Three retroviral sequences in amphibians are distinct from those in mammals and birds

The diversity and evolution of retroviruses: perspectives from viral “fossils”

Retroviruses exclusively infect vertebrates, causing a variety of diseases. The replication of retroviruses requires reverse transcription and integration into host genomes. When infecting germline cells, retroviruses become inherited vertically, forming endogenous retroviruses (ERVs). ERVs document past viral infections, providing molecular fossils for studying the evolutionary history of retroviruses. In this review, we summarize the recent advances in understanding the diversity and evolution of retroviruses from the perspectives of viral fossils, and discuss the effects of ERVs on the evolution of host biology.

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Recent advances in understanding the diversity and evolution of retroviruses.

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Methods to analyze ERVs.

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The effects of ERVs on the evolution of host biology.

Strong purifying selection in endogenous retroviruses in the saltwater crocodile (Crocodylus porosus) in the Northern Territory of Australia

Background

Endogenous retroviruses (ERVs) are remnants of exogenous retroviruses that have integrated into the nuclear DNA of a germ-line cell. Here we present the results of a survey into the ERV complement of Crocodylus porosus, the saltwater crocodile, representing 45 individuals from 17 sampling locations in the Northern Territory of Australia. These retroelements were compared with published ERVs from other species of Crocodylia (Crocodilians; alligators, caimans, gharials and crocodiles) as well as representatives from other vertebrates. This study represents one of the first in-depth studies of ERVs within a single reptilian species shedding light on the diversity of ERVs and proliferation mechanisms in crocodilians.

Results

Analyses of the retroviral pro-pol gene region have corroborated the presence of two major clades of ERVs in C. porosus and revealed 18 potentially functional fragments out of the 227 recovered that encode intact pro-pol ORFs. Interestingly, we have identified some patterns of diversification among those ERVs as well as a novel sequence that suggests the presence of an additional retroviral genus in C. porosus. In addition, considerable diversity but low genetic divergence within one of the C. porosus ERV lineages was identified.

Conclusions

We propose that the ERV complement of C. porosus has come about through a combination of recent infections and replication of ancestral ERVs. Strong purifying selection acting on these clades suggests that this activity is recent or still occurring in the genome of this species. The discovery of potentially functional elements is an interesting development that warrants further investigation.

Characterisation of retroviruses in the horse genome and their transcriptional activity via transcriptome sequencing

The recently released draft horse genome is incompletely characterised in terms of its repetitive element profile. This paper presents characterisation of the endogenous retrovirus (ERVs) of the horse genome based on a data-mining strategy using murine leukaemia virus proteins as queries. 978 ERV gene sequences were identified. Sequences were identified from the gamma, epsilon and betaretrovirus genera. At least one full length gammaretroviral locus was identified, though the gammaretroviral sequences are very degenerate. Using these data the RNA expression of these ERVs were derived from RNA transcriptome data from a variety of equine tissues. Unlike the well studied human and murine ERVs there do not appear to be particular phylogenetic groups of equine ERVs that are more transcriptionally active. Using this novel approach provided a more technically feasible method to characterise ERV expression than previous studies.

Characterization of a Xenopus tropicalis endogenous retrovirus with developmental and stress-dependent expression

We report on the identification and characterization of XTERV1, a full-length endogenous retrovirus (ERV) within the genome of the western clawed frog (Xenopus tropicalis). XTERV1 contains all the basic genetic elements common to ERVs, including the classical 5'-long terminal repeat (LTR)-gag-pol-env-3'-LTR architecture, as well as conserved functional motifs inherent to each retroviral protein. Using phylogenetic analysis, we show that XTERV1 is related to the Epsilonretrovirus genus. The X. tropicalis genome harbors a single full-length copy with intact gag and pol open reading frames that localizes to the centromeric region of chromosome 5. About 10 full-length defective copies of XTERV1 are found interspersed in the genome, and 2 of them could be assigned to chromosomes 1 and 3. We find that XTERV1 genes are zygotically transcribed in a regulated spatiotemporal manner during frog development, including metamorphosis. Moreover, XTERV1 transcription is upregulated under certain cellular stress conditions, including cytotoxic and metabolic stresses. Interestingly, XTERV1 Env is found to be homologous to FR47, a protein upregulated following cold exposure in the freeze-tolerant wood frog (Rana sylvatica). In addition, we find that R. sylvatica FR47 mRNA originated from a retroviral element. We discuss the potential role(s) of ERVs in physiological processes in vertebrates.

Amphibian virology

Amphibians are a diverse group of species; much work remains to be done to elucidate the viruses of amphibians. Viral diseases may play an important role in wild and captive amphibian populations. Iridoviruses are a leading cause of wild amphibian mortality events in the United States and are a common cause of amphibian mortality events worldwide. In addition to frank viral diseases, viral infections may play a role in the establishment of bacterial, fungal, and parasitic diseases and are an underlying cause of neoplasia. It is important for the amphibian clinician to recognize disease syndromes and pathology that are consistent with viral etiology.

Characterization and complete nucleotide sequence of an unusual reptilian retrovirus recovered from the order Crocodylia

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.

Viruses of lower vertebrates

Viruses of lower vertebrates recently became a field of interest to the public due to increasing epizootics and economic losses of poikilothermic animals. These were reported worldwide from both wildlife and collections of aquatic poikilothermic animals. Several RNA and DNA viruses infecting fish, amphibians and reptiles have been studied intensively during the last 20 years. Many of these viruses induce diseases resulting in important economic losses of lower vertebrates, especially in fish aquaculture. In addition, some of the DNA viruses seem to be emerging pathogens involved in the worldwide decline in wildlife. Irido-, herpes- and polyomavirus infections may be involved in the reduction in the numbers of endangered amphibian and reptile species. In this context the knowledge of several important RNA viruses such as orthomyxo-, paramyxo-, rhabdo-, retro-, corona-, calici-, toga-, picorna-, noda-, reo- and birnaviruses, and DNA viruses such as parvo-, irido-, herpes-, adeno-, polyoma- and poxviruses, is described in this review.

Identification and characterization of novel human endogenous retrovirus families by phylogenetic screening of the human genome mapping project database

Human endogenous retroviruses (HERVs) were first identified almost 20 years ago, and since then numerous families have been described. It has, however, been difficult to obtain a good estimate of both the total number of independently derived families and their relationship to each other as well as to other members of the family Retroviridae. In this study, I used sequence data derived from over 150 novel HERVs, obtained from the Human Genome Mapping Project database, and a variety of recently identified nonhuman retroviruses to classify the HERVs into 22 independently acquired families. Of these, 17 families were loosely assigned to the class I HERVs, 3 to the class II HERVs and 2 to the class III HERVs. Many of these families have been identified previously, but six are described here for the first time and another four, for which only partial sequence information was previously available, were further characterized. Members of each of the 10 families are defective, and calculation of their integration dates suggested that most of them are likely to have been present within the human lineage since it diverged from the Old World monkeys more than 25 million years ago.

Development of transgenic Xenopus laevis with a high C-src gene expression

Xenopus laevis larvae with an elevated expression of c-src were generated by mating a transgenic X. laevis male frog carrying proviral Rous sarcoma virus (RSV) long terminal repeat (LTR) and most of the pol gene sequences in its sperm DNA and a normal X. laevis female frog. Offspring (15-20%) with a higher dosage of c-Src, detected in disorganized myotomal musculature and in cerebral and spinal neuronal cells by immunohistochemical analysis, developed abnormally, with edemas (in most cases), head deformities, and eye and axial system defects. In the remaining embryos, a small increase in c-src expression seemed to be compatible with normal embryogenesis. The dosage of c-Src correlated with the dosage of RSV LTR integrated in frog DNA as revealed by Southern and polymerase chain reaction (PCR) analyses. Authenticity of the integrated RSV LTR including enhancer sequence was proved by sequencing. Probing of total RNA from aberrant larvae demonstrated several times higher dosage of c-src mRNA in their tissues than in control tadpoles. We hypothesize that the integrated RSV regulatory sequences can stimulate the expression of c-src proto-oncogene of X. laevis above a threshold that interferes with the early developmental program of frog embryos.

Retroviral diversity and distribution in vertebrates

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.

Two closely related but distinct retroviruses are associated with walleye discrete epidermal hyperplasia

Walleye discrete epidermal hyperplasia (WEH) is a hyperproliferative skin disease that is prevalent on adult walleye fish throughout North America. We have identified two retroviruses associated with WEH, designated here as walleye epidermal hyperplasia virus type 1 and type 2 (WEHV1 and WEHV2), that are closely related to one another (77% identity) and to walleye dermal sarcoma virus (64% identity) within the polymerase region. WEHV1 and/or WEHV2 viral DNA was readily detected by PCR in hyperplastic tissue samples, but only low levels of viral DNA were detected in uninvolved skin. Southern blot analysis showed one to three copies of integrated WEHV2 viral DNA in lesions but did not detect WEHV2 viral DNA in uninvolved skin from the same fish. Northern blots detected abundant levels of WEHV1 and/or WEHV2 virion RNA transcripts of approximately 13 kb in hyperplastic tissue, but virion RNA was not observed in uninvolved skin and muscle. These results suggest that WEHV1 and WEHV2 are the causative agents of discrete epidermal hyperplasia.

Human endogenous retrovirus type I-related viruses have an apparently widespread distribution within vertebrates

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.