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Progress towards a higher taxonomy of viruses
1CSIRO, Division of Biomolecular Engineering, Parkville, Victoria, Australia.
Research in Virology
|November 1, 1993
Summary
This study proposes a new virus taxonomy based on replication machinery, particularly RNA-dependent RNA polymerase, to address polyphyletic origins and modular evolution in viral classification.
Area of Science:
- Virology
- Bioinformatics
- Molecular Biology
Background:
- Current virus taxonomy faces challenges due to polyphyletic origins and modular gene acquisition.
- Viral adaptation through gene reassortment, duplication, and mutation complicates phylogenetic analysis.
Purpose of the Study:
- To establish a hierarchical taxonomy for viruses.
- To propose criteria for classifying viruses based on their evolutionary history and genetic makeup.
Main Methods:
- Analysis of RNA-dependent RNA polymerase sequence identity for positive-strand RNA viruses.
- Phylogenetic analysis of double-stranded RNA (dsRNA) viruses using polymerase dendrograms.
- Re-evaluation of existing virus family and genus classifications.
Main Results:
- Positive-strand RNA viruses are classified into five classes and fourteen orders.
- This classification confirms Togaviridae and Flaviridae separation but questions current assignments for pestiviruses, hepatitis C virus, and others.
- Coronaviruses and toroviruses are reclassified into distinct families and orders.
- Luteoviruses are split into two families, and apple chlorotic leaf spot virus is reclassified.
Conclusions:
- A unified virus kingdom with diverse phyla is proposed.
- Replication machinery, specifically RNA-dependent RNA polymerase, is a key criterion for virus classification.
- The proposed taxonomy offers a more robust framework for understanding viral evolution and relationships.