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

Katherine J. Siddle, Philomena Eromon, Kayla G. Barnes, Samar Mehta, Judith U. Oguzie, Ikponmwosa Odia, Stephen F. Schaffner, Sarah M. Winnicki, Rickey R. Shah, James Qu, Shirlee Wohl, Patrick Brehio, Christopher Iruolagbe, John Aiyepada, Eghosa Uyigue, Patience Akhilomen, Grace Okonofua, Simon Ye, Tolulope Kayode, Fehintola AjogbasileJessica Uwanibe, Amy Gaye, Mambu Momoh, Bridget Chak, Dylan Kotliar, Amber Carter, Adrianne Gladden-Young, Catherine A. Freije, Omigie Omoregie, Blessing Osiemi, Ekene B. Muoebonam, Michael Airende, Rachael Enigbe, Benevolence Ebo, Iguosadolo Nosamiefan, Paul Oluniyi, Mahan Nekoui, Ephraim Ogbaini-Emovon, Robert F. Garry, Kristian G. Andersen, Daniel J. Park, Nathan L. Yozwiak, George Akpede, Chikwe Ihekweazu, Oyewale Tomori, Sylvanus Okogbenin, Onikepe A. Folarin, Peter O. Okokhere, Bronwyn L. MacInnis, Pardis C. Sabeti, Christian T. Happi

Research output: Contribution to journalArticlepeer-review


During 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.

Original languageEnglish (US)
Pages (from-to)1745-1753
Number of pages9
JournalNew England Journal of Medicine
Issue number18
StatePublished - Nov 1 2018
Externally publishedYes

ASJC Scopus subject areas

  • General Medicine


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