Influenza Research Database: An integrated bioinformatics resource for influenza virus research

Abstract

The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research and development of vaccines, diagnostics and therapeutics against influenza virus by providing a comprehensive collection of influenza-related data integrated from various sources, a growing suite of analysis and visualization tools for data mining and hypothesis generation, personal workbench spaces for data storage and sharing, and active user community support. Here, we describe the recent improvements in IRD including the use of cloud and high performance computing resources, analysis and visualization of user-provided sequence data with associated metadata, predictions of novel variant proteins, annotations of phenotype-associated sequence markers and their predicted phenotypic effects, hemagglutinin (HA) clade classifications, an automated tool for HA subtype numbering conversion, linkouts to disease event data and the addition of host factor and antiviral drug components. All data and tools are freely available without restriction from the IRD website at https://www.fludb.org.

Regional patterns of genetic diversity in swine influenza A viruses in the United States from 2010 to 2016

“…The inferred phylogenetic trees were used to classify H1N1 and H1N2 sequences into previously defined genetic clades: H1‐α, H1‐β, H1‐γ, H1‐γ2, H1pdm09, H1‐ δ1, and H1‐ δ2 . These clades correspond to a recently released a global nomenclature for H1 HA genes from swine IAV . The clade designations are as follows: 1A.1 and 1A.1.1 (H1‐α), 1A.2 (H1‐β), 1A.3.3.3 (H1‐γ), 1A.3.2 (H1‐γ2), 1A.3.3.2 (H1pdm09), 1B.2.2 (H1‐δ1), 1B.2.2.1 (H1‐δ1a), 1B.2.2.2 (H1‐δ1b), and 1B.2.1 (H1‐ δ2).…”

A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses

“…To date, it has been applied successfully to classification of avian HA/H5 sequences, according to the nomenclature of the WHO/OIE/FAO H5N1 Working Group (29), to distinguishing new pandemic 2009 H1 viruses from earlier seasonal H1 viruses in humans and other hosts, and to classifying U.S. swine H1 HA phylogenetic clades. These three applications have been implemented on IRD (30, 31). …”

“…Classification by this web-based tool matched expertly curated, manual classification of the sequences >99% of the time. This tool will be released on the Influenza Research Database (IRD) at http://www.fludb.org (30, 31) to facilitate the adoption of the unified nomenclature.…”

Detection and characterization of an H4N6 avian-lineage influenza A virus in pigs in the Midwestern United States

“…Among the H4 HA sequences detected worldwide, publicly available in the Influenza Research Database, the majority were identified in avian species (2140/2235), a small number were found in mammals (5 in swine, 3 in sea mammals, and 2 in muskrats), 84 were detected in environmental samples and one was of unknown origin (Zhang et al, 2017). Pigs were experimentally challenged with 5 avian H4 strains from ducks in a comprehensive study that assessed the susceptibility of swine to 38 avian IAV strains (Kida et al, 1994).…”