retroviruses; mammals

[Eric Zurcher]

I gave an incorrect URL for the rules of viral nomenclature in my earlier
message. That URL ought to have been
<http://www.ncbi.nlm.nih.gov/ICTV/rules.html>.

At 08:44 30/09/99 -0400, Don McAllister wrote:
>Viruses are grouped by nucleic acid type, morphology, and the presence or
>absence of an envelope. The International Committee on Taxonomy of Viruses
has
>organized the 2000 known species into 73 families each of which share
>morphological characteristics and reproductive strategies.
>
>ICTV has not yet established order through kingdom categories, except the
>complex viruses will probably be placed in their own order and enveloped
>viruses with one negative strand of RNA have been classed in the newly
>established order Mononegavirales.

Don provided a good summary of higher-level virus taxonomy. But it's worth
noting that some of these morphological "groups" don't always correlate all
that well with the genetic makeup. Polyhedral viruses can be DNA or RNA,
single- or double- stranded - they largely run the gamut of genomic types.
On the other hand, some of the morphologic groups DO correlate pretty well
with the genomic type (e.g., the bullet-shaped enveloped particles of the
Rhabdoviridae (genomically ssRNA-) are fairly distinctive).

Anyone really interested in viral taxonomy should considering ordering a
copy of the 7th report of the ICTV, just published by Academic Press. This
work recognizes 3 named orders (which encompass only a smallish subset of
recognized viral species).

It is perhaps interesting to note that viral taxonomists are using named
ranks
at all, despite the lack of a Linnean legacy in their discipline.

For a thoughtful and up-to-date discussion of the problems of viral
taxonomy and phylogeny, I suggest examining the perspective given at
<http://www.ncbi.nlm.nih.gov/ICTV/perspective/future_of_taxonomy.html>.
Here is a portion:

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"We now know that many viruses have gained some functional genes from their
hosts (and hosts have gained some genes from viruses) and have gained other
genes from other viruses - that is, viral genomes seem to represent
more-or-less ancient "grab-bags" of genes, fine-tuned by the Darwinian
forces of selection into replicative machines with extraordinary functional
economy. We now know that the genomes of viruses in different families, in
most cases, are extremely different from each other, but we also know that
in some cases seemingly unrelated viruses (and taxa) are similar - similar
in gene order and arrangement, fine points of strategy of replication, and
even in conserved sequence domains encoding similarly functioning proteins.
Overall, the differences between most taxa are so great that it still seems
foolish to think of building a monophylogenous "tree" uniting all the
viruses. On the other hand, the unexpected similarities have prompted some
consideration of a partial phylogenetic taxonomy (Goldbach, 1986, 1987;
Gibbs, 1987; Goldbach and Wellink, 1988; Kingsbury, 1988; Morse, 1993)."
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Eric Zurcher
CSIRO Division of Entomology
Canberra, Australia
E-mail: ericz at ento.csiro.au