Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak.

ABSTRACT: The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strain

SUBMITTER: Kafetzopoulou LE 

PROVIDER: S-EPMC6855379 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature