The absence of bona fide viral fossils, i.e. ancient material from which viral nucleic acids can be recovered, might appear to make the origin of viral genomes an impenetrable mystery. However, the discovery of fragments of viral nucleic acids integrated into host genomes, coupled with an explosion in the determination of viral genome sequences, has allowed speculation on the evolutionary history of viruses. The origin of viruses is discussed in depth in Volume II, Chapter 10. How viruses with DNA or RNA genomes arose is a compelling question. A predominant hypothesis is that RNA viruses are relics of the “RNA world,” a period during which RNA was both genome and catalyst (no proteins yet existed). During this time, billions of years ago, life could have evolved from RNA, and the earliest organisms might have had RNA genomes. Viruses with RNA genomes might have evolved during this time.
Later, DNA replaced RNA as the genetic material, perhaps through the action of reverse transcriptases. With the emergence of DNA genomes came the evolution of DNA viruses. However, those with RNA genomes were and remain evolutionarily competitive, and hence they continue to survive to this day. There is no evidence that viruses are monophyletic, i.e., descended from a common ancestor: there is no single gene shared by all viruses. Nevertheless, viruses with different genomes and replication strategies do share a small set of viral hallmark genes that encode icosahedral capsid proteins, nucleic acid polymerases, helicases, integrases, and other enzymes. Tere are only distant homologs of these hallmark genes in cellular genomes. It seems likely that the widespread presence of viral hallmark genes implies their ancient, possibly precellular origin.
Viral genomes display a greater diversity of genome composition, structure, and reproduction than any other organism. Understanding the function of such diversity is an intriguing problem. As viral genomes are survivors of constant selective pressure, all configurations must provide advantages. One possibility is that different genome configurations allow unique mechanisms for control over gene expression. Tese mechanisms include synthesis of a polyprotein from () strand RNA genomes or production of subgenomic mRNAs from () strand RNA genomes. Tere is some evidence that segmented RNA genomes might have arisen from monopartite genomes, perhaps to allow regulation of the production of individual proteins (Box 3.4). Segmentation probably did not emerge to increase genome size, as the largest RNA genomes are monopartite.