Retroviral diversity and distribution in vertebrates

Abstract

We used the PCR to screen for the presence of endogenous retroviruses within the genomes of 18 vertebrate orders across eight classes, concentrating on reptilian, amphibian, and piscine hosts. Thirty novel retroviral sequences were isolated and characterized by sequencing approximately 1 kb of their encoded protease and reverse transcriptase genes. Isolation of novel viruses from so many disparate hosts suggests that retroviruses are likely to be ubiquitous within all but the most basal vertebrate classes and, furthermore, gives a good indication of the overall retroviral diversity within vertebrates. Phylogenetic analysis demonstrated that viruses clustering with (but not necessarily closely related to) the spumaviruses and murine leukemia viruses are widespread and abundant in vertebrate genomes. In contrast, we were unable to identify any viruses from hosts outside of mammals and birds which grouped with the other five currently recognized retroviral genera: the lentiviruses, human T-cell leukemia-related viruses, avian leukemia virus-related retroviruses, type D retroviruses, and mammalian type B retroviruses. There was also some indication that viruses isolated from individual vertebrate classes tended to cluster together in phylogenetic reconstructions. This implies that the horizontal transmission of at least some retroviruses, between some vertebrate classes, occurs relatively infrequently. It is likely that many of the retroviral sequences described here are distinct enough from those of previously characterized viruses to represent novel retroviral genera.

FIG. 1

Distribution of retroviral sequences within vertebrates and other Metazoa. The phylogeny is based on that described by Young (47). Endogenous retroviral sequences identified by PCR screening are indicated by a +, whereas a − represents screened taxa from which retroviral sequences have yet to be identified.

FIG. 2

Amino acid alignment derived from retroviral reverse transcriptase proteins, based on that described by Xiong and Eickbush (45). Sequences identified in this study are indicated in bold type. The underlined regions of the alignment were used in subsequent phylogenetic analysis. Asterisks represent in-frame stop codons, and missing data (due to frameshifts or deletions) are indicated by question marks. Three isolates, RV-brook trout, RV-brown trout, and RV-tiger salamanderI, contained large deletions and are not shown.

FIG. 2

Amino acid alignment derived from retroviral reverse transcriptase proteins, based on that described by Xiong and Eickbush (45). Sequences identified in this study are indicated in bold type. The underlined regions of the alignment were used in subsequent phylogenetic analysis. Asterisks represent in-frame stop codons, and missing data (due to frameshifts or deletions) are indicated by question marks. Three isolates, RV-brook trout, RV-brown trout, and RV-tiger salamanderI, contained large deletions and are not shown.

FIG. 3

Phylogenetic trees of the retroviruses based on the alignment shown in Fig. 2, with the addition of 30 residues derived from the protease protein. Exogenous isolates are indicated by bold type. The genera to which particular retroviruses have been assigned are also shown. (a) Unrooted neighbor-joining bootstrap tree. The figures on each branch represent bootstrap support (from 1,000 replicates), with percentage values on only those branches with support greater than 50 being shown. Unresolved branches are shown as polytomies. (b) Neighbor-joining tree rooted on several gypsy LTR retrotransposon sequences (gypsy, Del, Ty3, and micropia), with figures on each branch again showing percentage bootstrap support (1,000 replicates). (c) Rooted neighbor-joining tree with branch lengths proportional to the genetic distance between the sequences. The tree is rooted as described in the legend to panel a. (d) Strict consensus of six equal-length trees identified by maximum parsimony. Bootstrap values were generated from 100 replicates (each of 25 random-sequence additions) by using the unordered matrix. The tree is rooted as described in the legend to panel a.

FIG. 3

Phylogenetic trees of the retroviruses based on the alignment shown in Fig. 2, with the addition of 30 residues derived from the protease protein. Exogenous isolates are indicated by bold type. The genera to which particular retroviruses have been assigned are also shown. (a) Unrooted neighbor-joining bootstrap tree. The figures on each branch represent bootstrap support (from 1,000 replicates), with percentage values on only those branches with support greater than 50 being shown. Unresolved branches are shown as polytomies. (b) Neighbor-joining tree rooted on several gypsy LTR retrotransposon sequences (gypsy, Del, Ty3, and micropia), with figures on each branch again showing percentage bootstrap support (1,000 replicates). (c) Rooted neighbor-joining tree with branch lengths proportional to the genetic distance between the sequences. The tree is rooted as described in the legend to panel a. (d) Strict consensus of six equal-length trees identified by maximum parsimony. Bootstrap values were generated from 100 replicates (each of 25 random-sequence additions) by using the unordered matrix. The tree is rooted as described in the legend to panel a.

FIG. 3

Phylogenetic trees of the retroviruses based on the alignment shown in Fig. 2, with the addition of 30 residues derived from the protease protein. Exogenous isolates are indicated by bold type. The genera to which particular retroviruses have been assigned are also shown. (a) Unrooted neighbor-joining bootstrap tree. The figures on each branch represent bootstrap support (from 1,000 replicates), with percentage values on only those branches with support greater than 50 being shown. Unresolved branches are shown as polytomies. (b) Neighbor-joining tree rooted on several gypsy LTR retrotransposon sequences (gypsy, Del, Ty3, and micropia), with figures on each branch again showing percentage bootstrap support (1,000 replicates). (c) Rooted neighbor-joining tree with branch lengths proportional to the genetic distance between the sequences. The tree is rooted as described in the legend to panel a. (d) Strict consensus of six equal-length trees identified by maximum parsimony. Bootstrap values were generated from 100 replicates (each of 25 random-sequence additions) by using the unordered matrix. The tree is rooted as described in the legend to panel a.

FIG. 3

Phylogenetic trees of the retroviruses based on the alignment shown in Fig. 2, with the addition of 30 residues derived from the protease protein. Exogenous isolates are indicated by bold type. The genera to which particular retroviruses have been assigned are also shown. (a) Unrooted neighbor-joining bootstrap tree. The figures on each branch represent bootstrap support (from 1,000 replicates), with percentage values on only those branches with support greater than 50 being shown. Unresolved branches are shown as polytomies. (b) Neighbor-joining tree rooted on several gypsy LTR retrotransposon sequences (gypsy, Del, Ty3, and micropia), with figures on each branch again showing percentage bootstrap support (1,000 replicates). (c) Rooted neighbor-joining tree with branch lengths proportional to the genetic distance between the sequences. The tree is rooted as described in the legend to panel a. (d) Strict consensus of six equal-length trees identified by maximum parsimony. Bootstrap values were generated from 100 replicates (each of 25 random-sequence additions) by using the unordered matrix. The tree is rooted as described in the legend to panel a.

FIG. 4

Unrooted maximum parsimony tree of the group III viruses shown in Fig. 3. Branch lengths are proportional to the number of changes required to generate the observed variation. Numbers on each branch reflect percentage bootstrap support using maximum parsimony (upper value) or neighbor-joining (lower value).