. 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 Siddle¹, Philomena Eromon¹, Kayla G Barnes¹, Samar Mehta¹, Judith U Oguzie¹, Ikponmwosa Odia¹, Stephen F Schaffner¹, Sarah M Winnicki¹, Rickey R Shah¹, James Qu¹, Shirlee Wohl¹, Patrick Brehio¹, Christopher Iruolagbe¹, John Aiyepada¹, Eghosa Uyigue¹, Patience Akhilomen¹, Grace Okonofua¹, Simon Ye¹, Tolulope Kayode¹, Fehintola Ajogbasile¹, Jessica Uwanibe¹, Amy Gaye¹, Mambu Momoh¹, Bridget Chak¹, Dylan Kotliar¹, Amber Carter¹, Adrianne Gladden-Young¹, Catherine A Freije¹, Omigie Omoregie¹, Blessing Osiemi¹, Ekene B Muoebonam¹, Michael Airende¹, Rachael Enigbe¹, Benevolence Ebo¹, Iguosadolo Nosamiefan¹, Paul Oluniyi¹, Mahan Nekoui¹, Ephraim Ogbaini-Emovon¹, Robert F Garry¹, Kristian G Andersen¹, Daniel J Park¹, Nathan L Yozwiak¹, George Akpede¹, Chikwe Ihekweazu¹, Oyewale Tomori¹, Sylvanus Okogbenin¹, Onikepe A Folarin¹, Peter O Okokhere¹, Bronwyn L MacInnis¹, Pardis C Sabeti¹, Christian T Happi¹

Affiliations

Affiliation

¹ From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.).

PMID: 30332564
PMCID: PMC6181183
DOI: 10.1056/NEJMoa1804498

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

Katherine J Siddle et al. N Engl J Med. 2018.

. 2018 Nov 1;379(18):1745-1753.

doi: 10.1056/NEJMoa1804498. Epub 2018 Oct 17.

Authors

Affiliation

¹ From the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard University (K.J.S., K.G.B., S.M., S.F.S., S.M.W., R.R.S., J.Q., S.W., P.B., S.Y., B.C., D.K., A.C., A.G.-Y., C.A.F., D.J.P., N.L.Y., B.L.M., P.C.S.), the Center for Systems Biology, Department of Organismic and Evolutionary Biology (K.J.S., K.G.B., S.F.S., S.W., B.C., D.K., C.A.F., N.L.Y., P.C.S.), and the Faculty of Arts and Sciences (M.N.), Harvard University, Harvard University Extension School (R.R.S.), and Harvard-MIT Health Sciences and Technology, MIT (S.Y., P.C.S.), Cambridge, and the Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health (K.G.B., S.F.S., B.L.M., P.C.S., C.T.H.), and Beth Israel Deaconess Medical Center, Division of Infectious Diseases (S.M.), Boston - all in Massachusetts; the African Center of Excellence for Genomics of Infectious Diseases (P.E., J.U.O., E.U., T.K., F.A., J.U., A.G., M.M., I.N., P.O., O.T., O.A.F., C.T.H.) and the Department of Biological Sciences, College of Natural Sciences (J.U.O., E.U., T.K., F.A., J.U., P.O., O.A.F., C.T.H.), Redeemer's University, Ede, the Institute of Lassa Fever Research and Control (I.O., C. Iruolagbe, J.A., E.U., P.A., G.O., O.O., B.O., E.B.M., M.A., R.E., B.E., E.O.-E., G.A., S.O., P.O.O., C.T.H.) and the Department of Medicine (P.O.O.), Irrua Specialist Teaching Hospital, Irrua, the Nigeria Center for Disease Control, Abuja (C. Ihekweazu), and the Department of Medicine, Faculty of Clinical Sciences, Ambrose Alli University, Ekpoma (P.O.O.) - all in Nigeria; the Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, Dakar, Senegal (A.G.); Kenema Government Hospital, Kenema, Sierra Leone (M.M.); Tulane Health Sciences Center, Tulane University, New Orleans (R.F.G.); the Departments of Immunology and Microbial Science and Integrative Structural and Computational Biology, Scripps Research Institute, and the Scripps Translational Science Institute, La Jolla, CA (K.G.A.); and Howard Hughes Medical Institute, Chevy Chase, MD (P.C.S.).

PMID: 30332564
PMCID: PMC6181183
DOI: 10.1056/NEJMoa1804498

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.**
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.**
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.

See this image and copyright information in PMC

References

1. Geisbert TW. Predicting outcome and improving treatment for Lassa fever. Lancet Infect Dis 2018;18(6):594–5. - PubMed
1. The Lancet Infectious Diseases. Lassa fever and global health security. Lancet Infect Dis 2018;18(4):357. - PMC - PubMed
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1. WHO. 2018 Annual review of diseases prioritized under the R&D Blueprint [Internet]. 2018. Available from: http://www.who.int/emergencies/diseases/2018prioritization-report.pdf
1. McCormick JB, King IJ, Webb PA, et al. Lassa fever. Effective therapy with ribavirin. N Engl J Med 1986;314(1):20–6. - PubMed

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

Affiliation

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

Authors

Affiliation

Abstract

Figures

References

Publication types

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Molecular Biology Databases