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. 2018 Nov 1;379(18):1745-1753.
doi: 10.1056/NEJMoa1804498. Epub 2018 Oct 17.

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

Katherine J Siddle  1 , Philomena Eromon  1 , Kayla G Barnes  1 , Samar Mehta  1 , Judith U Oguzie  1 , Ikponmwosa Odia  1 , Stephen F Schaffner  1 , Sarah M Winnicki  1 , Rickey R Shah  1 , James Qu  1 , Shirlee Wohl  1 , Patrick Brehio  1 , Christopher Iruolagbe  1 , John Aiyepada  1 , Eghosa Uyigue  1 , Patience Akhilomen  1 , Grace Okonofua  1 , Simon Ye  1 , Tolulope Kayode  1 , Fehintola Ajogbasile  1 , Jessica Uwanibe  1 , Amy Gaye  1 , Mambu Momoh  1 , Bridget Chak  1 , Dylan Kotliar  1 , Amber Carter  1 , Adrianne Gladden-Young  1 , Catherine A Freije  1 , Omigie Omoregie  1 , Blessing Osiemi  1 , Ekene B Muoebonam  1 , Michael Airende  1 , Rachael Enigbe  1 , Benevolence Ebo  1 , Iguosadolo Nosamiefan  1 , Paul Oluniyi  1 , Mahan Nekoui  1 , Ephraim Ogbaini-Emovon  1 , Robert F Garry  1 , Kristian G Andersen  1 , Daniel J Park  1 , Nathan L Yozwiak  1 , George Akpede  1 , Chikwe Ihekweazu  1 , Oyewale Tomori  1 , Sylvanus Okogbenin  1 , Onikepe A Folarin  1 , Peter O Okokhere  1 , Bronwyn L MacInnis  1 , Pardis C Sabeti  1 , Christian T Happi  1
Affiliations

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

Katherine J Siddle et al. N Engl J Med. .

Abstract

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.

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Figures

Figure 1: Incidence of Lassa virus in Nigeria in recent years.
Figure 1: Incidence of Lassa virus in Nigeria in recent years.
a) Number of clinically suspected Lassa fever cases (blue) and RT-qPCR-positive cases (orange) tested at ISTH monthly from January 2012 to February 2018. Counts are those reported by ISTH. Gray shading denotes dry season months in Nigeria, when Lassa cases are typically highest. b) Samples processed at ISTH from January 1 to March 13, 2018. Outcome data, where available, are up to date as of March 22.
Figure 2. Distribution of Lassa virus genetic diversity in Nigeria.
Figure 2. Distribution of Lassa virus genetic diversity in Nigeria.
a) Maximum likelihood phylogenetic tree of the S segment of the Lassa virus genome. The tree incorporates the 77 new sequences presented here alongside 193 previously published sequences from Nigeria and the Mano River Union (in gray). The 77 new samples are coloured by geographic region in which the patient resides. Samples from 2018 are in bold. b) Map of Nigeria highlighting the states from which the 77 new sequences originate and the number of samples from each state. Colours are the same as in A. Kogi state, at the intersection of the 2 rivers, is shown in striped purple reflecting the clustering of the single sequenced sample from this state with others from the southwest region in A. The location of Irrua Specialist Teaching Hospital is marked in yellow.
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