Operational strategy for rapid detection and characterization of emergent viral pathogens using third next-generation sequencing technologies
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Global human health is challenged by emerging viral threats. Studies of these outbreaks have highlighted the impact of real-time sequencing of viral genomes for a better concerted public health response. Notably, the World Health Organization has recognized the need to deploy genomic surveillance approaches, especially in low and middle-resource
settings.
The setup of more robust sequencing/bioinformatics pipelines with low turnaround times could provide crucial insights into the understanding of outbreaks and enhanced monitoring of pathogen transmission, spread, and evolution. Thanks to its features (portability, short time of sequencing run, real-time data analysis), MinION devices, have opened the way
towards the implementation of field-applicable rapid next-generation sequencing.