Integrating reptilian herpesviruses into the family herpesviridae

Abstract

The phylogeny of reptilian herpesviruses (HVs) relative to mammalian and avian HVs was investigated by using available gene sequences and by alignment of encoded amino acid sequences and derivation of trees by maximum-likelihood and Bayesian methods. Phylogenetic loci were obtained for green turtle HV (GTHV) primarily on the basis of DNA polymerase (POL) and DNA binding protein sequences, and for lung-eye-trachea disease-associated HV (LETV) primarily from its glycoprotein B sequence; both have nodes on the branch leading to recognized species in the Alphaherpesvirinae subfamily and should be regarded as new members of that subfamily. A similar but less well defined locus was obtained for an iguanid HV based on a partial POL sequence. On the basis of short POL sequences (around 60 amino acid residues), it appeared likely that GTHV and LETV belong to a private clade and that three HVs of gerrhosaurs (plated lizards) are associated with the iguanid HV. Based on phylogenetic branching patterns for mammalian HV lineages that mirror those of host lineages, we estimated a date for the HV tree's root of around 400 million years ago. Estimated dates for branching events in the development of reptilian, avian, and mammalian Alphaherpesvirinae lineages could plausibly be accounted for in part but not completely by ancient coevolution of these virus lines with reptilian lineages and with the development of birds and mammals from reptilian progenitors.

FIG. 1.

POL and DBP trees, including GTHV. The top-scoring trees are shown based on HV POL amino acid sequences (A) and HV DBP amino acid sequences (B). The trees are presented as unrooted and in a condensed format showing genus-level groupings rather than individual species, with the multiple-branch region of each genus-level clade represented by a single heavy line. In each tree, the estimated position of the root is indicated by a filled arrowhead, calculated as the midpoint of the distance from the mean positions of branch tips in the alpha subfamily to the mean positions of branch tips in the beta and gamma subfamilies. A common scale bar is indicated for divergence (i.e., substitutions per amino acid site). Genus-equivalent labels are as follows: α1, Simplexvirus; α2, Varicellovirus; α3, Mardivirus; α4, Iltovirus; β1, Cytomegalovirus (including Muromegalovirus and Tupaia HV); β2, Roseolovirus (including porcine cytomegalovirus); β3, elephant endothelial HV; γ1, Lymphocryptovirus; γ2, Rhadinovirus. (A) The POL tree contains 44 species in addition to GTHV, distributed as follows: α1, 4 species; α2, 7 species; α3, 3 species; α4, 1 species; β1, 8 species; β2, 3 species; β3, 1 species; γ1, 3 species; γ2, 14 species. (B) The DBP tree contains 35 species in addition to GTHV, distributed as follows: α1, 4 species; α2, 6 species; α3, 3 species; α4, 1 species; β1, 7 species; β2, 2 species; γ1, 3 species; γ2, 9 species.

FIG. 2.

gB tree, including LETV. The top-scoring tree is shown based on HV gB amino acid sequences, obtained by two separate methods (Codeml and MrBayes). The format is as described for Fig. 1. The gB tree contains 60 species in addition to LETV, distributed as follows: α1, 10 species; α2, 13 species; α3, 3 species; α4, 1 species; β1, 9 species; β2, 3 species; β3, 1 species; γ1, 6 species; γ2, 14 species.

FIG. 3.

Trees based on a part of POL, including IgHV. The two top equal trees are shown based on a 226-amino-acid alignment of a section of POL. The alignment included 46 species: 45 as described for Fig. 1A plus IgHV. The format is as described for Fig. 1.

FIG. 4.

Molecular clock tree based on DBP plus POL sequences. A concatenated alignment for DBP and POL amino acid sequences of 36 species was used to produce a molecular clock, and a timescale was applied based on the correlation of divergence in the α2 lineage with paleontological dates as described in the text. Regions in the α1, α2, and α3 lineages occupied by multiple branches are shown as heavy lines, and the reduced outlines for the beta and gamma lineages are shown in gray.

FIG. 5.

Comparison of host and alphaherpesvirus trees. (A) Consensus tree for reptilian, avian, and mammalian lineages, derived from published data, with branch names chosen for comparison with the HV tree. The gray bar represents multiple branchings treated as unresolved. (B) Summary tree for alphaherpesvirus lineages, based on the gB tree and DBP plus POL molecular clock tree (Table 2). The gray bar and branch represent unresolved branching details for GTHV, LETV, and IgHV. In both trees, nodes that are discussed in the text are labeled. A common timescale is shown at the foot. inc., includes.