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

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Kafetzopoulou, L E, Pullan, S T, Lemey, P, Suchard, M A, Ehichioya, D U, Pahlmann, M, Thielebein, A, Hinzmann, J, Oestereich, L, Wozniak, D M, Efthymiadis, K, Schachten, D, Koenig, F, Matjeschk, J, Lorenzen, S, Lumley, S, Ighodalo, Y, Adomeh, D I, Olokor, T, Omomoh, E, Omiunu, R, Agbukor, J, Ebo, B, Aiyepada, J, Ebhodaghe, P, Osiemi, B, Ehikhametalor, S, Akhilomen, P, Airende, M, Esumeh, R, Muoebonam, E, Giwa, R, Ekanem, A, Igenegbale, G, Odigie, G, Okonofua, G, Enigbe, R, Oyakhilome, J, Yerumoh, E O, Odia, I, Aire, C, Okonofua, M, Atafo, R, Tobin, E, Asogun, D, Akpede, N, Okokhere, P O, Rafiu, M O, Iraoyah, K O, Iruolagbe, C O, Akhideno, P, Erameh, C, Akpede, G, Isibor, E, Naidoo, D, Hewson, Roger, Hiscox, J A, Vipond, R, Carroll, M W, Ihekweazu, C, Formenty, P, Okogbenin, S, Ogbaini-Emovon, E, Günther, S and Duraffour, S (2019) 'Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak.'. Science, Vol 363, Issue 6422, pp. 74-77.

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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.

Item Type: Article
Subjects: QU Biochemistry > Genetics > QU 550 Genetic techniques. PCR. Chromosome mapping
WA Public Health > Health Problems of Special Population Groups > WA 395 Health in developing countries
WC Communicable Diseases > Virus Diseases > Viral Hemorrhagic Fevers. Other Virus Diseases > WC 534 Viral hemorrhagic fevers
Faculty: Department: Clinical Sciences & International Health > International Public Health Department
Digital Object Identifer (DOI): https://doi.org/10.1126/science.aau9343
Depositing User: Stacy Murtagh
Date Deposited: 07 Jan 2019 11:49
Last Modified: 22 Jan 2019 14:23
URI: http://archive.lstmed.ac.uk/id/eprint/9937

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