The retroviruses are a very large group of viruses that infect invertebrates as well as vertebrates. Most of what we know about this group of viruses comes from studies of viruses that infect higher vertebrates. Hundreds have been studied and, although considerable divergences exist, they form a well-defined taxon. All are sufficiently similar to be classified as belonging to a single family, the Retroviridae. The family gets it name from the concept that these viruses use retrograde flow of information, from RNA to DNA, whereas the conventional flow of information in living organisms is from DNA to RNA.
The RTs of retroviruses are the most highly conserved elements of these viruses and have been used to study the relationships among them. Figure 5.1 illustrates the rela tionships among the retroviruses of higher vertebrates based on the sequences of their RTs. Included in the tree is a lineage of fish viruses, now classified as members of the genus Epsilonretrovirus. The tree is annotated to show where various new genes entered different virus lineages via recombination with the host or with other viruses. Based on these sequence relationships, the retroviruses that infect birds and mammals are classified into six genera, as illustrated in Fig. 5.1 and as listed in Table 5.1. Of these, members of three genera are characterized as simple retro-viruses, which encode only the genes gag, pro, pol, and env (and sometimes dut). The other three genera of retroviruses of higher vertebrates, as well as the fish viruses, encode, in addition, regulatory genes that control their life cycle, and they are called complex retroviruses. Notice that these regulatory genes independently entered the four different lineages of complex retroviruses represented by the four different genera (Fig. 5.1). Thus, recombination to acquire new functions has been an ongoing process in the retro-viruses. Also notice that the complex retroviruses do not group together. The epsilonretroviruses are more closely related to the gammaretroviruses, which are simple viruses,
(orfA, orfB, orfC
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