Introduction

One of the notable features of viruses is the exceptional diversity of their genome organization and of the modes of their genome expression. Viruses whose genome is RNA rather than DNA, as in all cellular organisms (Fig. 4.1), contribute greatly to virus diversity. The origin and evolution of RNA viruses has intrigued researchers for decades. Three classes of RNA viruses can be distinguished, depending on the type of genomic molecule (Baltimore, 1971; Fig. 4.1). These are RNA viruses that employ positive messenger-sense molecules as genomes (+RNA), those that have genome molecules with complementary polarity (negative) to that of their mRNAs (–RNA), and those that have genomes of double-stranded (ds) RNA molecules. A unique virusencoded enzyme RNA-dependent RNA polymerase (RdRp) directs the synthesis of all of these RNA species. Sometimes, viruses with RNA genomes which are replicated through a DNA stage, the retro viruses, are also regarded as RNA viruses (Chapter 27).

In order to sort out the diversity of viruses, a classification has been introduced which uses about a dozen different phenotypic characteristics (Francki et al., 1991). Thus, more than 60 RNA viral families and separate groups have been delineated, but this classification does not attempt to reflect the evolutionary relationships between the taxa.

A lack of virus fossils, and the apparent high rate of turnover of genome sequences, seemed to preclude our ability to understand RNA virus evolution. However, through the last decade, thanks primarily to the enormous increase in our knowledge of viral genome sequences, it became evident that some progress in evolutionary inference might be possible.