title: Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic.
abstract: An epidemic of Ebola virus disease of unprecedented scale has been ongoing for more than a year in West Africa. As of 29 April 2015, there have been 26,277 reported total cases (of which 14,895 have been laboratory confirmed) resulting in 10,899 deaths. The source of the outbreak was traced to the prefecture of Guéckédou in the forested region of southeastern Guinea. The virus later spread to the capital, Conakry, and to the neighbouring countries of Sierra Leone, Liberia, Nigeria, Senegal and Mali. In March 2014, when the first cases were detected in Conakry, the Institut Pasteur of Dakar, Senegal, deployed a mobile laboratory in Donka hospital to provide diagnostic services to the greater Conakry urban area and other regions of Guinea. Through this process we sampled 85 Ebola viruses (EBOV) from patients infected from July to November 2014, and report their full genome sequences here. Phylogenetic analysis reveals the sustained transmission of three distinct viral lineages co-circulating in Guinea, including the urban setting of Conakry and its surroundings. One lineage is unique to Guinea and closely related to the earliest sampled viruses of the epidemic. A second lineage contains viruses probably reintroduced from neighbouring Sierra Leone on multiple occasions, while a third lineage later spread from Guinea to Mali. Each lineage is defined by multiple mutations, including non-synonymous changes in the virion protein 35 (VP35), glycoprotein (GP) and RNA-dependent RNA polymerase (L) proteins. The viral GP is characterized by a glycosylation site modification and mutations in the mucin-like domain that could modify the outer shape of the virion. These data illustrate the ongoing ability of EBOV to develop lineage-specific and potentially phenotypically important variation.
authors.affiliation: 1] Institut Pasteur, Functional Genetics of Infectious Diseases Unit, 75724 Paris Cedex 15, France [2] CNRS URA3012, Paris 75015, France.
authors.forename: Etienne
authors.initials: E
authors.lastname: Simon-Loriere
authors.affiliation: Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar, Senegal.
authors.forename: Ousmane
authors.initials: O
authors.lastname: Faye
authors.affiliation: Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar, Senegal.
authors.forename: Oumar
authors.initials: O
authors.lastname: Faye
authors.affiliation: Institut National de Santé Publique de Guinée, Conakry, Guinea.
authors.forename: Lamine
authors.initials: L
authors.lastname: Koivogui
authors.affiliation: Projet de fièvres hémorragiques de Guinée, Université Gamal Abdel Nasser, BP 1147, Conakry, Guinea.
authors.forename: Nfaly
authors.initials: N
authors.lastname: Magassouba
authors.affiliation: Ministry of Health, BP 585 Conakry, Guinea.
authors.forename: Sakoba
authors.initials: S
authors.lastname: Keita
authors.affiliation: Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Thiberge
authors.affiliation: Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.
authors.forename: Laure
authors.initials: L
authors.lastname: Diancourt
authors.affiliation: Institut Pasteur, Genomic platform, 75724 Paris Cedex 15, France.
authors.forename: Christiane
authors.initials: C
authors.lastname: Bouchier
authors.affiliation: Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.
authors.forename: Matthias
authors.initials: M
authors.lastname: Vandenbogaert
authors.affiliation: Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Caro
authors.affiliation: Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar, Senegal.
authors.forename: Gamou
authors.initials: G
authors.lastname: Fall
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Jan P
authors.initials: JP
authors.lastname: Buchmann
authors.affiliation: Broad Institute, 75 Ames Street, Cambridge, Massachusetts 02142, USA.
authors.forename: Christan B
authors.initials: CB
authors.lastname: Matranga
authors.affiliation: 1] Broad Institute, 75 Ames Street, Cambridge, Massachusetts 02142, USA [2] FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, 52 Oxford Street, Cambridge, Massachusetts 02138, USA.
authors.forename: Pardis C
authors.initials: PC
authors.lastname: Sabeti
authors.affiliation: Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Manuguerra
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.affiliation: Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar, Senegal.
authors.forename: Amadou A
authors.initials: AA
authors.lastname: Sall
mesh_terms: D029043:Ebolavirus / Q000235:genetics* / Q000302:isolation & purification; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics*; D016679:Genome, Viral / Q000235:genetics; D006023:Glycoproteins / Q000235:genetics / Q000378:metabolism; D006031:Glycosylation; D016701:Guinea / Q000453:epidemiology; D019142:Hemorrhagic Fever, Ebola / Q000453:epidemiology* / Q000635:transmission / Q000821:virology*; D006801:Humans; D008302:Mali / Q000453:epidemiology; D008969:Molecular Sequence Data; D009077:Mucins / Q000737:chemistry; D009154:Mutation / Q000235:genetics*; D019590:Nucleocapsid Proteins; D009698:Nucleoproteins / Q000235:genetics; D010802:Phylogeny; D017434:Protein Structure, Tertiary / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D012807:Sierra Leone / Q000453:epidemiology; D014758:Viral Core Proteins / Q000235:genetics
chemical_list: D006023:Glycoproteins; D009077:Mucins; D019590:Nucleocapsid Proteins; D009698:Nucleoproteins; D014758:Viral Core Proteins; C084818:nucleoprotein VP35, Ebola virus; D012324:RNA-Dependent RNA Polymerase