Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100TM System
Véronique Hourdel, Aurélia Kwasiborski, Charlotte Balière, Séverine Matheus, Christophe Batéjat, Jean‐Claude Manuguerra, Jessica Vanhomwegen, Valérie Caro
Abstract
Global human health is increasingly challenged by emerging viral threats, especially those observed over the last twenty 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 establishing 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 iSeq100™ system. Our results highlighted the great potential of the amplicon-based approach to obtain consensus genomes of SARS-CoV-2 in just a few hours, in particular to explore clinical samples with low viral loads. 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