Influenza Research Database (IRD)
Influenza Research Database (IRD) is a US NIH/NIAID-funded, freely-available online bioinformatics resource for influenza virus data search, analysis and visualization. IRD is accessed ~1484 sessions per week (Google Analytics - 2016 average) and has been cited in more that 568 scientific publications.
Recently, several new influenza virus sequence annotation tools have been added to IRD, including: (1) a sequence auto-curation pipeline that checks for potential sequencing artifacts, (2) an H1 clade classification tool based on the USDA/OFFLU swine H1 classification scheme, (3) an H5 clade classification tool based on the CDC/WHO highly pathogenic avian influenza A H5N1 classification scheme, (4) a Sequence Feature Phenotypic Variant Type annotation tool based on the CDC H5 Genetic Changes Inventory, and (5) an HA subtype numbering conversion tool based on the cross-subtype HA numbering scheme proposed by Burke & Smith (PMID: 25391151). Additionally, a JavaScript based tree viewer Archaeopteryx-js and a user metadata capture utility have been developed and integrated into IRD.
Using the new annotation tools, influenza sequences in IRD have been comprehensively curated and annotated. Specifically, potential sequencing artifacts are flagged and users are provided with choices whether and how to include problematic sequences in their analyses. H1/H5 sequences are annotated with H1/H5 clade assignments. The presence/absence of Phenotypic Variant Types, in which particular sequence substitutions are predicted to give rise to phenotypic effects, have been computed for all influenza sequences in IRD. IRD users can also annotate their own sequences using any of these tools.
In addition to providing these expanded sequence annotations, IRD also now facilitates comparison of homologous residues between different HA subtypes using the new HA numbering conversion tool. This tool automatically converts the coordinates of user-provided and IRD-supported sequences into any other numbering schemes defined by selected reference strains.
Finally, IRD supports metadata-based comparative genomic analysis, such as phylogenetic tree coloring based on metadata values and metadata-driven Comparative Analysis Tool for Sequences (meta-CATS). Using the new Archaeopteryx-js tree viewer and the metadata capture utility, users can now upload their own sequence data with associated metadata to their personal Workbench space and subsequently analyze and visualize their sequence data and metadata along with IRD data using these analysis tools.
IRD provides comprehensive enriched influenza virus sequence annotations and supports custom sequence annotation, analysis and visualization as part of its mission to facilitate research and development of diagnostics, prophylactics and therapeutics for influenza viruses.
Publications
Zhang Y, Aevermann BD, Anderson TK, Burke DF, Dauphin G, Gu Z, He S, Kumar S, Larsen CN, Lee AJ, Li X, Macken C, Mahaffey C, Pickett BE, Reardon B, Smith T, Stewart L, Suloway C, Sun G, Tong L, Vincent AL, Walters B, Zaremba S, Zhao H, Zhou L, Zmasek C, Klem EB, Scheuermann RH
Influenza Research Database: An integrated bioinformatics resource for influenza virus research.
Nucleic acids research. 2017-01-04; 45.D1: D466-D474.
PMID: 27679478
Anderson TK, Macken CA, Lewis NS, Scheuermann RH, Van Reeth K, Brown IH, Swenson SL, Simon G, Saito T, Berhane Y, Ciacci-Zanella J, Pereda A, Davis CT, Donis RO, Webby RJ, Vincent AL
A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses.
mSphere. 2016-11-01; 1.6:
PMID: 27981236
Diversifying Selection Analysis Predicts Antigenic Evolution of 2009 Pandemic H1N1 Influenza A Virus in Humans.
Journal of virology. 2015-05-01; 89.10: 5427-40.
PMID: 25741011
A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway.
Evolutionary bioinformatics online. 2015-01-01; 11.43-8.
PMID: 25861210
Toward a method for tracking virus evolutionary trajectory applied to the pandemic H1N1 2009 influenza virus.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. 2014-12-01; 28.351-7.
PMID: 25064525
Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A, Bolles M, Carter V, Chang J, Clauss TR, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH
A comprehensive collection of systems biology data characterizing the host response to viral infection.
Scientific data. 2014-10-14; 1.140033.
PMID: 25977790
Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH
Standardized metadata for human pathogen/vector genomic sequences.
PloS one. 2014-06-17; 9.6: e99979.
PMID: 24936976
Pickett BE, Liu M, Sadat EL, Squires RB, Noronha JM, He S, Jen W, Zaremba S, Gu Z, Zhou L, Larsen CN, Bosch I, Gehrke L, McGee M, Klem EB, Scheuermann RH
Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes.
Virology. 2013-12-01; 447.1-2: 45-51.
PMID: 24210098
Squires RB, Noronha J, Hunt V, García-Sastre A, Macken C, Baumgarth N, Suarez D, Pickett BE, Zhang Y, Larsen CN, Ramsey A, Zhou L, Zaremba S, Kumar S, Deitrich J, Klem E, Scheuermann RH
Influenza research database: an integrated bioinformatics resource for influenza research and surveillance.
Influenza and other respiratory viruses. 2012-11-01; 6.6: 404-16.
PMID: 22260278
Noronha JM, Liu M, Squires RB, Pickett BE, Hale BG, Air GM, Galloway SE, Takimoto T, Schmolke M, Hunt V, Klem E, García-Sastre A, McGee M, Scheuermann RH
Influenza virus sequence feature variant type analysis: evidence of a role for NS1 in influenza virus host range restriction.
Journal of virology. 2012-05-01; 86.10: 5857-66.
PMID: 22398283
Greenbaum JA, Kotturi MF, Kim Y, Oseroff C, Vaughan K, Salimi N, Vita R, Ponomarenko J, Scheuermann RH, Sette A, Peters B
Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population.
Proceedings of the National Academy of Sciences of the United States of America. 2009-12-01; 106.48: 20365-70.
PMID: 19918065
Funding
This work is funded by the National Institute of Allergy and Infectious Diseases (NIH/DHHS) under contract no. HHSN272201400028C.
