Virus Pathogen Database and Analysis Resource (ViPR): A Comprehensive Bioinformatics Database and Analysis Resource for the Coronavirus Research Community

Abstract

Several viruses within the Coronaviridae family have been categorized as either emerging or re-emerging human pathogens, with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) being the most well known. The NIAID-sponsored Virus Pathogen Database and Analysis Resource (ViPR, ) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses, including the entire Coronaviridae family. ViPR provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, host factor data, and other data types through an intuitive web-based search interface. Records returned from these queries can then be subjected to web-based analyses including: multiple sequence alignment, phylogenetic inference, sequence variation determination, BLAST comparison, and metadata-driven comparative genomics statistical analysis. Additional tools exist to display multiple sequence alignments, view phylogenetic trees, visualize 3D protein structures, transfer existing reference genome annotations to new genomes, and store or share results from any search or analysis within personal private ‘Workbench’ spaces for future access. All of the data and integrated analysis and visualization tools in ViPR are made available without charge as a service to the Coronaviridae research community to facilitate the research and development of diagnostics, prophylactics, vaccines and therapeutics against these human pathogens.

Under-the-radar dengue virus infections in natural populations ofAedes aegyptimosquitoes

“…In 2019, 16 cases of locally acquired DENV were reported for the 11 state, including an area along the West-Central Florida Gulf Coast. Although the impacts of many ISVs on arboviral competence have yet to be 16 determined, the evidence to date clearly indicates that the mosquito virome cannot be safely 17 ignored and likely influences the risk of autochthonous DENV transmission once the virus is 18 introduced into an area. Although the impacts of many ISVs on arboviral competence have yet to be 16 determined, the evidence to date clearly indicates that the mosquito virome cannot be safely 17 ignored and likely influences the risk of autochthonous DENV transmission once the virus is 18 introduced into an area.…”

Immunogenicity of mumps virus vaccine candidates matching circulating genotypes in the United States and China

“…To compare the genome sequences among virus isolates from different locations over time, full length virus sequences were obtained from the Virus Pathogen Resource [27]. There were 94 complete genomes available at the time of analysis.…”

“…All available full length genome sequences were obtained from the Virus Pathogen Resource and a representative set was selected [27]. Using MEGA 7, the Maximum Likelyhood method based on the JTT matrix-based model was used to generate trees for the F and HN protein sequences.…”

The European Classical Swine Fever Virus Database: Blueprint for a Pathogen-Specific Sequence Database with Integrated Sequence Analysis Tools

“…The Virus Pathogen Resource (ViPR) is a different database project combining information from several primary databases (e.g., the GenBank sequence database). The ViPR covers a broad range of relevant viral human, animal, and zoonotic pathogens (e.g., hepatitis C, Ebola, dengue, and Zika viruses), allowing also for the comparison and phylogenetic analysis of viral sequences, primarily addressing needs for research activities [18,19]. The concept of the presented database is to provide information relevant for a specific pathogen and to focus on the needs with respect to the diagnosis and control of a disease.…”