Identification and classification of viruses that have not been propagated
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Identification and classification of viruses that have not been propagated* J. Maniloff Department of Microbiology and Immunology, University of Rochester, Rochester, New York, U.S.A.
Summary Microorganisms that cannot be grown in the laboratory can now be tentatively identified, by cloning and sequencing particular nucleic acid segments and then carrying out a comparative sequence analysis with an appropriate database. For bacteria, a few universally distributed genes and gene products have enabled comparative sequence analysis to be used for tentative identification and classification of uncultured bacteria. For viruses, there is no universally distributed viral gene or gene product. However, in a few cases, viruses that could not be propagated in the laboratory have been identified and classified. In these cases, either the entire viral genome sequence was determined or partial sequence information was supplemented with additional data. The Executive Committee of the International Committee on Taxonomy of Viruses (ICTV) has reviewed the issue of identification and classification of viruses that have not been propagated. Under the ICTV system, formal review of any taxonomic proposal is carried out by the relevant ICTV Subcommittee or Study Group. The few examples of unpropagated viruses that have arisen thus far have been readily accommodated within existing viral taxonomy, with the international group of experts comprising each Subcommittee and Study Group determining the necessary and sufficient amount of information needed for classification of an unpropagated virus on a case-by-case basis.
Introduction Recent advances in nucleic acid methodology now enable phylogenetic relationships between organisms to be investigated by analyses of nucleic acid and protein sequence similarities, signature sequences, and genome organization. For bacteria, reconstruction of a fairly detailed phylogenetic tree in the past few years has made it possible to design experiments to identify and classify uncultured bacteria. The general strategy has been to clone (with or without PCR amplification) and sequence specific genes or gene products, * Submitted on behalf of the Executive Committee of the International Committee on Taxonomy of Viruses.
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like 16S rRNA, and carry out comparative analyses of the sequence data from uncultured bacteria with a bacterial sequence database. A similar strategy has been applied to some unpropagated viruses - a couple of recent well-known cases are hepatitis C virus and Sin Nombre (also referred to as Four Corners) virus. For both uncultured bacteria and unpropagated viruses, it must be remembered that the adjective "uncultured" or "unpropagated" is an acknowledgment of current experimental limitations. Obviously, uncultured bacteria and unpropagated viruses grow or replicate in nature - the "uncultured" or "unpropagated" modifier simply indicates the inability, thus far, to devise appropriate growth conditions in the la
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