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Science. 2019 Jan 4;363(6422):74-77. doi: 10.1126/science.aau9343.

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

Author information

1
Public Health England, National Infection Service, Porton Down, UK.
2
National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.
3
Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
4
Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium.
5
Departments of Biomathematics, Biostatistics, and Human Genetics, University of California, Los Angeles, CA, USA.
6
German Center for Infection Research (DZIF), partner site Hamburg, Germany.
7
Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Brussels, Belgium.
8
Irrua Specialist Teaching Hospital, Irrua, Nigeria.
9
Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria.
10
World Health Organization, Geneva, Switzerland.
11
Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK.
12
Faculty of Clinical Sciences and International Public Health, Liverpool School of Tropical Medicine, Liverpool, UK.
13
Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore.
14
Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
15
Nigeria Centre for Disease Control, Abuja, Nigeria.
16
Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany. guenther@bni.uni-hamburg.de.
#
Contributed equally

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

PMID:
30606844
DOI:
10.1126/science.aau9343

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