ArticleJournal of virology2012
Partitioning the genetic diversity of a virus family: approach and evaluation through a case study of picornaviruses.
Article in Journal of virology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
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- Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism.mSystems · 2025Article
- Giant RNA genomes: Roles of host, translation elongation, genome architecture, and proteome in nidoviruses.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Intraspecific variation of the hedgehog arteriviruses, which may constitute a new genus in the subfamily Heroarterivirinae of the family Arteriviridae.Archives of virology · 2025Article
- Sequence Demarcation Tool (SDT), a Free User-Friendly Computer Program Using Pairwise Genetic Identity Calculations to Classify Nucleotide or Amino Acid Sequences.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Surveillance of coronaviruses in wild aquatic birds in Hong Kong: expanded genetic diversity and discovery of novel subgenus in theVirus evolution · 2025Article
- GRAViTy-V2: a grounded viral taxonomy application.NAR genomics and bioinformatics · 2024Article
- Rapid taxonomic categorization of short, abundant virus sequences for ecological analyses.Ecology and evolution · 2024Article
- Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates.PLoS pathogens · 2024Article
- Translating genomic exploration of the familyiScience · 2022Article
- The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes.Molecular biology and evolution · 2022Article
- Review
- Novel Filoviruses, Hantavirus, and Rhabdovirus in Freshwater Fish, Switzerland, 2017.Emerging infectious diseases · 2021Article
- SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.Nature communications · 2021Article
- Recognizing species as a new focus of virus research.PLoS pathogens · 2021Article
- Coronavirus replication-transcription complex: Vital and selective NMPylation of a conserved site in nsp9 by the NiRAN-RdRp subunit.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- A k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomes.Computational and structural biotechnology journal · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recent advent of genome sequences as the only source available to classify many newly discovered viruses challenges the development of virus taxonomy by expert virologists who traditionally rely on extensive virus characterization. In this proof-of-principle study, we address this issue by presenting a computational approach (DEmARC) to classify viruses of a family into groups at hierarchical levels using a sole criterion-intervirus genetic divergence. To quantify genetic divergence, we used pairwise evolutionary distances (PEDs) estimated by maximum likelihood inference on a multiple alignment of family-wide conserved proteins. PEDs were calculated for all virus pairs, and the resulting distribution was modeled via a mixture of probability density functions. The model enables the quantitative inference of regions of distance discontinuity in the family-wide PED distribution, which define the levels of hierarchy. For each level, a limit on genetic divergence, below which two viruses join the same group, was objectively selected among a set of candidates by minimizing violations of intragroup PEDs to the limit. In a case study, we applied the procedure to hundreds of genome sequences of picornaviruses and extensively evaluated it by modulating four key parameters. It was found that the genetics-based classification largely tolerates variations in virus sampling and multiple alignment construction but is affected by the choice of protein and the measure of genetic divergence. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3905-3915, 2012), we analyze the substantial insight gained with the genetics-based classification approach by comparing it with the expert-based picornavirus taxonomy.
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