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This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact

Medicine --- Immunology --- virus --- evolution --- human immunity --- endogenous retrovirus --- virus --- evolution --- human immunity --- endogenous retrovirus

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Retrotransposons are present in essentially all eukaryotic genomes and come in two basic flavors: those that are bracketed by long terminal repeats (LTRs) and share a common ancestor with retroviruses, and non-LTR retrotransposons that have a distinct lineage and remain transpositionally active in humans. Both types of retrotransposons replicate through an RNA intermediate, stably integrate into the host genome and have accumulated to a very high copy number in mammals and certain plant species. Autonomous elements produce transcripts capable of undergoing reverse transcription, and minimally encode proteins with reverse transcriptase, integrase/endonucleolytic, and nucleic acid chaperone activities. Retrotransposons are currently distinguished from viruses, since the process of retrotransposition is not infectious. However, this boundary may prove to be provisional as we learn more about these mobile genetic elements. The goal of this Special Issue of Viruses is to highlight progress in understanding the mechanism and consequences of retrotransposon movement. Several active research areas may be covered in reviews and research articles, including the roles of cellular modulators and defense systems, retrotransposon expression and replication, retrotransposon-induced mutations and their association with human diseases, and how these widely disseminated elements mold eukaryotic genomes.

Non-LTR retrotransposon --- Integration --- Human disease --- Endogenous retrovirus --- Reverse transcription --- Host factors --- Genome evolution --- LTR retrotransposon

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Foamy viruses, currently referred to as spumaretroviruses, are the most ancient retroviruses as evidenced by traces of viral sequences dispersed in all vertebrate classes from fish to mammals. Additionally, infectious foamy viruses circulate in a variety of mammalian species including simian, bovine, equine, caprine, and feline. Foamy viruses have many unique features which led to the division of the retrovirus family into two subfamilies, the Orthoretrovirinae and Spumaretrovirinae. In vitro, foamy viruses have a broad host range and in vivo, human infections have been described due to cross-species transmission from infected nonhuman primates. Thus far, there are no reports of virus-induced disease in humans or in the natural host species. These unique properties of foamy viruses have led researchers to develop foamy viruses as gene therapy vectors to study virus–virus and virus–host interactions for identifying factors involved in virus replication, transmission, and immune regulation that could influence potential clinical outcomes in humans as well as for using endogenous foamy virus sequences in the analysis of host species evolution.

Medicine --- Neurosciences --- spumavirus --- feline illness --- proviral load --- neglected virus --- bovine foamy virus --- infectious clone --- particle release --- cell-free transmission --- foamy virus --- spumaretrovirus --- cross-species virus transmission --- zoonosis --- restriction factors --- immune responses --- FV vectors --- virus replication --- latent infection --- feline foamy virus --- epidemiology --- retrovirus --- Spumaretrovirus --- mountain lion --- Puma concolor --- ELISA --- protease --- reverse transcriptase --- RNase H --- reverse transcription --- antiviral drugs --- resistance --- simian foamy virus --- gibbon --- lesser apes --- co-evolution --- complete viral genome --- equine foamy virus --- isolation --- Japan --- sero-epidemiology --- reptile foamy virus --- endogenous foamy virus --- endogenous retrovirus --- ancient retroviruses --- co-speciation --- foamy virus-host interactions --- viral tropism --- infection --- kidney --- cats --- chronic kidney disease --- chronic renal disease --- integrase --- integration --- co-infections --- NHP --- pathogenesis --- zoonoses --- viral prevalence --- Neotropical primates --- free-living primates --- Brazil --- new world primates --- simian retrovirus --- BFV --- spuma virus --- model system --- animal model --- animal experiment --- miRNA function --- gene expression --- antiviral host restriction --- gene therapy --- in-vivo gene therapy --- hematopoietic stem and progenitor cells --- foamy virus vector --- pre-clinical canine model --- SCID-X1 --- innate sensing --- cGAS --- STING --- foamy viruses --- wild ruminants --- European bison --- red deer --- roe deer --- fallow deer --- seroreactivity --- inter-species transmission --- HSC --- gene marking --- FV gene transfer to HSCs --- gene therapy alternatives --- serotype --- high-throughput sequencing --- replication kinetics --- cytopathic effect --- reverse transcriptase activity --- miRNA expression --- virus-host-interaction --- miRNA target gene identification --- innate immunity --- ANKRD17 --- Bif1 (SH3GLB1) --- replication in vitro --- spumavirus --- feline illness --- proviral load --- neglected virus --- bovine foamy virus --- infectious clone --- particle release --- cell-free transmission --- foamy virus --- spumaretrovirus --- cross-species virus transmission --- zoonosis --- restriction factors --- immune responses --- FV vectors --- virus replication --- latent infection --- feline foamy virus --- epidemiology --- retrovirus --- Spumaretrovirus --- mountain lion --- Puma concolor --- ELISA --- protease --- reverse transcriptase --- RNase H --- reverse transcription --- antiviral drugs --- resistance --- simian foamy virus --- gibbon --- lesser apes --- co-evolution --- complete viral genome --- equine foamy virus --- isolation --- Japan --- sero-epidemiology --- reptile foamy virus --- endogenous foamy virus --- endogenous retrovirus --- ancient retroviruses --- co-speciation --- foamy virus-host interactions --- viral tropism --- infection --- kidney --- cats --- chronic kidney disease --- chronic renal disease --- integrase --- integration --- co-infections --- NHP --- pathogenesis --- zoonoses --- viral prevalence --- Neotropical primates --- free-living primates --- Brazil --- new world primates --- simian retrovirus --- BFV --- spuma virus --- model system --- animal model --- animal experiment --- miRNA function --- gene expression --- antiviral host restriction --- gene therapy --- in-vivo gene therapy --- hematopoietic stem and progenitor cells --- foamy virus vector --- pre-clinical canine model --- SCID-X1 --- innate sensing --- cGAS --- STING --- foamy viruses --- wild ruminants --- European bison --- red deer --- roe deer --- fallow deer --- seroreactivity --- inter-species transmission --- HSC --- gene marking --- FV gene transfer to HSCs --- gene therapy alternatives --- serotype --- high-throughput sequencing --- replication kinetics --- cytopathic effect --- reverse transcriptase activity --- miRNA expression --- virus-host-interaction --- miRNA target gene identification --- innate immunity --- ANKRD17 --- Bif1 (SH3GLB1) --- replication in vitro

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Foamy viruses, currently referred to as spumaretroviruses, are the most ancient retroviruses as evidenced by traces of viral sequences dispersed in all vertebrate classes from fish to mammals. Additionally, infectious foamy viruses circulate in a variety of mammalian species including simian, bovine, equine, caprine, and feline. Foamy viruses have many unique features which led to the division of the retrovirus family into two subfamilies, the Orthoretrovirinae and Spumaretrovirinae. In vitro, foamy viruses have a broad host range and in vivo, human infections have been described due to cross-species transmission from infected nonhuman primates. Thus far, there are no reports of virus-induced disease in humans or in the natural host species. These unique properties of foamy viruses have led researchers to develop foamy viruses as gene therapy vectors to study virus–virus and virus–host interactions for identifying factors involved in virus replication, transmission, and immune regulation that could influence potential clinical outcomes in humans as well as for using endogenous foamy virus sequences in the analysis of host species evolution.

spumavirus --- feline illness --- proviral load --- neglected virus --- bovine foamy virus --- infectious clone --- particle release --- cell-free transmission --- foamy virus --- spumaretrovirus --- cross-species virus transmission --- zoonosis --- restriction factors --- immune responses --- FV vectors --- virus replication --- latent infection --- feline foamy virus --- epidemiology --- retrovirus --- Spumaretrovirus --- mountain lion --- Puma concolor --- ELISA --- protease --- reverse transcriptase --- RNase H --- reverse transcription --- antiviral drugs --- resistance --- simian foamy virus --- gibbon --- lesser apes --- co-evolution --- complete viral genome --- equine foamy virus --- isolation --- Japan --- sero-epidemiology --- reptile foamy virus --- endogenous foamy virus --- endogenous retrovirus --- ancient retroviruses --- co-speciation --- foamy virus-host interactions --- viral tropism --- infection --- kidney --- cats --- chronic kidney disease --- chronic renal disease --- integrase --- integration --- co-infections --- NHP --- pathogenesis --- zoonoses --- viral prevalence --- Neotropical primates --- free-living primates --- Brazil --- new world primates --- simian retrovirus --- BFV --- spuma virus --- model system --- animal model --- animal experiment --- miRNA function --- gene expression --- antiviral host restriction --- gene therapy --- in-vivo gene therapy --- hematopoietic stem and progenitor cells --- foamy virus vector --- pre-clinical canine model --- SCID-X1 --- innate sensing --- cGAS --- STING --- foamy viruses --- wild ruminants --- European bison --- red deer --- roe deer --- fallow deer --- seroreactivity --- inter-species transmission --- HSC --- gene marking --- FV gene transfer to HSCs --- gene therapy alternatives --- serotype --- high-throughput sequencing --- replication kinetics --- cytopathic effect --- reverse transcriptase activity --- miRNA expression --- virus-host-interaction --- miRNA target gene identification --- innate immunity --- ANKRD17 --- Bif1 (SH3GLB1) --- replication in vitro