ArticleJournal of virology2012
Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy 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 37 papers, 1 of them a synthesis that pooled it.
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Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A systematic review of evidence that enteroviruses may be zoonotic.Emerging microbes & infections · 2018Pooled it
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- Surveillance of coronaviruses in wild aquatic birds in Hong Kong: expanded genetic diversity and discovery of novel subgenus in theVirus evolution · 2025Article
- Four principles to establish a universal virus taxonomy.PLoS biology · 2023Article
- Molecular mechanism of antibody neutralization of coxsackievirus A16.Nature communications · 2022Article
- Review
- Recognizing species as a new focus of virus research.PLoS pathogens · 2021Article
- Enteroviruses from Humans and Great Apes in the Republic of Congo: Recombination within Enterovirus C Serotypes.Microorganisms · 2020Article
- The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks.Nature microbiology · 2020Review
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2.Nature microbiology · 2020Article
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- Phylogenetic Clustering by Linear Integer Programming (PhyCLIP).Molecular biology and evolution · 2019Article
- Exploiting the Legacy of the Arbovirus Hunters.Viruses · 2019Review
- Impact of rotavirus and hepatitis A virus by worldwide climatic changes during the period between 2000 and 2013.Bioinformation · 2019Article
- Increasing the number of available ranks in virus taxonomy from five to ten and adopting the Baltimore classes as taxa at the basal rank.Archives of virology · 2018Article
- Nidovirus-Associated Proliferative Pneumonia in the Green Tree Python (Morelia viridis).Journal of virology · 2017Article
- Coxsackievirus A16 utilizes cell surface heparan sulfate glycosaminoglycans as its attachment receptor.Emerging microbes & infections · 2017Article
- Identification of a Novel Enterovirus Species in Rhesus Macaque in China.Scientific reports · 2016Article
- Modification of the internal ribosome entry site element impairs the growth of foot-and-mouth disease virus in porcine-derived cells.The Journal of general virology · 2016Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Virus taxonomy has received little attention from the research community despite its broad relevance. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3890-3904, 2012), we have introduced a quantitative approach to hierarchically classify viruses of a family using pairwise evolutionary distances (PEDs) as a measure of genetic divergence. When applied to the six most conserved proteins of the Picornaviridae, it clustered 1,234 genome sequences in groups at three hierarchical levels (to which we refer as the "GENETIC classification"). In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification. To facilitate the analysis, we introduce two novel diagrams. The first connects the genetic diversity of taxa to both the PED distribution and the phylogeny of picornaviruses. The second depicts a classification and the accommodated genetic diversity in a standardized manner. Generally, we found striking agreement between the two classifications on species and genus taxa. A few disagreements concern the species Human rhinovirus A and Human rhinovirus C and the genus Aphthovirus, which were split in the GENETIC classification. Furthermore, we propose a new supergenus level and universal, level-specific PED thresholds, not reached yet by many taxa. Since the species threshold is approached mostly by taxa with large sampling sizes and those infecting multiple hosts, it may represent an upper limit on divergence, beyond which homologous recombination in the six most conserved genes between two picornaviruses might not give viable progeny.
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