Real-time, portable genome sequencing for Ebola surveillance
Identifieur interne : 000016 ( Pmc/Checkpoint ); précédent : 000015; suivant : 000017Real-time, portable genome sequencing for Ebola surveillance
Auteurs : Joshua Quick ; Nicholas J. Loman ; Sophie Duraffour ; Jared T. Simpson ; Ettore Severi ; Lauren Cowley ; Joseph Akoi Bore ; Raymond Koundouno ; Gytis Dudas ; Amy Mikhail ; Nobila Ouédraogo ; Babak Afrough ; Amadou Bah ; Jonathan Hj Baum ; Beate Becker-Ziaja ; Jan-Peter Boettcher ; Mar Cabeza-Cabrerizo ; Alvaro Camino-Sanchez ; Lisa L. Carter ; Juiliane Doerrbecker ; Theresa Enkirch ; Isabel Graciela García Dorival ; Nicole Hetzelt ; Julia Hinzmann ; Tobias Holm ; Liana Eleni Kafetzopoulou ; Michel Koropogui ; Abigail Kosgey ; Eeva Kuisma ; Christopher H. Logue ; Antonio Mazzarelli ; Sarah Meisel ; Marc Mertens ; Janine Michel ; Didier Ngabo ; Katja Nitzsche ; Elisa Pallash ; Livia Victoria Patrono ; Jasmine Portmann ; Johanna Gabriella Repits ; Natasha Yasmin Rickett ; Andrea Sachse ; Katrin Singethan ; Inês Vitoriano ; Rahel L. Yemanaberhan ; Elsa G. Zekeng ; Racine Trina ; Alexander Bello ; Amadou Alpha Sall ; Ousmane Faye ; Oumar Faye ; N Aly Magassouba ; Cecelia V. Williams ; Victoria Amburgey ; Linda Winona ; Emily Davis ; Jon Gerlach ; Franck Washington ; Vanessa Monteil ; Marine Jourdain ; Marion Bererd ; Alimou Camara ; Hermann Somlare ; Abdoulaye Camara ; Marianne Gerard ; Guillaume Bado ; Bernard Baillet ; Déborah Delaune ; Koumpingnin Yacouba Nebie ; Abdoulaye Diarra ; Yacouba Savane ; Raymond Bernard Pallawo ; Giovanna Jaramillo Gutierrez ; Natacha Milhano ; Isabelle Roger ; Christopher J. Williams ; Facinet Yattara ; Kuiama Lewandowski ; Jamie Taylor ; Philip Rachwal ; Daniel Turner ; Georgios Pollakis ; Julian A. Hiscox ; David A. Matthews ; Matthew K. O Hea ; Andrew Mcd Johnston ; Duncan Wilson ; Emma Hutley ; Erasmus Smit ; Antonino Di Caro ; Roman Woelfel ; Kilian Stoecker ; Erna Fleischmann ; Martin Gabriel ; Simon A. Weller ; Lamine Koivogui ; Boubacar Diallo ; Sakoba Keita ; Andrew Rambaut ; Pierre Formenty ; Stephan Gunther ; Miles W. CarrollSource :
- Nature [ 0028-0836 ] ; 2016.
Abstract
The Ebola virus disease (EVD) epidemic in West Africa is the largest on record, responsible for >28,599 cases and >11,299 deaths
Url:
DOI: 10.1038/nature16996
PubMed: 26840485
PubMed Central: 4817224
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
PMC:4817224Le document en format XML
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<author><name sortKey="Quick, Joshua" sort="Quick, Joshua" uniqKey="Quick J" first="Joshua" last="Quick">Joshua Quick</name>
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<author><name sortKey="Loman, Nicholas J" sort="Loman, Nicholas J" uniqKey="Loman N" first="Nicholas J." last="Loman">Nicholas J. Loman</name>
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<author><name sortKey="Duraffour, Sophie" sort="Duraffour, Sophie" uniqKey="Duraffour S" first="Sophie" last="Duraffour">Sophie Duraffour</name>
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<author><name sortKey="Simpson, Jared T" sort="Simpson, Jared T" uniqKey="Simpson J" first="Jared T." last="Simpson">Jared T. Simpson</name>
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<author><name sortKey="Severi, Ettore" sort="Severi, Ettore" uniqKey="Severi E" first="Ettore" last="Severi">Ettore Severi</name>
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<author><name sortKey="Cowley, Lauren" sort="Cowley, Lauren" uniqKey="Cowley L" first="Lauren" last="Cowley">Lauren Cowley</name>
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<author><name sortKey="Bore, Joseph Akoi" sort="Bore, Joseph Akoi" uniqKey="Bore J" first="Joseph Akoi" last="Bore">Joseph Akoi Bore</name>
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<author><name sortKey="Koundouno, Raymond" sort="Koundouno, Raymond" uniqKey="Koundouno R" first="Raymond" last="Koundouno">Raymond Koundouno</name>
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<author><name sortKey="Dudas, Gytis" sort="Dudas, Gytis" uniqKey="Dudas G" first="Gytis" last="Dudas">Gytis Dudas</name>
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<author><name sortKey="Mikhail, Amy" sort="Mikhail, Amy" uniqKey="Mikhail A" first="Amy" last="Mikhail">Amy Mikhail</name>
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<author><name sortKey="Ouedraogo, Nobila" sort="Ouedraogo, Nobila" uniqKey="Ouedraogo N" first="Nobila" last="Ouédraogo">Nobila Ouédraogo</name>
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<author><name sortKey="Afrough, Babak" sort="Afrough, Babak" uniqKey="Afrough B" first="Babak" last="Afrough">Babak Afrough</name>
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<author><name sortKey="Bah, Amadou" sort="Bah, Amadou" uniqKey="Bah A" first="Amadou" last="Bah">Amadou Bah</name>
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<author><name sortKey="Baum, Jonathan Hj" sort="Baum, Jonathan Hj" uniqKey="Baum J" first="Jonathan Hj" last="Baum">Jonathan Hj Baum</name>
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<author><name sortKey="Becker Ziaja, Beate" sort="Becker Ziaja, Beate" uniqKey="Becker Ziaja B" first="Beate" last="Becker-Ziaja">Beate Becker-Ziaja</name>
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<author><name sortKey="Boettcher, Jan Peter" sort="Boettcher, Jan Peter" uniqKey="Boettcher J" first="Jan-Peter" last="Boettcher">Jan-Peter Boettcher</name>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Cabeza Cabrerizo, Mar" sort="Cabeza Cabrerizo, Mar" uniqKey="Cabeza Cabrerizo M" first="Mar" last="Cabeza-Cabrerizo">Mar Cabeza-Cabrerizo</name>
<affiliation><nlm:aff>NONE</nlm:aff>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Camino Sanchez, Alvaro" sort="Camino Sanchez, Alvaro" uniqKey="Camino Sanchez A" first="Alvaro" last="Camino-Sanchez">Alvaro Camino-Sanchez</name>
<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Carter, Lisa L" sort="Carter, Lisa L" uniqKey="Carter L" first="Lisa L." last="Carter">Lisa L. Carter</name>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Doerrbecker, Juiliane" sort="Doerrbecker, Juiliane" uniqKey="Doerrbecker J" first="Juiliane" last="Doerrbecker">Juiliane Doerrbecker</name>
<affiliation><nlm:aff>NONE</nlm:aff>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Enkirch, Theresa" sort="Enkirch, Theresa" uniqKey="Enkirch T" first="Theresa" last="Enkirch">Theresa Enkirch</name>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Dorival, Isabel Graciela Garcia" sort="Dorival, Isabel Graciela Garcia" uniqKey="Dorival I" first="Isabel Graciela García" last="Dorival">Isabel Graciela García Dorival</name>
<affiliation><nlm:aff>NONE</nlm:aff>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Hetzelt, Nicole" sort="Hetzelt, Nicole" uniqKey="Hetzelt N" first="Nicole" last="Hetzelt">Nicole Hetzelt</name>
<affiliation><nlm:aff>NONE</nlm:aff>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Hinzmann, Julia" sort="Hinzmann, Julia" uniqKey="Hinzmann J" first="Julia" last="Hinzmann">Julia Hinzmann</name>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Holm, Tobias" sort="Holm, Tobias" uniqKey="Holm T" first="Tobias" last="Holm">Tobias Holm</name>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Kafetzopoulou, Liana Eleni" sort="Kafetzopoulou, Liana Eleni" uniqKey="Kafetzopoulou L" first="Liana Eleni" last="Kafetzopoulou">Liana Eleni Kafetzopoulou</name>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Koropogui, Michel" sort="Koropogui, Michel" uniqKey="Koropogui M" first="Michel" last="Koropogui">Michel Koropogui</name>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Kosgey, Abigail" sort="Kosgey, Abigail" uniqKey="Kosgey A" first="Abigail" last="Kosgey">Abigail Kosgey</name>
<affiliation><nlm:aff>NONE</nlm:aff>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Kuisma, Eeva" sort="Kuisma, Eeva" uniqKey="Kuisma E" first="Eeva" last="Kuisma">Eeva Kuisma</name>
<affiliation><nlm:aff>NONE</nlm:aff>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Logue, Christopher H" sort="Logue, Christopher H" uniqKey="Logue C" first="Christopher H" last="Logue">Christopher H. Logue</name>
<affiliation><nlm:aff>NONE</nlm:aff>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Mazzarelli, Antonio" sort="Mazzarelli, Antonio" uniqKey="Mazzarelli A" first="Antonio" last="Mazzarelli">Antonio Mazzarelli</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
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</author>
<author><name sortKey="Meisel, Sarah" sort="Meisel, Sarah" uniqKey="Meisel S" first="Sarah" last="Meisel">Sarah Meisel</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
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<author><name sortKey="Mertens, Marc" sort="Mertens, Marc" uniqKey="Mertens M" first="Marc" last="Mertens">Marc Mertens</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Michel, Janine" sort="Michel, Janine" uniqKey="Michel J" first="Janine" last="Michel">Janine Michel</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Ngabo, Didier" sort="Ngabo, Didier" uniqKey="Ngabo D" first="Didier" last="Ngabo">Didier Ngabo</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Nitzsche, Katja" sort="Nitzsche, Katja" uniqKey="Nitzsche K" first="Katja" last="Nitzsche">Katja Nitzsche</name>
<affiliation><nlm:aff>NONE</nlm:aff>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Pallash, Elisa" sort="Pallash, Elisa" uniqKey="Pallash E" first="Elisa" last="Pallash">Elisa Pallash</name>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Patrono, Livia Victoria" sort="Patrono, Livia Victoria" uniqKey="Patrono L" first="Livia Victoria" last="Patrono">Livia Victoria Patrono</name>
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<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Portmann, Jasmine" sort="Portmann, Jasmine" uniqKey="Portmann J" first="Jasmine" last="Portmann">Jasmine Portmann</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Repits, Johanna Gabriella" sort="Repits, Johanna Gabriella" uniqKey="Repits J" first="Johanna Gabriella" last="Repits">Johanna Gabriella Repits</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
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<author><name sortKey="Rickett, Natasha Yasmin" sort="Rickett, Natasha Yasmin" uniqKey="Rickett N" first="Natasha Yasmin" last="Rickett">Natasha Yasmin Rickett</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
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<author><name sortKey="Sachse, Andrea" sort="Sachse, Andrea" uniqKey="Sachse A" first="Andrea" last="Sachse">Andrea Sachse</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Singethan, Katrin" sort="Singethan, Katrin" uniqKey="Singethan K" first="Katrin" last="Singethan">Katrin Singethan</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Vitoriano, Ines" sort="Vitoriano, Ines" uniqKey="Vitoriano I" first="Inês" last="Vitoriano">Inês Vitoriano</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Yemanaberhan, Rahel L" sort="Yemanaberhan, Rahel L" uniqKey="Yemanaberhan R" first="Rahel L" last="Yemanaberhan">Rahel L. Yemanaberhan</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Zekeng, Elsa G" sort="Zekeng, Elsa G" uniqKey="Zekeng E" first="Elsa G" last="Zekeng">Elsa G. Zekeng</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Trina, Racine" sort="Trina, Racine" uniqKey="Trina R" first="Racine" last="Trina">Racine Trina</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bello, Alexander" sort="Bello, Alexander" uniqKey="Bello A" first="Alexander" last="Bello">Alexander Bello</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Sall, Amadou Alpha" sort="Sall, Amadou Alpha" uniqKey="Sall A" first="Amadou Alpha" last="Sall">Amadou Alpha Sall</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Faye, Ousmane" sort="Faye, Ousmane" uniqKey="Faye O" first="Ousmane" last="Faye">Ousmane Faye</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Faye, Oumar" sort="Faye, Oumar" uniqKey="Faye O" first="Oumar" last="Faye">Oumar Faye</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Magassouba, N Aly" sort="Magassouba, N Aly" uniqKey="Magassouba N" first="N Aly" last="Magassouba">N Aly Magassouba</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Williams, Cecelia V" sort="Williams, Cecelia V" uniqKey="Williams C" first="Cecelia V." last="Williams">Cecelia V. Williams</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Amburgey, Victoria" sort="Amburgey, Victoria" uniqKey="Amburgey V" first="Victoria" last="Amburgey">Victoria Amburgey</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Winona, Linda" sort="Winona, Linda" uniqKey="Winona L" first="Linda" last="Winona">Linda Winona</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Davis, Emily" sort="Davis, Emily" uniqKey="Davis E" first="Emily" last="Davis">Emily Davis</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Gerlach, Jon" sort="Gerlach, Jon" uniqKey="Gerlach J" first="Jon" last="Gerlach">Jon Gerlach</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Washington, Franck" sort="Washington, Franck" uniqKey="Washington F" first="Franck" last="Washington">Franck Washington</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Monteil, Vanessa" sort="Monteil, Vanessa" uniqKey="Monteil V" first="Vanessa" last="Monteil">Vanessa Monteil</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Jourdain, Marine" sort="Jourdain, Marine" uniqKey="Jourdain M" first="Marine" last="Jourdain">Marine Jourdain</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bererd, Marion" sort="Bererd, Marion" uniqKey="Bererd M" first="Marion" last="Bererd">Marion Bererd</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Camara, Alimou" sort="Camara, Alimou" uniqKey="Camara A" first="Alimou" last="Camara">Alimou Camara</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Somlare, Hermann" sort="Somlare, Hermann" uniqKey="Somlare H" first="Hermann" last="Somlare">Hermann Somlare</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Camara, Abdoulaye" sort="Camara, Abdoulaye" uniqKey="Camara A" first="Abdoulaye" last="Camara">Abdoulaye Camara</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Gerard, Marianne" sort="Gerard, Marianne" uniqKey="Gerard M" first="Marianne" last="Gerard">Marianne Gerard</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bado, Guillaume" sort="Bado, Guillaume" uniqKey="Bado G" first="Guillaume" last="Bado">Guillaume Bado</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Baillet, Bernard" sort="Baillet, Bernard" uniqKey="Baillet B" first="Bernard" last="Baillet">Bernard Baillet</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Delaune, Deborah" sort="Delaune, Deborah" uniqKey="Delaune D" first="Déborah" last="Delaune">Déborah Delaune</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Nebie, Koumpingnin Yacouba" sort="Nebie, Koumpingnin Yacouba" uniqKey="Nebie K" first="Koumpingnin Yacouba" last="Nebie">Koumpingnin Yacouba Nebie</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Diarra, Abdoulaye" sort="Diarra, Abdoulaye" uniqKey="Diarra A" first="Abdoulaye" last="Diarra">Abdoulaye Diarra</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Savane, Yacouba" sort="Savane, Yacouba" uniqKey="Savane Y" first="Yacouba" last="Savane">Yacouba Savane</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Pallawo, Raymond Bernard" sort="Pallawo, Raymond Bernard" uniqKey="Pallawo R" first="Raymond Bernard" last="Pallawo">Raymond Bernard Pallawo</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Gutierrez, Giovanna Jaramillo" sort="Gutierrez, Giovanna Jaramillo" uniqKey="Gutierrez G" first="Giovanna Jaramillo" last="Gutierrez">Giovanna Jaramillo Gutierrez</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Milhano, Natacha" sort="Milhano, Natacha" uniqKey="Milhano N" first="Natacha" last="Milhano">Natacha Milhano</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Roger, Isabelle" sort="Roger, Isabelle" uniqKey="Roger I" first="Isabelle" last="Roger">Isabelle Roger</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Williams, Christopher J" sort="Williams, Christopher J" uniqKey="Williams C" first="Christopher J" last="Williams">Christopher J. Williams</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Yattara, Facinet" sort="Yattara, Facinet" uniqKey="Yattara F" first="Facinet" last="Yattara">Facinet Yattara</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Lewandowski, Kuiama" sort="Lewandowski, Kuiama" uniqKey="Lewandowski K" first="Kuiama" last="Lewandowski">Kuiama Lewandowski</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Taylor, Jamie" sort="Taylor, Jamie" uniqKey="Taylor J" first="Jamie" last="Taylor">Jamie Taylor</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Rachwal, Philip" sort="Rachwal, Philip" uniqKey="Rachwal P" first="Philip" last="Rachwal">Philip Rachwal</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Turner, Daniel" sort="Turner, Daniel" uniqKey="Turner D" first="Daniel" last="Turner">Daniel Turner</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Pollakis, Georgios" sort="Pollakis, Georgios" uniqKey="Pollakis G" first="Georgios" last="Pollakis">Georgios Pollakis</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Hiscox, Julian A" sort="Hiscox, Julian A" uniqKey="Hiscox J" first="Julian A." last="Hiscox">Julian A. Hiscox</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Matthews, David A" sort="Matthews, David A" uniqKey="Matthews D" first="David A." last="Matthews">David A. Matthews</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="O Hea, Matthew K" sort="O Hea, Matthew K" uniqKey="O Hea M" first="Matthew K." last="O Hea">Matthew K. O Hea</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Johnston, Andrew Mcd" sort="Johnston, Andrew Mcd" uniqKey="Johnston A" first="Andrew Mcd" last="Johnston">Andrew Mcd Johnston</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Wilson, Duncan" sort="Wilson, Duncan" uniqKey="Wilson D" first="Duncan" last="Wilson">Duncan Wilson</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Hutley, Emma" sort="Hutley, Emma" uniqKey="Hutley E" first="Emma" last="Hutley">Emma Hutley</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Smit, Erasmus" sort="Smit, Erasmus" uniqKey="Smit E" first="Erasmus" last="Smit">Erasmus Smit</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Di Caro, Antonino" sort="Di Caro, Antonino" uniqKey="Di Caro A" first="Antonino" last="Di Caro">Antonino Di Caro</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Woelfel, Roman" sort="Woelfel, Roman" uniqKey="Woelfel R" first="Roman" last="Woelfel">Roman Woelfel</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Stoecker, Kilian" sort="Stoecker, Kilian" uniqKey="Stoecker K" first="Kilian" last="Stoecker">Kilian Stoecker</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Fleischmann, Erna" sort="Fleischmann, Erna" uniqKey="Fleischmann E" first="Erna" last="Fleischmann">Erna Fleischmann</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Gabriel, Martin" sort="Gabriel, Martin" uniqKey="Gabriel M" first="Martin" last="Gabriel">Martin Gabriel</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Weller, Simon A" sort="Weller, Simon A" uniqKey="Weller S" first="Simon A." last="Weller">Simon A. Weller</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Koivogui, Lamine" sort="Koivogui, Lamine" uniqKey="Koivogui L" first="Lamine" last="Koivogui">Lamine Koivogui</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Diallo, Boubacar" sort="Diallo, Boubacar" uniqKey="Diallo B" first="Boubacar" last="Diallo">Boubacar Diallo</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Keita, Sakoba" sort="Keita, Sakoba" uniqKey="Keita S" first="Sakoba" last="Keita">Sakoba Keita</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Rambaut, Andrew" sort="Rambaut, Andrew" uniqKey="Rambaut A" first="Andrew" last="Rambaut">Andrew Rambaut</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Formenty, Pierre" sort="Formenty, Pierre" uniqKey="Formenty P" first="Pierre" last="Formenty">Pierre Formenty</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Gunther, Stephan" sort="Gunther, Stephan" uniqKey="Gunther S" first="Stephan" last="Gunther">Stephan Gunther</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Carroll, Miles W" sort="Carroll, Miles W" uniqKey="Carroll M" first="Miles W." last="Carroll">Miles W. Carroll</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">26840485</idno>
<idno type="pmc">4817224</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817224</idno>
<idno type="RBID">PMC:4817224</idno>
<idno type="doi">10.1038/nature16996</idno>
<date when="2016">2016</date>
<idno type="wicri:Area/Pmc/Corpus">000675</idno>
<idno type="wicri:Area/Pmc/Curation">000675</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000016</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Real-time, portable genome sequencing for Ebola surveillance</title>
<author><name sortKey="Quick, Joshua" sort="Quick, Joshua" uniqKey="Quick J" first="Joshua" last="Quick">Joshua Quick</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Loman, Nicholas J" sort="Loman, Nicholas J" uniqKey="Loman N" first="Nicholas J." last="Loman">Nicholas J. Loman</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Duraffour, Sophie" sort="Duraffour, Sophie" uniqKey="Duraffour S" first="Sophie" last="Duraffour">Sophie Duraffour</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Simpson, Jared T" sort="Simpson, Jared T" uniqKey="Simpson J" first="Jared T." last="Simpson">Jared T. Simpson</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Severi, Ettore" sort="Severi, Ettore" uniqKey="Severi E" first="Ettore" last="Severi">Ettore Severi</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Cowley, Lauren" sort="Cowley, Lauren" uniqKey="Cowley L" first="Lauren" last="Cowley">Lauren Cowley</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bore, Joseph Akoi" sort="Bore, Joseph Akoi" uniqKey="Bore J" first="Joseph Akoi" last="Bore">Joseph Akoi Bore</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Koundouno, Raymond" sort="Koundouno, Raymond" uniqKey="Koundouno R" first="Raymond" last="Koundouno">Raymond Koundouno</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Dudas, Gytis" sort="Dudas, Gytis" uniqKey="Dudas G" first="Gytis" last="Dudas">Gytis Dudas</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Mikhail, Amy" sort="Mikhail, Amy" uniqKey="Mikhail A" first="Amy" last="Mikhail">Amy Mikhail</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ouedraogo, Nobila" sort="Ouedraogo, Nobila" uniqKey="Ouedraogo N" first="Nobila" last="Ouédraogo">Nobila Ouédraogo</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Afrough, Babak" sort="Afrough, Babak" uniqKey="Afrough B" first="Babak" last="Afrough">Babak Afrough</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bah, Amadou" sort="Bah, Amadou" uniqKey="Bah A" first="Amadou" last="Bah">Amadou Bah</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Baum, Jonathan Hj" sort="Baum, Jonathan Hj" uniqKey="Baum J" first="Jonathan Hj" last="Baum">Jonathan Hj Baum</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Becker Ziaja, Beate" sort="Becker Ziaja, Beate" uniqKey="Becker Ziaja B" first="Beate" last="Becker-Ziaja">Beate Becker-Ziaja</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Boettcher, Jan Peter" sort="Boettcher, Jan Peter" uniqKey="Boettcher J" first="Jan-Peter" last="Boettcher">Jan-Peter Boettcher</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Cabeza Cabrerizo, Mar" sort="Cabeza Cabrerizo, Mar" uniqKey="Cabeza Cabrerizo M" first="Mar" last="Cabeza-Cabrerizo">Mar Cabeza-Cabrerizo</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Camino Sanchez, Alvaro" sort="Camino Sanchez, Alvaro" uniqKey="Camino Sanchez A" first="Alvaro" last="Camino-Sanchez">Alvaro Camino-Sanchez</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Carter, Lisa L" sort="Carter, Lisa L" uniqKey="Carter L" first="Lisa L." last="Carter">Lisa L. Carter</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Doerrbecker, Juiliane" sort="Doerrbecker, Juiliane" uniqKey="Doerrbecker J" first="Juiliane" last="Doerrbecker">Juiliane Doerrbecker</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Enkirch, Theresa" sort="Enkirch, Theresa" uniqKey="Enkirch T" first="Theresa" last="Enkirch">Theresa Enkirch</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Dorival, Isabel Graciela Garcia" sort="Dorival, Isabel Graciela Garcia" uniqKey="Dorival I" first="Isabel Graciela García" last="Dorival">Isabel Graciela García Dorival</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Hetzelt, Nicole" sort="Hetzelt, Nicole" uniqKey="Hetzelt N" first="Nicole" last="Hetzelt">Nicole Hetzelt</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Hinzmann, Julia" sort="Hinzmann, Julia" uniqKey="Hinzmann J" first="Julia" last="Hinzmann">Julia Hinzmann</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Holm, Tobias" sort="Holm, Tobias" uniqKey="Holm T" first="Tobias" last="Holm">Tobias Holm</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Kafetzopoulou, Liana Eleni" sort="Kafetzopoulou, Liana Eleni" uniqKey="Kafetzopoulou L" first="Liana Eleni" last="Kafetzopoulou">Liana Eleni Kafetzopoulou</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Koropogui, Michel" sort="Koropogui, Michel" uniqKey="Koropogui M" first="Michel" last="Koropogui">Michel Koropogui</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Kosgey, Abigail" sort="Kosgey, Abigail" uniqKey="Kosgey A" first="Abigail" last="Kosgey">Abigail Kosgey</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Kuisma, Eeva" sort="Kuisma, Eeva" uniqKey="Kuisma E" first="Eeva" last="Kuisma">Eeva Kuisma</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Logue, Christopher H" sort="Logue, Christopher H" uniqKey="Logue C" first="Christopher H" last="Logue">Christopher H. Logue</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Mazzarelli, Antonio" sort="Mazzarelli, Antonio" uniqKey="Mazzarelli A" first="Antonio" last="Mazzarelli">Antonio Mazzarelli</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Meisel, Sarah" sort="Meisel, Sarah" uniqKey="Meisel S" first="Sarah" last="Meisel">Sarah Meisel</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Mertens, Marc" sort="Mertens, Marc" uniqKey="Mertens M" first="Marc" last="Mertens">Marc Mertens</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Michel, Janine" sort="Michel, Janine" uniqKey="Michel J" first="Janine" last="Michel">Janine Michel</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Ngabo, Didier" sort="Ngabo, Didier" uniqKey="Ngabo D" first="Didier" last="Ngabo">Didier Ngabo</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Nitzsche, Katja" sort="Nitzsche, Katja" uniqKey="Nitzsche K" first="Katja" last="Nitzsche">Katja Nitzsche</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Pallash, Elisa" sort="Pallash, Elisa" uniqKey="Pallash E" first="Elisa" last="Pallash">Elisa Pallash</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Patrono, Livia Victoria" sort="Patrono, Livia Victoria" uniqKey="Patrono L" first="Livia Victoria" last="Patrono">Livia Victoria Patrono</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Portmann, Jasmine" sort="Portmann, Jasmine" uniqKey="Portmann J" first="Jasmine" last="Portmann">Jasmine Portmann</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Repits, Johanna Gabriella" sort="Repits, Johanna Gabriella" uniqKey="Repits J" first="Johanna Gabriella" last="Repits">Johanna Gabriella Repits</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Rickett, Natasha Yasmin" sort="Rickett, Natasha Yasmin" uniqKey="Rickett N" first="Natasha Yasmin" last="Rickett">Natasha Yasmin Rickett</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Sachse, Andrea" sort="Sachse, Andrea" uniqKey="Sachse A" first="Andrea" last="Sachse">Andrea Sachse</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Singethan, Katrin" sort="Singethan, Katrin" uniqKey="Singethan K" first="Katrin" last="Singethan">Katrin Singethan</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Vitoriano, Ines" sort="Vitoriano, Ines" uniqKey="Vitoriano I" first="Inês" last="Vitoriano">Inês Vitoriano</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Yemanaberhan, Rahel L" sort="Yemanaberhan, Rahel L" uniqKey="Yemanaberhan R" first="Rahel L" last="Yemanaberhan">Rahel L. Yemanaberhan</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Zekeng, Elsa G" sort="Zekeng, Elsa G" uniqKey="Zekeng E" first="Elsa G" last="Zekeng">Elsa G. Zekeng</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Trina, Racine" sort="Trina, Racine" uniqKey="Trina R" first="Racine" last="Trina">Racine Trina</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bello, Alexander" sort="Bello, Alexander" uniqKey="Bello A" first="Alexander" last="Bello">Alexander Bello</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Sall, Amadou Alpha" sort="Sall, Amadou Alpha" uniqKey="Sall A" first="Amadou Alpha" last="Sall">Amadou Alpha Sall</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Faye, Ousmane" sort="Faye, Ousmane" uniqKey="Faye O" first="Ousmane" last="Faye">Ousmane Faye</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Faye, Oumar" sort="Faye, Oumar" uniqKey="Faye O" first="Oumar" last="Faye">Oumar Faye</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Magassouba, N Aly" sort="Magassouba, N Aly" uniqKey="Magassouba N" first="N Aly" last="Magassouba">N Aly Magassouba</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Williams, Cecelia V" sort="Williams, Cecelia V" uniqKey="Williams C" first="Cecelia V." last="Williams">Cecelia V. Williams</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Amburgey, Victoria" sort="Amburgey, Victoria" uniqKey="Amburgey V" first="Victoria" last="Amburgey">Victoria Amburgey</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Winona, Linda" sort="Winona, Linda" uniqKey="Winona L" first="Linda" last="Winona">Linda Winona</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Davis, Emily" sort="Davis, Emily" uniqKey="Davis E" first="Emily" last="Davis">Emily Davis</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Gerlach, Jon" sort="Gerlach, Jon" uniqKey="Gerlach J" first="Jon" last="Gerlach">Jon Gerlach</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Washington, Franck" sort="Washington, Franck" uniqKey="Washington F" first="Franck" last="Washington">Franck Washington</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Monteil, Vanessa" sort="Monteil, Vanessa" uniqKey="Monteil V" first="Vanessa" last="Monteil">Vanessa Monteil</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Jourdain, Marine" sort="Jourdain, Marine" uniqKey="Jourdain M" first="Marine" last="Jourdain">Marine Jourdain</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bererd, Marion" sort="Bererd, Marion" uniqKey="Bererd M" first="Marion" last="Bererd">Marion Bererd</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Camara, Alimou" sort="Camara, Alimou" uniqKey="Camara A" first="Alimou" last="Camara">Alimou Camara</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Somlare, Hermann" sort="Somlare, Hermann" uniqKey="Somlare H" first="Hermann" last="Somlare">Hermann Somlare</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Camara, Abdoulaye" sort="Camara, Abdoulaye" uniqKey="Camara A" first="Abdoulaye" last="Camara">Abdoulaye Camara</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Gerard, Marianne" sort="Gerard, Marianne" uniqKey="Gerard M" first="Marianne" last="Gerard">Marianne Gerard</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Bado, Guillaume" sort="Bado, Guillaume" uniqKey="Bado G" first="Guillaume" last="Bado">Guillaume Bado</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Baillet, Bernard" sort="Baillet, Bernard" uniqKey="Baillet B" first="Bernard" last="Baillet">Bernard Baillet</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Delaune, Deborah" sort="Delaune, Deborah" uniqKey="Delaune D" first="Déborah" last="Delaune">Déborah Delaune</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Nebie, Koumpingnin Yacouba" sort="Nebie, Koumpingnin Yacouba" uniqKey="Nebie K" first="Koumpingnin Yacouba" last="Nebie">Koumpingnin Yacouba Nebie</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Diarra, Abdoulaye" sort="Diarra, Abdoulaye" uniqKey="Diarra A" first="Abdoulaye" last="Diarra">Abdoulaye Diarra</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Savane, Yacouba" sort="Savane, Yacouba" uniqKey="Savane Y" first="Yacouba" last="Savane">Yacouba Savane</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Pallawo, Raymond Bernard" sort="Pallawo, Raymond Bernard" uniqKey="Pallawo R" first="Raymond Bernard" last="Pallawo">Raymond Bernard Pallawo</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Gutierrez, Giovanna Jaramillo" sort="Gutierrez, Giovanna Jaramillo" uniqKey="Gutierrez G" first="Giovanna Jaramillo" last="Gutierrez">Giovanna Jaramillo Gutierrez</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Milhano, Natacha" sort="Milhano, Natacha" uniqKey="Milhano N" first="Natacha" last="Milhano">Natacha Milhano</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Roger, Isabelle" sort="Roger, Isabelle" uniqKey="Roger I" first="Isabelle" last="Roger">Isabelle Roger</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Williams, Christopher J" sort="Williams, Christopher J" uniqKey="Williams C" first="Christopher J" last="Williams">Christopher J. Williams</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Yattara, Facinet" sort="Yattara, Facinet" uniqKey="Yattara F" first="Facinet" last="Yattara">Facinet Yattara</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Lewandowski, Kuiama" sort="Lewandowski, Kuiama" uniqKey="Lewandowski K" first="Kuiama" last="Lewandowski">Kuiama Lewandowski</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Taylor, Jamie" sort="Taylor, Jamie" uniqKey="Taylor J" first="Jamie" last="Taylor">Jamie Taylor</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Rachwal, Philip" sort="Rachwal, Philip" uniqKey="Rachwal P" first="Philip" last="Rachwal">Philip Rachwal</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Turner, Daniel" sort="Turner, Daniel" uniqKey="Turner D" first="Daniel" last="Turner">Daniel Turner</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Pollakis, Georgios" sort="Pollakis, Georgios" uniqKey="Pollakis G" first="Georgios" last="Pollakis">Georgios Pollakis</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Hiscox, Julian A" sort="Hiscox, Julian A" uniqKey="Hiscox J" first="Julian A." last="Hiscox">Julian A. Hiscox</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Matthews, David A" sort="Matthews, David A" uniqKey="Matthews D" first="David A." last="Matthews">David A. Matthews</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="O Hea, Matthew K" sort="O Hea, Matthew K" uniqKey="O Hea M" first="Matthew K." last="O Hea">Matthew K. O Hea</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Johnston, Andrew Mcd" sort="Johnston, Andrew Mcd" uniqKey="Johnston A" first="Andrew Mcd" last="Johnston">Andrew Mcd Johnston</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Wilson, Duncan" sort="Wilson, Duncan" uniqKey="Wilson D" first="Duncan" last="Wilson">Duncan Wilson</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Hutley, Emma" sort="Hutley, Emma" uniqKey="Hutley E" first="Emma" last="Hutley">Emma Hutley</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Smit, Erasmus" sort="Smit, Erasmus" uniqKey="Smit E" first="Erasmus" last="Smit">Erasmus Smit</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Di Caro, Antonino" sort="Di Caro, Antonino" uniqKey="Di Caro A" first="Antonino" last="Di Caro">Antonino Di Caro</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Woelfel, Roman" sort="Woelfel, Roman" uniqKey="Woelfel R" first="Roman" last="Woelfel">Roman Woelfel</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Stoecker, Kilian" sort="Stoecker, Kilian" uniqKey="Stoecker K" first="Kilian" last="Stoecker">Kilian Stoecker</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Fleischmann, Erna" sort="Fleischmann, Erna" uniqKey="Fleischmann E" first="Erna" last="Fleischmann">Erna Fleischmann</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Gabriel, Martin" sort="Gabriel, Martin" uniqKey="Gabriel M" first="Martin" last="Gabriel">Martin Gabriel</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Weller, Simon A" sort="Weller, Simon A" uniqKey="Weller S" first="Simon A." last="Weller">Simon A. Weller</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Koivogui, Lamine" sort="Koivogui, Lamine" uniqKey="Koivogui L" first="Lamine" last="Koivogui">Lamine Koivogui</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Diallo, Boubacar" sort="Diallo, Boubacar" uniqKey="Diallo B" first="Boubacar" last="Diallo">Boubacar Diallo</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Keita, Sakoba" sort="Keita, Sakoba" uniqKey="Keita S" first="Sakoba" last="Keita">Sakoba Keita</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Rambaut, Andrew" sort="Rambaut, Andrew" uniqKey="Rambaut A" first="Andrew" last="Rambaut">Andrew Rambaut</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Formenty, Pierre" sort="Formenty, Pierre" uniqKey="Formenty P" first="Pierre" last="Formenty">Pierre Formenty</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Gunther, Stephan" sort="Gunther, Stephan" uniqKey="Gunther S" first="Stephan" last="Gunther">Stephan Gunther</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Carroll, Miles W" sort="Carroll, Miles W" uniqKey="Carroll M" first="Miles W." last="Carroll">Miles W. Carroll</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
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</analytic>
<series><title level="j">Nature</title>
<idno type="ISSN">0028-0836</idno>
<idno type="eISSN">1476-4687</idno>
<imprint><date when="2016">2016</date>
</imprint>
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<front><div type="abstract" xml:lang="en"><p id="P3">The Ebola virus disease (EVD) epidemic in West Africa is the largest on record, responsible for >28,599 cases and >11,299 deaths <sup><xref rid="R1" ref-type="bibr">1</xref>
</sup>
. Genome sequencing in viral outbreaks is desirable in order to characterize the infectious agent to determine its evolutionary rate, signatures of host adaptation, identification and monitoring of diagnostic targets and responses to vaccines and treatments. The Ebola virus genome (EBOV) substitution rate in the Makona strain has been estimated at between 0.87 × 10<sup>−3</sup>
to 1.42 × 10<sup>−3</sup>
mutations per site per year. This is equivalent to 16 to 27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic <sup><xref rid="R2" ref-type="bibr">2</xref>
-<xref rid="R7" ref-type="bibr">7</xref>
</sup>
. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought-after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions <sup><xref rid="R8" ref-type="bibr">8</xref>
</sup>
. Genomic surveillance during the epidemic has been sporadic due to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities <sup><xref rid="R9" ref-type="bibr">9</xref>
</sup>
. In order to address this problem, we devised a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. Here we present sequence data and analysis of 142 Ebola virus (EBOV) samples collected during the period March to October 2015. We were able to generate results in less than 24 hours after receiving an Ebola positive sample, with the sequencing process taking as little as 15-60 minutes. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.</p>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">0410462</journal-id>
<journal-id journal-id-type="pubmed-jr-id">6011</journal-id>
<journal-id journal-id-type="nlm-ta">Nature</journal-id>
<journal-id journal-id-type="iso-abbrev">Nature</journal-id>
<journal-title-group><journal-title>Nature</journal-title>
</journal-title-group>
<issn pub-type="ppub">0028-0836</issn>
<issn pub-type="epub">1476-4687</issn>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">26840485</article-id>
<article-id pub-id-type="pmc">4817224</article-id>
<article-id pub-id-type="doi">10.1038/nature16996</article-id>
<article-id pub-id-type="manuscript">EMS66776</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Real-time, portable genome sequencing for Ebola surveillance</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" equal-contrib="yes"><name><surname>Quick</surname>
<given-names>Joshua</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
</contrib>
<contrib contrib-type="author" equal-contrib="yes"><name><surname>Loman</surname>
<given-names>Nicholas J.</given-names>
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<contrib contrib-type="author" equal-contrib="yes"><name><surname>Duraffour</surname>
<given-names>Sophie</given-names>
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<given-names>Jared T.</given-names>
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<xref ref-type="aff" rid="A29">29</xref>
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<given-names>Ettore</given-names>
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<xref ref-type="aff" rid="A35">35</xref>
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<given-names>Lauren</given-names>
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<given-names>Joseph Akoi</given-names>
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<given-names>Raymond</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Dudas</surname>
<given-names>Gytis</given-names>
</name>
<xref ref-type="aff" rid="A5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mikhail</surname>
<given-names>Amy</given-names>
</name>
<xref ref-type="aff" rid="A4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ouédraogo</surname>
<given-names>Nobila</given-names>
</name>
<xref ref-type="aff" rid="A6">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Afrough</surname>
<given-names>Babak</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A11">11</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bah</surname>
<given-names>Amadou</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A7">7</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Baum</surname>
<given-names>Jonathan HJ</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Becker-Ziaja</surname>
<given-names>Beate</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Boettcher</surname>
<given-names>Jan-Peter</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A8">8</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Cabeza-Cabrerizo</surname>
<given-names>Mar</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Camino-Sanchez</surname>
<given-names>Alvaro</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Carter</surname>
<given-names>Lisa L.</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A9">9</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Doerrbecker</surname>
<given-names>Juiliane</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Enkirch</surname>
<given-names>Theresa</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A37">37</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Dorival</surname>
<given-names>Isabel Graciela García</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A10">10</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hetzelt</surname>
<given-names>Nicole</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A8">8</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hinzmann</surname>
<given-names>Julia</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A8">8</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Holm</surname>
<given-names>Tobias</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kafetzopoulou</surname>
<given-names>Liana Eleni</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A38">38</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Koropogui</surname>
<given-names>Michel</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A26">26</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kosgey</surname>
<given-names>Abigail</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A39">39</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kuisma</surname>
<given-names>Eeva</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A11">11</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Logue</surname>
<given-names>Christopher H</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A11">11</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mazzarelli</surname>
<given-names>Antonio</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A31">31</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Meisel</surname>
<given-names>Sarah</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Mertens</surname>
<given-names>Marc</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A12">12</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Michel</surname>
<given-names>Janine</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A8">8</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ngabo</surname>
<given-names>Didier</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A11">11</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Nitzsche</surname>
<given-names>Katja</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pallash</surname>
<given-names>Elisa</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Patrono</surname>
<given-names>Livia Victoria</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Portmann</surname>
<given-names>Jasmine</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A13">13</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Repits</surname>
<given-names>Johanna Gabriella</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A14">14</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rickett</surname>
<given-names>Natasha Yasmin</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A10">10</xref>
<xref ref-type="aff" rid="A45">45</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sachse</surname>
<given-names>Andrea</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A8">8</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Singethan</surname>
<given-names>Katrin</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A40">40</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Vitoriano</surname>
<given-names>Inês</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A11">11</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Yemanaberhan</surname>
<given-names>Rahel L</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Zekeng</surname>
<given-names>Elsa G</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A10">10</xref>
<xref ref-type="aff" rid="A45">45</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Trina</surname>
<given-names>Racine</given-names>
</name>
<xref ref-type="aff" rid="A15">15</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bello</surname>
<given-names>Alexander</given-names>
</name>
<xref ref-type="aff" rid="A15">15</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sall</surname>
<given-names>Amadou Alpha</given-names>
</name>
<xref ref-type="aff" rid="A16">16</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Faye</surname>
<given-names>Ousmane</given-names>
</name>
<xref ref-type="aff" rid="A16">16</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Faye</surname>
<given-names>Oumar</given-names>
</name>
<xref ref-type="aff" rid="A16">16</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Magassouba</surname>
<given-names>N’Faly</given-names>
</name>
<xref ref-type="aff" rid="A17">17</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Williams</surname>
<given-names>Cecelia V.</given-names>
</name>
<xref ref-type="aff" rid="A18">18</xref>
<xref ref-type="aff" rid="A19">19</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Amburgey</surname>
<given-names>Victoria</given-names>
</name>
<xref ref-type="aff" rid="A18">18</xref>
<xref ref-type="aff" rid="A19">19</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Winona</surname>
<given-names>Linda</given-names>
</name>
<xref ref-type="aff" rid="A18">18</xref>
<xref ref-type="aff" rid="A19">19</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Davis</surname>
<given-names>Emily</given-names>
</name>
<xref ref-type="aff" rid="A19">19</xref>
<xref ref-type="aff" rid="A20">20</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gerlach</surname>
<given-names>Jon</given-names>
</name>
<xref ref-type="aff" rid="A19">19</xref>
<xref ref-type="aff" rid="A20">20</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Washington</surname>
<given-names>Franck</given-names>
</name>
<xref ref-type="aff" rid="A19">19</xref>
<xref ref-type="aff" rid="A20">20</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Monteil</surname>
<given-names>Vanessa</given-names>
</name>
<xref ref-type="aff" rid="A21">21</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Jourdain</surname>
<given-names>Marine</given-names>
</name>
<xref ref-type="aff" rid="A21">21</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bererd</surname>
<given-names>Marion</given-names>
</name>
<xref ref-type="aff" rid="A21">21</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Camara</surname>
<given-names>Alimou</given-names>
</name>
<xref ref-type="aff" rid="A21">21</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Somlare</surname>
<given-names>Hermann</given-names>
</name>
<xref ref-type="aff" rid="A21">21</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Camara</surname>
<given-names>Abdoulaye</given-names>
</name>
<xref ref-type="aff" rid="A21">21</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gerard</surname>
<given-names>Marianne</given-names>
</name>
<xref ref-type="aff" rid="A21">21</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bado</surname>
<given-names>Guillaume</given-names>
</name>
<xref ref-type="aff" rid="A21">21</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Baillet</surname>
<given-names>Bernard</given-names>
</name>
<xref ref-type="aff" rid="A21">21</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Delaune</surname>
<given-names>Déborah</given-names>
</name>
<xref ref-type="aff" rid="A22">22</xref>
<xref ref-type="aff" rid="A23">23</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Nebie</surname>
<given-names>Koumpingnin Yacouba</given-names>
</name>
<xref ref-type="aff" rid="A24">24</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Diarra</surname>
<given-names>Abdoulaye</given-names>
</name>
<xref ref-type="aff" rid="A24">24</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Savane</surname>
<given-names>Yacouba</given-names>
</name>
<xref ref-type="aff" rid="A24">24</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pallawo</surname>
<given-names>Raymond Bernard</given-names>
</name>
<xref ref-type="aff" rid="A24">24</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gutierrez</surname>
<given-names>Giovanna Jaramillo</given-names>
</name>
<xref ref-type="aff" rid="A42">42</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Milhano</surname>
<given-names>Natacha</given-names>
</name>
<xref ref-type="aff" rid="A41">41</xref>
<xref ref-type="aff" rid="A35">35</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Roger</surname>
<given-names>Isabelle</given-names>
</name>
<xref ref-type="aff" rid="A24">24</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Williams</surname>
<given-names>Christopher J</given-names>
</name>
<xref ref-type="aff" rid="A43">43</xref>
<xref ref-type="aff" rid="A35">35</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Yattara</surname>
<given-names>Facinet</given-names>
</name>
<xref ref-type="aff" rid="A26">26</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lewandowski</surname>
<given-names>Kuiama</given-names>
</name>
<xref ref-type="aff" rid="A11">11</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Taylor</surname>
<given-names>Jamie</given-names>
</name>
<xref ref-type="aff" rid="A27">27</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rachwal</surname>
<given-names>Philip</given-names>
</name>
<xref ref-type="aff" rid="A27">27</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Turner</surname>
<given-names>Daniel</given-names>
</name>
<xref ref-type="aff" rid="A28">28</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Pollakis</surname>
<given-names>Georgios</given-names>
</name>
<xref ref-type="aff" rid="A10">10</xref>
<xref ref-type="aff" rid="A45">45</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hiscox</surname>
<given-names>Julian A.</given-names>
</name>
<xref ref-type="aff" rid="A10">10</xref>
<xref ref-type="aff" rid="A45">45</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Matthews</surname>
<given-names>David A.</given-names>
</name>
<xref ref-type="aff" rid="A30">30</xref>
</contrib>
<contrib contrib-type="author"><name><surname>O’Shea</surname>
<given-names>Matthew K.</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
<xref ref-type="aff" rid="A46">46</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Johnston</surname>
<given-names>Andrew McD</given-names>
</name>
<xref ref-type="aff" rid="A46">46</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wilson</surname>
<given-names>Duncan</given-names>
</name>
<xref ref-type="aff" rid="A46">46</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hutley</surname>
<given-names>Emma</given-names>
</name>
<xref ref-type="aff" rid="A47">47</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Smit</surname>
<given-names>Erasmus</given-names>
</name>
<xref ref-type="aff" rid="A48">48</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Di Caro</surname>
<given-names>Antonino</given-names>
</name>
<xref ref-type="aff" rid="A31">31</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Woelfel</surname>
<given-names>Roman</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A32">32</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Stoecker</surname>
<given-names>Kilian</given-names>
</name>
<xref ref-type="aff" rid="A3">3</xref>
<xref ref-type="aff" rid="A32">32</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Fleischmann</surname>
<given-names>Erna</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A32">32</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gabriel</surname>
<given-names>Martin</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Weller</surname>
<given-names>Simon A.</given-names>
</name>
<xref ref-type="aff" rid="A27">27</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Koivogui</surname>
<given-names>Lamine</given-names>
</name>
<xref ref-type="aff" rid="A25">25</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Diallo</surname>
<given-names>Boubacar</given-names>
</name>
<xref ref-type="aff" rid="A24">24</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Keita</surname>
<given-names>Sakoba</given-names>
</name>
<xref ref-type="aff" rid="A26">26</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rambaut</surname>
<given-names>Andrew</given-names>
</name>
<xref ref-type="aff" rid="A5">5</xref>
<xref ref-type="aff" rid="A33">33</xref>
<xref ref-type="aff" rid="A34">34</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Formenty</surname>
<given-names>Pierre</given-names>
</name>
<xref ref-type="aff" rid="A24">24</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gunther</surname>
<given-names>Stephan</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Carroll</surname>
<given-names>Miles W.</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
<xref ref-type="aff" rid="A11">11</xref>
<xref ref-type="aff" rid="A36">36</xref>
<xref ref-type="aff" rid="A49">49</xref>
</contrib>
</contrib-group>
<aff id="A1"><label>(1)</label>
Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK</aff>
<aff id="A2"><label>(2)</label>
The European Mobile Laboratory Consortium, Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany</aff>
<aff id="A3"><label>(3)</label>
Bernhard-Nocht-Institute for Tropical Medicine, D-20359 Hamburg, Germany</aff>
<aff id="A4"><label>(4)</label>
National Infection Service, Public Health England, London, UK</aff>
<aff id="A5"><label>(5)</label>
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 2FL, UK</aff>
<aff id="A6"><label>(6)</label>
Postgraduate Training for Applied Epidemiology (PAE, German FETP), Robert Koch Institute, Berlin, Germany</aff>
<aff id="A7"><label>(7)</label>
Swiss Tropical and Public Health Institute, Basel, Switzerland</aff>
<aff id="A8"><label>(8)</label>
Robert Koch Institute, Berlin, Germany</aff>
<aff id="A9"><label>(9)</label>
University College London, London, UK</aff>
<aff id="A10"><label>(10)</label>
Institute of Infection and Global Health, University of Liverpool, Liverpool, UK</aff>
<aff id="A11"><label>(11)</label>
Public Health England, Porton Down, Wiltshire SP4 0JG, UK</aff>
<aff id="A12"><label>(12)</label>
Friedrich-Loeffler-Institute, Greifswald, Germany</aff>
<aff id="A13"><label>(13)</label>
Spiez Laboratory, Spiez, Switzerland</aff>
<aff id="A14"><label>(14)</label>
Janssen-Cilag, Stockholm, Sweden</aff>
<aff id="A15"><label>(15)</label>
Public Health Agency of Canada, Winnipeg, Canada</aff>
<aff id="A16"><label>(16)</label>
Institut Pasteur Dakar, Dakar, Senegal</aff>
<aff id="A17"><label>(17)</label>
Laboratoire de Fièvres Hémorragiques de Guinée, Conakry, Guinea</aff>
<aff id="A18"><label>(18)</label>
Sandia National Laboratories, Albuquerque, New Mexico, USA</aff>
<aff id="A19"><label>(19)</label>
Ratoma Ebola Diagnostic Center, Conakry, Guinea</aff>
<aff id="A20"><label>(20)</label>
MRIGlobal, Kansas City, USA</aff>
<aff id="A21"><label>(21)</label>
Expertise France, Laboratoire K-plan de Forecariah en Guinée, Paris, France</aff>
<aff id="A22"><label>(22)</label>
Fédération des Laboratoires - HIA Bégin, Paris, France</aff>
<aff id="A23"><label>(23)</label>
Laboratoire de Biologie - Centre de Traitement des Soignants, Conakry, Guinée</aff>
<aff id="A24"><label>(24)</label>
World Health Organization, Conakry, Guinea</aff>
<aff id="A25"><label>(25)</label>
Institut National de Santé Publique, Conakry, Guinea</aff>
<aff id="A26"><label>(26)</label>
Ministry of Health Guinea, Conakry, Guinea</aff>
<aff id="A27"><label>(27)</label>
Defence Science and Technology Laboratory (Dstl) Porton Down, Salisbury SP4 0JQ, UK</aff>
<aff id="A28"><label>(28)</label>
Oxford Nanopore Technologies, Oxford, UK</aff>
<aff id="A29"><label>(29)</label>
Ontario Institute for Cancer Research, Toronto, Canada</aff>
<aff id="A30"><label>(30)</label>
Department of Cellular and Molecular Medicine, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK</aff>
<aff id="A31"><label>(31)</label>
National Institute for Infectious Diseases L. Spallanzani, Rome, Italy</aff>
<aff id="A32"><label>(32)</label>
Bundeswehr Institute of Microbiology, Munich, Germany</aff>
<aff id="A33"><label>(33)</label>
Fogarty International Center, National Institutes of Health, Bethesda, USA</aff>
<aff id="A34"><label>(34)</label>
Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh EH9 2FL, UK</aff>
<aff id="A35"><label>(35)</label>
European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden</aff>
<aff id="A36"><label>(36)</label>
University of Southampton, South General Hospital, Southampton SO16 6YD, UK</aff>
<aff id="A37"><label>(37)</label>
Paul-Ehrlich-Institut, Division of Veterinary Medicine, Langen, Germany</aff>
<aff id="A38"><label>(38)</label>
Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, KU Leuven, Belgium</aff>
<aff id="A39"><label>(39)</label>
Kenya Medical Research Institute, Nairobi, Kenya</aff>
<aff id="A40"><label>(40)</label>
Institute of Virology, Technische Universität München, Munich, Germany</aff>
<aff id="A41"><label>(41)</label>
Norwegian Institute of Public Health, Oslo, Norway</aff>
<aff id="A42"><label>(42)</label>
London School of Hygiene and Tropical Medicine, London, UK</aff>
<aff id="A43"><label>(43)</label>
Public Health Wales, Cardiff, UK</aff>
<aff id="A44"><label>(44)</label>
Department of Computer Science, University of Toronto, Toronto, Canada</aff>
<aff id="A45"><label>(45)</label>
NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, L69 7BE</aff>
<aff id="A46"><label>(46)</label>
Academic Department of Military Medicine, Royal Centre for Defence Medicine, Birmingham, UK</aff>
<aff id="A47"><label>(47)</label>
Centre of Defence Pathology, Royal Centre of Defence Medicine, Birmingham UK.</aff>
<aff id="A48"><label>(48)</label>
Queen Elizabeth Hospital, Birmingham, UK</aff>
<aff id="A49"><label>(49)</label>
NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, PHE Porton Down, UK</aff>
<author-notes><corresp id="CR1">Manuscript correspondence should be directed to Nicholas James Loman (<email>n.j.loman@bham.ac.uk</email>
)</corresp>
<fn id="FN1"><p id="P1"><bold>Author contributions</bold>
</p>
<p id="P2">N.L., J.Q., M.O’S, D.W., S.G., M.W.C. conceived the study. N.L., J.Q., M.O'S., S.W., J.T., P.R., D.T. designed the lab in a suitcase and laboratory protocol and initial validation. J.Q., S.D., L.C., J.B., R.K., L.E.F., and A.M. performed MinION sequencing. N.L., J.Q. and J.T.S. performed bioinformatics analysis and wrote software. J.T.S. added variant calling support to the nanopolish software. N.L., J.Q., S.D., E.S., P.F., L.C., A.M., N.M. and I.R. analysed the data. G.D., A.R., N.L., J.Q. and G.P. performed phylogenetic analysis. J.H., D.M., G.P., K.L., B.A. assisted further validation experiments. M.W.C., M.G., S.G., A.D.C., K.S., E.F. and R.W. coordinated activities for the European Mobile Laboratories. N.L., J.Q., S.D., M.W.C., S.G., M.O’Shea, A.R., E.S., P.F., I.R., A.M., and L.C. wrote the manuscript. All other authors were involved either in sample collection, and/or logistical support and strategic oversight for the work.</p>
</fn>
</author-notes>
<pub-date pub-type="nihms-submitted"><day>25</day>
<month>2</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="epub"><day>03</day>
<month>2</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="ppub"><day>11</day>
<month>2</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>11</day>
<month>8</month>
<year>2016</year>
</pub-date>
<volume>530</volume>
<issue>7589</issue>
<fpage>228</fpage>
<lpage>232</lpage>
<pmc-comment>elocation-id from pubmed: 10.1038/nature16996</pmc-comment>
<permissions><license><license-p>Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:<uri xlink:type="simple" xlink:href="http://www.nature.com/authors/editorial_policies/license.html#terms">http://www.nature.com/authors/editorial_policies/license.html#terms</uri>
</license-p>
</license>
</permissions>
<abstract><p id="P3">The Ebola virus disease (EVD) epidemic in West Africa is the largest on record, responsible for >28,599 cases and >11,299 deaths <sup><xref rid="R1" ref-type="bibr">1</xref>
</sup>
. Genome sequencing in viral outbreaks is desirable in order to characterize the infectious agent to determine its evolutionary rate, signatures of host adaptation, identification and monitoring of diagnostic targets and responses to vaccines and treatments. The Ebola virus genome (EBOV) substitution rate in the Makona strain has been estimated at between 0.87 × 10<sup>−3</sup>
to 1.42 × 10<sup>−3</sup>
mutations per site per year. This is equivalent to 16 to 27 mutations in each genome, meaning that sequences diverge rapidly enough to identify distinct sub-lineages during a prolonged epidemic <sup><xref rid="R2" ref-type="bibr">2</xref>
-<xref rid="R7" ref-type="bibr">7</xref>
</sup>
. Genome sequencing provides a high-resolution view of pathogen evolution and is increasingly sought-after for outbreak surveillance. Sequence data may be used to guide control measures, but only if the results are generated quickly enough to inform interventions <sup><xref rid="R8" ref-type="bibr">8</xref>
</sup>
. Genomic surveillance during the epidemic has been sporadic due to a lack of local sequencing capacity coupled with practical difficulties transporting samples to remote sequencing facilities <sup><xref rid="R9" ref-type="bibr">9</xref>
</sup>
. In order to address this problem, we devised a genomic surveillance system that utilizes a novel nanopore DNA sequencing instrument. In April 2015 this system was transported in standard airline luggage to Guinea and used for real-time genomic surveillance of the ongoing epidemic. Here we present sequence data and analysis of 142 Ebola virus (EBOV) samples collected during the period March to October 2015. We were able to generate results in less than 24 hours after receiving an Ebola positive sample, with the sequencing process taking as little as 15-60 minutes. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.</p>
</abstract>
</article-meta>
</front>
<floats-group><fig id="F1" orientation="portrait" position="float"><label>Figure 1</label>
<caption><title>Deployment of the portable genome surveillance system in Guinea</title>
<p>We were able to pack all instruments, reagents and disposable consumables within aircraft baggage (<bold>Panel A</bold>
). We initially established the genomic surveillance laboratory in Donka Hospital, Conakry (<bold>Panel B</bold>
). Later we moved the laboratory to a dedicated sequencing laboratory in Coyah prefecture (<bold>Panel C</bold>
). Within this laboratory (<bold>Panel</bold>
D) we separated the sequencing instruments (on the left) from the PCR bench (to the right). An uninterruptable power supply can be seen in the middle which provides power to the thermocycler. (Photographs taken by Josh Quick and Sophie Duraffour.)</p>
</caption>
<graphic xlink:href="emss-66776-f0001"></graphic>
</fig>
<fig id="F2" orientation="portrait" position="float"><label>Figure 2</label>
<caption><title>Real-time genomics surveillance in context of the Guinea EVD epidemic</title>
<p>Here we show the number of reported cases of EVD in Guinea (red) in relation to the number of EBOV new patient samples (<italic>n</italic>
=137, in blue) generated during this study (<bold>Panel A</bold>
). For each of the 142 sequenced samples, we show the relationship between sample collection date (red) and the date of sequencing (blue) (<bold>Panel B</bold>
). Twenty-eight samples were sequenced within three days of the sample being taken, and sixty-eight samples within a week. Larger gaps represent retrospective sequencing of cases to provide additional epidemiological context.</p>
</caption>
<graphic xlink:href="emss-66776-f0002"></graphic>
</fig>
<fig id="F3" orientation="portrait" position="float"><label>Figure 3</label>
<caption><title>Evolution of EBOV over the course of the EVD epidemic</title>
<p>Time-scaled phylogeny of 603 published sequences with 125 high quality sequences from this study (<bold>Panel A</bold>
). The shape of nodes on the tree demonstrates country of origin. Our results show Guinean samples (coloured circles) belong to two previously identified lineages, GN1 and SL3. GN1 is deeply branching with early epidemic samples (<bold>Panel B</bold>
). SL3 is related to cases identified in Sierra Leone (<bold>Panel C</bold>
). Samples are frequently clustered by geography (indicated by colour of circle) and this provides information as to origins of new introductions, such as in the Boké epidemic in May 2015. Map figure adapted from SimpleMaps website (<ext-link ext-link-type="uri" xlink:href="http://simplemaps.com/resources/svg-gn">http://simplemaps.com/resources/svg-gn</ext-link>
).</p>
</caption>
<graphic xlink:href="emss-66776-f0003"></graphic>
</fig>
</floats-group>
</pmc>
<affiliations><list></list>
<tree><noCountry><name sortKey="Afrough, Babak" sort="Afrough, Babak" uniqKey="Afrough B" first="Babak" last="Afrough">Babak Afrough</name>
<name sortKey="Amburgey, Victoria" sort="Amburgey, Victoria" uniqKey="Amburgey V" first="Victoria" last="Amburgey">Victoria Amburgey</name>
<name sortKey="Bado, Guillaume" sort="Bado, Guillaume" uniqKey="Bado G" first="Guillaume" last="Bado">Guillaume Bado</name>
<name sortKey="Bah, Amadou" sort="Bah, Amadou" uniqKey="Bah A" first="Amadou" last="Bah">Amadou Bah</name>
<name sortKey="Baillet, Bernard" sort="Baillet, Bernard" uniqKey="Baillet B" first="Bernard" last="Baillet">Bernard Baillet</name>
<name sortKey="Baum, Jonathan Hj" sort="Baum, Jonathan Hj" uniqKey="Baum J" first="Jonathan Hj" last="Baum">Jonathan Hj Baum</name>
<name sortKey="Becker Ziaja, Beate" sort="Becker Ziaja, Beate" uniqKey="Becker Ziaja B" first="Beate" last="Becker-Ziaja">Beate Becker-Ziaja</name>
<name sortKey="Bello, Alexander" sort="Bello, Alexander" uniqKey="Bello A" first="Alexander" last="Bello">Alexander Bello</name>
<name sortKey="Bererd, Marion" sort="Bererd, Marion" uniqKey="Bererd M" first="Marion" last="Bererd">Marion Bererd</name>
<name sortKey="Boettcher, Jan Peter" sort="Boettcher, Jan Peter" uniqKey="Boettcher J" first="Jan-Peter" last="Boettcher">Jan-Peter Boettcher</name>
<name sortKey="Bore, Joseph Akoi" sort="Bore, Joseph Akoi" uniqKey="Bore J" first="Joseph Akoi" last="Bore">Joseph Akoi Bore</name>
<name sortKey="Cabeza Cabrerizo, Mar" sort="Cabeza Cabrerizo, Mar" uniqKey="Cabeza Cabrerizo M" first="Mar" last="Cabeza-Cabrerizo">Mar Cabeza-Cabrerizo</name>
<name sortKey="Camara, Abdoulaye" sort="Camara, Abdoulaye" uniqKey="Camara A" first="Abdoulaye" last="Camara">Abdoulaye Camara</name>
<name sortKey="Camara, Alimou" sort="Camara, Alimou" uniqKey="Camara A" first="Alimou" last="Camara">Alimou Camara</name>
<name sortKey="Camino Sanchez, Alvaro" sort="Camino Sanchez, Alvaro" uniqKey="Camino Sanchez A" first="Alvaro" last="Camino-Sanchez">Alvaro Camino-Sanchez</name>
<name sortKey="Carroll, Miles W" sort="Carroll, Miles W" uniqKey="Carroll M" first="Miles W." last="Carroll">Miles W. Carroll</name>
<name sortKey="Carter, Lisa L" sort="Carter, Lisa L" uniqKey="Carter L" first="Lisa L." last="Carter">Lisa L. Carter</name>
<name sortKey="Cowley, Lauren" sort="Cowley, Lauren" uniqKey="Cowley L" first="Lauren" last="Cowley">Lauren Cowley</name>
<name sortKey="Davis, Emily" sort="Davis, Emily" uniqKey="Davis E" first="Emily" last="Davis">Emily Davis</name>
<name sortKey="Delaune, Deborah" sort="Delaune, Deborah" uniqKey="Delaune D" first="Déborah" last="Delaune">Déborah Delaune</name>
<name sortKey="Di Caro, Antonino" sort="Di Caro, Antonino" uniqKey="Di Caro A" first="Antonino" last="Di Caro">Antonino Di Caro</name>
<name sortKey="Diallo, Boubacar" sort="Diallo, Boubacar" uniqKey="Diallo B" first="Boubacar" last="Diallo">Boubacar Diallo</name>
<name sortKey="Diarra, Abdoulaye" sort="Diarra, Abdoulaye" uniqKey="Diarra A" first="Abdoulaye" last="Diarra">Abdoulaye Diarra</name>
<name sortKey="Doerrbecker, Juiliane" sort="Doerrbecker, Juiliane" uniqKey="Doerrbecker J" first="Juiliane" last="Doerrbecker">Juiliane Doerrbecker</name>
<name sortKey="Dorival, Isabel Graciela Garcia" sort="Dorival, Isabel Graciela Garcia" uniqKey="Dorival I" first="Isabel Graciela García" last="Dorival">Isabel Graciela García Dorival</name>
<name sortKey="Dudas, Gytis" sort="Dudas, Gytis" uniqKey="Dudas G" first="Gytis" last="Dudas">Gytis Dudas</name>
<name sortKey="Duraffour, Sophie" sort="Duraffour, Sophie" uniqKey="Duraffour S" first="Sophie" last="Duraffour">Sophie Duraffour</name>
<name sortKey="Enkirch, Theresa" sort="Enkirch, Theresa" uniqKey="Enkirch T" first="Theresa" last="Enkirch">Theresa Enkirch</name>
<name sortKey="Faye, Oumar" sort="Faye, Oumar" uniqKey="Faye O" first="Oumar" last="Faye">Oumar Faye</name>
<name sortKey="Faye, Ousmane" sort="Faye, Ousmane" uniqKey="Faye O" first="Ousmane" last="Faye">Ousmane Faye</name>
<name sortKey="Fleischmann, Erna" sort="Fleischmann, Erna" uniqKey="Fleischmann E" first="Erna" last="Fleischmann">Erna Fleischmann</name>
<name sortKey="Formenty, Pierre" sort="Formenty, Pierre" uniqKey="Formenty P" first="Pierre" last="Formenty">Pierre Formenty</name>
<name sortKey="Gabriel, Martin" sort="Gabriel, Martin" uniqKey="Gabriel M" first="Martin" last="Gabriel">Martin Gabriel</name>
<name sortKey="Gerard, Marianne" sort="Gerard, Marianne" uniqKey="Gerard M" first="Marianne" last="Gerard">Marianne Gerard</name>
<name sortKey="Gerlach, Jon" sort="Gerlach, Jon" uniqKey="Gerlach J" first="Jon" last="Gerlach">Jon Gerlach</name>
<name sortKey="Gunther, Stephan" sort="Gunther, Stephan" uniqKey="Gunther S" first="Stephan" last="Gunther">Stephan Gunther</name>
<name sortKey="Gutierrez, Giovanna Jaramillo" sort="Gutierrez, Giovanna Jaramillo" uniqKey="Gutierrez G" first="Giovanna Jaramillo" last="Gutierrez">Giovanna Jaramillo Gutierrez</name>
<name sortKey="Hetzelt, Nicole" sort="Hetzelt, Nicole" uniqKey="Hetzelt N" first="Nicole" last="Hetzelt">Nicole Hetzelt</name>
<name sortKey="Hinzmann, Julia" sort="Hinzmann, Julia" uniqKey="Hinzmann J" first="Julia" last="Hinzmann">Julia Hinzmann</name>
<name sortKey="Hiscox, Julian A" sort="Hiscox, Julian A" uniqKey="Hiscox J" first="Julian A." last="Hiscox">Julian A. Hiscox</name>
<name sortKey="Holm, Tobias" sort="Holm, Tobias" uniqKey="Holm T" first="Tobias" last="Holm">Tobias Holm</name>
<name sortKey="Hutley, Emma" sort="Hutley, Emma" uniqKey="Hutley E" first="Emma" last="Hutley">Emma Hutley</name>
<name sortKey="Johnston, Andrew Mcd" sort="Johnston, Andrew Mcd" uniqKey="Johnston A" first="Andrew Mcd" last="Johnston">Andrew Mcd Johnston</name>
<name sortKey="Jourdain, Marine" sort="Jourdain, Marine" uniqKey="Jourdain M" first="Marine" last="Jourdain">Marine Jourdain</name>
<name sortKey="Kafetzopoulou, Liana Eleni" sort="Kafetzopoulou, Liana Eleni" uniqKey="Kafetzopoulou L" first="Liana Eleni" last="Kafetzopoulou">Liana Eleni Kafetzopoulou</name>
<name sortKey="Keita, Sakoba" sort="Keita, Sakoba" uniqKey="Keita S" first="Sakoba" last="Keita">Sakoba Keita</name>
<name sortKey="Koivogui, Lamine" sort="Koivogui, Lamine" uniqKey="Koivogui L" first="Lamine" last="Koivogui">Lamine Koivogui</name>
<name sortKey="Koropogui, Michel" sort="Koropogui, Michel" uniqKey="Koropogui M" first="Michel" last="Koropogui">Michel Koropogui</name>
<name sortKey="Kosgey, Abigail" sort="Kosgey, Abigail" uniqKey="Kosgey A" first="Abigail" last="Kosgey">Abigail Kosgey</name>
<name sortKey="Koundouno, Raymond" sort="Koundouno, Raymond" uniqKey="Koundouno R" first="Raymond" last="Koundouno">Raymond Koundouno</name>
<name sortKey="Kuisma, Eeva" sort="Kuisma, Eeva" uniqKey="Kuisma E" first="Eeva" last="Kuisma">Eeva Kuisma</name>
<name sortKey="Lewandowski, Kuiama" sort="Lewandowski, Kuiama" uniqKey="Lewandowski K" first="Kuiama" last="Lewandowski">Kuiama Lewandowski</name>
<name sortKey="Logue, Christopher H" sort="Logue, Christopher H" uniqKey="Logue C" first="Christopher H" last="Logue">Christopher H. Logue</name>
<name sortKey="Loman, Nicholas J" sort="Loman, Nicholas J" uniqKey="Loman N" first="Nicholas J." last="Loman">Nicholas J. Loman</name>
<name sortKey="Magassouba, N Aly" sort="Magassouba, N Aly" uniqKey="Magassouba N" first="N Aly" last="Magassouba">N Aly Magassouba</name>
<name sortKey="Matthews, David A" sort="Matthews, David A" uniqKey="Matthews D" first="David A." last="Matthews">David A. Matthews</name>
<name sortKey="Mazzarelli, Antonio" sort="Mazzarelli, Antonio" uniqKey="Mazzarelli A" first="Antonio" last="Mazzarelli">Antonio Mazzarelli</name>
<name sortKey="Meisel, Sarah" sort="Meisel, Sarah" uniqKey="Meisel S" first="Sarah" last="Meisel">Sarah Meisel</name>
<name sortKey="Mertens, Marc" sort="Mertens, Marc" uniqKey="Mertens M" first="Marc" last="Mertens">Marc Mertens</name>
<name sortKey="Michel, Janine" sort="Michel, Janine" uniqKey="Michel J" first="Janine" last="Michel">Janine Michel</name>
<name sortKey="Mikhail, Amy" sort="Mikhail, Amy" uniqKey="Mikhail A" first="Amy" last="Mikhail">Amy Mikhail</name>
<name sortKey="Milhano, Natacha" sort="Milhano, Natacha" uniqKey="Milhano N" first="Natacha" last="Milhano">Natacha Milhano</name>
<name sortKey="Monteil, Vanessa" sort="Monteil, Vanessa" uniqKey="Monteil V" first="Vanessa" last="Monteil">Vanessa Monteil</name>
<name sortKey="Nebie, Koumpingnin Yacouba" sort="Nebie, Koumpingnin Yacouba" uniqKey="Nebie K" first="Koumpingnin Yacouba" last="Nebie">Koumpingnin Yacouba Nebie</name>
<name sortKey="Ngabo, Didier" sort="Ngabo, Didier" uniqKey="Ngabo D" first="Didier" last="Ngabo">Didier Ngabo</name>
<name sortKey="Nitzsche, Katja" sort="Nitzsche, Katja" uniqKey="Nitzsche K" first="Katja" last="Nitzsche">Katja Nitzsche</name>
<name sortKey="O Hea, Matthew K" sort="O Hea, Matthew K" uniqKey="O Hea M" first="Matthew K." last="O Hea">Matthew K. O Hea</name>
<name sortKey="Ouedraogo, Nobila" sort="Ouedraogo, Nobila" uniqKey="Ouedraogo N" first="Nobila" last="Ouédraogo">Nobila Ouédraogo</name>
<name sortKey="Pallash, Elisa" sort="Pallash, Elisa" uniqKey="Pallash E" first="Elisa" last="Pallash">Elisa Pallash</name>
<name sortKey="Pallawo, Raymond Bernard" sort="Pallawo, Raymond Bernard" uniqKey="Pallawo R" first="Raymond Bernard" last="Pallawo">Raymond Bernard Pallawo</name>
<name sortKey="Patrono, Livia Victoria" sort="Patrono, Livia Victoria" uniqKey="Patrono L" first="Livia Victoria" last="Patrono">Livia Victoria Patrono</name>
<name sortKey="Pollakis, Georgios" sort="Pollakis, Georgios" uniqKey="Pollakis G" first="Georgios" last="Pollakis">Georgios Pollakis</name>
<name sortKey="Portmann, Jasmine" sort="Portmann, Jasmine" uniqKey="Portmann J" first="Jasmine" last="Portmann">Jasmine Portmann</name>
<name sortKey="Quick, Joshua" sort="Quick, Joshua" uniqKey="Quick J" first="Joshua" last="Quick">Joshua Quick</name>
<name sortKey="Rachwal, Philip" sort="Rachwal, Philip" uniqKey="Rachwal P" first="Philip" last="Rachwal">Philip Rachwal</name>
<name sortKey="Rambaut, Andrew" sort="Rambaut, Andrew" uniqKey="Rambaut A" first="Andrew" last="Rambaut">Andrew Rambaut</name>
<name sortKey="Repits, Johanna Gabriella" sort="Repits, Johanna Gabriella" uniqKey="Repits J" first="Johanna Gabriella" last="Repits">Johanna Gabriella Repits</name>
<name sortKey="Rickett, Natasha Yasmin" sort="Rickett, Natasha Yasmin" uniqKey="Rickett N" first="Natasha Yasmin" last="Rickett">Natasha Yasmin Rickett</name>
<name sortKey="Roger, Isabelle" sort="Roger, Isabelle" uniqKey="Roger I" first="Isabelle" last="Roger">Isabelle Roger</name>
<name sortKey="Sachse, Andrea" sort="Sachse, Andrea" uniqKey="Sachse A" first="Andrea" last="Sachse">Andrea Sachse</name>
<name sortKey="Sall, Amadou Alpha" sort="Sall, Amadou Alpha" uniqKey="Sall A" first="Amadou Alpha" last="Sall">Amadou Alpha Sall</name>
<name sortKey="Savane, Yacouba" sort="Savane, Yacouba" uniqKey="Savane Y" first="Yacouba" last="Savane">Yacouba Savane</name>
<name sortKey="Severi, Ettore" sort="Severi, Ettore" uniqKey="Severi E" first="Ettore" last="Severi">Ettore Severi</name>
<name sortKey="Simpson, Jared T" sort="Simpson, Jared T" uniqKey="Simpson J" first="Jared T." last="Simpson">Jared T. Simpson</name>
<name sortKey="Singethan, Katrin" sort="Singethan, Katrin" uniqKey="Singethan K" first="Katrin" last="Singethan">Katrin Singethan</name>
<name sortKey="Smit, Erasmus" sort="Smit, Erasmus" uniqKey="Smit E" first="Erasmus" last="Smit">Erasmus Smit</name>
<name sortKey="Somlare, Hermann" sort="Somlare, Hermann" uniqKey="Somlare H" first="Hermann" last="Somlare">Hermann Somlare</name>
<name sortKey="Stoecker, Kilian" sort="Stoecker, Kilian" uniqKey="Stoecker K" first="Kilian" last="Stoecker">Kilian Stoecker</name>
<name sortKey="Taylor, Jamie" sort="Taylor, Jamie" uniqKey="Taylor J" first="Jamie" last="Taylor">Jamie Taylor</name>
<name sortKey="Trina, Racine" sort="Trina, Racine" uniqKey="Trina R" first="Racine" last="Trina">Racine Trina</name>
<name sortKey="Turner, Daniel" sort="Turner, Daniel" uniqKey="Turner D" first="Daniel" last="Turner">Daniel Turner</name>
<name sortKey="Vitoriano, Ines" sort="Vitoriano, Ines" uniqKey="Vitoriano I" first="Inês" last="Vitoriano">Inês Vitoriano</name>
<name sortKey="Washington, Franck" sort="Washington, Franck" uniqKey="Washington F" first="Franck" last="Washington">Franck Washington</name>
<name sortKey="Weller, Simon A" sort="Weller, Simon A" uniqKey="Weller S" first="Simon A." last="Weller">Simon A. Weller</name>
<name sortKey="Williams, Cecelia V" sort="Williams, Cecelia V" uniqKey="Williams C" first="Cecelia V." last="Williams">Cecelia V. Williams</name>
<name sortKey="Williams, Christopher J" sort="Williams, Christopher J" uniqKey="Williams C" first="Christopher J" last="Williams">Christopher J. Williams</name>
<name sortKey="Wilson, Duncan" sort="Wilson, Duncan" uniqKey="Wilson D" first="Duncan" last="Wilson">Duncan Wilson</name>
<name sortKey="Winona, Linda" sort="Winona, Linda" uniqKey="Winona L" first="Linda" last="Winona">Linda Winona</name>
<name sortKey="Woelfel, Roman" sort="Woelfel, Roman" uniqKey="Woelfel R" first="Roman" last="Woelfel">Roman Woelfel</name>
<name sortKey="Yattara, Facinet" sort="Yattara, Facinet" uniqKey="Yattara F" first="Facinet" last="Yattara">Facinet Yattara</name>
<name sortKey="Yemanaberhan, Rahel L" sort="Yemanaberhan, Rahel L" uniqKey="Yemanaberhan R" first="Rahel L" last="Yemanaberhan">Rahel L. Yemanaberhan</name>
<name sortKey="Zekeng, Elsa G" sort="Zekeng, Elsa G" uniqKey="Zekeng E" first="Elsa G" last="Zekeng">Elsa G. Zekeng</name>
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</tree>
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</record>
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