BioHealthBase: informatics support in the elucidation of influenza virus host–pathogen interactions and virulence

Abstract

The BioHealthBase Bioinformatics Resource Center (BRC) (http://www.biohealthbase.org) is a public bioinformatics database and analysis resource for the study of specific biodefense and public health pathogens—Influenza virus, Francisella tularensis, Mycobacterium tuberculosis, Microsporidia species and ricin toxin. The BioHealthBase serves as an extensive integrated repository of data imported from public databases, data derived from various computational algorithms and information curated from the scientific literature. The goal of the BioHealthBase is to facilitate the development of therapeutics, diagnostics and vaccines by integrating all available data in the context of host–pathogen interactions, thus allowing researchers to understand the root causes of virulence and pathogenicity. Genome and protein annotations can be viewed either as formatted text or graphically through a genome browser. 3D visualization capabilities allow researchers to view proteins with key structural and functional features highlighted. Influenza virus host–pathogen interactions at the molecular/cellular and systemic levels are represented. Host immune response to influenza infection is conveyed through the display of experimentally determined antibody and T-cell epitopes curated from the scientific literature or as derived from computational predictions. At the molecular/cellular level, the BioHealthBase BRC has developed biological pathway representations relevant to influenza virus host–pathogen interaction in collaboration with the Reactome database (http://www.reactome.org).

Highly Pathogenic Avian Influenza Virus Subtype H5N1 Escaping Neutralization: More than HA Variation

“…The reference three-dimensional (3D) structure (accession no. 2FFP) was obtained from the NIAID Influenza Research Database (IRD) through the website at http://www.fludb.org (39). For visualization of the altered amino acids, Jmol (http://www.fludb.org) was used.…”

PB2 Residue 271 Plays a Key Role in Enhanced Polymerase Activity of Influenza A Viruses in Mammalian Host Cells

“…To further evaluate the potential role of residue 271 in swine influenza infection, we next collected 220 full-length PB2 sequences of swine influenza viruses from the Influenza Research Database (41) and examined the residues at positions 271, 627, and 701 (Table 2). Among the swine viruses that contain 627E, 51% have 271A and 28% contain 701N, suggesting that these two residues can compensate for the lack of 627K in PB2.…”

Computational analysis in Influenza virus

“…The Influenza Research Database (IRD) is paying attention to data related to influenza virus. IRD is distinctive in the size and intensity of the data and analysis tools provided and in its approach to data and workflow integration that aid in the development of vaccines, therapeutics, and diagnostics [3] . A number of influenza-focused web-accessible databases exist: the NCBI Influenza Virus Resource (IVR) [8] , Global Initiative on Sharing Avian Influenza Data (GISAID) EpiFlu Database [9] , Korea Influenza Sequence & Epitope Database (KISED) [10] , the Influenza Virus Database (IVDB) [11] , and the OpenFlu Database [12] .…”

“…Furthermore, during the 20th century, three major influenza pandemics have taken place with a total mortality of 50 -100 million people [2] . The recent appearance of the 2009 pandemic influenza A⁄H1N1 virus has decorated the cost of free and undoes access to influenza virus genome sequence data integrated with information about other significant virus characteristics [3] . Influenza belongs to the genus orthomyxovirus in the family of Orthomyxoviridae.…”