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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 strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.

Original publication

DOI

10.1126/science.aau9343

Type

Journal article

Journal

Science (New York, N.Y.)

Publication Date

01/2019

Volume

363

Pages

74 - 77

Addresses

Public Health England, National Infection Service, Porton Down, UK.

Keywords

Animals, Humans, Lassa virus, Zoonoses, Lassa Fever, Disease Outbreaks, Phylogeny, Genome, Viral, Nigeria, Molecular Epidemiology, Metagenomics