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.Retroviruses (family Retroviridae) are characterized by a unique replication strategy. The RNA genome of an extracellular retrovirus is first copied into DNA by virus-encoded reverse transcriptase (RT) and is then integrated into the nuclear DNA of the host cell (35). Integration is highly stable and, consequently, infection of germ line cells can lead to vertical transmission of retroviruses from parent to offspring as Mendelian alleles (8). These retroviruses are termed endogenous (to distinguish them from their horizontally transmitted, exogenous counterparts), and they have been identified in almost all vertebrate orders examined (8, 16). Some endogenous retroviruses (ERVs) represent endogenized copies of extant exogenous retroviruses, but the majority are very old and appear to lack closely related exogenous counterparts (8,16). Analysis of these ERVs in the genomes of humans, mice, and other species indicates a longstanding association between retroviruses and vertebrates, probably dating back several hundred million years, during which retroviruses have repeatedly colonized host genomes (12,19,20,23).Most ERVs show clear homology to one another and to modern exogenous retroviruses, especially across the RT gene, which is relatively refractory to nonsynonymous substitution. Diverse retrovirus sequences can therefore be aligned in order to investigate phylogenetic relationships, and this has been instrumental in the classification of exogenous retroviruses into seven genera (alpha-, beta-, gamma-, delta-, and epsilonretroviruses; lentivirus; and spumavirus) (12,26,34,37). Although many ERVs have not been assigned to particular genera, there is a growing tendency to group them ...

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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.The Retroviridae are a family of selfish genetic elements with a host range restricted to vertebrates (2, 5-7, 9, 22). They are currently subdivided into seven genera, all but one of which are harbored by mammalian or avian hosts (8,11,20,21). There are currently no full-length retroviral sequences recovered from amphibians or reptiles, but analysis of PCR-amplified fragments from both vertebrate classes indicates that they harbor many elements that are only distantly related to other retroviruses (9,18,19).We have previously described a large number of novel retroviruses via PCR amplification of approximately 1kb of the pol gene, followed by phylogenetic analysis (9,14). During these studies, we characterized eight very unusual retroelements recovered from the order Crocodylia. The elements were present in all three extant families (the Alligatoridae, Crocodylidae, and Gavialidae (Table 1), and it is likely that similar elements remain to be found in many of the remaining 14 species constituting the order Crocodylia (1).All eight elements were found to encode at least one inframe stop codon or frameshift mutation, indicating they were endogenous in origin. We were unable to detect related elements in other organisms, either by PCR screening of other vertebrate taxa or by low-stringency hybridization of genomic DNA obtained from several birds, reptiles, amphibians, and fish. It is therefore likely that related elements are not widespread within vertebrate genomes.To characterize these elements further, we constructed a genomic DNA library from liver tissue derived from a captive Nile crocodile (Crocodylus niloticus). Genomic DNA was digested with Sau3A and 10-to 15-kb fragments were ligated into BamHI-digested lambda EMBL3, packaged, and plated. Nine plaque-purified positive clones were identified; three, termed CnEVI to -III, were fully sequenced.Open reading frame (ORF) maps of CnEVI to -III revealed that each carried multiple in-frame stop codons and frameshift mutations. Analysis of a consensus sequence constructed from all three elements indicated that their original genomic organization probably consisted of two large ORFs, corresponding to the major retroviral genes gag and pol, and a small third ORF immediately upstream of the 3Ј long terminal repeat (LTR).CnEVI contains a 593-bp 5Ј LTR and a 585-bp 3Ј LTR which differ from each other by approximately 7%, indicating that integration occurred some time ago. We were unable to unambiguously identify promoter or polyadenylation signals, but a putative polypurine tract and primer binding site were identified adjacent to the 3Ј and 5Ј LTRs, respectively. The primer binding site showed 14 of 18 matches to human tRNA (Ser).The CnEVI Gag polypr...

We report the first full-length sequence of an endogenous amphibian retrovirus derived from the African clawed toad Xenopus laevis. The virus, termed Xen1, has one of the largest endogenous retroviral genomes described to date of over 10 kb in length and it also has a relatively complex genomic organisation consisting of LTR-orf1, orf2, gag, pol, env-LTR. Orfs 1 and 2 are novel, duplicated genes of unknown function. Phylogenetic analysis indicates that Xen1 is most closely related to the epsilon -retroviruses WDSV and WEHV types 1 and 2, which are large, complex exogenous retroviruses present within Walleye fish.

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