ViruSurf: an integrated database to investigate viral sequences

• Published in: Nucleic Acids Research Vol. 49; no. D1; pp. D817 - D824
• Main Authors: Canakoglu, Arif, Pinoli, Pietro, Bernasconi, Anna, Alfonsi, Tommaso, Melidis, Damianos P, Ceri, Stefano
• Format: Journal Article Web Resource
• Language: English
• Published: England Oxford University Press 08.01.2021
• Subjects: Computational Biology - methods; COVID-19 - epidemiology; COVID-19 - prevention & control; COVID-19 - virology; Data Curation - methods; Database Issue; Databases, Genetic; Genetic Variation; Genome, Viral - genetics; Humans; Information Storage and Retrieval - methods; Internet; Pandemics; SARS-CoV-2 - genetics; SARS-CoV-2 - physiology; User-Computer Interface
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkaa846

Abstract ViruSurf, available at http://gmql.eu/virusurf/, is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database, available at http://gmql.eu/virusurf_gisaid/, offers a subset of these functionalities. Given the current pandemic outbreak, SARS-CoV-2 data are collected from the four sources; but ViruSurf contains other virus species harmful to humans, including SARS-CoV, MERS-CoV, Ebola and Dengue. The database is centered on sequences, described from their biological, technological and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences. Several example queries on the database confirm and possibly improve results from recent research papers; results can be recomputed over time and upon selected populations. Effective search over large and curated sequence data may enable faster responses to future threats that could arise from new viruses.