Virus Pathogen Resource (ViPR)

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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.

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.
Viruses. 2010-10-01; 2.10: 2258-68.
PMID: 21994619
Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community.
Viruses. 2012-11-19; 4.11: 3209-26.
PMID: 23202522
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
ViPR: an open bioinformatics database and analysis resource for virology research.
Nucleic acids research. 2012-01-01; 40.Database issue: D593-8.
PMID: 22006842
Zika virus: designate standardized names.
Nature. 2016-03-10; 531.7593: 173.
PMID: 26961650
A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway.
Evolutionary bioinformatics online. 2015-01-01; 11.43-8.
PMID: 25861210
Comprehensive Annotation of Mature Peptides and Genotypes for Zika Virus.
PloS one. 2017-01-01; 12.12: e0170462.
PMID: 28125631
Genetic changes found in a distinct clade of Enterovirus D68 associated with paralysis during the 2014 outbreak.
Virus evolution. 2016-01-01; 2.1: vew015.
PMID: 28512577
Identification of diagnostic peptide regions that distinguish Zika virus from related mosquito-borne Flaviviruses.
PloS one. 2017-01-01; 12.12: e0178199.
PMID: 28562637

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