ArticlemSystems2022
Elimination of Foreign Sequences in Eukaryotic Viral Reference Genomes Improves the Accuracy of Virome Analysis.
Article in mSystems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Virome profiling of long-tailed marmots reveals tissue tropism and cross-species transmission of a diversity of uncharacterized mammalian viruses.Microbiome · 2025Article
- Node role of wild boars in virus circulation among wildlife and domestic animals.Nature communications · 2025Article
- A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics.Nature microbiology · 2025Article
- The gut and circulating virome: emerging players in aging and longevity.Frontiers in aging · 2025Review
- Viromics-based precision diagnosis of reproductive abnormalities in cows reveals a reassortant Akabane disease virus.BMC veterinary research · 2024Article
- The links between dietary diversity and RNA virus diversity harbored by the great evening bat (Ia io).Microbiome · 2024Article
- Isolation, characterization, and circulation sphere of a filovirus in fruit bats.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Isolation and Identification of Severe Fever with Thrombocytopenia Syndrome Virus from Farmed Mink in Shandong, China.Transboundary and emerging diseases · 2024Article
- Ten common issues with reference sequence databases and how to mitigate them.Frontiers in bioinformatics · 2024Review
- The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses.Virus evolution · 2024Article
- Virome Profiling of Chickens with Hepatomegaly Rupture Syndrome Reveals Coinfection of Multiple Viruses.Viruses · 2023Article
- DNA virome of ticks in the Northeast and Hubei provinces of China reveals diverse single-stranded circular DNA viruses.Parasites & vectors · 2023Article
- Virome Profiling of an Eastern Roe Deer Reveals Spillover of Viruses from Domestic Animals to Wildlife.Pathogens (Basel, Switzerland) · 2023Article
- Virome Profiling of anVeterinary sciences · 2022Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Widespread in public databases, foreign contaminant sequences pose a substantial obstacle in genomic analyses. Such contamination in viral genome databases is also notorious but more complicated and often causes questionable results in various applications, particularly in virome-based virus detection. Here, we conducted comprehensive screening and identification of the foreign sequences hidden in the largest eukaryotic viral genome collections of GenBank and UniProt using a scrutiny pipeline, which enables us to rigorously detect those problematic viral sequences (PVSs) with origins in hosts, vectors, and laboratory components. As a result, a total of 766 nucleotide PVSs and 276 amino acid PVSs with lengths up to 6,605 bp were determined, which were widely distributed in 39 families with many involving highly public health-concerning viruses, such as hepatitis C virus, Crimean-Congo hemorrhagic fever virus, and filovirus. The majority of these PVSs are genomic fragments of hosts including humans and bacteria. However, they cannot simply be regarded as foreign contaminants, since parts of them are results of natural occurrence or artificial engineering of viruses. Nevertheless, they severely disturb such sequence-based analyses as genome annotation, taxonomic assignment, and virome profiling. Therefore, we provide a clean version of the eukaryotic viral reference data set by the removal of these PVSs, which allows more accurate virome analysis with less time consumed than with other comprehensive databases.
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