Toward a Comprehensive Phylogeny for Mammalian and Avian Herpesviruses

Abstract

With the aim of deriving a definitive phylogenetic tree for as many mammalian and avian herpesvirus species as possible, alignments were made of amino acid sequences from eight conserved and ubiquitously present genes of herpesviruses, with 48 virus species each represented by at least one gene. Phylogenetic trees for both single-gene and concatenated alignments were evaluated thoroughly by maximum-likelihood methods, with each of the three herpesvirus subfamilies (the Alpha-, Beta-, and Gammaherpesvirinae) examined independently. Composite trees were constructed starting with the top-scoring tree based on the broadest set of genes and supplemented by addition of virus species from trees based on narrower gene sets, to give finally a 46-species tree; branching order for three regions within the tree remained unresolved. Sublineages of the Alpha-and Betaherpesvirinae showed extensive cospeciation with host lineages by criteria of congruence in branching patterns and consistency in extent of divergence. The Gammaherpesvirinae presented a more complex picture, with both higher and lower substitution rates in different sublineages. The final tree obtained represents the most detailed view to date of phylogenetic relationships in any family of large-genome viruses.The Herpesviridae are a numerous family of large DNA viruses which have as their natural hosts humans, other mammals and vertebrates, and in one described case, an invertebrate (11, 16). The genomes of herpesviruses of mammals and birds clearly evince descent from a common ancestor, but with a great range of variation in terms of nucleotide substitution, gene content, and genomic arrangement (15). The Herpesviridae have been divided into three subfamilies, the Alpha-, Beta-, and Gammaherpesvirinae, initially from their distinct biological properties and latterly more precisely on the basis of their genomic attributes (16). Over the last two decades an extensive body of herpesvirus DNA sequence data has been built up, from single-gene analyses to studies of whole genomes (in the range 120 to 240 kbp). Phylogenetic studies using herpesvirus sequences have been undertaken, demonstrating clear division into the three subfamilies and, in some sublineages, patterns of divergence consistent with cospeciation of virus and host (7,9,13,14). Herpesviruses of fish (2, 3), amphibians (4), and invertebrates (A. J. Davison, personal communication) are only remotely related to the mammalian and avian viruses, while certain turtle viruses (the only reptile herpesviruses for which some sequence is known) probably group with the mammalian and avian viruses (18).We describe in this report a major update of herpesvirus phylogenetic analysis, using the greatly increased number of gene sequences now available from a wide range of mammalian and avian herpesviruses, and enabled by advances both in processing power of modern computers and in methods for analysis of relationships among gene sequences. We aimed to produce by good current practice a single phylogenetic tree that would...

Aggregating Homologous Protein Families in Evolutionary Reconstructions of Herpesviruses

“…Additional support for this being a suitable tree is that very similar trees have been constructed by us using more comprehensive data, such as the genome phylogenetic profiles formed by the 257 HPFs that are present in two or more of the genomes [2]. Second, our tree is similar to that published in [11] and reproduced in [5] on the subset of 25 herpesvirus genomes common to our tree. The latter tree is based on comprehensive data including expert knowledge.…”

“…The latter tree is based on comprehensive data including expert knowledge. Our tree in Figure 1 differs from the tree in [11,5] on two clusters rooted at nodes 43 (four β genomes) and 53 (seven γ genomes), respectively. This difference, however, falls within the margin of uncertainty of the tree topology indicated in [11,5].…”

Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates

“…Although nearly all RNA viruses seem to experience very rapid evolutionary change-usually expressed as rates of nucleotide substitution per site-far lower rates are observed in some large double-stranded DNA (dsDNA) viruses. For example, the nucleotide substitution rates for variola virus and herpes simplex virus (dsDNA) have been reported to be as low as 9.32 Â 10 -6 and 3 Â 10 29 substitutions per site per year, respectively [6,7], and hence between three to six orders of magnitude lower than that of influenza virus A (negative-sense singlestranded RNA; 2ssRNA) at 4.1 Â 10 23 substitutions per site per year [8]. Overall, most RNA viruses seem to exhibit evolutionary rates of around 10 23 to 10 24 substitutions per site per year [9].…”

Herpesviral infection and Toll-like receptor 2

“…The herpesviruses have co-evolved with their vertebrate hosts for more than one hundred million years to establish lifelong infections (Soderberg-Naucler and Nelson, 1999;McGeoch et al, 2000). This co-evolution has created viruses which are well adapted to the human host and environment.…”