Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic.
Identifieur interne : 002A34 ( PubMed/Curation ); précédent : 002A33; suivant : 002A35Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic.
Auteurs : Etienne Simon-Loriere [France] ; Ousmane Faye [Sénégal] ; Oumar Faye [Sénégal] ; Lamine Koivogui [Guinée] ; Nfaly Magassouba [Guinée] ; Sakoba Keita [Guinée] ; Jean-Michel Thiberge [France] ; Laure Diancourt [France] ; Christiane Bouchier [France] ; Matthias Vandenbogaert [France] ; Valérie Caro [France] ; Gamou Fall [Sénégal] ; Jan P. Buchmann [Australie] ; Christan B. Matranga [États-Unis] ; Pardis C. Sabeti [États-Unis] ; Jean-Claude Manuguerra [France] ; Edward C. Holmes [Australie] ; Amadou A. Sall [Sénégal]Source :
- Nature [ 1476-4687 ] ; 2015.
Descripteurs français
- KwdFr :
- Données de séquences moléculaires, Ebolavirus (génétique), Ebolavirus (isolement et purification), Fièvre hémorragique à virus Ebola (transmission), Fièvre hémorragique à virus Ebola (virologie), Fièvre hémorragique à virus Ebola (épidémiologie), Glycoprotéines (génétique), Glycoprotéines (métabolisme), Glycosylation, Guinée (épidémiologie), Génome viral (génétique), Humains, Mali (épidémiologie), Mucines (), Mutation (génétique), Nucléoprotéines (génétique), Phylogénie, Protéines du core viral (génétique), RNA replicase (génétique), Sierra Leone (épidémiologie), Structure tertiaire des protéines (génétique), Variation génétique (génétique), Évolution moléculaire.
- MESH :
- génétique : Ebolavirus, Glycoprotéines, Génome viral, Mutation, Nucléoprotéines, Protéines du core viral, RNA replicase, Structure tertiaire des protéines, Variation génétique.
- isolement et purification : Ebolavirus.
- métabolisme : Glycoprotéines.
- virologie : Fièvre hémorragique à virus Ebola.
- épidémiologie : Fièvre hémorragique à virus Ebola, Guinée, Mali, Sierra Leone.
- Données de séquences moléculaires, Glycosylation, Humains, Mucines, Phylogénie, Évolution moléculaire.
- Wicri :
- geographic : Guinée, Mali, Sierra Leone.
English descriptors
- KwdEn :
- Ebolavirus (genetics), Ebolavirus (isolation & purification), Evolution, Molecular, Genetic Variation (genetics), Genome, Viral (genetics), Glycoproteins (genetics), Glycoproteins (metabolism), Glycosylation, Guinea (epidemiology), Hemorrhagic Fever, Ebola (epidemiology), Hemorrhagic Fever, Ebola (transmission), Hemorrhagic Fever, Ebola (virology), Humans, Mali (epidemiology), Molecular Sequence Data, Mucins (chemistry), Mutation (genetics), Nucleoproteins (genetics), Phylogeny, Protein Structure, Tertiary (genetics), RNA Replicase (genetics), Sierra Leone (epidemiology), Viral Core Proteins (genetics).
- MESH :
- chemical , chemistry : Mucins.
- chemical , genetics : Glycoproteins, Nucleoproteins, RNA Replicase, Viral Core Proteins.
- geographic , epidemiology : Guinea, Mali, Sierra Leone.
- epidemiology : Hemorrhagic Fever, Ebola.
- genetics : Ebolavirus, Genetic Variation, Genome, Viral, Mutation, Protein Structure, Tertiary.
- isolation & purification : Ebolavirus.
- chemical , metabolism : Glycoproteins.
- transmission : Hemorrhagic Fever, Ebola.
- virology : Hemorrhagic Fever, Ebola.
- Evolution, Molecular, Glycosylation, Humans, Molecular Sequence Data, Phylogeny.
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.
DOI: 10.1038/nature14612
PubMed: 26106863
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Viral Hemorrhagic Fever Unit, BP 220, Dakar, Senegal.</nlm:affiliation><country xml:lang="fr">Sénégal</country><wicri:regionArea>Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar</wicri:regionArea></affiliation></author><author><name sortKey="Buchmann, Jan P" sort="Buchmann, Jan P" uniqKey="Buchmann J" first="Jan P" last="Buchmann">Jan P. 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African epidemic.</title><author><name sortKey="Simon Loriere, Etienne" sort="Simon Loriere, Etienne" uniqKey="Simon Loriere E" first="Etienne" last="Simon-Loriere">Etienne Simon-Loriere</name><affiliation wicri:level="1"><nlm:affiliation>1] Institut Pasteur, Functional Genetics of Infectious Diseases Unit, 75724 Paris Cedex 15, France [2] CNRS URA3012, Paris 75015, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>1] Institut Pasteur, Functional Genetics of Infectious Diseases Unit, 75724 Paris Cedex 15, France [2] CNRS URA3012, Paris 75015</wicri:regionArea></affiliation></author><author><name sortKey="Faye, Ousmane" sort="Faye, Ousmane" uniqKey="Faye O" first="Ousmane" last="Faye">Ousmane Faye</name><affiliation wicri:level="1"><nlm:affiliation>Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar, Senegal.</nlm:affiliation><country xml:lang="fr">Sénégal</country><wicri:regionArea>Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar</wicri:regionArea></affiliation></author><author><name sortKey="Faye, Oumar" sort="Faye, Oumar" uniqKey="Faye O" first="Oumar" last="Faye">Oumar Faye</name><affiliation wicri:level="1"><nlm:affiliation>Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar, Senegal.</nlm:affiliation><country xml:lang="fr">Sénégal</country><wicri:regionArea>Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar</wicri:regionArea></affiliation></author><author><name sortKey="Koivogui, Lamine" sort="Koivogui, Lamine" uniqKey="Koivogui L" first="Lamine" last="Koivogui">Lamine Koivogui</name><affiliation wicri:level="1"><nlm:affiliation>Institut National de Santé Publique de Guinée, Conakry, Guinea.</nlm:affiliation><country xml:lang="fr">Guinée</country><wicri:regionArea>Institut National de Santé Publique de Guinée, Conakry</wicri:regionArea></affiliation></author><author><name sortKey="Magassouba, Nfaly" sort="Magassouba, Nfaly" uniqKey="Magassouba N" first="Nfaly" last="Magassouba">Nfaly Magassouba</name><affiliation wicri:level="1"><nlm:affiliation>Projet de fièvres hémorragiques de Guinée, Université Gamal Abdel Nasser, BP 1147, Conakry, Guinea.</nlm:affiliation><country xml:lang="fr">Guinée</country><wicri:regionArea>Projet de fièvres hémorragiques de Guinée, Université Gamal Abdel Nasser, BP 1147, Conakry</wicri:regionArea></affiliation></author><author><name sortKey="Keita, Sakoba" sort="Keita, Sakoba" uniqKey="Keita S" first="Sakoba" last="Keita">Sakoba Keita</name><affiliation wicri:level="1"><nlm:affiliation>Ministry of Health, BP 585 Conakry, Guinea.</nlm:affiliation><country xml:lang="fr">Guinée</country><wicri:regionArea>Ministry of Health, BP 585 Conakry</wicri:regionArea></affiliation></author><author><name sortKey="Thiberge, Jean Michel" sort="Thiberge, Jean Michel" uniqKey="Thiberge J" first="Jean-Michel" last="Thiberge">Jean-Michel Thiberge</name><affiliation wicri:level="1"><nlm:affiliation>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15</wicri:regionArea></affiliation></author><author><name sortKey="Diancourt, Laure" sort="Diancourt, Laure" uniqKey="Diancourt L" first="Laure" last="Diancourt">Laure Diancourt</name><affiliation wicri:level="1"><nlm:affiliation>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15</wicri:regionArea></affiliation></author><author><name sortKey="Bouchier, Christiane" sort="Bouchier, Christiane" uniqKey="Bouchier C" first="Christiane" last="Bouchier">Christiane Bouchier</name><affiliation wicri:level="1"><nlm:affiliation>Institut Pasteur, Genomic platform, 75724 Paris Cedex 15, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Pasteur, Genomic platform, 75724 Paris Cedex 15</wicri:regionArea></affiliation></author><author><name sortKey="Vandenbogaert, Matthias" sort="Vandenbogaert, Matthias" uniqKey="Vandenbogaert M" first="Matthias" last="Vandenbogaert">Matthias Vandenbogaert</name><affiliation wicri:level="1"><nlm:affiliation>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15</wicri:regionArea></affiliation></author><author><name sortKey="Caro, Valerie" sort="Caro, Valerie" uniqKey="Caro V" first="Valérie" last="Caro">Valérie Caro</name><affiliation wicri:level="1"><nlm:affiliation>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15</wicri:regionArea></affiliation></author><author><name sortKey="Fall, Gamou" sort="Fall, Gamou" uniqKey="Fall G" first="Gamou" last="Fall">Gamou Fall</name><affiliation wicri:level="1"><nlm:affiliation>Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar, Senegal.</nlm:affiliation><country xml:lang="fr">Sénégal</country><wicri:regionArea>Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar</wicri:regionArea></affiliation></author><author><name sortKey="Buchmann, Jan P" sort="Buchmann, Jan P" uniqKey="Buchmann J" first="Jan P" last="Buchmann">Jan P. Buchmann</name><affiliation wicri:level="1"><nlm: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.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>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</wicri:regionArea></affiliation></author><author><name sortKey="Matranga, Christan B" sort="Matranga, Christan B" uniqKey="Matranga C" first="Christan B" last="Matranga">Christan B. Matranga</name><affiliation wicri:level="1"><nlm:affiliation>Broad Institute, 75 Ames Street, Cambridge, Massachusetts 02142, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute, 75 Ames Street, Cambridge, Massachusetts 02142</wicri:regionArea></affiliation></author><author><name sortKey="Sabeti, Pardis C" sort="Sabeti, Pardis C" uniqKey="Sabeti P" first="Pardis C" last="Sabeti">Pardis C. Sabeti</name><affiliation wicri:level="1"><nlm: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.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>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</wicri:regionArea></affiliation></author><author><name sortKey="Manuguerra, Jean Claude" sort="Manuguerra, Jean Claude" uniqKey="Manuguerra J" first="Jean-Claude" last="Manuguerra">Jean-Claude Manuguerra</name><affiliation wicri:level="1"><nlm:affiliation>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15</wicri:regionArea></affiliation></author><author><name sortKey="Holmes, Edward C" sort="Holmes, Edward C" uniqKey="Holmes E" first="Edward C" last="Holmes">Edward C. Holmes</name><affiliation wicri:level="1"><nlm: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.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>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</wicri:regionArea></affiliation></author><author><name sortKey="Sall, Amadou A" sort="Sall, Amadou A" uniqKey="Sall A" first="Amadou A" last="Sall">Amadou A. Sall</name><affiliation wicri:level="1"><nlm:affiliation>Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar, Senegal.</nlm:affiliation><country xml:lang="fr">Sénégal</country><wicri:regionArea>Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar</wicri:regionArea></affiliation></author></analytic><series><title level="j">Nature</title><idno type="eISSN">1476-4687</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Ebolavirus (genetics)</term><term>Ebolavirus (isolation & purification)</term><term>Evolution, Molecular</term><term>Genetic Variation (genetics)</term><term>Genome, Viral (genetics)</term><term>Glycoproteins (genetics)</term><term>Glycoproteins (metabolism)</term><term>Glycosylation</term><term>Guinea (epidemiology)</term><term>Hemorrhagic Fever, Ebola (epidemiology)</term><term>Hemorrhagic Fever, Ebola (transmission)</term><term>Hemorrhagic Fever, Ebola (virology)</term><term>Humans</term><term>Mali (epidemiology)</term><term>Molecular Sequence Data</term><term>Mucins (chemistry)</term><term>Mutation (genetics)</term><term>Nucleoproteins (genetics)</term><term>Phylogeny</term><term>Protein Structure, Tertiary (genetics)</term><term>RNA Replicase (genetics)</term><term>Sierra Leone (epidemiology)</term><term>Viral Core Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Données de séquences moléculaires</term><term>Ebolavirus (génétique)</term><term>Ebolavirus (isolement et purification)</term><term>Fièvre hémorragique à virus Ebola (transmission)</term><term>Fièvre hémorragique à virus Ebola (virologie)</term><term>Fièvre hémorragique à virus Ebola (épidémiologie)</term><term>Glycoprotéines (génétique)</term><term>Glycoprotéines (métabolisme)</term><term>Glycosylation</term><term>Guinée (épidémiologie)</term><term>Génome viral (génétique)</term><term>Humains</term><term>Mali (épidémiologie)</term><term>Mucines ()</term><term>Mutation (génétique)</term><term>Nucléoprotéines (génétique)</term><term>Phylogénie</term><term>Protéines du core viral (génétique)</term><term>RNA replicase (génétique)</term><term>Sierra Leone (épidémiologie)</term><term>Structure tertiaire des protéines (génétique)</term><term>Variation génétique (génétique)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Mucins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Glycoproteins</term><term>Nucleoproteins</term><term>RNA Replicase</term><term>Viral Core Proteins</term></keywords><keywords scheme="MESH" type="geographic" qualifier="epidemiology" xml:lang="en"><term>Guinea</term><term>Mali</term><term>Sierra Leone</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Hemorrhagic Fever, Ebola</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Ebolavirus</term><term>Genetic Variation</term><term>Genome, Viral</term><term>Mutation</term><term>Protein Structure, Tertiary</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Ebolavirus</term><term>Glycoprotéines</term><term>Génome viral</term><term>Mutation</term><term>Nucléoprotéines</term><term>Protéines du core viral</term><term>RNA replicase</term><term>Structure tertiaire des protéines</term><term>Variation génétique</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Ebolavirus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Ebolavirus</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Glycoproteins</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Glycoprotéines</term></keywords><keywords scheme="MESH" qualifier="transmission" xml:lang="en"><term>Hemorrhagic Fever, Ebola</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Fièvre hémorragique à virus Ebola</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Hemorrhagic Fever, Ebola</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Fièvre hémorragique à virus Ebola</term><term>Guinée</term><term>Mali</term><term>Sierra Leone</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Glycosylation</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Données de séquences moléculaires</term><term>Glycosylation</term><term>Humains</term><term>Mucines</term><term>Phylogénie</term><term>Évolution moléculaire</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Guinée</term><term>Mali</term><term>Sierra Leone</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26106863</PMID><DateCreated><Year>2015</Year><Month>08</Month><Day>06</Day></DateCreated><DateCompleted><Year>2016</Year><Month>05</Month><Day>01</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1476-4687</ISSN><JournalIssue CitedMedium="Internet"><Volume>524</Volume><Issue>7563</Issue><PubDate><Year>2015</Year><Month>Aug</Month><Day>06</Day></PubDate></JournalIssue><Title>Nature</Title><ISOAbbreviation>Nature</ISOAbbreviation></Journal><ArticleTitle>Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic.</ArticleTitle><Pagination><MedlinePgn>102-4</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/nature14612</ELocationID><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Simon-Loriere</LastName><ForeName>Etienne</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>1] Institut Pasteur, Functional Genetics of Infectious Diseases Unit, 75724 Paris Cedex 15, France [2] CNRS URA3012, Paris 75015, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Faye</LastName><ForeName>Ousmane</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar, Senegal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Faye</LastName><ForeName>Oumar</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar, Senegal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Koivogui</LastName><ForeName>Lamine</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Institut National de Santé Publique de Guinée, Conakry, Guinea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Magassouba</LastName><ForeName>Nfaly</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Projet de fièvres hémorragiques de Guinée, Université Gamal Abdel Nasser, BP 1147, Conakry, Guinea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Keita</LastName><ForeName>Sakoba</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Ministry of Health, BP 585 Conakry, Guinea.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Thiberge</LastName><ForeName>Jean-Michel</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Diancourt</LastName><ForeName>Laure</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bouchier</LastName><ForeName>Christiane</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Institut Pasteur, Genomic platform, 75724 Paris Cedex 15, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vandenbogaert</LastName><ForeName>Matthias</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Caro</LastName><ForeName>Valérie</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fall</LastName><ForeName>Gamou</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar, Senegal.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Buchmann</LastName><ForeName>Jan P</ForeName><Initials>JP</Initials><AffiliationInfo><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.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Matranga</LastName><ForeName>Christan B</ForeName><Initials>CB</Initials><AffiliationInfo><Affiliation>Broad Institute, 75 Ames Street, Cambridge, Massachusetts 02142, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sabeti</LastName><ForeName>Pardis C</ForeName><Initials>PC</Initials><AffiliationInfo><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.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Manuguerra</LastName><ForeName>Jean-Claude</ForeName><Initials>JC</Initials><AffiliationInfo><Affiliation>Institut Pasteur, Unité Environnement et Risques Infectieux, Cellule d'Intervention Biologique d'Urgence, 75724 Paris Cedex 15, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Holmes</LastName><ForeName>Edward C</ForeName><Initials>EC</Initials><AffiliationInfo><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.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sall</LastName><ForeName>Amadou A</ForeName><Initials>AA</Initials><AffiliationInfo><Affiliation>Institut Pasteur de Dakar, Arbovirus and Viral Hemorrhagic Fever Unit, BP 220, Dakar, Senegal.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList 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MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016679" MajorTopicYN="N">Genome, Viral</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006023" MajorTopicYN="N">Glycoproteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006031" MajorTopicYN="N">Glycosylation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016701" MajorTopicYN="N" Type="Geographic">Guinea</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="N">epidemiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019142" MajorTopicYN="N">Hemorrhagic Fever, Ebola</DescriptorName><QualifierName UI="Q000453" MajorTopicYN="Y">epidemiology</QualifierName><QualifierName UI="Q000635" 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