title: The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses.
abstract: Combining epidemiological information, genetic characterization and geomapping in the analysis of influenza can contribute to a better understanding and description of influenza epidemiology and ecology, including possible virus reassortment events. Furthermore, integration of information such as agroecological farming system characteristics can provide new knowledge on risk factors of influenza emergence and spread. Integrating viral characteristics into an animal disease information system is therefore expected to provide a unique tool to trace-and-track particular virus strains; generate clade distributions and spatiotemporal clusters; screen for distribution of viruses with specific molecular markers; identify potential risk factors; and analyze or map viral characteristics related to vaccines used for control and/or prevention. For this purpose, a genetic module was developed within EMPRES-i (FAO's global animal disease information system) linking epidemiological information from influenza events with virus characteristics and enabling combined analysis. An algorithm was developed to act as the interface between EMPRES-i disease event data and publicly available influenza virus sequences in OpenfluDB. This algorithm automatically computes potential links between outbreak event and sequences, which are subsequently manually validated by experts. Subsequently, other virus characteristics such as antiviral resistance can then be associated to outbreak data. To visualize such characteristics on a geographic map, shape files with virus characteristics to overlay on other EMPRES-i map layers (e.g. animal densities) can be generated. The genetic module allows export of associated epidemiological and sequence data for further analysis. FAO has made this tool available for scientists and policy makers. Contributions are expected from users to improve and validate the number of linked influenza events and isolate information as well as the quality of information. Possibilities to interconnect with other influenza sequence databases or to expand the genetic module to other viral diseases (e.g. foot and mouth disease) are being explored. Database OpenfluDB URL: http://openflu.vital-it.ch Database EMPRES-i URL: http://EMPRES-i.fao.org/.
authors.affiliation: Animal Health Service, Food and Agriculture Organization of the United Nations (FAO), Viale delle Terme di Caracalla, 10532 Rome, Italy and Vital-IT/Swiss-Prot Groups, SIB, Swiss Institute for Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.
authors.forename: Filip
authors.initials: F
authors.lastname: Claes
authors.forename: Dmitry
authors.initials: D
authors.lastname: Kuznetsov
authors.forename: Robin
authors.initials: R
authors.lastname: Liechti
authors.forename: Sophie
authors.initials: S
authors.lastname: Von Dobschuetz
authors.forename: Bao Dinh
authors.initials: BD
authors.lastname: Truong
authors.forename: Anne
authors.initials: A
authors.lastname: Gleizes
authors.forename: Daniele
authors.initials: D
authors.lastname: Conversa
authors.forename: Alessandro
authors.initials: A
authors.lastname: Colonna
authors.forename: Ettore
authors.initials: E
authors.lastname: Demaio
authors.forename: Sabina
authors.initials: S
authors.lastname: Ramazzotto
authors.forename: Fairouz
authors.initials: F
authors.lastname: Larfaoui
authors.forename: Julio
authors.initials: J
authors.lastname: Pinto
authors.forename: Philippe
authors.initials: P
authors.lastname: Le Mercier
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.forename: Gwenaelle
authors.initials: G
authors.lastname: Dauphin
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D004196:Disease Outbreaks; D006801:Humans; D007251:Influenza, Human / Q000453:epidemiology* / Q000235:genetics / Q000821:virology*; D009975:Orthomyxoviridae / Q000235:genetics* / Q000302:isolation & purification; D015203:Reproducibility of Results