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.

Relaciones de estructura-función en la P-glicoproteína humana (ABCB1): Perspectivas de las simulaciones de dinámica molecular

“…En 2002-2003, el coronavirus del síndrome respiratorio agudo severo (SARS-CoV) fue la primera enfermedad infecciosa para la cual, los científicos compartieron software y datos genéticos de patógenos a través de Internet para responder rápidamente a la enfermedad. A partir de entonces, la epidemiología genómica se consolidó con las respuestas a H5N1, H1N1-2009 y otras cepas de influenza como H7N9 [2] y se ha expandido para responder a las enfermedades transmitidas por los alimentos y de transmisión sexual [3][4][5]. El primer genoma del SARS-CoV se compartió después de la publicación [6,7] en el sitio web GenBank del Centro Nacional de Información Biotecnológica (NCBI), lo cual era lo habitual.…”

Phylogenetic visualization of the spread of H7 influenza A viruses

“…The H7 subtype consists of both high and low pathogenic strains (Horimoto and Kawaoka, 2005). Highly pathogenic strains are demarcated by a polybasic cleavage site in the HA segment (Chen et al, 1998;Janies et al, 2012). Furthermore, the H7 subtype is designated by the Office Internationale des Epizooties (2012) as a notifiable disease.…”