Endogenous viral elements
Also in 鈥� Scientific meeting鈥�
Theo Murphy meeting organised by Dr Katy Brown, Dr Emma Harding and Professor Rachael Tarlinton
This meeting will discuss current endogenous viral element (EVE) research. EVEs are viruses which have become part of their host’s genome through germline integration, and can represent extinct or current viruses. We will discuss endogenous retroviral, RNA viral and DNA viral elements, including their diversity, roles in host biology and impacts on human and veterinary disease.
The full programme, including speaker biographies and abstracts, will be available soon. A draft programme is shown below. Please note the programme may be subject to change.
Poster session
There will be a poster session on Monday 8 February 2027. Registered attendees will be invited to submit a proposed poster title and abstract (up to 200 words). Acceptances may be made on a rolling basis so we recommend submitting as soon as possible in case the session becomes full. Submissions made within one month of the meeting may not be included in the programme booklet.
Attending the event
This event is intended for researchers in relevant fields.
- Free to attend and in-person only
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- Requests are reviewed by the meeting organisers on a rolling basis. You will receive a link to register if your request has been successful
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Enquiries: Scientific Programmes team
Image credit © iStock.com / quantic69
Organisers
Schedule
Chair
Dr Emma Harding
University of Oxford, UK
Dr Emma Harding
University of Oxford, UK
Emma has a background in molecular virology and begun her studies with the development of broad-spectrum antivirals against flavivirus RdRp proteins. Transitioning to bioinformatics during her PhD, she expanded her work to encompass workflow development, viral discovery and virus evolution. She completed her PhD at the University of New South Wales (UNSW) in Sydney, Australia and now works at the University of Oxford in the paleovirology lab with Professor Aris Katzourakis.
Using and developing bioinformatic methods, her current work integrates endogenous viral elements to answer questions about viral molecular evolution, host immunity, horizontal gene transfer and vertebrate genomics.
| 09:00-09:05 |
Welcome by the lead organiser
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| 09:05-09:35 |
Domesticated endogenous viral elements of parasitoid wasps are a major source of horizontal gene transfer among insects
Parasitoid wasps carry gene delivery agents called polydnaviruses (PDVs). These domesticated endogenous viral elements mediate the integration of wasp genes into the genome of parasitized hosts, thereby protecting developing larvae from immune defenses. Using bulk DNA sequencing of parasitized lepidopterans, we have shown that PDV integration occurs massively in all surveyed tissues (from 12 to 85 integration events per host haploid genome). We also demonstrated that integrations of the PDV encoded by the wasp Cotesia typhae persist up to the adult stage in individuals of its natural host, the moth Sesamia nonagrioides, that survived parasitism. C. typhae PDV can even integrate massively into the chromosomes of other lepidopteran species that are not normally targeted by the wasp in the wild. Finally, a search for canonical PDV integrations in 6,814 publicly available protostome genomes unveiled no less than 6,556 integrations, all of which were in insects. While most integrations were found in lepidopterans, the main hosts of parasitoid wasps (6,260 integrations in 303 species), a few were retrieved in sawflies (139 integrations in 14 species) and leaf beetles (four integrations in two species), also known to be parasitized by some of these wasps. Remarkably, we found a total of 232 integrations in stick insects and one integration in an orthopteran, two insect lineages not known to be attacked by PDV-encoding wasps. Our results set PDV as major vectors of horizontal gene transfer (HGT) in insects, and they show that PDV-mediated HGT can be used to uncovered hitherto unknown ecological interactions. 
Dr Clement GilbertCNRS-IRD-Université Paris Saclay, France
Dr Clement GilbertCNRS-IRD-Université Paris Saclay, France Dr Gilbert obtained a PhD in Zoology from Stellenbosch University, South Africa, in 2008, where he studied the chromosomal evolution of golden moles and tenrecs. He then completed a postdoctoral fellowship in the Feschotte lab, then located at the University of Texas at Arlington, USA, where he became interested in the horizontal transfer of transposable elements (HTT) and viral evolution through the discovery of endogenous viral elements (EVEs). Now a senior researcher in the Evolution, Genome, Behavior and Ecology lab at Paris-Saclay University, he and his team pursue several lines of research on HTT and EVEs, including the characterisation of so-called polydnaviruses in parasitoid wasps and the propensity of these EVEs to facilitate horizontal transfer between insects. |
| 09:35-10:05 |
Population genomics of Aedes albopictus to investigate whether piRNA clusters are traps for nonretroviral endogenous viral elements
Professor Mariangela BonizzoniUniversity of Pavia, Italy
Professor Mariangela BonizzoniUniversity of Pavia, Italy Mariangela Bonizzoni is currently Professor of Zoology in the Department of Biology and Biotechnology of the University of Pavia in Italy. She received her PhD from both the University of Pavia and the Universite’ de Paris XI through a joint Italian- French PhD program in 2004. In 2005, she moved to University of California, Irvine to study insecticide resistance in malaria vectors with Professor Guiyun Yan and arboviral vector competence in Aedes mosquitoes with Professor Anthony A James. She joined the Department of Biology and Biotechnology of the University of Pavia in 2015. She is interested in understanding the evolutionary adaptations in mosquito genomes that foster their invasion success and vector competence. |
| 10:05-10:35 |
Endogenous viral elements of arthropods
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| 10:35-11:00 |
Break
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| 11:00-11:30 |
Repetitive EVEs in invertebrates
Dr Katy BrownUniversity of Cambridge, UK
Dr Katy BrownUniversity of Cambridge, UK Katy is a postdoctoral researcher and bioinformatician in the Virology Division, Department of Pathology, at the University of Cambridge, where she works with Prof Andrew Firth. Her research focuses on the discovery of RNA viruses in public sequencing datasets, particularly those from non-model organisms, with a special interest in endogenous RNA viral elements (EVEs). More recently, she has been investigating EVEs in butterflies and moths. She is also interested in developing approaches to integrate EVE data with other types of genome annotation. Katy has worked on EVEs periodically throughout her research career, beginning with her PhD, completed in 2014, which focused on endogenous retroviruses in primates. Before joining Cambridge, she was a member of the Computational Genomics Analysis and Training (CGAT) team at the University of Oxford. |
| 11:30-12:00 |
From viral fossils to host proteins: functional domestication of non-retroviral endogenous viral elements in hemipteran insects
Non-retroviral endogenous viral elements (nrEVEs) are widespread in insect genomes and are generally regarded as molecular records of ancient virus-host interactions. Increasing evidence, however, suggests that some nrEVEs have been retained and repurposed by their hosts, yet how these elements become functionally domesticated and what biological roles they acquire remain poorly understood. Using planthoppers and related hemipteran insects as model systems, we investigate how nrEVEs derived from diverse RNA viruses become functionally domesticated after integration into host genomes. Our studies have identified multiple transcriptionally active nrEVEs with preserved or remodeled open reading frames, several of which give rise to proteins with host biological functions. Functional analyses show that nrEVE-derived genes and proteins can participate in distinct aspects of insect biology, including development, reproduction, antiviral immunity and interactions with contemporary viruses. Together, these examples reveal multiple routes by which ancient viral coding sequences can be incorporated into modern host biological networks. We are also tracing homologous nrEVEs across related insects and broader arthropod lineages to reconstruct their evolutionary origins and subsequent fates. These comparisons suggest that homologous integrations can be differentially retained, lost or remodeled during host diversification, ranging from genomic remnants and transcribed elements to protein-coding forms. Together, our work highlights the domestication of nrEVEs into functional proteins as an important evolutionary outcome of nrEVE integration and illustrates how ancient viral sequences can become components of contemporary insect biology. 
Professor Jun-Min LiNingbo University, China
Professor Jun-Min LiNingbo University, China Jun-Min Li is a Professor at Ningbo University, China. His research focuses on the diversity and evolution of RNA viruses in agriculturally important insect vectors, particularly hemipteran insects such as planthoppers, and their coevolution with insect hosts. His recent work explores the origin, evolution and functional domestication of non-retroviral endogenous viral elements (nrEVEs), with particular interest in how virus-derived sequences contribute to host genetic innovation and antiviral functions. He also contributes to virus taxonomy through the International Committee on Taxonomy of Viruses (ICTV), serving as Chair of the Lispiviridae Study Group and a member of the Kitaviridae Study Group. |
| 12:00-12:30 |
Cryptic infections and genome integration in giant viruses of green algae
The recent discovery of giant endogenous viral elements (GEVEs) across a wide range of protist genomes presents an opportunity to investigate a possible latent viral infection strategy within giant viruses. Although these elements can be prominent features of eukaryotic genomes, GEVEs frequently exhibit clear signs of genomic erosion, including duplications, methylation, and intron invasion, raising questions about their viability. Chlamydomonas reinhardtii is a unicellular green alga long recognized as a model organism, but its potential interaction with viruses in the environment has remained elusive. Recently, my group described a 617 kbp integrated giant virus in the genome of a C. reinhardtii field isolate that can reactivate and form virions. Here, I will present recent results from our ongoing work to examine the reactivation dynamics and host-virus coevolution in this unique system. 
Dr Frank AylwardVirginia Tech, US
Dr Frank AylwardVirginia Tech, US Frank received a Bachelor’s degree in Biochemistry from the University of Arizona in 2008 and a PhD in Microbiology from the University of Wisconsin-Madison in 2013. For his PhD work he studied symbiotic microbial communities associated with leaf-cutter ants in Panama. He completed a postdoc at the University of Hawaii at Manoa, where he examined diel cycling of marine microbial and viral activities. He then joined the Biological Sciences department at Virginia Tech in 2017, where he is now an associate professor. Frank has worked with a wide range of microbial and viral systems, and currently focuses mostly on large DNA viruses, especially “giant viruses” and large bacteriophages. In particular, he is interested in endogenous giant viruses of eukaryotes. |
Chair
Dr Muriel Ritsch
Friedrich Schiller University Jena, Germany
Dr Muriel Ritsch
Friedrich Schiller University Jena, Germany
Muriel Ritsch is a bioinformatician who recently completed her PhD at Friedrich Schiller University Jena, Germany, under the supervision of Professor Manja Marz. Her research focuses on endogenous viral elements (EVEs) and the computational challenges associated with their identification and characterisation in host genomes.
Her work includes a comprehensive review of EVE research from a bioinformatics perspective, exploring their diversity across viral and host groups as well as methodological challenges in their detection. She has also investigated the quality and diversity of viral sequence databases and their impact on virus-related genomic analyses. In bats, she identified a novel, widely conserved bornavirus-derived EVE and its associated antisense transcript.
Her current research focuses on RNA virus-derived EVEs in the human genome, particularly on distinguishing genuine viral integrations from misleading homology signals.
| 13:30-14:00 |
EVEs in virus metagenomics: Happy little accidents painting a deeper picture of virus evolution
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| 14:00-14:30 |
Origin and evolution of retroviruses and the functional versatility of endogenous retroviruses
Retroviruses exclusively infect vertebrates, leaving behind endogenous retroviral (ERV) fossils that serve as molecular archives of past infections. Recent phylogenomic surveys have dramatically reshaped our understanding of retroviral diversity, evolution, and functional impact. The discovery of lokiretroviruses as a sister lineage to all known retroviruses, along with the identification of Odin retrotransposons in cnidarians, has narrowed the evolutionary gap between retrotransposons and retroviruses, providing insights into the origin of retroviruses. Large-scale pan-vertebrate ERV mining has revealed complex retroviral repertoires shaped by both coevolution and cross-species transmission in birds and cetaceans and ongoing retroviral invasions in over 120 vertebrate species. Beyond their role as genomic remnants, retroviral genes have been repeatedly repurposed for host functions. A comprehensive survey identified hundreds of independent co-option events across vertebrates, with remarkable examples including retrovirus-driven iridescence in swordtail fish and multiple syncytin-like env genes essential for placentation in ruminants. Collectively, these findings illuminate the ancient origins, intricate evolutionary trajectories, and functional versatility of retroviruses. 
Professor Guan-Zhu HanNanjing Normal University, China
Professor Guan-Zhu HanNanjing Normal University, China Dr Guan-Zhu Han is a full professor at Nanjing Normal University, China. He received his PhD in Ecology and Evolutionary Biology from the University of Arizona in 2014. His research program investigates the origins, evolution, and diversity of viruses, as well as the evolutionary innovations forged by host–microbe conflicts. By integrating comparative genomics, molecular evolution, and molecular biology, his group has uncovered fundamental patterns in viral evolution, shed light on the ancient origins of major viral lineages, and revealed the evolutionary origins of diverse immune systems across eukaryotes. |
| 14:30-15:00 |
Paleovirology: what have ancient viruses revealed about viral evolution and host biology?
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| 15:00-15:30 |
Break
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| 15:30-16:00 |
The process and consequences of retroviral endogenisation at its earliest stage
Retroviral vertebrate germline infections have made endogenous retroviruses (ERVs) ubiquitous features of mammalian genomes. However, millions of years of evolution obscure many of the repercussions of retroviral endogenisation on host health or the changes that the colonizing virus may make to adapt to its host. We have examined retroviral endogenisation during its earliest stages in the koala (Phascolarctos cinereus), a species undergoing germline colonization by koala retrovirus (KoRV) and affected by high cancer prevalence. We have characterised integration sites (IS) discovering that recombinant versions of KoRV, replacing much of the KoRV genome with the highly degraded genome of an older ERV, are proliferating within and among koalas. This may represent a genomic defense against retroviral germline colonization. We also characterised the accumulation of KoRV integration sites (IS) in tumour versus healthy tissues. We find that tumours accumulate novel IS, with proximate genes over-represented for cancer associations. In a large-scale pedigree analysis, we observe the genesis of new endogenous KoRVs, purging of detrimental KoRVs and the presence of potentially beneficial IS. We have generated genetic risk scores to improve koala fitness in at least, captive koala populations. We have also determined the effects of founder events on KoRV endogenisation. Our data provide insights into the tremendous mutational load suffered by the host during active retroviral germline colonisation and some of the countermeasures employed by the host genome, a process repeatedly experienced and overcome during the evolution of vertebrate lineages. 
Professor Alex GreenwoodLeibniz Institute for Zoo and Wildlife Research, Germany
Professor Alex GreenwoodLeibniz Institute for Zoo and Wildlife Research, Germany Alex D Greenwood is Head of the Department of Wildlife Diseases at the Leibniz Institute for Zoo and Wildlife Research and Professor of Wildlife Diseases at the Freie Universität Berlin in the Department of Veterinary Medicine in Berlin, Germany. Professor Greenwood is an evolutionary virologist focusing on retroviruses, herpesviruses and the role of wildlife in One Health related research. He has a long-standing interest in evolutionary mechanisms underlying retroviral colonisation of vertebrate genomes. He applies various high throughput-sequencing methods to answer short term, medium term and long-term evolutionary questions regarding the mechanisms. Recently, where possible, he tries to employ the results of his research to achieve better conservation outcomes for the species under study including captive and free living koalas. For other species, he focuses on developing and using non-invasive approaches to disease research such as environmental DNA and RNA. |
| 16:00-17:00 |
Poster session
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Chair
Dr Katy Brown
University of Cambridge, UK
Dr Katy Brown
University of Cambridge, UK
Katy is a postdoctoral researcher and bioinformatician in the Virology Division, Department of Pathology, at the University of Cambridge, where she works with Prof Andrew Firth. Her research focuses on the discovery of RNA viruses in public sequencing datasets, particularly those from non-model organisms, with a special interest in endogenous RNA viral elements (EVEs). More recently, she has been investigating EVEs in butterflies and moths. She is also interested in developing approaches to integrate EVE data with other types of genome annotation.
Katy has worked on EVEs periodically throughout her research career, beginning with her PhD, completed in 2014, which focused on endogenous retroviruses in primates. Before joining Cambridge, she was a member of the Computational Genomics Analysis and Training (CGAT) team at the University of Oxford.
| 09:00-09:30 |
T2T repeat curation in great apes uncovers a high tolerance for multiple retroviral infections and ongoing mobilisation in gorilla
Interspersed repeats are present in the genomes of virtually all life on Earth, making up the bulk of most eukaryotic genomes. Remnants of transposable element (TE) copies often play roles in gene regulation, the formation of novel genes, and global genomic rearrangements. Leveraging data generated by the T2T Primate Consortium, we present a comparative analysis of the activity of two endogenous retroviruses (ERVs), PtERV and LTR5/HERVK, across the great ape lineage. We found roughly equal numbers of solo-LTRs and proviruses among PtERV insertions in gorilla, bonobo, and chimpanzee genomes, indicating a slower rate of LTR-LTR ectopic recombination - the process that reduces a provirus to a solo-LTR - possibly due to tandem duplications specific to PtERV LTRs. We also found that previous estimates of species-specific PtERV insertions in the chimpanzee genome were inflated, owing to the lack of a bonobo genome for comparison at the time of those analyses. Our data instead show high levels of insertions shared between chimpanzee and bonobo, with low levels of species-specific insertions in either genome. Divergence distribution and complementary phylogenetic clustering of PtERV LTRs indicate two independent infection events: one in the Pan lineage prior to the diversification of bonobo and chimpanzee, and an earlier one in the gorilla lineage. A similar aging analysis of LTR5/HERVK proviral insertions points to a recent infection and expansion in gorillas: 78% of insertions remain heterozygous in the gorilla genome, and four of these retain intact ERV open reading frames (ORFs), providing evidence of ongoing mobilisation. 
Professor Rachel O'NeillUniversity of Connecticut, US
Professor Rachel O'NeillUniversity of Connecticut, US Rachel O'Neill is a Board of Trustees Distinguished Professor and the John and Donna Krenicki Professor in Genomics and Personalized Healthcare at the University of Connecticut, as well as a member of the Connecticut Academy of Science and Engineering. She serves as Director of the Institute for Systems Genomics and Director of the Center for Genome Innovation. Her research in genome biology focuses on telomere-to-telomere (T2T)-scale genome assemblies and comparative genomics across the tree of life, driving discoveries in repeat biology and chromosome evolution. Her recent work bridges de-extinction science and conservation genomics. Author of more than 150 publications, O'Neill has produced T2T and chromosome-level assemblies for a wide range of model and non-traditional species, including humans, non-human primates, mammals and birds broadly, marsupials, and deep-sea marine organisms. |
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| 09:30-10:00 |
Endogenous viral elements and the deep evolutionary history of vertebrate viruses
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| 10:00-10:30 |
New insights into endogenous viral elements (EVEs) in vertebrate species
Dr Joana ArbantesUniversidade do Porto, Portugal
Dr Joana ArbantesUniversidade do Porto, Portugal Joana Abrantes PhD is Assistant Professor in the Department of Biology, Faculty of Sciences, University of Porto, and Assistant Researcher at BIOPOLIS-CIBIO in the Immunity and Emerging Diseases (IMED) group. Her research focuses on host-pathogen co鈥慹volution, using rabbits and hares and their viral diseases as model systems. She studies viral evolution (recombination, mutation, selection), emergence, spillover, and epidemiology. Her work also addresses the immunogenetic basis of host susceptibility and resistance, including genes of the innate and adaptive immune system (Toll鈥憀ike receptors (TLRs), guanylate鈥慴inding proteins (GBPs), chemokines and their receptors, interleukins, among others). More recently, she has expanded her research into wildlife virome diversity for zoonotic surveillance within a One Health framework. She further investigates endogenous viral elements in vertebrate genomes, exploring how ancient viral integrations shape host genome evolution and may influence antiviral immunity and susceptibility to contemporary infections. |
| 10:30-11:00 |
Break
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| 11:00-11:30 |
False-positive viral signals in the human genome: Guidelines for EVE detection using homology-based approaches
Endogenous viral elements (EVEs) provide valuable insights into virus evolution and ancient host–virus interactions and are commonly identified through genome-wide homology searches. However, distinguishing authentic viral integrations from spurious sequence similarities remains a major challenge. Here, we systematically screened the human genome using comprehensive viral datasets and developed a two-stage validation guideline combining automated candidate filtering with manual evaluation. Initial homology searches identified more than 1.18 million apparent viral signals, spanning approximately 17% of the human genome. After excluding well-characterised endogenous retroviruses, more than 350,000 non-retroviral candidate loci remained, despite only a small number of non-retroviral EVEs having been described in humans. Sequential automated filtering reduced these signals to a few hundred candidates, which were subsequently assessed using a structured manual validation guideline. Ultimately, more than 99.9% of the initial non-retroviral candidates were rejected, leaving only a small number of plausible loci. Most false-positive predictions originated from recurrent artefact classes, including erroneous viral database records and biologically meaningful viral–host chimeric sequences. The remaining candidates included previously reported bornavirus-derived EVEs and potentially novel loci. Our results demonstrate that viral homology alone is insufficient evidence for an endogenous viral origin. Understanding the sources of misleading homology signals enables their systematic identification and provides a practical framework for robust EVE discovery across host genomes and other homology-based analyses.
Dr Muriel RitschFriedrich Schiller University Jena, Germany
Dr Muriel RitschFriedrich Schiller University Jena, Germany Muriel Ritsch is a bioinformatician who recently completed her PhD at Friedrich Schiller University Jena, Germany, under the supervision of Professor Manja Marz. Her research focuses on endogenous viral elements (EVEs) and the computational challenges associated with their identification and characterisation in host genomes. Her work includes a comprehensive review of EVE research from a bioinformatics perspective, exploring their diversity across viral and host groups as well as methodological challenges in their detection. She has also investigated the quality and diversity of viral sequence databases and their impact on virus-related genomic analyses. In bats, she identified a novel, widely conserved bornavirus-derived EVE and its associated antisense transcript. Her current research focuses on RNA virus-derived EVEs in the human genome, particularly on distinguishing genuine viral integrations from misleading homology signals. |
| 11:30-12:00 |
Invasion patterns of ERVs in mammals
Dr Emma HardingUniversity of Oxford, UK
Dr Emma HardingUniversity of Oxford, UK Emma has a background in molecular virology and begun her studies with the development of broad-spectrum antivirals against flavivirus RdRp proteins. Transitioning to bioinformatics during her PhD, she expanded her work to encompass workflow development, viral discovery and virus evolution. She completed her PhD at the University of New South Wales (UNSW) in Sydney, Australia and now works at the University of Oxford in the paleovirology lab with Professor Aris Katzourakis. Using and developing bioinformatic methods, her current work integrates endogenous viral elements to answer questions about viral molecular evolution, host immunity, horizontal gene transfer and vertebrate genomics. |
| 12:00-12:30 |
Endogenous retroviruses are essential for vertebrate embryonic development
Professor Cédric FeschotteCornell University, USA
Professor Cédric FeschotteCornell University, USA Cédric Feschotte received his PhD in 2001 from the University Pierre & Marie Curie in Paris during which he characterized mosquito transposable elements with Professor Claude Mouchès. He then joined the group of Dr Susan Wessler at the University of Georgia in Athens, GA as a postdoctoral fellow where he contributed to elucidate the origin and amplification mechanism of 'MITE' transposons in plant genomes. In 2004, he became an Assistant Professor in the Department of Biology at the University of Texas, Arlington where he was promoted to Associate Professor in 2009. In 2012, he joined the Department of Human Genetics at the University of Utah School of Medicine in Salt Lake City. Since July 2017 he has been a Professor in the Department of Molecular Biology and Genetics at Cornell University in Ithaca, NY. His laboratory uses an integrative approach to study the evolution and biological impact of various forms of mobile DNA, with an emphasis on the genomes of vertebrates. |
| 13:30-14:00 |
What happens to a host species when a new retrovirus enters its germ line? The Koala example.
Professor Rachael TarlintonUniversity of Nottingham, UK
Professor Rachael TarlintonUniversity of Nottingham, UK Rachael is a veterinary virologist who has worked on endogenous viruses since her PhD on koala retrovirus at the University of Sydney 20 years ago. She is based at the Vet School at the University of Nottingham where she teaches vet students and leads a research programme in animal viruses both endogenous and exogenous. Recent work includes koalas (KoRV), Humans (HERVs in multiple sclerosis), Sheep (Maedi Visna, Bluetongue and Schmallenberg), Cats (FeLV, feline morbillivirus) and assorted wildlife (Coronaviruses of mustelids, bats and hedgehogs). Her group focus on genomics and transcriptomics of both host and virus and she is particularly fascinated with the host genetics of viral resistance. |
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| 14:00-14:30 |
Human endogenous retrovirus activity underlies major psychiatric disorders
Dr Nicholas DopkinsVirginia Commonwealth University, US
Dr Nicholas DopkinsVirginia Commonwealth University, US To advance our understanding of human physiology, Dr Dopkins studies how endogenous retroelements (EREs) participate in molecular genetics, cellular biology, and immune pathways. Making up over 40% of the human genome, these abundant, highly repetitive elements are active in healthy tissues but show distinct activity patterns in various diseases. Despite their ubiquity, their precise biological functions remain poorly understood. For more than a decade, Dr Dopkins has investigated host-microbe and host-ERE interactions across immunology, genomics, molecular biology, bacteriology, and neuroscience to uncover their roles in health and disease. Dr Dopkins is currently a member of the Center for Biomarker Research and Precision Medicine in the Department of Pharmaceutics at the Virginia Commonwealth University School of Pharmacy in Richmond, VA. |
| 14:30-15:00 |
Transposon-mediated evolution of immune gene regulatory networks
Mammalian genomes harbour millions of transposon insertions, but most are expected to be inert or silenced. Despite this, our research has uncovered numerous transposons that have been co-opted as infection-inducible enhancers and exons for immune genes, shaping the regulation of host defence responses. These transposons are often species-specific and show context-dependent activity, providing an evolutionary mechanism for rapid regulatory evolution. The recurrent co-option of transposons as regulatory substrates for immune genes is consistent their role as catalysts for regulatory innovations in the face of pathogen pressure. 
Dr Edward Boyi ChuongUniversity of Colorado Boulder, US
Dr Edward Boyi ChuongUniversity of Colorado Boulder, US Edward Chuong is an Associate Professor in the BioFrontiers Institute and the Department of Molecular, Cellular and Developmental Biology at the University of Colorado Boulder. His laboratory studies how transposable elements are co-opted into host gene regulatory networks, with a focus on innate immunity and cancer. His work established endogenous retroviruses as a source of interferon-inducible enhancers and showed that Alu exonization generates a decoy interferon receptor that tunes human interferon signalling. The lab combines comparative genomics, long-read transcriptomics and CRISPR screening across primates, rodents, bats and ruminants to test how transposon-derived regulatory variation shapes immune function and its dysregulation in tumours. He received his PhD in genetics from Stanford University and was an Jane Coffin Childs postdoctoral fellow at the University of Utah. He is a Packard Fellow, a Sloan Research Fellow and a Cancer Research Institute Lloyd J Old STAR Investigator. |
| 15:00-15:30 |
Break
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| 15:30-16:00 |
Dynamic evolution of envelope-derived genes in mammalian species
A substantial portion of mammalian genomes consists of virus-derived sequences, the majority of which are endogenous retroviruses (ERVs). ERVs carry an envelope (env) gene encoding a fusogenic protein. Although most env genes have been inactivated by mutation, a small number have been co-opted for host functions, most notably placental development through trophoblast cell fusion. We have characterised such co-opted env-derived genes in cows, cats, mice, primates, and monotremes. We recently examined env open reading frames (ORFs) across 247 primate genomes and identified 8,683 nearly intact ORFs encoding proteins of at least 400 amino acids. Copy number varied among lineages, from 3 to 429 per genome. Sequence-similarity clustering revealed an evolutionary signature distinguishing the small set of long-term co-opted env-derived genes, which are retained at low copy number across lineages, from the broader pool of rapidly turning-over env-ORFs. Most conserved orthologs recovered by this approach corresponded to previously characterised genes, including syncytin-1. Applying this framework, we identified a previously unrecognised single-copy env ortholog conserved across Tarsiiformes, named env-Tar1, and experimentally demonstrated its cell fusion activity in vitro, indicating that env co-option has also occurred in a lineage where it had not been reported. We further found that certain co-opted env-derived genes have been inactivated by nonsense or indel mutations within specific primate lineages. Since many env-derived genes are maintained at low copy number and under purifying selection, we hypothesise that this dynamic turnover is driven by host-virus arms races, as exogenous viruses and ERVs often share cell-surface receptors. 
Professor So NakagawaTokai University School of Medicine, Japan
Professor So NakagawaTokai University School of Medicine, Japan So Nakagawa is Associate Professor at Tokai University School of Medicine, Japan, and a Visiting Researcher at the IDEC Institute, Hiroshima University. He received his PhD from Tokyo Medical and Dental University in 2008, then trained at the National Institute of Genetics/DDBJ Center and at Harvard University's Department of Organismic and Evolutionary Biology before joining Tokai University in 2013. His group combines comparative genomics, molecular evolution, and large-scale sequence analysis to study endogenous viral elements and retrotransposons, with a particular interest in how retroviral envelope genes are co-opted for host functions. He has also worked on RNA virus discovery from metagenomic data and on RNA virus evolutionary genomic analyses. He serves as an editor for Virus Evolution, FEBS Open Bio, mSphere, and Frontiers in Virology, and has received several awards, including the Young Investigator Award and the GGS Prize from the Genetics Society of Japan. |
| 16:00-17:00 |
Panel discussion/overview (future directions)
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