Emerging infectious diseases (EIDs), especially the viral ones, are a serious threat to public health, significantly challenging global security, social economy and human's life. Rapid and accurate diagnosis of EIDs is a prerequisite for timely formulating and implementing prevention and control measures. High-throughput sequencing (HTS)-based metagenomics is a promising approach for rapid diagnosis and identification of EIDs because it does not require ‘a priori’ information and is capable of identifying a comprehensive spectrum of potential agents, especially those new ones, by a single test. Metagenomic diagnosis highly depends on the similarity-based analyses of reads or contigs against reference database. Hence, the high quality of reference database that is of complete representativeness, functional robustness, and informational accuracy provides an important guarantee of diagnostic reliability. However, widespread in public databases, the notorious contamination in virus reference databases often leads to confusing even wrong conclusions in applications like viral disease diagnosis and viromic analysis, highlighting the need of a high-quality database. To that end, we established a stringent scrutiny pipeline (http://github.com/BH-Lab/EVRD) to systematically analyze and identify problematic viral sequences (PVSs) hidden in the largest viral nt (GenBank) and aa (UniProt) reference collections, resulting in a nonredundant (collapsed at 90% identity) and well-refined eukaryotic viral reference database. To augment its function for diagnosis, we incorporated risk (LCD- and Vector-tagging) and vaccine (Vaccine-tagging) information into the database, which helps identify possible exotic contamination and distinguish vaccine strains from field viruses. The database will be annually updated and is expected to provide a more accurate reference for EID diagnosis, new virus identification, viromic analysis, and other virologic studies.

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Citation

If you use our databases, please kindly cite this article:

Chen, Junjie et al. “Elimination of Foreign Sequences in Eukaryotic Viral Reference Genomes Improves the Accuracy of Virome Analysis.” mSystems, e0090722. 26 Oct. 2022, doi:10.1128/msystems.00907-22

Contact

Any questions or comments should be addressed to heb-001001@163.com (Prof. and Dr. Biao He at Changchun Veterinary Research Institute)