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Article: Wildlife endogenous retroviruses: colonization, consequences, and cooption.

Jern, Patric / Greenwood, Alex D

2023 Volume 40, Issue 2, Page(s) 149–159

Abstract: Endogenous retroviruses (ERVs) are inherited genomic remains of past germline retroviral infections. Research on human ERVs has focused on medical implications of their dysregulation on various diseases. However, recent studies incorporating wildlife are ...

Abstract	Endogenous retroviruses (ERVs) are inherited genomic remains of past germline retroviral infections. Research on human ERVs has focused on medical implications of their dysregulation on various diseases. However, recent studies incorporating wildlife are yielding remarkable perspectives on long-term retrovirus-host interactions. These initial forays into broader taxonomic analysis, including sequencing of multiple individuals per species, show the incredible plasticity and variation of ERVs within and among wildlife species. This demonstrates that stochastic processes govern much of the vertebrate genome. In this review, we elaborate on discoveries pertaining to wildlife ERV origins and evolution, genome colonization, and consequences for host biology.
MeSH term(s)	Animals ; Humans ; Endogenous Retroviruses ; Animals, Wild/genetics ; Vertebrates/genetics ; Genomics ; Evolution, Molecular ; Phylogeny
Language	English
Publishing date	2023-11-19
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	619240-3
ISSN	1362-4555 ; 0168-9525 ; 0168-9479
ISSN (online)	1362-4555
ISSN	0168-9525 ; 0168-9479
DOI	10.1016/j.tig.2023.10.014
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Article ; Online: Contrasting segregation patterns among endogenous retroviruses across the koala population.

Lillie, Mette / Pettersson, Mats / Jern, Patric

Communications biology

2024 Volume 7, Issue 1, Page(s) 350

Abstract: Koalas (Phascolarctos cinereus) have experienced a history of retroviral epidemics leaving their trace as heritable endogenous retroviruses (ERVs) in their genomes. A recently identified ERV lineage, named phaCin-β, shows a pattern of recent, possibly ... ...

Abstract	Koalas (Phascolarctos cinereus) have experienced a history of retroviral epidemics leaving their trace as heritable endogenous retroviruses (ERVs) in their genomes. A recently identified ERV lineage, named phaCin-β, shows a pattern of recent, possibly current, activity with high insertional polymorphism in the population. Here, we investigate geographic patterns of three focal ERV lineages of increasing estimated ages, from the koala retrovirus (KoRV) to phaCin-β and to phaCin-β-like, using the whole-genome sequencing of 430 koalas from the Koala Genome Survey. Thousands of ERV loci were found across the population, with contrasting patterns of polymorphism. Northern individuals had thousands of KoRV integrations and hundreds of phaCin-β ERVs. In contrast, southern individuals had higher phaCin-β frequencies, possibly reflecting more recent activity and a founder effect. Overall, our findings suggest high ERV burden in koalas, reflecting historic retrovirus-host interactions. Importantly, the ERV catalogue supplies improved markers for conservation genetics in this endangered species.
MeSH term(s)	Humans ; Animals ; Endogenous Retroviruses/genetics ; Phascolarctidae/genetics ; Retroviridae Infections/genetics ; Gammaretrovirus/genetics ; Whole Genome Sequencing
Language	English
Publishing date	2024-03-21
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-024-06049-0
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Article: ZBED6 binding motifs correlate with endogenous retroviruses and

Pettersson, Mats E / Jern, Patric

Virus evolution

2020 Volume 7, Issue 1, Page(s) veaa083

Abstract: Retroviruses have infiltrated vertebrate germlines for millions of years as inherited endogenous retroviruses (ERVs). Mammalian genomes host large numbers of ERVs and transposable elements (TEs), including retrotransposons and DNA transposons, that ... ...

Abstract	Retroviruses have infiltrated vertebrate germlines for millions of years as inherited endogenous retroviruses (ERVs). Mammalian genomes host large numbers of ERVs and transposable elements (TEs), including retrotransposons and DNA transposons, that contribute to genomic innovation and evolution as coopted genes and regulators of diverse functions. To explore features distinguishing coopted ERVs and TEs from other integrations, we focus on the potential role of ZBED6 and repeated ERV domestication as repurposed
Language	English
Publishing date	2020-11-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/veaa083
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Article ; Online: Expansion of a retrovirus lineage in the koala genome.

Lillie, Mette / Hill, Jason / Pettersson, Mats E / Jern, Patric

Proceedings of the National Academy of Sciences of the United States of America

2022 Volume 119, Issue 25, Page(s) e2201844119

Abstract: Retroviruses have left their legacy in host genomes over millions of years as endogenous retroviruses (ERVs), and their structure, diversity, and prevalence provide insights into the historical dynamics of retrovirus-host interactions. In bioinformatic ... ...

Abstract	Retroviruses have left their legacy in host genomes over millions of years as endogenous retroviruses (ERVs), and their structure, diversity, and prevalence provide insights into the historical dynamics of retrovirus-host interactions. In bioinformatic analyses of koala (
MeSH term(s)	Animals ; Betaretrovirus/genetics ; Endogenous Retroviruses/genetics ; Evolution, Molecular ; Genome ; Genomics ; Host Microbial Interactions ; Phascolarctidae/genetics ; Phascolarctidae/virology ; Retroviridae Infections/veterinary ; Retroviridae Infections/virology
Language	English
Publishing date	2022-06-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2201844119
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Article: Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups.

Pettersson, Mats E / Jern, Patric

Genes

2019 Volume 10, Issue 2

Abstract: Retroviruses have invaded vertebrate hosts for millions of years and left an extensive endogenous retrovirus (ERV) record in the host genomes, which provides a remarkable source for an evolutionary perspective on retrovirus-host associations. Here we ... ...

Abstract	Retroviruses have invaded vertebrate hosts for millions of years and left an extensive endogenous retrovirus (ERV) record in the host genomes, which provides a remarkable source for an evolutionary perspective on retrovirus-host associations. Here we identified ERV variation across whole-genomes from two chicken lines, derived from a common founder population subjected to 50 years of bi-directional selection on body weight, and a distantly related domestic chicken line as a comparison outgroup. Candidate ERV loci, where at least one of the chicken lines indicated distinct differences, were analyzed for adjacent host genomic landscapes, selective sweeps, and compared by sequence associations to reference assembly ERVs in phylogenetic analyses. Current data does not support selection acting on specific ERV loci in the domestic chicken lines, as determined by presence inside selective sweeps or composition of adjacent host genes. The varying ERV records among the domestic chicken lines associated broadly across the assembly ERV phylogeny, indicating that the observed insertion differences result from pre-existing and segregating ERV loci in the host populations. Thus, data suggest that the observed differences between the host lineages are best explained by substantial standing ERV variation within host populations, and indicates that even truncated, presumably old, ERVs have not yet become fixed in the host population.
MeSH term(s)	Animals ; Chickens/genetics ; Chickens/virology ; Endogenous Retroviruses/classification ; Endogenous Retroviruses/genetics ; Evolution, Molecular ; Genome ; Phylogeny ; Polymorphism, Genetic
Language	English
Publishing date	2019-02-20
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes10020162
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Article ; Online: Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.

Hill, Jason / Lillie, Mette / Pettersson, Mats E / Rubin, Carl-Johan / Grant, B Rosemary / Grant, Peter R / Andersson, Leif / Jern, Patric

Nature communications

2022 Volume 13, Issue 1, Page(s) 6033

Abstract: Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin's finches, a system synonymous ... ...

Abstract	Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin's finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin's finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin's finches' radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin's finches.
MeSH term(s)	Animals ; Biological Evolution ; Ecuador ; Endogenous Retroviruses/genetics ; Finches/genetics ; Gene Flow ; Passeriformes/genetics ; Phylogeny
Language	English
Publishing date	2022-10-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-33723-w
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Article ; Online: Single-cell transcriptomics of human traumatic brain injury reveals activation of endogenous retroviruses in oligodendroglia.

Garza, Raquel / Sharma, Yogita / Atacho, Diahann A M / Thiruvalluvan, Arun / Abu Hamdeh, Sami / Jönsson, Marie E / Horvath, Vivien / Adami, Anita / Ingelsson, Martin / Jern, Patric / Hammell, Molly Gale / Englund, Elisabet / Kirkeby, Agnete / Jakobsson, Johan / Marklund, Niklas

Cell reports

2023 Volume 42, Issue 11, Page(s) 113395

Abstract: Traumatic brain injury (TBI) is a leading cause of chronic brain impairment and results in a robust, but poorly understood, neuroinflammatory response that contributes to the long-term pathology. We used single-nuclei RNA sequencing (snRNA-seq) to study ... ...

Abstract	Traumatic brain injury (TBI) is a leading cause of chronic brain impairment and results in a robust, but poorly understood, neuroinflammatory response that contributes to the long-term pathology. We used single-nuclei RNA sequencing (snRNA-seq) to study transcriptomic changes in different cell populations in human brain tissue obtained acutely after severe, life-threatening TBI. This revealed a unique transcriptional response in oligodendrocyte precursors and mature oligodendrocytes, including the activation of a robust innate immune response, indicating an important role for oligodendroglia in the initiation of neuroinflammation. The activation of an innate immune response correlated with transcriptional upregulation of endogenous retroviruses in oligodendroglia. This observation was causally linked in vitro using human glial progenitors, implicating these ancient viral sequences in human neuroinflammation. In summary, this work provides insight into the initiating events of the neuroinflammatory response in TBI, which has therapeutic implications.
MeSH term(s)	Humans ; Animals ; Mice ; Endogenous Retroviruses/genetics ; Neuroinflammatory Diseases ; Transcriptome/genetics ; Brain Injuries, Traumatic/pathology ; Brain Injuries/pathology ; Oligodendroglia/pathology ; Inflammation/genetics ; Inflammation/pathology ; Mice, Inbred C57BL
Language	English
Publishing date	2023-11-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2023.113395
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Article: Characterization of the endogenous retrovirus insertion in

Li, Jingyi / Davis, Brian W / Jern, Patric / Dorshorst, Ben J / Siegel, Paul B / Andersson, Leif

Mobile DNA

2019 Volume 10, Page(s) 38

Abstract: Background: Henny feathering in chickens is determined by a dominant mutation that transforms male-specific plumage to female-like plumage. Previous studies indicated that this phenotype is caused by ectopic expression in skin of : Results: We used ... ...

Abstract	Background: Henny feathering in chickens is determined by a dominant mutation that transforms male-specific plumage to female-like plumage. Previous studies indicated that this phenotype is caused by ectopic expression in skin of Results: We used publicly available whole genome sequence data to determine the flanking sequences of the ERV, and then PCR amplified the entire insertion and sequenced it using Nanopore long reads and Sanger sequencing. The 7524 bp insertion contains an intact endogenous retrovirus that was not found in chickens representing 31 different breeds not showing henny feathering or in samples of the ancestral red junglefowl. The sequence shows over 99% sequence identity to the avian leukosis virus ev-1 and ev-21 strains, suggesting a recent integration. The ERV 3'LTR, containing a powerful transcriptional enhancer and core promoter with TATA box together with binding sites for EFIII and Ig/EBP inside the Conclusions: We demonstrate that the henny feathering allele harbors an insertion of an intact avian leukosis virus at the 5'end of
Language	English
Publishing date	2019-08-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2536054-1
ISSN	1759-8753
ISSN	1759-8753
DOI	10.1186/s13100-019-0181-4
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Article ; Online: Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations.

Rivas-Carrillo, Salvador Daniel / Pettersson, Mats E / Rubin, Carl-Johan / Jern, Patric

Proceedings of the National Academy of Sciences of the United States of America

2018 Volume 115, Issue 43, Page(s) 11012–11017

Abstract: Although recent advances in sequencing and computational analyses have facilitated use of endogenous retroviruses (ERVs) for deciphering coevolution among retroviruses and their hosts, sampling effects from different host populations present major ... ...

Abstract	Although recent advances in sequencing and computational analyses have facilitated use of endogenous retroviruses (ERVs) for deciphering coevolution among retroviruses and their hosts, sampling effects from different host populations present major challenges. Here we utilize available whole-genome data from wild and domesticated European rabbit (
MeSH term(s)	Animals ; Animals, Domestic/virology ; Comparative Genomic Hybridization/methods ; DNA/genetics ; Endogenous Retroviruses/genetics ; Genome, Viral/genetics ; Genome-Wide Association Study/methods ; Genomics/methods ; Host Specificity/genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Rabbits
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2018-10-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1815056115
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Article ; Online: Pan-vertebrate comparative genomics unmasks retrovirus macroevolution.

Hayward, Alexander / Cornwallis, Charlie K / Jern, Patric

Proceedings of the National Academy of Sciences of the United States of America

2015 Volume 112, Issue 2, Page(s) 464–469

Abstract: Although extensive research has demonstrated host-retrovirus microevolutionary dynamics, it has been difficult to gain a deeper understanding of the macroevolutionary patterns of host-retrovirus interactions. Here we use recent technological advances to ... ...

Abstract	Although extensive research has demonstrated host-retrovirus microevolutionary dynamics, it has been difficult to gain a deeper understanding of the macroevolutionary patterns of host-retrovirus interactions. Here we use recent technological advances to infer broad patterns in retroviral diversity, evolution, and host-virus relationships by using a large-scale phylogenomic approach using endogenous retroviruses (ERVs). Retroviruses insert a proviral DNA copy into the host cell genome to produce new viruses. ERVs are provirus insertions in germline cells that are inherited down the host lineage and consequently present a record of past host-viral associations. By mining ERVs from 65 host genomes sampled across vertebrate diversity, we uncover a great diversity of ERVs, indicating that retroviral sequences are much more prevalent and widespread across vertebrates than previously appreciated. The majority of ERV clades that we recover do not contain known retroviruses, implying either that retroviral lineages are highly transient over evolutionary time or that a considerable number of retroviruses remain to be identified. By characterizing the distribution of ERVs, we show that no major vertebrate lineage has escaped retroviral activity and that retroviruses are extreme host generalists, having an unprecedented ability for rampant host switching among distantly related vertebrates. In addition, we examine whether the distribution of ERVs can be explained by host factors predicted to influence viral transmission and find that internal fertilization has a pronounced effect on retroviral colonization of host genomes. By capturing the mode and pattern of retroviral evolution and contrasting ERV diversity with known retroviral diversity, our study provides a cohesive framework to understand host-virus coevolution better.
MeSH term(s)	Animals ; Ecosystem ; Endogenous Retroviruses/genetics ; Endogenous Retroviruses/pathogenicity ; Endogenous Retroviruses/physiology ; Evolution, Molecular ; Genetic Variation ; Genome, Viral ; Genomics ; Host Specificity/genetics ; Host-Pathogen Interactions/genetics ; Humans ; Phylogeny ; Retroviridae/genetics ; Retroviridae/pathogenicity ; Retroviridae/physiology ; Vertebrates/genetics ; Vertebrates/virology
Language	English
Publishing date	2015-01-13
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1414980112
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