 2020, 11, pp.571328. ⟨10.3389/fmicb.2020.571328⟩. ⟨pasteur-02976015⟩

Share

Metrics

Record views

33

Files downloads

55