Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak.

Science

Authors	Stephen Gire Augustine Goba Kristian Andersen Rachel Sealfon Daniel Park Lansana Kanneh Simbirie Jalloh Mambu Momoh Mohamed Fullah Gytis Dudas Shirlee Wohl Lina Moses Nathan Yozwiak Sarah Winnicki Christian Matranga Christine Malboeuf James Qu Adrianne Gladden Stephen Schaffner Xiao Yang Pan-Pan Jiang Mahan Nekoui Andres Colubri Moinya Coomber Mbalu Fonnie Alex Moigboi Michael Gbakie Fatima Kamara Veronica Tucker Edwin Konuwa Sidiki Saffa Josephine Sellu Abdul Jalloh Alice Kovoma James Koninga Ibrahim Mustapha Kandeh Kargbo Momoh Foday Mohamed Yillah Franklyn Kanneh Willie Robert James Massally Sinéad Chapman James Bochicchio Cheryl Murphy Chad Nusbaum Sarah Young Bruce Birren Donald Grant John Scheiffelin Eric Lander Christian Happi Sahr Gevao Andreas Gnirke Andrew Rambaut Robert Garry S Humarr Khan Pardis Sabeti
Keywords	Humans Mutation Base Sequence Genomics Genetic Variation Sequence Analysis, DNA Ebolavirus Hemorrhagic Fever, Ebola Genome, Viral Disease Outbreaks Sierra Leone Epidemiological Monitoring
Abstract	In its largest outbreak, Ebola virus disease is spreading through Guinea, Liberia, Sierra Leone, and Nigeria. We sequenced 99 Ebola virus genomes from 78 patients in Sierra Leone to ~2000× coverage. We observed a rapid accumulation of interhost and intrahost genetic variation, allowing us to characterize patterns of viral transmission over the initial weeks of the epidemic. This West African variant likely diverged from central African lineages around 2004, crossed from Guinea to Sierra Leone in May 2014, and has exhibited sustained human-to-human transmission subsequently, with no evidence of additional zoonotic sources. Because many of the mutations alter protein sequences and other biologically meaningful targets, they should be monitored for impact on diagnostics, vaccines, and therapies critical to outbreak response.
Year of Publication	2014
Journal	Science
Volume	345
Issue	6202
Pages	1369-72
Date Published	2014 Sep 12
ISSN	1095-9203
URL
DOI	10.1126/science.1259657
PubMed ID	25214632
PubMed Central ID	PMC4431643
Links
Grant list	U19 AI115589 / AI / NIAID NIH HHS / United States 1U01HG007480-01 / HG / NHGRI NIH HHS / United States 1DP2OD006514-01 / OD / NIH HHS / United States U01 HG007480 / HG / NHGRI NIH HHS / United States T32 GM080177 / GM / NIGMS NIH HHS / United States GM080177 / GM / NIGMS NIH HHS / United States 095831 / Wellcome Trust / United Kingdom HHSN272200900049C / AI / NIAID NIH HHS / United States 260864 / European Research Council / International DP2 OD006514 / OD / NIH HHS / United States U19 AI110818 / AI / NIAID NIH HHS / United States HHSN272200900049C / PHS HHS / United States