@article{133433de672144219e0669a540c71ad1,
title = "Lassa virus circulating in Liberia: a retrospective genomic characterisation",
abstract = "Background: An alarming rise in reported Lassa fever cases continues in west Africa. Liberia has the largest reported per capita incidence of Lassa fever cases in the region, but genomic information on the circulating strains is scarce. The aim of this study was to substantially increase the available pool of data to help foster the generation of targeted diagnostics and therapeutics. Methods: Clinical serum samples collected from 17 positive Lassa fever cases originating from Liberia (16 cases) and Guinea (one case) within the past decade were processed at the Liberian Institute for Biomedical Research using a targeted-enrichment sequencing approach, producing 17 near-complete genomes. An additional 17 Lassa virus sequences (two from Guinea, seven from Liberia, four from Nigeria, and four from Sierra Leone) were generated from viral stocks at the US Centers for Disease Control and Prevention (Atlanta, GA) from samples originating from the Mano River Union (Guinea, Liberia, and Sierra Leone) region and Nigeria. Sequences were compared with existing Lassa virus genomes and published Lassa virus assays. Findings: The 23 new Liberian Lassa virus genomes grouped within two clades (IV.A and IV.B) and were genetically divergent from those circulating elsewhere in west Africa. A time-calibrated phylogeographic analysis incorporating the new genomes suggests Liberia was the entry point of Lassa virus into the Mano River Union region and estimates the introduction to have occurred between 300–350 years ago. A high level of diversity exists between the Liberian Lassa virus genomes. Nucleotide percent difference between Liberian Lassa virus genomes ranged up to 27% in the L segment and 18% in the S segment. The commonly used Lassa Josiah-MGB assay was up to 25% divergent across the target sites when aligned to the Liberian Lassa virus genomes. Interpretation: The large amount of novel genomic diversity of Lassa virus observed in the Liberian cases emphasises the need to match deployed diagnostic capabilities with locally circulating strains and underscores the importance of evaluating cross-lineage protection in the development of vaccines and therapeutics. Funding: Defense Biological Product Assurance Office of the US Department of Defense and the Armed Forces Health Surveillance Branch and its Global Emerging Infections Surveillance and Response Section.",
author = "Wiley, {Michael R.} and Lawrence Fakoli and Letizia, {Andrew G.} and Welch, {Stephen R.} and Ladner, {Jason T.} and Karla Prieto and Daniel Reyes and Nicole Espy and Chitty, {Joseph A.} and Pratt, {Catherine B.} and {Di Paola}, Nicholas and Fahn Taweh and Desmond Williams and Jon Saindon and Davis, {William G.} and Ketan Patel and Mitchell Holland and Daniel Negr{\'o}n and Ute Str{\"o}her and Nichol, {Stuart T.} and Shanmuga Sozhamannan and Rollin, {Pierre E.} and John Dogba and Tolbert Nyenswah and Fatorma Bolay and Albari{\~n}o, {C{\'e}sar G.} and Mosoka Fallah and Gustavo Palacios",
note = "Funding Information: Lassa virus consensus genomes are available on GenBank under accession numbers MG812630-MG812685 and MH215278-MH215289. Acknowledgments The views expressed in this article are those of the authors and do not necessarily reflect the official policy or position of the Department of the Army, the Department of the Navy, the Department of Defense, the US Department of Health and Human Services, the US Government, nor the institutions or companies affiliated with the authors. Financial support for this work was provided by the Defense Biological Product Assurance Office through task order awarded to the National Strategic Research Institute under FA4600–12-D-9000, the Armed Forces Health Surveillance Branch and its Global Emerging Infections Surveillance and Response (GEIS) Section (funding year 2017, ProMIS ID P2052_16_N3), and GEIS outbreak funds through Navy Medical Research Unit Three Ghana Detachment. CDR AGL is a military service member of the US Government. This work was prepared as part of his official duties. Title 17 of the United States Code §105 provides that “Copyright protection under this title is not available for any work of the United States Government.” Title 17 of the United States Code §101 defines a US Government work as a work prepared by a military service member or employee of the US Government as part of that person's official duties. JT Ladner was funded under the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. Funding Information: The views expressed in this article are those of the authors and do not necessarily reflect the official policy or position of the Department of the Army, the Department of the Navy, the Department of Defense, the US Department of Health and Human Services, the US Government, nor the institutions or companies affiliated with the authors. Financial support for this work was provided by the Defense Biological Product Assurance Office through task order awarded to the National Strategic Research Institute under FA4600?12-D-9000, the Armed Forces Health Surveillance Branch and its Global Emerging Infections Surveillance and Response (GEIS) Section (funding year 2017, ProMIS ID P2052_16_N3), and GEIS outbreak funds through Navy Medical Research Unit Three Ghana Detachment. CDR AGL is a military service member of the US Government. This work was prepared as part of his official duties. Title 17 of the United States Code ?105 provides that ?Copyright protection under this title is not available for any work of the United States Government.? Title 17 of the United States Code ?101 defines a US Government work as a work prepared by a military service member or employee of the US Government as part of that person's official duties. JT Ladner was funded under the State of Arizona Technology and Research Initiative Fund (TRIF), administered by the Arizona Board of Regents, through Northern Arizona University. Publisher Copyright: {\textcopyright} 2019 Elsevier Ltd",
year = "2019",
month = dec,
doi = "10.1016/S1473-3099(19)30486-4",
language = "English (US)",
volume = "19",
pages = "1371--1378",
journal = "The Lancet Infectious Diseases",
issn = "1473-3099",
publisher = "Lancet Publishing Group",
number = "12",
}