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Cell. 2015 Aug 13;162(4):738-50. doi: 10.1016/j.cell.2015.07.020.

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus.

Author information

1
FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; The Scripps Research Institute, Scripps Translational Science Institute, La Jolla, CA 92037, USA. Electronic address: andersen@scripps.edu.
2
FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Department of Biological Sciences, University of Montréal, Montréal, QC H2V 2S9, Canada.
3
Broad Institute, Cambridge, MA 02142, USA.
4
Broad Institute, Cambridge, MA 02142, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
5
FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA.
6
Tulane Health Sciences Center, Tulane University, New Orleans, LA 70118, USA.
7
Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria; Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Redemption City, Osun State, Nigeria.
8
Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone.
9
Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria.
10
Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Eastern Province, Sierra Leone; Eastern Polytechnic College, Kenema, Eastern Province, Sierra Leone.
11
Zalgen Labs, Germantown, MD 20876, USA.
12
FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
13
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA.
14
Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA 02115, USA.
15
College of Medicine, Columbia University, New York, NY 10032, USA.
16
Nigerian Federal Ministry of Health, Abuja, Federal Capital Territory, Nigeria.
17
The National Aeronautics and Space Administration, Johnson Space Center, Houston, TX 77058, USA.
18
The University of Texas School of Public Health, Brownsville, TX 77030, USA.
19
Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, 20259 Hamburg, Germany.
20
NIAID Integrated Research Facility, Frederick, MD 21702, USA.
21
Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Edo State, Nigeria; Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Redemption City, Osun State, Nigeria. Electronic address: happic@run.edu.ng.
22
FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA 02115, USA. Electronic address: psabeti@oeb.harvard.edu.

Abstract

The 2013-2015 West African epidemic of Ebola virus disease (EVD) reminds us of how little is known about biosafety level 4 viruses. Like Ebola virus, Lassa virus (LASV) can cause hemorrhagic fever with high case fatality rates. We generated a genomic catalog of almost 200 LASV sequences from clinical and rodent reservoir samples. We show that whereas the 2013-2015 EVD epidemic is fueled by human-to-human transmissions, LASV infections mainly result from reservoir-to-human infections. We elucidated the spread of LASV across West Africa and show that this migration was accompanied by changes in LASV genome abundance, fatality rates, codon adaptation, and translational efficiency. By investigating intrahost evolution, we found that mutations accumulate in epitopes of viral surface proteins, suggesting selection for immune escape. This catalog will serve as a foundation for the development of vaccines and diagnostics. VIDEO ABSTRACT.

Comment in

PMID:
26276630
PMCID:
PMC4537774
DOI:
10.1016/j.cell.2015.07.020
[Indexed for MEDLINE]
Free PMC Article

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