Abstract: Endogenous retroviruses (ERVs) are widespread in vertebrate genomes and have been loosely grouped into "classes" on the basis of their phylogenetic relatedness to the established genera of exogenous retroviruses. Four of these genera-the lentiviruses, alpharetroviruses, betaretroviruses, and deltaretroviruses-form a well-supported clade in retroviral phylogenies, and ERVs that group with these genera have been termed class II ERVs. We used PCR amplification and sequencing of retroviral fragments from more than 130 vertebrate taxa to investigate the evolution of the class II retroviruses in detail. We confirm that class II retroviruses are largely confined to mammalian and avian hosts and provide evidence for a major novel group of avian retroviruses, and we identify additional members of both the alpha- and the betaretrovirus genera. Phylogenetic analyses demonstrated that the avian and mammalian viruses form distinct monophyletic groups, implying that interclass transmission has occurred only rarely during the evolution of the class II retroviruses. In contrast to previous reports, the lentiviruses clustered as sister taxa to several endogenous retroviruses derived from rodents and insectivores. This topology was further supported by the shared loss of both the class II PR-Pol frameshift site and the class II retrovirus G-patch domain.
Abstract: A novel group of retroviruses found within the order Crocodylia are described. Phylogenetic analyses demonstrate that they are probably the most divergent members of the Retroviridae described to date; even the most conserved regions of Pol show an average of only 23% amino acid identity when compared to other retroviruses.
Abstract: We developed a degenerate PCR procedure to simultaneously amplify products from divergent retrotransposon families within the genomes of Anopheles mosquitoes. The procedure required cloning of multiple PCR products, but more than half of the clones subsequently sequenced were of retrotransposon origin. These included Copia-like and LINE retrotransposons, as well as the first Gypsy-like retrotransposons reported from mosquitoes. Furthermore, some Anopheles retrotransposon sequences showed similarity to the divergent Pao element from the silkmoth Bombyx mori. Phylogenetic analyses provided consistently strong bootstrap support (> 95%) for a major clade of Pao-like retrotransposons, which includes five mosquito sequences and the recently discovered Drosophila retrotransposons BEL and ninja. This appears to represent a new family of Pao-like LTR-retrotransposons distinct from the Copia and Gypsy families.
Abstract: Retroviruses are capable of infectious horizontal transmission between hosts, usually between individuals within a single species, although a number of probable zoonotic infections resulting from transmission between different species of placental mammals have also been reported. Despite these data, it remains unclear how often interspecies transmission events occur or whether their frequency is influenced by the evolutionary distance between host taxa. To address this problem we used PCR to amplify and characterize endogenous retroviruses related to the murine leukemia viruses. We show that members of this retroviral genus are harbored by considerably more organisms than previously thought and that phylogenetic analysis demonstrates that viruses isolated from a particular host class generally cluster together, suggesting that infectious virus horizontal transfer between vertebrate classes occurs only rarely. However, two recent instances of transmission of zoonotic infections between distantly related host organisms were identified. One, from mammals to birds, has led to a rapid adaptive radiation into other avian hosts. The other, between placental and marsupial mammals, involves viruses clustering with recently described porcine retroviruses, adding to concerns regarding the xenotransplantation of pig organs to humans.
Abstract: Gypsy LTR-retrotransposons have been identified in the genomes of many organisms, but only a small number of vertebrate examples have been reported to date. Here we show that members of this family are likely to be widespread in many vertebrate classes with the possible exceptions of mammals and birds. Phylogenetic analyses demonstrate that although there are several distinct lineages of vertebrate gypsy LTR-retrotransposons, the majority clusters into one monophyletic clade. Groups of fungal, plant, and insect elements were also observed, suggesting horizontal transfer between phyla may be infrequent. However, in contrast to this, there was little evidence to support sister relationships between elements derived from vertebrate and insect hosts. In fact, the majority of the vertebrate elements appeared to be most closely related to a group of gypsy LTR-retrotransposons present within fungi. This implies either that at least one horizontal transmission between these two phyla has occurred previously or that a gypsy LTR-retrotransposon lineage has been lost from insect taxa.
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.
Abstract: Retroviruses from lower vertebrate hosts have been poorly characterized to date. Few sequences have been isolated, and those which have been reported are all highly divergent when compared to the retroviruses known to be harbored by mammals and birds. Here we show that retroviruses with significant homology to the human endogenous retrovirus type I (HERV-I) are present within the genomes of fish, reptiles, birds, and mammals and that they may well be widespread within many vertebrates. Phylogenetic analysis of nucleotide sequences strongly supported the inclusion of viruses from each of these vertebrate classes into one monophyletic group. This analysis also demonstrated that the HERV-I-related viruses are more closely related to retroviruses belonging to the murine leukemia virus genus than to members of the other retroviral genera. The presence of HERV-I-related retroviruses in so many disparate vertebrate hosts suggests that other endogenous human retroviruses may also have a much wider distribution than is currently appreciated.
