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 SQLiteDB is converted to SQL 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.

Unclustered

Unclustered (U-) nucleotide sequence files.

RVDB Version (Release date) Sequence files in FASTA format Sequence files in SQL format Release notes in plain text file
Current Release v20.0 (Sept, 3 2020) U-RVDBv20.0.fasta U-RVDBv20.0.sql U-RVDBv20.0.release notes
v19.0 (Jun 29, 2020) U-RVDBv19.0.fasta U-RVDBv19.0.sql U-RVDBv19.0.release notes
v18.0 (Mar 2, 2020) U-RVDBv18.0.fasta U-RVDBv18.0.sql U-RVDBv18.0.release notes
v17.0 (Nov 6, 2019) U-RVDBv17.0.fasta U-RVDBv17.0.sql U-RVDBv17.0.release notes
v16.0 (May 29, 2019) U-RVDBv16.0.fasta U-RVDBv16.0.sql U-RVDBv16.0.release notes
v15.1 (Feb 6, 2019) U-RVDBv15.1.fasta U-RVDBv15.1.sql U-RVDBv15.1.release notes
v14.0 (Oct 1, 2018) U-RVDBv14.0.fasta U-RVDBv14.0.sql U-RVDBv14.0.release notes
v13.0 (Jun 11, 2018) U-RVDBv13.0.fasta U-RVDBv13.0.sql U-RVDBv13.0.release notes
v12.2 (Feb 12, 2018) U-RVDBv12.2.fasta Not Available U-RVDBv12.2.release notes
v11.5 (Sept 27, 2017) U-RVDBv11.5.fasta Not Available U-RVDBv11.5.release notes
v11.3 (Aug 1, 2017) U-RVDBv11.3.fasta Not Available U-RVDBv11.3.release notes
v10.2 (U-May 5, 2017; C-Dec. 28, 2016) U-RVDBv10.2.fasta Not Available U-RVDBv10.2.release notes

Clustered

Clustered (C-) nucleotide sequence files.

RVDB Version (Release date) Sequence files in FASTA format Release notes in plain text file
Current Release v20.0 (Sept, 3 2020) C-RVDBv20.0.fasta C-RVDBv20.0.release notes
v19.0 (Jun 29, 2020) C-RVDBv19.0.fasta C-RVDBv19.0.release notes
v18.0 (Mar 2, 2020) C-RVDBv18.0.fasta C-RVDBv18.0.release notes
v17.0 (Nov 6, 2019) C-RVDBv17.0.fasta C-RVDBv17.0.release notes
v16.0 (May 29, 2019) C-RVDBv16.0.fasta C-RVDBv16.0.release notes
v15.1 (Feb 6, 2019) C-RVDBv15.1.fasta C-RVDBv15.1.release notes
v14.0 (Oct 1, 2018) C-RVDBv14.0.fasta C-RVDBv14.0.release notes
v13.0 (Jun 11, 2018) C-RVDBv13.0.fasta C-RVDBv13.0.release notes
v12.2 (Feb 12, 2018) C-RVDBv12.2.fasta C-RVDBv12.2.release notes
v11.5 (Sept 27, 2017) C-RVDBv11.5.fasta C-RVDBv11.5.release notes
v11.3 (Aug 1, 2017) C-RVDBv11.3.fasta C-RVDBv11.3.release notes
v10.2 (U-May 5, 2017; C-Dec. 28, 2016) C-RVDBv10.2.fasta C-RVDBv10.2.release notes

Citing RVDB

Goodacre N, Aljanahi A, Nandakumar S, Mikailov M, Khan AS. A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection. mSphere. 2018 Mar 14;3(2). pii: e00069-18. doi: 10.1128/mSphereDirect.00069-18. eCollection 2018 Mar-Apr. PubMed PMID: 29564396; PubMed Central PMCID: PMC5853486.

Questions/Comments

If you have any questions or comments regarding RVDB nucleotidic databases, please contact Arifa Khan (Arifa.Khan@fda.hhs.gov). If you have any technical questions or comments regarding the website, please contact the Bioinformatics Core at University of Delaware help@bioinformatics.udel.edu.