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

• DOI: 10.1126/science.aau9343
• Publication Date: 2019-01-04T00:05:31Z
• Authors: L. E. Kafetzopoulou; S. T. Pullan; P. Lemey; M. A. Suchard; D. U. Ehichioya; M. Pahlmann; A. Thielebein; J. Hinzmann; L. Oestereich; D. M. Wozniak; K. Efthymiadis; D. Schachten; F. Koenig; J. Matjeschk; S. Lorenzen; S. Lumley; Y. Ighodalo; D. I. Adomeh; T. Olokor; E. Omomoh; R. Omiunu; J. Agbukor; B. Ebo; J. Aiyepada; P. Ebhodaghe; B. Osiemi; S. Ehikhametalor; P. Akhilomen; M. Airende; R. Esumeh; E. Muoebonam; R. Giwa; A. Ekanem; G. Igenegbale; G. Odigie; G. Okonofua; R. Enigbe; J. Oyakhilome; E. O. Yerumoh; I. Odia; C. Aire; M. Okonofua; R. Atafo; E. Tobin; D. Asogun; N. Akpede; P. O. Okokhere; M. O. Rafiu; K. O. Iraoyah; C. O. Iruolagbe; P. Akhideno; C. Erameh; G. Akpede; E. Isibor; D. Naidoo; R. Hewson; J. A. Hiscox; R. Vipond; M. W. Carroll; C. Ihekweazu; P. Formenty; S. Okogbenin; E. Ogbaini-Emovon; S. Günther; S. Duraffour
• Keywords: Pandemic; Strain (injury); Phylogenomics

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