Dataset Information

Analysis and visualization of H7 influenza using genomic, evolutionary and geographic information in a modular web service.

ABSTRACT: We have reported previously on use of a web-based application, Supramap (http://supramap.org) for the study of biogeographic, genotypic, and phenotypic evolution. Using Supramap we have developed maps of the spread of drug-resistant influenza and host shifts in H1N1 and H5N1 influenza and coronaviruses such as SARS. Here we report on another zoonotic pathogen, H7 influenza, and provide an update on the implementation of Supramap as a web service. We find that the emergence of pathogenic strains of H7 is labile with many transitions from high to low pathogenicity, and from low to high pathogenicity. We use Supramap to put these events in a temporal and geospatial context. We identify several lineages of H7 influenza with biomarkers of high pathogenicity in regions that have not been reported in the scientific literature. The original implementation of Supramap was built with tightly coupled client and server software. Now we have decoupled the components to provide a modular web service for POY (http://poyws.org) that can be consumed by a data provider to create a novel application. To demonstrate the web service, we have produced an application, Geogenes (http://geogenes.org). Unlike in Supramap, in which the user is required to create and upload data files, in Geogenes the user works from a graphical interface to query an underlying dataset. Geogenes demonstrates how the web service can provide underlying processing for any sequence and metadata database. © The Willi Hennig Society 2012.

SUBMITTER: Janies DA

PROVIDER: S-EPMC7162197 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature

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Analysis and visualization of H7 influenza using genomic, evolutionary and geographic information in a modular web service.

Janies Daniel A DA Pomeroy Laura W LW Aaronson Jacob M JM Handelman Samuel S Hardman Jori J Kawalec Kevin K Bitterman Thomas T Wheeler Ward C WC

Cladistics : the international journal of the Willi Hennig Society 20120521 5

We have reported previously on use of a web-based application, Supramap (http://supramap.org) for the study of biogeographic, genotypic, and phenotypic evolution. Using Supramap we have developed maps of the spread of drug-resistant influenza and host shifts in H1N1 and H5N1 influenza and coronaviruses such as SARS. Here we report on another zoonotic pathogen, H7 influenza, and provide an update on the implementation of Supramap as a web service. We find that the emergence of pathogenic strains ...[more]

PMID: 32313365

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Project description:BackgroundNowadays there is a worldwide consensus on the importance of conducting wildlife disease surveillance. Indeed, 60% of emerging infectious diseases are zoonotic in nature, and the majority of these (71.8%) originate in wildlife. Surveillance of wildlife diseases is crucial to prevent negative effects on human and animal health. Data digitization and sharing are among the main goals for the present and coming years. Geographic Information Systems (GIS) are increasingly used to analyze the geographical distribution of diseases and the relationships between pathogenic factors and their geographic environments.MethodsWild animal's samples collected in the Abruzzo and Molise regions and delivered to our laboratory are entered in our Laboratory Information System and processed to be displayed through the Web-GIS mash-up presented in this paper. We built it using both open source and proprietary solutions, to produce data driven interactive maps, charts and tables to help to understand the epidemiology of wild animal diseases, their spread and trend.ResultsSince 2013, 9.606 samples collected from wild animals have been analyzed in the laboratories of the IZS-Teramo and have been recorded in the system, facilitating the reporting to the judicial authorities and the identification of highly risky areas to set up control and repression measures. Moreover, thanks to the monitoring health protocol, a canine distemper epidemic in wolves has been detected and monitored in its temporal and spatial evolution, as well as cases of bovine tuberculosis in wild boars.ConclusionsWhile it is more evident that the starting point is to choose the right sampling method, it is for sure less obvious that the information system in which data is stored is equally important. In fact, it should give the possibility to consult it in an easy and instructive way. GIS allows immediately grasping the spatial relationships between the data itself and those between the data and the territory; it is an important tool to support veterinary services in managing epidemic and non-epidemic emergencies and performing epidemiological investigations, but also to examine control plans and identify new gaps and challenges.

Dataset Information

Analysis and visualization of H7 influenza using genomic, evolutionary and geographic information in a modular web service.

Publications

Analysis and visualization of H7 influenza using genomic, evolutionary and geographic information in a modular web service.

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