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

Katherine J. Siddle; Philomena Eromon; Kayla 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 Ajogbasile; Jessica 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

doi:10.1056/nejmoa1804498

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

Katherine J. Siddle, Philomena Eromon, Kayla 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

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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.

Original language	English
Pages (from-to)	1745-1753
Number of pages	9
Journal	New England Journal of Medicine
Volume	379
Issue number	18
DOIs	https://doi.org/10.1056/nejmoa1804498
Publication status	Published - 1 Nov 2018
Externally published	Yes

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Siddle, K. J., Eromon, P., Barnes, K., Mehta, S., Oguzie, J. U., Odia, I., Schaffner, S. F., Winnicki, S. M., Shah, R. R., Qu, J., Wohl, S., Brehio, P., Iruolagbe, C., Aiyepada, J., Uyigue, E., Akhilomen, P., Okonofua, G., Ye, S., Kayode, T., ... Happi, C. T. (2018). Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018. New England Journal of Medicine, 379(18), 1745-1753. https://doi.org/10.1056/nejmoa1804498

@article{23ad5c7522924341a1abf8876343b108,

title = "Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018",

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.",

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

year = "2018",

month = nov,

day = "1",

doi = "10.1056/nejmoa1804498",

language = "English",

volume = "379",

pages = "1745--1753",

journal = "New England Journal of Medicine",

issn = "0028-4793",

publisher = "Massachussetts Medical Society",

number = "18",

}

Siddle, KJ, Eromon, P, Barnes, K, Mehta, S, Oguzie, JU, Odia, I, Schaffner, SF, Winnicki, SM, Shah, RR, Qu, J, Wohl, S, Brehio, P, Iruolagbe, C, Aiyepada, J, Uyigue, E, Akhilomen, P, Okonofua, G, Ye, S, Kayode, T, Ajogbasile, F, Uwanibe, J, Gaye, A, Momoh, M, Chak, B, Kotliar, D, Carter, A, Gladden-Young, A, Freije, CA, Omoregie, O, Osiemi, B, Muoebonam, EB, Airende, M, Enigbe, R, Ebo, B, Nosamiefan, I, Oluniyi, P, Nekoui, M, Ogbaini-Emovon, E, Garry, RF, Andersen, KG, Park, DJ, Yozwiak, NL, Akpede, G, Ihekweazu, C, Tomori, O, Okogbenin, S, Folarin, OA, Okokhere, PO, MacInnis, BL, Sabeti, PC & Happi, CT 2018, 'Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018', New England Journal of Medicine, vol. 379, no. 18, pp. 1745-1753. https://doi.org/10.1056/nejmoa1804498

TY - JOUR

T1 - Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018

AU - Siddle, Katherine J.

AU - Eromon, Philomena

AU - Barnes, Kayla

AU - Mehta, Samar

AU - Oguzie, Judith U.

AU - Odia, Ikponmwosa

AU - Schaffner, Stephen F.

AU - Winnicki, Sarah M.

AU - Shah, Rickey R.

AU - Qu, James

AU - Wohl, Shirlee

AU - Brehio, Patrick

AU - Iruolagbe, Christopher

AU - Aiyepada, John

AU - Uyigue, Eghosa

AU - Akhilomen, Patience

AU - Okonofua, Grace

AU - Ye, Simon

AU - Kayode, Tolulope

AU - Ajogbasile, Fehintola

AU - Uwanibe, Jessica

AU - Gaye, Amy

AU - Momoh, Mambu

AU - Chak, Bridget

AU - Kotliar, Dylan

AU - Carter, Amber

AU - Gladden-Young, Adrianne

AU - Freije, Catherine A.

AU - Omoregie, Omigie

AU - Osiemi, Blessing

AU - Muoebonam, Ekene B.

AU - Airende, Michael

AU - Enigbe, Rachael

AU - Ebo, Benevolence

AU - Nosamiefan, Iguosadolo

AU - Oluniyi, Paul

AU - Nekoui, Mahan

AU - Ogbaini-Emovon, Ephraim

AU - Garry, Robert F.

AU - Andersen, Kristian G.

AU - Park, Daniel J.

AU - Yozwiak, Nathan L.

AU - Akpede, George

AU - Ihekweazu, Chikwe

AU - Tomori, Oyewale

AU - Okogbenin, Sylvanus

AU - Folarin, Onikepe A.

AU - Okokhere, Peter O.

AU - MacInnis, Bronwyn L.

AU - Sabeti, Pardis C.

AU - Happi, Christian T.

PY - 2018/11/1

Y1 - 2018/11/1

N2 - 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.

AB - 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.

U2 - 10.1056/nejmoa1804498

DO - 10.1056/nejmoa1804498

M3 - Article

SN - 0028-4793

VL - 379

SP - 1745

EP - 1753

JO - New England Journal of Medicine

JF - New England Journal of Medicine

IS - 18

ER -

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

Abstract

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