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A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection.
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Who cites it
116 citing papers in PubMed.
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- Omics-Level Approaches to Studying Gammaherpesvirus Infection.Pathogens (Basel, Switzerland) · 2026Review
- Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication.Nature communications · 2026Article
- A fold switch regulates conformation of an alphavirus RNA-dependent RNA polymerase.Nucleic acids research · 2026Article
- VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses.Nucleic acids research · 2026Article
- ViMOP: a user-friendly and field-applicable pipeline for untargeted viral genome nanopore sequencing.Bioinformatics (Oxford, England) · 2026Article
- A new lineage ofFrontiers in veterinary science · 2026Article
- A framework of Microbial Genomic Database for clinical metagenomic pathogen diagnosis: development and multi-cohort evaluation.Frontiers in cellular and infection microbiology · 2026Article
- Evaluation of high-throughput sequencing for replacing the conventional adventitious virus detection assays used for biologics.NPJ vaccines · 2025Article
- ViTrace detects viral signatures in tumor transcriptomes using a hybrid language model.Communications biology · 2025Article
- Whole-genome characterization of Newcastle disease virus isolates of sub-genotype VII.1.1 from chickens in Ethiopia.Virus genes · 2025Article
- Report of the fourth conference on next-generation sequencing (NGS) for adventitious virus detection in biologics for humans and animals: Validation and implementation of NGS.Biologicals : journal of the International Association of Biological Standardization · 2025Article
- Seasonal patterns of viromes in urban aquatic environments of Manitoba.Applied and environmental microbiology · 2025Article
- Fluke-borne viruses are a risk factor for diseases caused by carcinogenic trematodes.bioRxiv : the preprint server for biology · 2025Article
- AntiviralDB: an expert-curated database of antiviral agents against human infectious diseases.mBio · 2025Article
- Pig-to-human lung xenotransplantation into a brain-dead recipient.Nature medicine · 2025Article
- Article
- Distinct virome compositions and lack of viral diversification indicate that viral spillover is a dead-end between the western honey bee and the common eastern bumblebee.Communications biology · 2025Article
56 more citing papers are in PubMed but not listed here.
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB). This database was manually and computationally reviewed, resulting in refined, semantic selection criteria (SEM-R), which were applied to a new download of updated GenBank sequences to create a second-generation VDB. Viral entries in the latter were clustered at 98% by CD-HIT-EST to reduce redundancy while retaining high viral sequence diversity. The viral identity of the clustered representative sequences (creps) was confirmed by BLAST searches in NCBI databases and HMMER searches in PFAM and DFAM databases. The resulting RVDB contained a broad representation of viral families, sequence diversity, and a reduced cellular content; it includes full-length and partial sequences and endogenous nonretroviral elements, endogenous retroviruses, and retrotransposons. Testing of RVDBv10.2, with an in-house HTS transcriptomic data set indicated a significantly faster run for virus detection than interrogating the entirety of the NCBI nonredundant nucleotide database, which contains all viral sequences but also nonviral sequences. RVDB is publically available for facilitating HTS analysis, particularly for novel virus detection. It is meant to be updated on a regular basis to include new viral sequences added to GenBank.
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