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

Autor: Kafetzopoulou LE; Public Health England, National Infection Service, Porton Down, UK.; National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany., Pullan ST; Public Health England, National Infection Service, Porton Down, UK.; National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK., Lemey P; Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium., Suchard MA; Departments of Biomathematics, Biostatistics, and Human Genetics, University of California, Los Angeles, CA, USA., Ehichioya DU; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.; German Center for Infection Research (DZIF), partner site Hamburg, Germany., Pahlmann M; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.; German Center for Infection Research (DZIF), partner site Hamburg, Germany., Thielebein A; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.; German Center for Infection Research (DZIF), partner site Hamburg, Germany., Hinzmann J; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.; German Center for Infection Research (DZIF), partner site Hamburg, Germany., Oestereich L; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.; German Center for Infection Research (DZIF), partner site Hamburg, Germany., Wozniak DM; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.; German Center for Infection Research (DZIF), partner site Hamburg, Germany., Efthymiadis K; Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Brussels, Belgium., Schachten D; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany., Koenig F; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany., Matjeschk J; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany., Lorenzen S; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany., Lumley S; Public Health England, National Infection Service, Porton Down, UK., Ighodalo Y; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Adomeh DI; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Olokor T; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Omomoh E; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Omiunu R; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Agbukor J; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Ebo B; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Aiyepada J; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Ebhodaghe P; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Osiemi B; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Ehikhametalor S; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Akhilomen P; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Airende M; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Esumeh R; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Muoebonam E; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Giwa R; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Ekanem A; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Igenegbale G; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Odigie G; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Okonofua G; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Enigbe R; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Oyakhilome J; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Yerumoh EO; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Odia I; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Aire C; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Okonofua M; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Atafo R; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Tobin E; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Asogun D; Irrua Specialist Teaching Hospital, Irrua, Nigeria.; Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria., Akpede N; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Okokhere PO; Irrua Specialist Teaching Hospital, Irrua, Nigeria.; Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria., Rafiu MO; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Iraoyah KO; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Iruolagbe CO; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Akhideno P; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Erameh C; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Akpede G; Irrua Specialist Teaching Hospital, Irrua, Nigeria.; Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria., Isibor E; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Naidoo D; World Health Organization, Geneva, Switzerland., Hewson R; Public Health England, National Infection Service, Porton Down, UK.; National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.; Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK.; Faculty of Clinical Sciences and International Public Health, Liverpool School of Tropical Medicine, Liverpool, UK., Hiscox JA; National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.; Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore.; Institute of Infection and Global Health, University of Liverpool, Liverpool, UK., Vipond R; Public Health England, National Infection Service, Porton Down, UK.; National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK., Carroll MW; Public Health England, National Infection Service, Porton Down, UK.; National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK., Ihekweazu C; Nigeria Centre for Disease Control, Abuja, Nigeria., Formenty P; World Health Organization, Geneva, Switzerland., Okogbenin S; Irrua Specialist Teaching Hospital, Irrua, Nigeria.; Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria., Ogbaini-Emovon E; Irrua Specialist Teaching Hospital, Irrua, Nigeria., Günther S; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany. guenther@bni.uni-hamburg.de.; German Center for Infection Research (DZIF), partner site Hamburg, Germany., Duraffour S; Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.; German Center for Infection Research (DZIF), partner site Hamburg, Germany.
Jazyk: angličtina
Zdroj: Science (New York, N.Y.) [Science] 2019 Jan 04; Vol. 363 (6422), pp. 74-77.
DOI: 10.1126/science.aau9343
Abstrakt: 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.
(Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)
Databáze: MEDLINE
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