| Virol J. 2008; 5: 34. Published online 2008 February 27. doi: 10.1186/1743-422X-5-34. | PMCID: PMC2275254 |
Copyright © 2008 Voevodin and Marx; licensee BioMed Central Ltd. Frag-Virus: a new term to distinguish presumptive viruses known primarily from sequence data Alexander Voevodin 1 and Preston A Marx 21Vir&Gen, Toronto, Canada 2Division of Microbiology, Tulane National Primate Research Center, Covington, Louisiana USA Received February 18, 2008; Accepted February 27, 2008. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
The wide availability of PCR-based methods for the amplification of nucleic acids homologous to known viral genomes plus automated DNA sequencing have led to explosive growth of a new field, 'proxy' virus isolation. Typically, genomic fragments are amplified and subjected to phylogenetic analysis showing that they are related to, but distinct from, known ' bona fide' viruses. These "new viruses" are now commonly reported in the virological literature and are too numerous to cite here, two studies are given as typical examples [ 1, 2]. Although unintentional, these reports may, mislead the readership of scientific journals and the general press. Having no distinction between preliminary genome-based evidence and conclusive proof by biological isolation and characterization of a replication-competent virus blurs the meaning of new virus. To distinguish presumptive viruses known primarily through genomic sequence fragments from bona fide viruses we propose the term 'frag-virus'. The 'frag-virus status' may be intermediary between 'full' recognition as a new virus, as occurred, for example, with hepatitis C virus and Kaposi sarcoma herpesvirus [3-6]. Frag-virus designation may also be a category for such virus that likely exists, but there is neither sufficient motivation nor resources to pursue its elevation from frag-virus limbo to bona fide virus status. At the same time the frag-virus status will be a 'career end-point' for sequences belonging to non-infectious 'pseudo-viruses' or those having their origins in artifact. Whatever the 'fate' of frag-viruses, this simple term is highly informative and may prove useful in preventing misconceptions about new viruses. |
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