Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018

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Summ a r yDuring 2018, an unusual increase in Lassa fever cases occurred in Nigeria, raising concern among national and international public health agencies.We analyzed 220 Lassa virus genomes from infected patients, including 129 from the 2017-2018 transmission season, to understand the viral populations underpinning the increase.A total of 14 initial genomes from 2018 samples were generated at Redeemer's University in Nigeria, and the findings were shared with the Nigerian Center for Disease Control in real time.We found that the increase in cases was not attributable to a particular Lassa virus strain or sustained by human-to-human transmission.Instead, the data were consistent with ongoing cross-species transmission from local rodent populations.Phylogenetic analysis also revealed extensive viral diversity that was structured according to geography, with major rivers appearing to act as barriers to migration of the rodent reservoir.L assa fever is a viral hemorrhagic illness that is endemic to parts of West Africa and causes more than 300,000 cases of illness and 3000 deaths each year. 1 Despite the burden of disease, there is currently no approved vaccine, and the only available pharmacologic therapy is early intravenous administration of the antiviral agent ribavirin.[2][3][4] For these reasons, Lassa fever has been recognized by the World Health Organization (WHO) and the Coalition for Epidemic Preparedness Innovations as an important threat to global health and asThe authors' affiliations are listed in the Appendix.