Viruses 2012, 4(9), 1425-1437; doi:10.3390/v4091425
Article

Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences

1email and 1,2,* email
Received: 3 July 2012; in revised form: 23 August 2012 / Accepted: 24 August 2012 / Published: 31 August 2012
(This article belongs to the Special Issue Advances in Filovirus Research 2012)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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
PDF Full-text Download PDF Full-Text [1174 KB, uploaded 31 August 2012 13:33 CEST]

Export to BibTeX |
EndNote


MDPI and ACS Style

Lauber, C.; Gorbalenya, A.E. Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences. Viruses 2012, 4, 1425-1437.

AMA Style

Lauber C, Gorbalenya AE. Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences. Viruses. 2012; 4(9):1425-1437.

Chicago/Turabian Style

Lauber, Chris; Gorbalenya, Alexander E. 2012. "Genetics-Based Classification of Filoviruses Calls for Expanded Sampling of Genomic Sequences." Viruses 4, no. 9: 1425-1437.


Viruses EISSN 1999-4915 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert