Characterization of a
            <i>Xenopus tropicalis</i>
            Endogenous Retrovirus with Developmental and Stress-Dependent Expression

Sinzelle, Ludivine; Carradec, Quentin; Paillard, Elodie; Bronchain, Odile; Pollet, Nicolas

doi:10.1128/jvi.01979-10

Cited by 17 publications

(15 citation statements)

References 65 publications

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“…By tracing the process backwards, and assuming host neutral evolution, it is possible to estimate the ERV integration date. This method has been used to date many ERV integration events, revealing that most retroviral families are many millions of years old (Brown et al, 2014;Katzourakis and Tristem, 2005;Lavie et al, 2004;Martins and Villesen, 2011;Sinzelle et al, 2011;Tristem, 2000). These methods are based on a reasonable assumption that EVE sequences evolve at the host neutral rate after the duplication process.…”

Section: Dating Eves and Generating Robust Viral Evolutionary Timescalesmentioning

confidence: 98%

Endogenous viruses: Connecting recent and ancient viral evolution

2015

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The rapid rates of viral evolution allow us to reconstruct the recent history of viruses in great detail. This feature, however, also results in rapid erosion of evolutionary signal within viral molecular data, impeding studies of their deep history. Thus, the further back in time, the less accurate the inference becomes. Furthermore, reconstructing complex histories of transmission can be challenging, especially where extinct viral lineages are concerned. This problem has been partially solved by the discovery of viruses embedded in host genomes, known as endogenous viral elements (EVEs). Some of these endogenous viruses are derived from ancient relatives of extant viruses, allowing us to better examine ancient viral host range, geographical distribution and transmission routes. Moreover, our knowledge of viral evolutionary timescales and rate dynamics has also been greatly improved by their discovery, thereby bridging the gap between recent and ancient viral evolution.

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Section: Dating Eves and Generating Robust Viral Evolutionary Timescalesmentioning

confidence: 98%

Endogenous viruses: Connecting recent and ancient viral evolution

2015

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“…psilonretroviruses are a genus of retrovirus usually associated with fish (1). Several common proliferative diseases in commercially important fish species are caused by these viruses.…”

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confidence: 99%

Multiple Groups of Endogenous Epsilon-Like Retroviruses Conserved across Primates

Brown

Emes

Tarlinton

2014

J Virol

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Several types of cancer in fish are caused by retroviruses, including those responsible for major outbreaks of disease, such as walleye dermal sarcoma virus and salmon swim bladder sarcoma virus. These viruses form a phylogenetic group often described as the epsilonretrovirus genus. Epsilon-like retroviruses have become endogenous retroviruses (ERVs) on several occasions, integrating into germ line cells to become part of the host genome, and sections of fish and amphibian genomes are derived from epsilon-like retroviruses. However, epsilon-like ERVs have been identified in very few mammals. We have developed a pipeline to screen full genomes for ERVs, and using this pipeline, we have located over 800 endogenous epsilon-like ERV fragments in primate genomes. Genomes from 32 species of mammals and birds were screened, and epsilon-like ERV fragments were found in all primate and tree shrew genomes but no others. These viruses appear to have entered the genome of a common ancestor of Old and New World monkeys between 42 million and 65 million years ago. Based on these results, there is an ancient evolutionary relationship between epsilon-like retroviruses and primates. Clearly, these viruses had the potential to infect the ancestors of primates and were at some point a common pathogen in these hosts. Therefore, this result raises questions about the potential of epsilonretroviruses to infect humans and other primates and about the evolutionary history of these retroviruses. IMPORTANCEEpsilonretroviruses are a group of retroviruses that cause several important diseases in fish. Retroviruses have the ability to become a permanent part of the DNA of their host by entering the germ line as endogenous retroviruses (ERVs), where they lose their infectivity over time but can be recognized as retroviruses for millions of years. Very few mammals are known to have epsilon-like ERVs; however, we have identified over 800 fragments of endogenous epsilon-like ERVs in the genomes of all major groups of primates, including humans. These viruses seem to have circulated and infected primate ancestors 42 to 65 million years ago. We are now interested in how these viruses have evolved and whether they have the potential to infect modern humans or other primates.

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“…Furthermore, the genome sequence of the cane toad harbors 8 full-length ( Fig. 3C) and 21 truncated genomic copies of RMERV, a number comparable with those of an X. tropicalis ERV, XTERV1 (n ϭ 11) (35). We also identified 204 partial RMERV transcripts in publicly available splenic transcriptomes (Table S3), indicating the widespread genomic insertion and transcription of RMERV-like sequences in cane toads across Australia.…”

Section: Discussionmentioning

confidence: 79%

“…A novel full-length epsilonretrovirus sequence was detected in cane toad liver. There is a considerable gap in the scientific literature on amphibian retroviruses, with only two endogenous retroviruses (ERVs) identified so far in Xenopus laevis and Xenopus tropicalis (35,36). To address this, we aimed to identify novel retroviruses in the cane toad.…”

Section: Resultsmentioning

confidence: 99%

Viral Discovery in the Invasive Australian Cane Toad (Rhinella marina) Using Metatranscriptomic and Genomic Approaches

Russo

Eden

Tuipulotu

et al. 2018

J Virol

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Cane toads are a notorious invasive species, inhabiting over 1.2 million km of Australia and threatening native biodiversity. The release of pathogenic cane toad viruses is one possible biocontrol strategy yet is currently hindered by the poorly described cane toad virome. Metatranscriptomic analysis of 16 cane toad livers revealed the presence of a novel and full-length picornavirus, Rhimavirus A (RhiV-A), a member of a reptile- and amphibian-specific cluster of the basal to the-like group. In the combined liver transcriptome, we also identified a complete genome sequence of a distinct epsilonretrovirus, Rhinella marina endogenous retrovirus (RMERV). The recently sequenced cane toad genome contains 8 complete RMERV proviruses as well as 21 additional truncated insertions. The oldest full-length RMERV provirus was estimated to have inserted 1.9 million years ago (MYA). To screen for these viral sequences in additional toads, we analyzed publicly available transcriptomes from six diverse Australian locations. RhiV-A transcripts were identified in toads sampled from three locations across 1,000 km of Australia, stretching to the current Western Australia (WA) invasion front, while RMERV transcripts were observed at all six sites. Finally, we scanned the cane toad genome for nonretroviral endogenous viral elements, finding three sequences related to small DNA viruses in the family This shows ancestral circoviral infection with subsequent genomic integration. The identification of these current and past viral infections enriches our knowledge of the cane toad virome, an understanding of which will facilitate future work on infection and disease in this important invasive species. Cane toads are poisonous amphibians that were introduced to Australia in 1935 for insect control. Since then, their population has increased dramatically, and they now threaten many native Australian species. One potential method to control the population is to release a cane toad virus with high mortality rates, yet few cane toad viruses have been characterized. This study samples cane toads from different Australian locations and uses an RNA sequencing and computational approach to find new viruses. We report novel complete picornavirus and retrovirus sequences that were genetically similar to viruses infecting frogs, reptiles, and fish. Using data generated in other studies, we show that these viral sequences are present in cane toads from distinct Australian locations. Three sequences related to circoviruses were also found in the toad genome. The identification of new viral sequences will aid future studies that investigate their prevalence and potential as agents for biocontrol.

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Characterization of a Xenopus tropicalis Endogenous Retrovirus with Developmental and Stress-Dependent Expression

Cited by 17 publications

References 65 publications

Endogenous viruses: Connecting recent and ancient viral evolution

Endogenous viruses: Connecting recent and ancient viral evolution

Multiple Groups of Endogenous Epsilon-Like Retroviruses Conserved across Primates

Viral Discovery in the Invasive Australian Cane Toad (Rhinella marina) Using Metatranscriptomic and Genomic Approaches

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