Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus

• Published in: Cell Vol. 162; no. 4; pp. 738 - 750
• Main Authors: Andersen, Kristian G., Shapiro, B. Jesse, Matranga, Christian B., Sealfon, Rachel, Lin, Aaron E., Moses, Lina M., Folarin, Onikepe A., Goba, Augustine, Odia, Ikponmwonsa, Ehiane, Philomena E., Momoh, Mambu, England, Eleina M., Winnicki, Sarah, Branco, Luis M., Gire, Stephen K., Phelan, Eric, Tariyal, Ridhi, Tewhey, Ryan, Omoniwa, Omowunmi, Fullah, Mohammed, Fonnie, Richard, Fonnie, Mbalu, Kanneh, Lansana, Jalloh, Simbirie, Gbakie, Michael, Saffa, Sidiki, Karbo, Kandeh, Gladden, Adrianne D., Qu, James, Stremlau, Matthew, Nekoui, Mahan, Finucane, Hilary K., Tabrizi, Shervin, Vitti, Joseph J., Birren, Bruce, Fitzgerald, Michael, McCowan, Caryn, Ireland, Andrea, Berlin, Aaron M., Bochicchio, James, Tazon-Vega, Barbara, Lennon, Niall J., Ryan, Elizabeth M., Bjornson, Zach, Milner, Danny A., Lukens, Amanda K., Broodie, Nisha, Rowland, Megan, Heinrich, Megan, Akdag, Marjan, Schieffelin, John S., Levy, Danielle, Akpan, Henry, Bausch, Daniel G., Rubins, Kathleen, McCormick, Joseph B., Lander, Eric S., Günther, Stephan, Hensley, Lisa, Okogbenin, Sylvanus, Schaffner, Stephen F., Okokhere, Peter O., Khan, S. Humarr, Grant, Donald S., Akpede, George O., Asogun, Danny A., Gnirke, Andreas, Levin, Joshua Z., Happi, Christian T., Garry, Robert F., Sabeti, Pardis C.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 13-08-2015
• Subjects: Africa, Western - epidemiology; Animals; Biological Evolution; Disease Reservoirs; Ebolavirus - genetics; Genetic Variation; Genome, Viral; Glycoproteins - genetics; Hemorrhagic Fever, Ebola - virology; Humans; Lassa Fever - epidemiology; Lassa Fever - transmission; Lassa Fever - virology; Lassa virus - classification; Lassa virus - genetics; Lassa virus - physiology; Murinae - genetics; Mutation; Nigeria - epidemiology; RNA, Viral - genetics; Viral Proteins - genetics; Zoonoses - epidemiology; Zoonoses - virology; Nigeria; Africa, Western
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2015.07.020

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.
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•Lassa virus is a life-threatening pathogen that is endemic in West Africa•Lassa virus has diverse and ancient origins in Nigeria•Viral strains from Nigeria and Sierra Leone differ in their translation efficiency•The virus evolves within hosts to evade immune-determined selection pressures
Sequencing analysis of ∼200 Lassa virus genomes reveals its ancient origins and distinct evolutionary features compared to the Ebola virus.