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Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences
Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119899 Moscow, Russia
* Author to whom correspondence should be addressed.
Received: 3 July 2012; in revised form: 23 August 2012 / Accepted: 24 August 2012 / Published: 31 August 2012
Abstract: We have recently developed a computational approach for hierarchical, genome-based classification of viruses of a family (DEmARC). In DEmARC, virus clusters are delimited objectively by devising a universal family-wide threshold on intra-cluster genetic divergence of viruses that is specific for each level of the classification. Here, we apply DEmARC to a set of 56 filoviruses with complete genome sequences and compare the resulting classification to the ICTV taxonomy of the family Filoviridae. We find in total six candidate taxon levels two of which correspond to the species and genus ranks of the family. At these two levels, the six filovirus species and two genera officially recognized by ICTV, as well as a seventh tentative species for Lloviu virus and prototyping a third genus, are reproduced. DEmARC lends the highest possible support for these two as well as the four other levels, implying that the actual number of valid taxon levels remains uncertain and the choice of levels for filovirus species and genera is arbitrary. Based on our experience with other virus families, we conclude that the current sampling of filovirus genomic sequences needs to be considerably expanded in order to resolve these uncertainties in the framework of genetics-based classification.
Keywords: genetics-based classification; taxonomy; DEmARC; filoviruses; ebolavirus; virus species; genetic diversity; pairwise evolutionary distances
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Lauber, C.; Gorbalenya, A.E. Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences. Viruses 2012, 4, 1425-1437.
Lauber C, Gorbalenya AE. Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences. Viruses. 2012; 4(9):1425-1437.
Lauber, Chris; Gorbalenya, Alexander E. 2012. "Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences." Viruses 4, no. 9: 1425-1437.