Comprehensive New Database an “Efficient and Helpful Tool” for Accessing HCV Research

August 16, 2016
Dava Stewart

“Each entry contains contextual information pertaining to the entry such as the HCV genotypic background and links to the original publication,” say the authors.

A new database gives researchers a way to access information about the hepatitis C virus (HCV) generally, and also about the internal ribosomal entry site (IRES), which exists in all HCV genotypes. A paper published in the journal BMC Microbiology, authored by Evan Floden, of the Department of Genetics & Microbiology at Charles University in Prague, and colleagues, describes the database.

The authors say that the “possible high impact of variations in HCV IRES on viral protein production and thus virus replication” motivated them to collect the available and known data on nucleotide variants in the HCV IRES. The database is called the HCV IRES variation database or HCVIVdb. “Each entry contains contextual information pertaining to the entry such as the HCV genotypic background and links to the original publication,” say the authors.

Although 150 to 200 million people around the world have HCV, the virus was only proven to exist in 1989. The authors say, “The data generated from thousands of experiments are spread across many journal articles, with no standardized reporting format.” The database was constructed using information manually gathered, and is “arranged to reflect the availability of published information including HCV genotype, nucleotide changes, systems used to monitor translation efficiency, activity in translation assays, plasmid constructs and reporter genes used, clinical data and the original publication reference,” say the researchers.

One goal of the database was to provide an accessible, efficient tool, in order to encourage more scientists to make use of it. Each entry includes a PubMed ID, and the authors say, “the entries have been organized so that searching for a distinct variation allows evaluation of other entries with identical mutations along with mutations at the same location.”

Other databases specializing in HCV data do exist, though the authors report that many are outdated and not regularly updated. They conclude by saying that “The HCVIVdb is an efficient and helpful tool for people working in both the HCV and IRES fields and can aid in the understanding of the IRES function, development and design of new experiments and in a targeted drug design.”

The database can be accessed online at http://hcvivdb.org.

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