Efforts were initiated to refine RVDB from version 19.0. This included removal of misannotated sequences and sequences determined to be irrelevant for virus detection in RVDB. This is indicated in the Release Notes and the list of removed accession numbers is included in the Annotation sheet.

Objective

Reference Viral Database (RVDB) is developed by Arifa Khan's group at CBER, FDA for enhancing virus detection using next-generation sequencing (NGS) technologies. RVDB is available as Unclustered (U-) and Clustered (C-) nucleotide sequence files. The scripts and steps involved in generating and updating RVDB have been assembled into a pipeline (reported in mSphere) and is available with instructions at GitHub.

The SQLite form of U-RVDB is provided using the sqlite3 module available in python, as described by GitHub. From version 15.1 and thereafter, the RVDB SQLDB is converted to SQLite to provide a flexible import format.

A proteic version of RVDB, was developed by Marc Eloit’s group at Institut Pasteur (RVDB-prot and RVDB-prot-HMM). The proteic RVDB may be used to complement analysis using these nucleotidic databases.