ViPR: an open bioinformatics database and analysis resource for virology research

Pickett, Brett E.; Sadat, Eva L.; Zhang, Yun; Noronha, Jyothi M.; Squires, R. Burke; Hunt, Victoria; Liu, Mengya; Kumar, Sanjeev; Zaremba, Sam; Gu, Zhiping; Zhou, Liwei; Larson, Christopher N.; Dietrich, Jonathan; Klem, Edward B.; Scheuermann, Richard H.

Dengue virus is an arthropod-borne virus native to tropical regions of the world and endemic in areas where it colocalizes with the preferred Aedes aegypti mosquito vector. Because of these restrictions, it can be assumed that DENV infections reported in clinics located in non-tropical regions of the world are likely due to recent travel by the patient to an endemic area. These imported cases can thus establish viral lineage in new regions as a result of human travel. The CDC has recently demonstrated that the travel history of US residents having been clinically diagnosed with DENV between 1999 and 2000 validates such an explanation (30) . As an example use case, we will extend the CDC study by performing an in-depth comparative genomics analysis of all DENV serotype 1-4 isolates taken between the years of 1999 and 2000, involving the following bioinformatics workflow: (i) identify sequence records using the ViPR Genome Search interface; (ii) save the matching sequence records as a working set in a personal Workbench; (iii) reconstruct a phylogenetic tree; (iv) visualize the multiple sequence alignment; (v) perform a metadata-driven statistical analysis of sequence variation; (vi) determine where these differentiating residues are located in relation to validated Sequence Features; and (vii) examine the 3D structure associated with a homologous protein from a related DENV-2 strain. Although this illustration is focused on Dengue virus, it should be noted that similar tasks can be performed for other virus species to address other biological questions by combining the wealth of relevant data with the suite of bioinformatics tools integrated into ViPR (Supplementary Figure S4) .