Virus Pathogen Resource (ViPR)

In order to support research focused on newly emerging pathogens, the Division of Microbiology and Infectious Diseases (DMID) of the National Institute of Allergy and Infectious Diseases (NIAID), at the US National Institutes of Health (NIH), is supporting a variety of resources for researchers including: the Genomic Sequencing Centers for Infectious Diseases, Structural Genomics Centers for Infectious Diseases, Systems Biology for Infectious Diseases Research, and BEI Resources Repository programs to increase public availability of genome sequence data, 3D protein structures, systems biology models, isolated organisms and experiment reagents. The Bioinformatics Resource Centers (BRC) for Infectious Diseases were created to serve as database resources for the integration of research and surveillance data being generated by these DMID-sponsored resources and by other primary investigators working on infectious diseases caused by different groups of human pathogens and their insect vectors. The objective of the BRC program is to provide a one-stop-shop for data and analytical tools to support data mining and analysis workflows for both basic and applied research.

The Virus Pathogen Resource (ViPR) is a US NIH/NIAID-funded, freely-available online bioinformatics resource for search, analysis and visualization of data about 14 different families of human pathogenic viruses, including Coronaviridae (SARS, MERS), Flaviviridae (Dengue, Zika, West Nile, Yellow fever, Hepatitis C), Picornaviridae (Polio, Enterovirus D68), Togaviridae (Chikungunya, EEEV, VEEV, Rubella), Arenaviridae (Lassa), Filoviridae (Ebola, Marburg), Herpesviridae (HSV, EBV, CMV), and Poxviridae (Smallpox). Cross-referencing data and integrating computational tools into the online ViPR resource allows complex analyses to be easily performed by researchers regardless of their bioinformatics training or expertise. 

ViPR is accessed ~1638 sessions per week (Google Analytics - 2016 average) and has been cited in more that 255 scientific publications.


Methods in molecular biology (Clifton, N.J.). 2019-01-01; 1911.47-69.
Hepatitis C Virus Database and Bioinformatics Analysis Tools in the Virus Pathogen Resource (ViPR)
Zhang Y, Zmasek C, Sun G, Larsen CN, Scheuermann RH
PMID: 30593617
PloS one. 2017-05-31; 12.5: e0178199.
Identification of diagnostic peptide regions that distinguish Zika virus from related mosquito-borne Flaviviruses
Lee AJ, Bhattacharya R, Scheuermann RH, Pickett BE
PMID: 28562637
PloS one. 2017-01-01; 12.12: e0170462.
Comprehensive Annotation of Mature Peptides and Genotypes for Zika Virus
Sun G, Larsen CN, Baumgarth N, Klem EB, Scheuermann RH
PMID: 28125631
Virus evolution. 2016-06-15; 2.1: vew015.
Genetic changes found in a distinct clade of Enterovirus D68 associated with paralysis during the 2014 outbreak
Zhang Y, Cao J, Zhang S, Lee AJ, Sun G, Larsen CN, Zhao H, Gu Z, He S, Klem EB, Scheuermann RH
PMID: 28512577
Nature. 2016-03-10; 531.7593: 173.
Zika virus: designate standardized names
Scheuermann RH
PMID: 26961650
Evolutionary bioinformatics online. 2015-03-16; 11.43-8.
A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway
Miller MA, Schwartz T, Pickett BE, He S, Klem EB, Scheuermann RH, Passarotti M, Kaufman S, O'Leary MA
PMID: 25861210
Scientific data. 2014-10-14; 1.140033.
A comprehensive collection of systems biology data characterizing the host response to viral infection
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
PMID: 25977790
PloS one. 2014-06-17; 9.6: e99979.
Standardized metadata for human pathogen/vector genomic sequences
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
PMID: 24936976
Virology. 2013-12-01; 447.1-2: 45-51.
Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes
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
PMID: 24210098
Viruses. 2012-11-19; 4.11: 3209-26.
Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community
Pickett BE, Greer DS, Zhang Y, Stewart L, Zhou L, Sun G, Gu Z, Kumar S, Zaremba S, Larsen CN, Jen W, Klem EB, Scheuermann RH
PMID: 23202522
Nucleic acids research. 2012-01-01; 40.Database issue: D593-8.
ViPR: an open bioinformatics database and analysis resource for virology research
Pickett BE, Sadat EL, Zhang Y, Noronha JM, Squires RB, Hunt V, Liu M, Kumar S, Zaremba S, Gu Z, Zhou L, Larson CN, Dietrich J, Klem EB, Scheuermann RH
PMID: 22006842
Viruses. 2010-10-13; 2.10: 2258-2268.
Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop
Brister JR, Bao Y, Kuiken C, Lefkowitz EJ, Mercier PL, Le Mercier P, Leplae R, Madupu R, Scheuermann RH, Schobel S, Seto D, Shrivastava S, Sterk P, Zeng Q, Klimke W, Tatusova T
PMID: 21994619


This work is funded by the National Institute of Allergy and Infectious Diseases (NIH/DHHS) under contract no. HHSN272201400028C.

Principal Investigator

Key Staff


Morgan Craft, Vincent Desborough, Ed Klem, Xiaomei Li, Angela Mundi, Jyothsna Reddy, Sam Zaremba, and Shujia Zhou
Northrop Grumman

Chris Larsen and Guangyu Sun

Catherine A. Macken
University of Auckland

Nicole Baumgarth
University of California Davis

Slobodan Paessler
University of Texas Medical Branch, Galveston

Richard Kuhn
Purdue University

David Knipe
Harvard University


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