Molecular Evolution of the Herpesvirales

McGeoch, Duncan J. and Davison, Andrew J. and Dolan, Aidan and Gatherer, Derek and Sevilla-Reyes, Edgar E. (2008) Molecular Evolution of the Herpesvirales. In: Origin and Evolution of Viruses. Elsevier Ltd, pp. 447-475. ISBN 9780123741530

Abstract

The herpesviruses are a group of large DNA viruses, originally defined by their characteristic virion structure. On the basis of genome sequences they have been assigned to an order, Herpesvirales, containing three families: the Herpesviridae, infecting mammals, birds and reptiles; the Alloherpesviridae, infecting amphibians and fish; and the Malacoherpesviridae, populated only by an oyster virus. Viruses in the Herpesviridae are descended from a common ancestor, as are those in the Alloherpesviridae, but connections between the families are tenuous.The Herpesviridae include eight human viruses. Three widely diverged subfamilies, the Alpha -, Beta -, and Gammaherpesvirinae, are defined. A robust phylogenetic tree has been constructed for this family, based on amino acid sequences from conserved genes. Within sub-families, aspects of branching patterns resemble those of mammalian host lineages, indicating long-term co-evolution of virus and host lines and thus enabling inference of a timeframe for the tree. On this basis the tree is estimated to be about 400 million years in depth. Some 40 genes are conserved across the Herpesviridae, with recognized roles mainly in capsid structure and DNA replication machinery. Functions of non-conserved genes include roles in immune modulation and latency. Some herpesvirus genes appear to have originated by capture from cellular genomes, and others by genesis de novo. Multigene families are common, notably in the Betaherpesvirinae. Aspects of DNA replication systems have diverged among subfamilies, with complex arrangements for initiation of DNA synthesis in the Gammaherpesvirinae and part of the Betaherpesvirinae, and disabling in the Betaherpesvirinae ofgenes for nucleotide anabolism. Comparative genomic sequenc-ing of herpesvirus isolates is revealing novel aspects of recent evolution. Recombination among strains has emerged as a general phenomenon. Also, certain latent cycle genes of gammaherpesviruses uniquely evince signs of widespread diversifying selection. Genomic organizations in theAlloherpes-viridae and Malacoherpesviridae look gener-ally similar to those of the Herpesviridae, and the Alloherpesviridae are also widely diverse.