1
|
Chen Y, Fachko DN, Wu HL, Sacha JB, Skalsky RL. Sequence Analysis of microRNAs Encoded by Simian Lymphocryptoviruses. Viruses 2024; 16:1923. [PMID: 39772230 PMCID: PMC11680086 DOI: 10.3390/v16121923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 12/09/2024] [Accepted: 12/10/2024] [Indexed: 01/11/2025] Open
Abstract
Lymphocryptoviruses (LCVs) are ubiquitous gamma-herpesviruses that establish life-long infections in both humans and non-human primates (NHPs). In immunocompromised hosts, LCV infections are commonly associated with B cell disorders and malignancies such as lymphoma. In this study, we evaluated simian LCV-encoded small microRNAs (miRNAs) present in lymphoblastoid cell lines (LCLs) derived from a Mauritian cynomolgus macaque (Macaca fascicularis) with cyLCV-associated post-transplant lymphoproliferative disease (PTLD) as well as the viral miRNAs expressed in a baboon (Papio hamadryas) LCL that harbors CeHV12. Via sequence comparisons, we further predicted viral miRNAs encoded by LCVs that infect two additional NHP species: stump-tailed macaques (Macaca arctoides) and bonobos (Pan paniscus). Together, these species represent two arms of the primate phylogeny: Hominoids (Pan) and Old-World monkeys (Macaca, Papio). Through our analysis, we defined sequences for >95 viral miRNAs encoded by these four NHP LCVs. Our study provides the most comprehensive annotation of NHP LCV miRNAs to date, yielding a resource for developing sequence-specific reagents to detect these molecules. Importantly, we further demonstrate that cyLCV miRNAs can be detected in circulation in vivo and have biomarker potential for LCV-related PTLD.
Collapse
Affiliation(s)
- Yan Chen
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA; (Y.C.); (D.N.F.); (J.B.S.)
| | - Devin N. Fachko
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA; (Y.C.); (D.N.F.); (J.B.S.)
| | - Helen L. Wu
- Oregon National Primate Research Center, Beaverton, OR 97006, USA;
| | - Jonah B. Sacha
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA; (Y.C.); (D.N.F.); (J.B.S.)
- Oregon National Primate Research Center, Beaverton, OR 97006, USA;
| | - Rebecca L. Skalsky
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR 97006, USA; (Y.C.); (D.N.F.); (J.B.S.)
- Oregon National Primate Research Center, Beaverton, OR 97006, USA;
| |
Collapse
|
2
|
Blanco-Melo D, Campbell MA, Zhu H, Dennis TPW, Modha S, Lytras S, Hughes J, Gatseva A, Gifford RJ. A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record. Genome Biol 2024; 25:120. [PMID: 38741126 PMCID: PMC11089739 DOI: 10.1186/s13059-024-03258-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes. RESULTS Using DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses. CONCLUSIONS We comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.
Collapse
Affiliation(s)
- Daniel Blanco-Melo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | | | - Henan Zhu
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Tristan P W Dennis
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Sejal Modha
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Anna Gatseva
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK.
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
| |
Collapse
|
3
|
Kunze PE, Cortés-Hinojosa G, Williams CV, Archer LL, Ferrante JA, Wellehan JFX. Identification of 3 novel herpesviruses in prosimians with lymphoproliferative disease. J Vet Diagn Invest 2023; 35:514-520. [PMID: 37381927 PMCID: PMC10467458 DOI: 10.1177/10406387231183431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023] Open
Abstract
Although many studies have characterized catarrhine and platyrrhine primate herpesviruses, little is known about herpesviruses in prosimians. We aimed to identify and characterize herpesviruses in prosimians with proliferative lymphocytic disease. DNA was extracted from tissues of 9 gray mouse lemurs (Microcebus murinus) and 3 pygmy slow lorises (Nycticebus pygmaeus) with lymphoproliferative lesions, and we performed nested PCR and sequencing for detection of herpesviruses and polyomaviruses. We identified 3 novel herpesviruses and performed phylogenetic analyses to characterize their relationship with other herpesviruses. A gray mouse lemur herpesvirus clustered with other primate herpesviruses within the subfamily Betaherpesvirinae, just basal to the genus Cytomegalovirus. The other gray mouse lemur herpesvirus and the pygmy slow loris herpesvirus clustered within the subfamily Gammaherpesvirinae, although the relationships within the subfamily were less resolved. Quantitative PCR assays were developed for the 2 new gray mouse lemur viruses, providing specific, faster, less expensive, and quantitative detection tools. Further studies are needed to elucidate the relationship between the presence of these viruses and the severity or presence of lymphoproliferative lesions in prosimians.
Collapse
Affiliation(s)
- Patricia E. Kunze
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Galaxia Cortés-Hinojosa
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Linda L. Archer
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Jason A. Ferrante
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - James F. X. Wellehan
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| |
Collapse
|
4
|
Clouthier S, Tomczyk M, Schroeder T, Klassen C, Dufresne A, Emmenegger E, Nalpathamkalam T, Wang Z, Thiruvahindrapuram B. A New Sturgeon Herpesvirus from Juvenile Lake Sturgeon Acipenser fulvescens Displaying Epithelial Skin Lesions. Pathogens 2023; 12:1115. [PMID: 37764923 PMCID: PMC10537993 DOI: 10.3390/pathogens12091115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Herpesvirus infections of sturgeon pose a potential threat to sturgeon culture efforts worldwide. A new epitheliotropic herpesvirus named Acipenser herpesvirus 3 (AciHV-3) was detected in hatchery-reared Lake Sturgeon Acipenser fulvescens displaying skin lesions in central Canada. The growths were discovered in the fall, reached average prevalence levels of 0.2-40% and eventually regressed. No unusual mortality was observed. The cellular changes within the lesions included epithelial hyperplasia and were reminiscent of other herpesvirus infections. The virus was not evident in lesions examined by electron microscopy. Skin tissue homogenates from symptomatic sturgeon produced atypical cytopathic effects on a primary Lake Sturgeon cell line, and next-generation sequence analysis of the DNA samples revealed the presence of an alloherpesvirus. A new genotyping PCR assay targeting the major capsid protein sequence detected AciHV-3 in symptomatic Lake Sturgeon as well as other apparently healthy sturgeon species. Bayesian inference of phylogeny reconstructed with a concatenation of five alloherpesvirus core proteins revealed a new Alloherpesviridae lineage isomorphic with a new genus. The presence of AciHV-3 homologs in cell lines and sturgeon sequence datasets, low sequence divergence among these homologs and branching patterns within the genotyping phylogeny provide preliminary evidence of an endogenous virus lifestyle established in an ancestral sturgeon.
Collapse
Affiliation(s)
- Sharon Clouthier
- Freshwater Institute, Department of Fisheries and Oceans, 501 University Crescent, Winnipeg, MB R3T 2N6, Canada;
| | - Marek Tomczyk
- Manitoba Agriculture & Resource Development Veterinary Diagnostic Services, 545 University Crescent, Winnipeg, MB R3T 5S6, Canada;
| | - Tamara Schroeder
- Freshwater Institute, Department of Fisheries and Oceans, 501 University Crescent, Winnipeg, MB R3T 2N6, Canada;
| | - Cheryl Klassen
- Manitoba Hydro, 360 Portage Ave, Winnipeg, MB R3C 0G8, Canada;
| | - André Dufresne
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, 1015 Arlington Street, Winnipeg, MB R3E 3M4, Canada;
| | - Eveline Emmenegger
- Western Fisheries Research Center, U.S. Geological Survey, 6505 NE 65th Street, Seattle, WA 98115, USA;
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; (T.N.); (Z.W.); (B.T.)
| | - Zhuozhi Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; (T.N.); (Z.W.); (B.T.)
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; (T.N.); (Z.W.); (B.T.)
| |
Collapse
|
5
|
Inoue Y, Takeda H. Teratorn and its relatives - a cross-point of distinct mobile elements, transposons and viruses. Front Vet Sci 2023; 10:1158023. [PMID: 37187934 PMCID: PMC10175614 DOI: 10.3389/fvets.2023.1158023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Mobile genetic elements (e.g., transposable elements and plasmids) and viruses display significant diversity with various life cycles, but how this diversity emerges remains obscure. We previously reported a novel and giant (180 kb long) mobile element, Teratorn, originally identified in the genome of medaka, Oryzias latipes. Teratorn is a composite DNA transposon created by a fusion of a piggyBac-like DNA transposon (piggyBac) and a novel herpesvirus of the Alloherpesviridae family. Genomic survey revealed that Teratorn-like herpesviruses are widely distributed among teleost genomes, the majority of which are also fused with piggyBac, suggesting that fusion with piggyBac is a trigger for the life-cycle shift of authentic herpesviruses to an intragenomic parasite. Thus, Teratorn-like herpesvirus provides a clear example of how novel mobile elements emerge, that is to say, the creation of diversity. In this review, we discuss the unique sequence and life-cycle characteristics of Teratorn, followed by the evolutionary process of piggyBac-herpesvirus fusion based on the distribution of Teratorn-like herpesviruses (relatives) among teleosts. Finally, we provide other examples of evolutionary associations between different classes of elements and propose that recombination could be a driving force generating novel mobile elements.
Collapse
Affiliation(s)
- Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
6
|
Inoue Y, Takeda H. Teratorn and Its Related Elements – a Novel Group of Herpesviruses Widespread in Teleost Genomes. Zoolog Sci 2023; 40:83-90. [PMID: 37042688 DOI: 10.2108/zs220069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 12/12/2022] [Indexed: 03/08/2023]
Abstract
Herpesviruses are a large family of DNA viruses infecting vertebrates and invertebrates, and are important pathogens in the field of aquaculture. In general, herpesviruses do not have the ability to integrate into the host genomes since they do not have a chromosomal integration step in their life cycles. Recently, we identified a novel group of herpesviruses, "Teratorn" and its related elements, in the genomes of various teleost fish species. At least some of the Teratorn-like herpesviruses are fused with a piggyBac-like DNA transposon, suggesting that they have acquired the transposon-like intragenomic lifestyle by hijacking the transposon system. In this review, we describe the sequence characteristics of Teratorn-like herpesviruses and phylogenetic relationships with other herpesviruses. Then we discuss the process of transposon-herpesvirus fusion, their life cycle, and the generality of transposon-virus fusion. Teratorn-like herpesviruses provide a piece of concrete evidence that even non-retroviral elements can become intragenomic parasites retaining replication capacity, by acquiring transposition machinery from other sources.
Collapse
Affiliation(s)
- Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| |
Collapse
|
7
|
Campbell MA, Loncar S, Kotin RM, Gifford RJ. Comparative analysis reveals the long-term coevolutionary history of parvoviruses and vertebrates. PLoS Biol 2022; 20:e3001867. [PMID: 36445931 PMCID: PMC9707805 DOI: 10.1371/journal.pbio.3001867] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/04/2022] [Indexed: 12/03/2022] Open
Abstract
Parvoviruses (family Parvoviridae) are small DNA viruses that cause numerous diseases of medical, veterinary, and agricultural significance and have important applications in gene and anticancer therapy. DNA sequences derived from ancient parvoviruses are common in animal genomes and analysis of these endogenous parvoviral elements (EPVs) has demonstrated that the family, which includes twelve vertebrate-specific genera, arose in the distant evolutionary past. So far, however, such "paleovirological" analysis has only provided glimpses into the biology of ancient parvoviruses and their long-term evolutionary interactions with hosts. Here, we comprehensively map EPV diversity in 752 published vertebrate genomes, revealing defining aspects of ecology and evolution within individual parvovirus genera. We identify 364 distinct EPV sequences and show these represent approximately 200 unique germline incorporation events, involving at least five distinct parvovirus genera, which took place at points throughout the Cenozoic Era. We use the spatiotemporal and host range calibrations provided by these sequences to infer defining aspects of long-term evolution within individual parvovirus genera, including mammalian vicariance for genus Protoparvovirus, and interclass transmission for genus Dependoparvovirus. Moreover, our findings support a model of virus evolution in which the long-term cocirculation of multiple parvovirus genera in vertebrates reflects the adaptation of each viral genus to fill a distinct ecological niche. Our findings show that efforts to develop parvoviruses as therapeutic tools can be approached from a rational foundation based on comparative evolutionary analysis. To support this, we published our data in the form of an open, extensible, and cross-platform database designed to facilitate the wider utilisation of evolution-related domain knowledge in parvovirus research.
Collapse
Affiliation(s)
- Matthew A. Campbell
- University of Alaska Museum of the North, Fishes and Marine Invertebrates, Fairbanks, Alaska, United States of America
- * E-mail:
| | - Shannon Loncar
- University of Massachusetts Medical School, Department of Microbiology and Physiological Systems, Gene Therapy Center, Worcester, Massachusetts, United States of America
| | - Robert M. Kotin
- University of Massachusetts Medical School, Department of Microbiology and Physiological Systems, Gene Therapy Center, Worcester, Massachusetts, United States of America
- Carbon Biosciences, Lexington, Massachusetts, United States of America
| | - Robert J. Gifford
- MRC-University of Glasgow Centre for Virus Research, Bearsden, Glasgow, United Kingdom
- * E-mail:
| |
Collapse
|
8
|
Li Y, Bletsa M, Zisi Z, Boonen I, Gryseels S, Kafetzopoulou L, Webster JP, Catalano S, Pybus OG, Van de Perre F, Li H, Li Y, Li Y, Abramov A, Lymberakis P, Lemey P, Lequime S. Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History. Mol Biol Evol 2022; 39:msac190. [PMID: 36063436 PMCID: PMC9550988 DOI: 10.1093/molbev/msac190] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large data set of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.
Collapse
Affiliation(s)
- Yiqiao Li
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Magda Bletsa
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Zafeiro Zisi
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Ine Boonen
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Sophie Gryseels
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Belgium Evolutionary Ecology Group, University of Antwerp, 2610 Wilrijk, Belgium
| | - Liana Kafetzopoulou
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Virology Department, Belgium Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Joanne P Webster
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - Stefano Catalano
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - Oliver G Pybus
- Department of Pathobiology and Population Science, Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | | | - Haotian Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Yaoyao Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Yuchun Li
- Marine College, Shandong University (Weihai), 264209 Weihai, China
| | - Alexei Abramov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, 190121 Saint Petersburg, Russia
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Sébastian Lequime
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747 AG Groningen, the Netherlands
| |
Collapse
|
9
|
Barreat JGN, Katzourakis A. Paleovirology of the DNA viruses of eukaryotes. Trends Microbiol 2021; 30:281-292. [PMID: 34483047 DOI: 10.1016/j.tim.2021.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022]
Abstract
Paleovirology is the study of ancient viruses and how they have coevolved with their hosts. An increasingly detailed understanding of the diversity, origins, and evolution of the DNA viruses of eukaryotes has been obtained through the lens of paleovirology in recent years. Members of multiple viral families have been found integrated in the genomes of eukaryotes, providing a rich fossil record to study. These elements have extended our knowledge of exogenous viral diversity, host ranges, and the timing of viral evolution, and are revealing the existence of entire new families of eukaryotic integrating dsDNA viruses and transposons. Future work in paleovirology will continue to provide insights into antiviral immunity, viral diversity, and potential applications, and reveal other secrets of the viral world.
Collapse
Affiliation(s)
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford, OX1 3SY, UK.
| |
Collapse
|
10
|
Aswad A, Aimola G, Wight D, Roychoudhury P, Zimmermann C, Hill J, Lassner D, Xie H, Huang ML, Parrish NF, Schultheiss HP, Venturini C, Lager S, Smith GCS, Charnock-Jones DS, Breuer J, Greninger AL, Kaufer BB. Evolutionary History of Endogenous Human Herpesvirus 6 Reflects Human Migration out of Africa. Mol Biol Evol 2021; 38:96-107. [PMID: 32722766 PMCID: PMC7782865 DOI: 10.1093/molbev/msaa190] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Human herpesvirus 6A and 6B (HHV-6) can integrate into the germline, and as a result, ∼70 million people harbor the genome of one of these viruses in every cell of their body. Until now, it has been largely unknown if 1) these integrations are ancient, 2) if they still occur, and 3) whether circulating virus strains differ from integrated ones. Here, we used next-generation sequencing and mining of public human genome data sets to generate the largest and most diverse collection of circulating and integrated HHV-6 genomes studied to date. In genomes of geographically dispersed, only distantly related people, we identified clades of integrated viruses that originated from a single ancestral event, confirming this with fluorescent in situ hybridization to directly observe the integration locus. In contrast to HHV-6B, circulating and integrated HHV-6A sequences form distinct clades, arguing against ongoing integration of circulating HHV-6A or “reactivation” of integrated HHV-6A. Taken together, our study provides the first comprehensive picture of the evolution of HHV-6, and reveals that integration of heritable HHV-6 has occurred since the time of, if not before, human migrations out of Africa.
Collapse
Affiliation(s)
- Amr Aswad
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Giulia Aimola
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Darren Wight
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA
| | | | - Joshua Hill
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Dirk Lassner
- HighTech Center, Vinmec Hospital, Hanoi, Vietnam.,Institut Kardiale Diagnostik und Therapie, Berlin, Germany
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA
| | - Nicholas F Parrish
- Genome Immunobiology RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Cristina Venturini
- Division of Infection and Immunity, UCL Research Department of Infection, UCL, London, United Kingdom
| | - Susanne Lager
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.,Department of Obstetrics and Gynaecology, Cambridge University, United Kingdom
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, Cambridge University, United Kingdom
| | | | - Judith Breuer
- Division of Infection and Immunity, UCL Research Department of Infection, UCL, London, United Kingdom
| | - Alexander L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, WA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Centre, Seattle, WA
| | | |
Collapse
|
11
|
Endogenization of a Prosimian Retrovirus during Lemur Evolution. Viruses 2021; 13:v13030383. [PMID: 33673677 PMCID: PMC7997422 DOI: 10.3390/v13030383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 02/23/2021] [Indexed: 01/08/2023] Open
Abstract
Studies of viruses that coevolved with lemurs provide an opportunity to understand the basal traits of primate viruses and provide an evolutionary context for host-virus interactions. Germline integration of endogenous retroviruses (ERVs) are fossil evidence of past infections. Hence, characterization of novel ERVs provides insight into the ancient precursors of extant viruses and the evolutionary history of their hosts. Here, we report the discovery of a novel endogenous retrovirus present in the genome of a lemur, Coquerel's sifaka (Propithecus coquereli). Using next-generation sequencing, we identified and characterized the complete genome sequence of a retrovirus, named prosimian retrovirus 1 (PSRV1). Phylogenetic analyses indicate that PSRV1 is a gamma-type betaretrovirus basal to the other primate betaretroviruses and most closely related to simian retroviruses. Molecular clock analysis of PSRV1 long terminal repeat (LTR) sequences estimated the time of endogenization within 4.56 MYA (± 2.4 MYA), placing it after the divergence of Propithecus species. These results indicate that PSRV1 is an important milestone of lemur evolution during the radiation of the Propithecus genus. These findings may have implications for both human and animal health in that the acquisition of a gamma-type env gene within an endogenized betaretrovirus could facilitate a cross-species jump between vertebrate class hosts.
Collapse
|
12
|
The U94 Gene of Human Herpesvirus 6: A Narrative Review of Its Role and Potential Functions. Cells 2020; 9:cells9122608. [PMID: 33291793 PMCID: PMC7762089 DOI: 10.3390/cells9122608] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/02/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022] Open
Abstract
Human herpesvirus 6 (HHV-6) is a β-herpesvirus that is highly prevalent in the human population. HHV-6 comprises two recognized species (HHV-6A and HHV-6B). Despite different cell tropism and disease association, HHV-6A/B show high genome homology and harbor the conserved U94 gene, which is limited to HHV-6 and absent in all the other human herpesviruses. U94 has key functions in the virus life cycle and associated diseases, having demonstrated or putative roles in virus replication, integration, and reactivation. During natural infection, U94 elicits an immune response, and the prevalence and extent of the anti-U94 response are associated with specific diseases. Notably, U94 can entirely reproduce some virus effects at the cell level, including inhibition of cell migration, induction of cytokines and HLA-G expression, and angiogenesis inhibition, supporting a direct U94 role in the development of HHV-6-associated diseases. Moreover, specific U94 properties, such as the ability to modulate angiogenesis pathways, have been exploited to counteract cancer development. Here, we review the information available on this key HHV-6 gene, highlighting its potential uses.
Collapse
|
13
|
Maghodia AB, Geisler C, Jarvis DL. A new nodavirus-negative Trichoplusia ni cell line for baculovirus-mediated protein production. Biotechnol Bioeng 2020; 117:3248-3264. [PMID: 32662870 DOI: 10.1002/bit.27494] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/21/2020] [Accepted: 07/12/2020] [Indexed: 12/22/2022]
Abstract
Cell lines derived from Trichoplusia ni (Tn) are widely used as hosts in the baculovirus-insect cell system (BICS). One advantage of Tn cell lines is they can produce recombinant proteins at higher levels than cell lines derived from other insects. However, Tn cell lines are persistently infected with an alphanodavirus, Tn5 cell-line virus (TnCLV), which reduces their utility as a host for the BICS. Several groups have isolated TnCLV-negative Tn cell lines, but none were thoroughly characterized and shown to be free of other adventitious viruses. Thus, we isolated and extensively characterized a new TnCLV-negative line, Tn-nodavirus-negative (Tn-NVN). Tn-NVN cells have no detectable TnCLV, no other previously identified viral contaminants of lepidopteran insect cell lines, and no sequences associated with any replicating virus or other viral adventitious agents. Tn-NVN cells tested negative for >60 species of Mycoplasma, Acholeplasma, Spiroplasma, and Ureaplasma. Finally, Tn-NVN cells grow well as a single-cell suspension culture in serum-free medium, produce recombinant proteins at levels similar to High Five™ cells, and do not produce recombinant glycoproteins with immunogenic core α1,3-fucosylation. Thus, Tn-NVN is a new, well-characterized TnCLV-negative cell line with several other features enhancing its utility as a host for the BICS.
Collapse
Affiliation(s)
| | | | - Donald L Jarvis
- GlycoBac, LLC, Laramie, Wyoming.,Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| |
Collapse
|
14
|
van der Kuyl AC, Berkhout B. Viruses in the reproductive tract: On their way to the germ line? Virus Res 2020; 286:198101. [PMID: 32710926 DOI: 10.1016/j.virusres.2020.198101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 01/13/2023]
Abstract
Studies of vertebrate genomes have indicated that all species contain in their chromosomes stretches of DNA with sequence similarity to viral genomes. How such 'endogenous' viral elements (EVEs) ended up in host genomes is usually explained in general terms such as 'they entered the germ line at some point during evolution'. This seems a correct statement, but is also rather imprecise. The vast number of endogenous viral sequences suggest that common routes to the 'germ line' may exist, as relying on chance alone may not easily explain the abundance of EVEs in modern mammalian genomes. An increasing number of virus types have been detected in human semen and a growing number of studies have reported on viral infections that cause male infertility or subfertility and on viral infections that threaten in vitro fertilisation practices. Thus, it is timely to survey the pathway(s) that viruses can use to gain access to the human germ line. Embryo transfer and semen quality studies in livestock form another source of relevant information because virus infection during reproduction is clearly unwanted, as is the case for the human situation. In this review, studies on viruses in the male and female reproductive tract and in the early embryo will be discussed to propose a plausible viral route to the mammalian germ line.
Collapse
Affiliation(s)
- Antoinette Cornelia van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| |
Collapse
|
15
|
Three decades of Philippine nonhuman primate studies: research gaps and opportunities for Philippine primatology. Primates 2020; 62:233-239. [PMID: 32681352 DOI: 10.1007/s10329-020-00847-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/09/2020] [Indexed: 10/23/2022]
Abstract
The Philippines is considered a megadiverse country. However, there are few published studies on its nonhuman primate (NHP) species (Carlito syrichta, Macaca fascicularis, and Nycticebus menagensis). Understanding the nature and extent of existing NHP research in the Philippines would help us to determine research gaps and opportunities. Thus, studies on NHPs of Philippine origin were retrieved from online databases including Google Scholar, ResearchGate, Primate Lit, the Integrated Taxonomic Information System (ITIS), and relevant authors. Of a total of 107 studies on Philippine NHP from 1989 to 2019, most focused on Philippine long-tailed macaque (52.78%), and Philippine tarsier (42.59%), with far fewer on Philippine slow loris (4.63%). Fewer studies were based on fieldwork (26.17%); more were based on research on captive animals or that undertaken in the laboratory (34.58%), or used only existing specimens or data (33.64%). Studies on wild NHPs were mostly conducted in Bohol Island. In terms of the type of research, studies on diseases (38.60%) were the most prevalent for macaques; ecological studies (23.91%) for tarsiers; evolutionary, taxonomic, and systematic studies (40%), and ecological and natural history studies (40%) for lorises. Philippine researchers and collaborations with foreign researchers contributed fewer studies (43.93%) than foreign-only researchers (56.07%). In conclusion, although research on Philippine NHPs is increasing, there is a bias with regards to the species studied, the type of research, and study location. Conservation-driven studies are also lacking. These gaps offer opportunities for further research to identify threats to the survival of NHPs in the Philippines, and for the development of plans and effective strategies for their conservation.
Collapse
|
16
|
Türsen Ü, Türsen B, Lotti T. Coronavirus-days ın dermatology. Dermatol Ther 2020; 33:e13438. [PMID: 32307810 PMCID: PMC7235478 DOI: 10.1111/dth.13438] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 04/16/2020] [Indexed: 12/27/2022]
Abstract
Severe acute respiratory syndrome-corona virus-2, which causes coronavirus disease 2019 (COVID-19), is highly contagious and a particularly popular problem in all around the World and also in all departments of every hospital. In order to protect the well-being of health care providers while providing a sufficient workforce to respond to the COVID-19 are vital for pandemic planning. In this article, we will discuss this problem from a dermatological aspect.
Collapse
Affiliation(s)
- Ümit Türsen
- Department of Dermatology, School of MedicineMersin UniversityMersinTurkey
| | - Belma Türsen
- Department of Medical SciencesToros UniversityMersinTurkey
| | - Torello Lotti
- Department of Dermatology and VenereologyUniversity of Rome G. MarconiRomeItaly
| |
Collapse
|
17
|
Current understanding of human herpesvirus 6 (HHV-6) chromosomal integration. Antiviral Res 2020; 176:104720. [PMID: 32044155 DOI: 10.1016/j.antiviral.2020.104720] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/12/2022]
Abstract
Human herpesvirus 6A (HHV-6A) and 6B (HHV-6B) are members of the genus Roseolovirus in the Betaherpesvirinae subfamily. HHV-6B infects humans in the first years of life, has a seroprevalence of more than 90% and causes Roseola Infantum, but less is known about HHV-6A. While most other herpesviruses maintain their latent genome as a circular episome, HHV-6A and HHV-6B (HHV-6A/B) have been shown to integrate their genome into the telomeres of infected cells. HHV-6A/B can also integrate into the chromosomes of germ cells, resulting in individuals carrying a copy of the virus genome in every nucleated cell of their bodies. This review highlights our current understanding of HHV-6A/B integration and reactivation as well as aspects that should be addressed in the future of this relatively young research area. It forms part of an online symposium on the prevention and therapy of DNA virus infections, dedicated to the memory of Mark Prichard.
Collapse
|
18
|
Murthy S, O'Brien K, Agbor A, Angedakin S, Arandjelovic M, Ayimisin EA, Bailey E, Bergl RA, Brazzola G, Dieguez P, Eno-Nku M, Eshuis H, Fruth B, Gillespie TR, Ginath Y, Gray M, Herbinger I, Jones S, Kehoe L, Kühl H, Kujirakwinja D, Lee K, Madinda NF, Mitamba G, Muhindo E, Nishuli R, Ormsby LJ, Petrzelkova KJ, Plumptre AJ, Robbins MM, Sommer V, Ter Heegde M, Todd A, Tokunda R, Wessling E, Jarvis MA, Leendertz FH, Ehlers B, Calvignac-Spencer S. Cytomegalovirus distribution and evolution in hominines. Virus Evol 2019; 5:vez015. [PMID: 31384482 PMCID: PMC6671425 DOI: 10.1093/ve/vez015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Herpesviruses are thought to have evolved in very close association with their hosts. This is notably the case for cytomegaloviruses (CMVs; genus Cytomegalovirus) infecting primates, which exhibit a strong signal of co-divergence with their hosts. Some herpesviruses are however known to have crossed species barriers. Based on a limited sampling of CMV diversity in the hominine (African great ape and human) lineage, we hypothesized that chimpanzees and gorillas might have mutually exchanged CMVs in the past. Here, we performed a comprehensive molecular screening of all 9 African great ape species/subspecies, using 675 fecal samples collected from wild animals. We identified CMVs in eight species/subspecies, notably generating the first CMV sequences from bonobos. We used this extended dataset to test competing hypotheses with various degrees of co-divergence/number of host switches while simultaneously estimating the dates of these events in a Bayesian framework. The model best supported by the data involved the transmission of a gorilla CMV to the panine (chimpanzee and bonobo) lineage and the transmission of a panine CMV to the gorilla lineage prior to the divergence of chimpanzees and bonobos, more than 800,000 years ago. Panine CMVs then co-diverged with their hosts. These results add to a growing body of evidence suggesting that viruses with a double-stranded DNA genome (including other herpesviruses, adenoviruses, and papillomaviruses) often jumped between hominine lineages over the last few million years.
Collapse
Affiliation(s)
- Sripriya Murthy
- Division 12 "Measles, Mumps, Rubella and Viruses Affecting Immune-Compromised Patients" Robert Koch Institute, Berlin, Germany
| | - Kathryn O'Brien
- School of Biomedical and Healthcare Sciences, University of Plymouth, Devon, UK
| | - Anthony Agbor
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany.,African Parks Network, Lonehill, Republic of South Africa
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | | | - Emma Bailey
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | | | - Gregory Brazzola
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | | | - Henk Eshuis
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | - Barbara Fruth
- Faculty of Science, School of Natural Sciences and hPsychology, Liverpool John Moores University, Liverpool, UK.,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Thomas R Gillespie
- Department of Environmental Sciences and Program in Population Biology, Ecology, and Evolutionary Biology, Emory University, Atlanta, USA
| | - Yisa Ginath
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | - Maryke Gray
- International Gorilla Conservation Programme, Kigali, Rwanda.,Batavia Coast Maritime Institute, Geraldton, WA, Australia
| | | | - Sorrel Jones
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany.,Royal Holloway, University of London, Egham, UK
| | - Laura Kehoe
- Wild Chimpanzee Foundation (WCF), Leipzig, Germany.,Department of Biology, University of Victoria, Victoria, Canada.,Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| | - Hjalmar Kühl
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | | | - Kevin Lee
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany.,School of Human Evolution and Social Change, Arizona State University, Tempe, USA
| | - Nadège F Madinda
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany.,Epidemiology of highly pathogenic microorganisms, Robert Koch Institute, Berlin, Germany
| | | | | | - Radar Nishuli
- Réserve de Faune à Okapis, Institut Congolais pour la Conservation de la Nature, Kinshasa, Democratic Republic of the Congo
| | - Lucy J Ormsby
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | - Klara J Petrzelkova
- Institute of Vertebrate Biology, Academy of Sciences, Brno, Czech Republic.,Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic.,Biology Centre, Institute of Parasitology, Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic.,Liberec Zoo, Liberec, Czech Republic
| | - Andrew J Plumptre
- Wildlife Conservation Society, NY, USA.,KBA Secretariat, c/o BirdLife International, Cambridge, UK.,Zoology Department, Conservation Science Group, University of Cambridge, Cambridge, UK
| | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany
| | - Volker Sommer
- Gashaka Primate Project, Nigeria c/o Department of Anthropology, University College London, London, UK
| | - Martijn Ter Heegde
- Epidemiology of highly pathogenic microorganisms, Robert Koch Institute, Berlin, Germany
| | - Angelique Todd
- Dzanga Sangha Protected Areas, WWF Central African Republic, Bangui, Central African Republic
| | - Raymond Tokunda
- Institute of Vertebrate Biology, Academy of Sciences, Brno, Czech Republic
| | - Erin Wessling
- Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig, Germany.,Dzanga Sangha Protected Areas, WWF Central African Republic, Bangui, Central African Republic
| | - Michael A Jarvis
- School of Biomedical and Healthcare Sciences, University of Plymouth, Devon, UK
| | - Fabian H Leendertz
- Epidemiology of highly pathogenic microorganisms, Robert Koch Institute, Berlin, Germany
| | - Bernhard Ehlers
- Division 12 "Measles, Mumps, Rubella and Viruses Affecting Immune-Compromised Patients" Robert Koch Institute, Berlin, Germany
| | - Sébastien Calvignac-Spencer
- Epidemiology of highly pathogenic microorganisms, Robert Koch Institute, Berlin, Germany.,Viral Evolution, Robert Koch Institute, Berlin, Germany
| |
Collapse
|
19
|
Broecker F, Moelling K. What viruses tell us about evolution and immunity: beyond Darwin? Ann N Y Acad Sci 2019; 1447:53-68. [PMID: 31032941 PMCID: PMC6850104 DOI: 10.1111/nyas.14097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/09/2019] [Accepted: 03/20/2019] [Indexed: 12/14/2022]
Abstract
We describe mechanisms of genetic innovation mediated by viruses and related elements that, during evolution, caused major genetic changes beyond what was anticipated by Charles Darwin. Viruses and related elements introduced genetic information and have shaped the genomes and immune systems of all cellular life forms. None of these mechanisms contradict Darwin's theory of evolution but extend it by means of sequence information that has recently become available. Not only do small increments of genetic information contribute to evolution, but also do major events such as infection by viruses or bacteria, which can supply new genetic information to a host by horizontal gene transfer. Thereby, viruses and virus-like elements act as major drivers of evolution.
Collapse
Affiliation(s)
- Felix Broecker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Karin Moelling
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Max Planck Institute for Molecular Genetics, Berlin, Germany
| |
Collapse
|
20
|
Systematic survey of non-retroviral virus-like elements in eukaryotic genomes. Virus Res 2019; 262:30-36. [DOI: 10.1016/j.virusres.2018.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/30/2017] [Accepted: 02/05/2018] [Indexed: 01/31/2023]
|
21
|
Broecker F, Moelling K. Evolution of Immune Systems From Viruses and Transposable Elements. Front Microbiol 2019; 10:51. [PMID: 30761103 PMCID: PMC6361761 DOI: 10.3389/fmicb.2019.00051] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 01/14/2019] [Indexed: 12/20/2022] Open
Abstract
Virus-derived sequences and transposable elements constitute a substantial portion of many cellular genomes. Recent insights reveal the intimate evolutionary relationship between these sequences and various cellular immune pathways. At the most basic level, superinfection exclusion may be considered a prototypical virus-mediated immune system that has been described in both prokaryotes and eukaryotes. More complex immune mechanisms fully or partially derived from mobile genetic elements include CRISPR-Cas of prokaryotes and the RAG1/2 system of vertebrates, which provide immunological memory of foreign genetic elements and generate antibody and T cell receptor diversity, respectively. In this review, we summarize the current knowledge on the contribution of mobile genetic elements to the evolution of cellular immune pathways. A picture is emerging in which the various cellular immune systems originate from and are spread by viruses and transposable elements. Immune systems likely evolved from simple superinfection exclusion to highly complex defense strategies.
Collapse
Affiliation(s)
- Felix Broecker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Karin Moelling
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Max Planck Institute for Molecular Genetics, Berlin, Germany
| |
Collapse
|
22
|
Iyer MS, Joshi AG, Sowdhamini R. Genome-wide survey of remote homologues for protein domain superfamilies of known structure reveals unequal distribution across structural classes. Mol Omics 2018; 14:266-280. [PMID: 29971307 DOI: 10.1039/c8mo00008e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Domains are the basic building blocks of proteins which can combine to give rise to different domain architectures. Annotation of domains in a sequence is the first step towards understanding the biological function. Since there are a limited number of folds and evolutionarily related proteins have a similar structure, function can be inferred through remote homology. Computational sequence searches were performed for remote homologues on genomes of around ∼160 000 different organisms, starting from nearly 11 000 superfamily queries of known structure. Case studies revealed that most of the associated domains are involved in the same biological process. Using all the proteins predicted to have at least one structural domain, a coverage of 61% of Pfam families was achieved which is higher than the existing methods (43.36% by SIFTS). Taxonomic analysis of the proteins revealed 493 superfamilies in all the major kingdoms of life and a few lateral gene transfers between viruses and cellular organisms. The distribution of remote homologues across different classes, folds and superfamilies was studied and reveals that sequences are unequally distributed across structural classes. Finally, domain architectures were computed for the homologues and these data were compiled for each superfamily and organism.
Collapse
Affiliation(s)
- Meenakshi S Iyer
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, Karnataka 560 065, India.
| | | | | |
Collapse
|
23
|
Inoue Y, Kumagai M, Zhang X, Saga T, Wang D, Koga A, Takeda H. Fusion of piggyBac-like transposons and herpesviruses occurs frequently in teleosts. ZOOLOGICAL LETTERS 2018; 4:6. [PMID: 29484202 PMCID: PMC5822658 DOI: 10.1186/s40851-018-0089-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 02/06/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND Endogenous viral elements play important roles in eukaryotic evolution by giving rise to genetic novelties. Herpesviruses are a large family of DNA viruses, most of which do not have the ability to endogenize into host genomes. Recently, we identified a novel type of endogenous herpesvirus, which we named "Teratorn", from the medaka (Oryzias latipes) genome, in which the herpesvirus is fused with a piggyBac-like DNA transposon, forming a novel mobile element. Teratorn is a unique herpesvirus that retains its viral genes intact and has acquired the endogenized lifestyle by hijacking the transposon system. However, it is unclear how this novel element evolved in the teleost lineage and whether fusion of two mobile elements is a general phenomenon in vertebrates. RESULTS Here we performed a comprehensive genomic survey searching for Teratorn-like viruses in publicly available genome data and found that they are widely distributed in teleosts, forming a clade within Alloherpesviridae. Importantly, at least half of the identified Teratorn-like viruses contain piggyBac-like transposase genes, suggesting the generality of the transposon-herpesvirus fusion in teleosts. Phylogenetic tree topologies between the piggyBac-like transposase gene and herpesvirus-like genes are nearly identical, supporting the idea of a long-term evolutionary relationship between them. CONCLUSION We propose that piggyBac-like elements and Teratorn-like viruses have co-existed for a long time, and that fusion of the two mobile genetic elements occurred frequently in teleosts.
Collapse
Affiliation(s)
- Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Masahiko Kumagai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Xianbo Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715 China
| | - Tomonori Saga
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715 China
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506 Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| |
Collapse
|
24
|
Complete fusion of a transposon and herpesvirus created the Teratorn mobile element in medaka fish. Nat Commun 2017; 8:551. [PMID: 28916771 PMCID: PMC5601938 DOI: 10.1038/s41467-017-00527-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 07/05/2017] [Indexed: 01/02/2023] Open
Abstract
Mobile genetic elements (e.g., transposable elements and viruses) display significant diversity with various life cycles, but how novel elements emerge remains obscure. Here, we report a giant (180-kb long) transposon, Teratorn, originally identified in the genome of medaka, Oryzias latipes. Teratorn belongs to the piggyBac superfamily and retains the transposition activity. Remarkably, Teratorn is largely derived from a herpesvirus of the Alloherpesviridae family that could infect fish and amphibians. Genomic survey of Teratorn-like elements reveals that some of them exist as a fused form between piggyBac transposon and herpesvirus genome in teleosts, implying the generality of transposon-herpesvirus fusion. We propose that Teratorn was created by a unique fusion of DNA transposon and herpesvirus, leading to life cycle shift. Our study supports the idea that recombination is the key event in generation of novel mobile genetic elements. Teratorn is a large mobile genetic element originally identified in the small teleost fish medaka. Here, the authors show that Teratorn is derived from the fusion of a piggyBac superfamily DNA transposon and an alloherpesvirus and that it is widely found across teleost fish.
Collapse
|
25
|
Disentangling the origins of virophages and polintons. Curr Opin Virol 2017; 25:59-65. [PMID: 28802203 DOI: 10.1016/j.coviro.2017.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/10/2017] [Accepted: 07/14/2017] [Indexed: 01/04/2023]
Abstract
Virophages and polintons are part of a complex system that also involves eukaryotes, giant viruses, as well as other viruses and transposable elements. Virophages are cosmopolitan, being found in environments ranging from the Amazon River to Antarctic hypersaline lakes, while polintons are found in many single celled and multicellular eukaryotes. Virophages and polintons have a shared ancestry, but their exact origins are unknown and obscured by antiquity and extensive horizontal gene transfer (HGT). Paleovirology can help disentangle the complicated gene flow between these two, as well as their giant viral and eukaryotic hosts. We outline the evidence and theoretical support for polintons being descended from viruses and not vice versa. In order to disentangle the natural history of polintons and virophages, we suggest that there is much to be gained by embracing rigorous metagenomics and evolutionary analyses. Methods from paleovirology will play a pivotal role in unravelling ancient relationships, HGT and patterns of cross-species transmission.
Collapse
|
26
|
Aswad A, Katzourakis A. A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence data. Virus Evol 2017; 3:vex016. [PMID: 28798873 PMCID: PMC5544889 DOI: 10.1093/ve/vex016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pathogenic viruses represent a small fraction of viral diversity, and emerging diseases are frequently the result of cross-species transmissions. Therefore, we need to develop high-throughput techniques to investigate a broader range of viral biodiversity across a greater number of species. This is especially important in the context of new practices in agriculture that have arisen to tackle the challenges of global food security, including the rising number of marine and freshwater species that are used in aquaculture. In this study, we demonstrate the utility of combining evolutionary approaches with bioinformatics to mine non-viral genome data for viruses, by adapting methods from paleovirology. We report the discovery of a new lineage of dsDNA viruses that are associated with at least fifteen different species of fish. This approach also enabled us to simultaneously identify sequences that likely represent endogenous viral elements, which we experimentally confirmed in commercial salmon samples. Moreover, genomic analysis revealed that the endogenous sequences have co-opted PiggyBac-like transposable elements, possibly as a mechanism of intragenomic proliferation. The identification of novel viruses from genome data shows that our approach has applications in genomics, virology, and the development of best practices for aquaculture and farming.
Collapse
Affiliation(s)
- Amr Aswad
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS Oxford, UK
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS Oxford, UK
| |
Collapse
|
27
|
The biological significance of bornavirus-derived genes in mammals. Curr Opin Virol 2017; 25:1-6. [PMID: 28666136 DOI: 10.1016/j.coviro.2017.06.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/06/2017] [Accepted: 06/13/2017] [Indexed: 02/01/2023]
Abstract
The discoveries of sequences derived from non-retroviral viruses in eukaryotic genomes have significantly expanded our knowledge about virus evolution as well as the co-evolution between viruses and eukaryotes. However, the biological functions of such sequences in the host are largely unknown. Endogenous bornavirus-like elements (EBLs) have been relatively well studied by molecular biological methods, which have provided evidence that some EBLs have been co-opted by their hosts. This review highlights the current knowledge on the biological significance of EBLs, and discusses possible functions of EBLs. Further, we highlight the importance of extensive surveillance of exogenous viruses for a better understanding of endogenous viral sequences as well as the co-evolution of viruses and eukaryotes.
Collapse
|
28
|
Abstract
This paper reports on the various nuances of the origins of life on Earth and highlights the latest findings in that arena as reported at the Network of Researchers on Horizontal Gene Transfer and the Last Universal Common Ancestor (NoR HGT and LUCA) which was held from the 3–4th November 2016 at the Open University, UK. Although the answers to the question of the origin of life on Earth will not be fathomable anytime soon, a wide variety of subject matter was able to be covered, ranging from examining what constitutes a LUCA, looking at viral connections and “from RNA to DNA”, i.e., could DNA have been formed simultaneously with RNA, rather than RNA first and then describing the emergence of DNA from RNA. Also discussed are proteins and the origins of genomes as well as various ideas that purport to explain the origin of life here on Earth and potentially further afield elsewhere on other planets.
Collapse
Affiliation(s)
- Sohan Jheeta
- Network of Researchers on Horizontal Gene Transfer and the Last Universal Common Ancestor (NoR HGT & LUCA), Leeds LS7 3RB, UK.
| |
Collapse
|
29
|
Blinov VM, Zverev VV, Krasnov GS, Filatov FP, Shargunov AV. Viral component of the human genome. Mol Biol 2017; 51:205-215. [PMID: 32214476 PMCID: PMC7089383 DOI: 10.1134/s0026893317020066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 04/27/2016] [Indexed: 12/17/2022]
Abstract
Relationships between viruses and their human host are traditionally described from the point of view taking into consideration hosts as victims of viral aggression, which results in infectious diseases. However, these relations are in fact two-sided and involve modifications of both the virus and host genomes. Mutations that accumulate in the populations of viruses and hosts may provide them advantages such as the ability to overcome defense barriers of host cells or to create more efficient barriers to deal with the attack of the viral agent. One of the most common ways of reinforcing anti-viral barriers is the horizontal transfer of viral genes into the host genome. Within the host genome, these genes may be modified and extensively expressed to compete with viral copies and inhibit the synthesis of their products or modulate their functions in other ways. This review summarizes the available data on the horizontal gene transfer between viral and human genomes and discusses related problems.
Collapse
Affiliation(s)
- V M Blinov
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | - V V Zverev
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| | - G S Krasnov
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia.,2Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 111911 Russia.,3Orekhovich Research Institute of Biomedical Chemistry, Moscow, 119121 Russia
| | - F P Filatov
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia.,Gamaleya Research Center of Epidemiology and Microbiology, Moscow, 123098 Russia
| | - A V Shargunov
- 1Mechnikov Research Institute of Vaccines and Sera, Moscow, 105064 Russia
| |
Collapse
|
30
|
Schönrich G, Abdelaziz MO, Raftery MJ. Herpesviral capture of immunomodulatory host genes. Virus Genes 2017; 53:762-773. [PMID: 28451945 DOI: 10.1007/s11262-017-1460-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/18/2017] [Indexed: 12/27/2022]
Abstract
Herpesviruses have acquired numerous genes from their hosts. Although these homologs are not essential for viral replication, they often have important immunomodulatory functions that ensure viral persistence in the host. Some of these viral molecules are called virokines as they mimic cellular cytokines of their host such as interleukin-10 (cIL-10). In recent years, many viral homologs of IL-10 (vIL-10s) have been discovered in the genome of members of the order Herpesvirales. For some, gene and protein structure as well as biological activity and potential use in the clinical context have been explored. Besides virokines, herpesviruses have also captured genes encoding membrane-bound host immunomodulatory proteins such as major histocompatibility complex (MHC) molecules. These viral MHC mimics also retain many of the functions of the cellular genes, in particular directly or indirectly modulating the activity of natural killer cells. The mechanisms underlying capture of cellular genes by large DNA viruses are still enigmatic. In this review, we provide an update of the advances in the field of herpesviral gene piracy and discuss possible scenarios that could explain how the gene transfer from host to viral genome was achieved.
Collapse
Affiliation(s)
- Günther Schönrich
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.
| | - Mohammed O Abdelaziz
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Martin J Raftery
- Institute of Medical Virology, Helmut-Ruska-Haus, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| |
Collapse
|
31
|
Abstract
Although genetic transfer between viruses and vertebrate hosts occurs less frequently than gene flow between bacteriophages and prokaryotes, it is extensive and has affected the evolution of both parties. With retroviruses, the integration of proviral DNA into chromosomal DNA can result in the activation of adjacent host gene expression and in the transduction of host transcripts into retroviral genomes as oncogenes. Yet in contrast to lysogenic phage, there is little evidence that viral oncogenes persist in a chain of natural transmission or that retroviral transduction is a significant driver of the horizontal spread of host genes. Conversely, integration of proviruses into the host germ line has generated endogenous retroviral genomes (ERV) in all vertebrate genomes sequenced to date. Some of these genomes retain potential infectivity and upon reactivation may transmit to other host species. During mammalian evolution, sequences of retroviral origin have been repurposed to serve host functions, such as the viral envelope glycoproteins crucial to the development of the placenta. Beyond retroviruses, DNA viruses with complex genomes have acquired numerous genes of host origin which influence replication, pathogenesis and immune evasion, while host species have accumulated germline sequences of both DNA and RNA viruses. A codicil is added on lateral transmission of cancer cells between hosts and on migration of host mitochondria into cancer cells.
Collapse
Affiliation(s)
- Robin A Weiss
- Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
32
|
Weiss RA. Human endogenous retroviruses: friend or foe? APMIS 2016; 124:4-10. [PMID: 26818257 DOI: 10.1111/apm.12476] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/12/2015] [Indexed: 01/21/2023]
Abstract
The integration of proviral DNA into host chromosomal DNA as an obligatory step in the replication cycle of retroviruses is a natural event of genetic recombination between virus and host. When integration occurs in cells of the germ line, it results in mendelian inheritance of viral sequences that we call endogenous retroviruses (ERV) and HERV for humans. HERVs and host often establish a symbiotic relationship, especially in the placenta and in pluripotent embryonic stem cells, but HERVs occasionally have deleterious consequences for the host. This special issue of APMIS features the fascinating relationships between HERV and humans in health and disease.
Collapse
Affiliation(s)
- Robin A Weiss
- Division of Infection & Immunity, University College London, London, UK
| |
Collapse
|
33
|
Houldcroft CJ, Underdown SJ. Neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:379-88. [PMID: 27063929 DOI: 10.1002/ajpa.22985] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 02/10/2016] [Accepted: 03/03/2016] [Indexed: 12/13/2022]
Abstract
High quality Altai Neanderthal and Denisovan genomes are revealing which regions of archaic hominin DNA have persisted in the modern human genome. A number of these regions are associated with response to infection and immunity, with a suggestion that derived Neanderthal alleles found in modern Europeans and East Asians may be associated with autoimmunity. As such Neanderthal genomes are an independent line of evidence of which infectious diseases Neanderthals were genetically adapted to. Sympathetically, human genome adaptive introgression is an independent line of evidence of which infectious diseases were important for AMH coming in to Eurasia and interacting with Neanderthals. The Neanderthals and Denisovans present interesting cases of hominin hunter-gatherers adapted to a Eurasian rather than African infectious disease package. Independent sources of DNA-based evidence allow a re-evaluation of the first epidemiologic transition and how infectious disease affected Pleistocene hominins. By combining skeletal, archaeological and genetic evidence from modern humans and extinct Eurasian hominins, we question whether the first epidemiologic transition in Eurasia featured a new package of infectious diseases or a change in the impact of existing pathogens. Coupled with pathogen genomics, this approach supports the view that many infectious diseases are pre-Neolithic, and the list continues to expand. The transfer of pathogens between hominin populations, including the expansion of pathogens from Africa, may also have played a role in the extinction of the Neanderthals and offers an important mechanism to understand hominin-hominin interactions well back beyond the current limits for aDNA extraction from fossils alone. Am J Phys Anthropol 160:379-388, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Charlotte J Houldcroft
- Division of Biological Anthropology, Department of Archaeology & Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.,Infection, Inflammation and Rheumatology Section, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Simon J Underdown
- Human Origins and Palaeoenvironmental Research Group (HOPE), Department of Anthropology & Geography, Oxford Brookes University, Oxford, OX3 0BP, UK
| |
Collapse
|
34
|
Tweedy J, Spyrou MA, Pearson M, Lassner D, Kuhl U, Gompels UA. Complete Genome Sequence of Germline Chromosomally Integrated Human Herpesvirus 6A and Analyses Integration Sites Define a New Human Endogenous Virus with Potential to Reactivate as an Emerging Infection. Viruses 2016; 8:v8010019. [PMID: 26784220 PMCID: PMC4728579 DOI: 10.3390/v8010019] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/25/2015] [Accepted: 12/01/2015] [Indexed: 12/23/2022] Open
Abstract
Human herpesvirus-6A and B (HHV-6A, HHV-6B) have recently defined endogenous genomes, resulting from integration into the germline: chromosomally-integrated “CiHHV-6A/B”. These affect approximately 1.0% of human populations, giving potential for virus gene expression in every cell. We previously showed that CiHHV-6A was more divergent than CiHHV-6B by examining four genes in 44 European CiHHV-6A/B cardiac/haematology patients. There was evidence for gene expression/reactivation, implying functional non-defective genomes. To further define the relationship between HHV-6A and CiHHV-6A we used next-generation sequencing to characterize genomes from three CiHHV-6A cardiac patients. Comparisons to known exogenous HHV-6A showed CiHHV-6A genomes formed a separate clade; including all 85 non-interrupted genes and necessary cis-acting signals for reactivation as infectious virus. Greater single nucleotide polymorphism (SNP) density was defined in 16 genes and the direct repeats (DR) terminal regions. Using these SNPs, deep sequencing analyses demonstrated superinfection with exogenous HHV-6A in two of the CiHHV-6A patients with recurrent cardiac disease. Characterisation of the integration sites in twelve patients identified the human chromosome 17p subtelomere as a prevalent site, which had specific repeat structures and phylogenetically related CiHHV-6A coding sequences indicating common ancestral origins. Overall CiHHV-6A genomes were similar, but distinct from known exogenous HHV-6A virus, and have the capacity to reactivate as emerging virus infections.
Collapse
Affiliation(s)
- Joshua Tweedy
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, University of London, London WC1E 7HT, UK.
| | - Maria Alexandra Spyrou
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, University of London, London WC1E 7HT, UK.
| | - Max Pearson
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, University of London, London WC1E 7HT, UK.
| | - Dirk Lassner
- Institute of Cardiac diagnostics (IKDT), Charite University, D-12203 Berlin, Germany.
| | - Uwe Kuhl
- Institute of Cardiac diagnostics (IKDT), Charite University, D-12203 Berlin, Germany.
| | - Ursula A Gompels
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, University of London, London WC1E 7HT, UK.
| |
Collapse
|
35
|
Abstract
Epstein-Barr virus (EBV) orthologues from non-human primates (NHPs) have been studied for nearly as long as EBV itself. Cross-reactive sera and DNA hybridization studies provided the first glimpses of the closely related herpesviruses that belonged to the same gamma-1 herpesvirus, or lymphocryptovirus, genus, as EBV. Over the years, detailed molecular and sequence analyses of LCVs that infect humans and other NHPs revealed similar colinear genome structures and homologous viral proteins expressed during latent and lytic infection. Despite these similarities, experimental infection of NHPs with EBV did not result in acute symptoms or persistent infection as observed in humans, suggesting some degree of host species restriction. Genome sequencing and a molecular clone of an LCV isolate from naturally infected rhesus macaques combined with domestic colonies of LCV-naïve rhesus macaques have opened the door to a unique experimental animal model that accurately reproduces the normal transmission, acute viremia, lifelong persistence, and immune responses found in EBV-infected humans. This chapter will summarize the advances made over the last 50 years in our understanding of LCVs that naturally infect both Old and New World NHPs, the recent, groundbreaking developments in the use of rhesus macaques as an animal model for EBV infection, and how NHP LCVs and the rhLCV animal model can advance future EBV research and the development of an EBV vaccine.
Collapse
Affiliation(s)
- Janine Mühe
- Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, 02115
- Department of Molecular Biology and Immunobiology, Harvard Medical School, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, 02115
| | - Fred Wang
- Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, 02115.
- Department of Molecular Biology and Immunobiology, Harvard Medical School, Brigham and Women's Hospital, 181 Longwood Ave, Boston, MA, 02115.
- Infectious Diseases Division, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, USA.
| |
Collapse
|
36
|
Abstract
EBV expresses a number of viral noncoding RNAs (ncRNAs) during latent infection, many of which have known regulatory functions and can post-transcriptionally regulate viral and/or cellular gene expression. With recent advances in RNA sequencing technologies, the list of identified EBV ncRNAs continues to grow. EBV-encoded RNAs (EBERs) , the BamHI-A rightward transcripts (BARTs) , a small nucleolar RNA (snoRNA) , and viral microRNAs (miRNAs) are all expressed during EBV infection in a variety of cell types and tumors. Recently, additional novel EBV ncRNAs have been identified. Viral miRNAs, in particular, have been under extensive investigation since their initial identification over ten years ago. High-throughput studies to capture miRNA targets have revealed a number of miRNA-regulated viral and cellular transcripts that tie into important biological networks. Functions for many EBV ncRNAs are still unknown; however, roles for many EBV miRNAs in latency and in tumorigenesis have begun to emerge. Ongoing mechanistic studies to elucidate the functions of EBV ncRNAs should unravel additional roles for ncRNAs in the viral life cycle. In this chapter, we will discuss our current knowledge of the types of ncRNAs expressed by EBV, their potential roles in viral latency, and their potential involvement in viral pathogenesis.
Collapse
|
37
|
Weiss RA. What's the host and what's the microbe? The Marjory Stephenson Prize Lecture 2015. J Gen Virol 2015; 96:2501-2510. [PMID: 26296666 DOI: 10.1099/jgv.0.000220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The interchange between retroviruses and their hosts is an intimate one because retroviruses integrate proviral DNA into host chromosomal DNA as an obligate step in the replication cycle. This has resulted in the occasional transduction of host genes into retroviral genomes as oncogenes, and also led to the integration of viral genomes into the host germ line that gives rise to endogenous retroviruses. I shall reflect on the evolutionary consequences of these events for virus and host. Then, I shall discuss the emergence of non-viral infections of host origin, namely, how malignant cells can give rise to eukaryotic single cell 'parasites' that colonize new hosts and how these in turn have been colonized by host mitochondria.
Collapse
Affiliation(s)
- Robin A Weiss
- Division of Infection & Immunity, University College London, Gower Street, London WC1E 6BT, UK
| |
Collapse
|
38
|
Jheeta S. The Routes of Emergence of Life from LUCA during the RNA and Viral World: A Conspectus. Life (Basel) 2015; 5:1445-53. [PMID: 26057871 PMCID: PMC4500147 DOI: 10.3390/life5021445] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/20/2015] [Indexed: 11/16/2022] Open
Abstract
How did life emerge on Earth? The aim of the Network of Researchers on Horizontal Gene Transfer and the Last Universal Cellular Ancestor (NoR HGT & LUCA) is to understand how the genetics of LUCAs were reorganised prior to the advent of the three domains of life. This paper reports the research of eminent scientists who have come together within the network and are making significant contributions to the wider knowledge base surrounding this, one of science’s remaining mysteries. I also report on their relevance in relation to LUCAs and life’s origins, as well as ask a question: what next?
Collapse
Affiliation(s)
- Sohan Jheeta
- Network of Researchers on Horizontal Gene Transfer and the Last Universal Cellular Ancestor (NoR HGT & LUCA †), 1 Scott Hall Crescent, Leeds LS7 3RB, UK.
| |
Collapse
|
39
|
Houldcroft CJ, Breuer J. Tales from the crypt and coral reef: the successes and challenges of identifying new herpesviruses using metagenomics. Front Microbiol 2015; 6:188. [PMID: 25821447 PMCID: PMC4358218 DOI: 10.3389/fmicb.2015.00188] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/20/2015] [Indexed: 12/14/2022] Open
Abstract
Herpesviruses are ubiquitous double-stranded DNA viruses infecting many animals, with the capacity to cause disease in both immunocompetent and immunocompromised hosts. Different herpesviruses have different cell tropisms, and have been detected in a diverse range of tissues and sample types. Metagenomics—encompassing viromics—analyses the nucleic acid of a tissue or other sample in an unbiased manner, making few or no prior assumptions about which viruses may be present in a sample. This approach has successfully discovered a number of novel herpesviruses. Furthermore, metagenomic analysis can identify herpesviruses with high degrees of sequence divergence from known herpesviruses and does not rely upon culturing large quantities of viral material. Metagenomics has had success in two areas of herpesvirus sequencing: firstly, the discovery of novel exogenous and endogenous herpesviruses in primates, bats and cnidarians; and secondly, in characterizing large areas of the genomes of herpesviruses previously only known from small fragments, revealing unexpected diversity. This review will discuss the successes and challenges of using metagenomics to identify novel herpesviruses, and future directions within the field.
Collapse
Affiliation(s)
- Charlotte J Houldcroft
- Infection, Inflammation and Rheumatology, Institute of Child Health, University College London , London, UK
| | - Judith Breuer
- Infection, Inflammation and Rheumatology, Institute of Child Health, University College London , London, UK ; Division of Infection and Immunity, University College London , London, UK
| |
Collapse
|
40
|
Aiewsakun P, Katzourakis A. Endogenous viruses: Connecting recent and ancient viral evolution. Virology 2015; 479-480:26-37. [PMID: 25771486 DOI: 10.1016/j.virol.2015.02.011] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/15/2014] [Accepted: 02/04/2015] [Indexed: 12/17/2022]
Abstract
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.
Collapse
Affiliation(s)
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
| |
Collapse
|
41
|
Abstract
UNLABELLED The roles of host genetics versus exposure and contact frequency in driving cross-species transmission remain the subject of debate. Here, we used a multitaxon lemur collection at the Saint Louis Zoo in the United States as a model to gain insight into viral transmission in a setting of high interspecies contact. Lemurs are a diverse and understudied group of primates that are highly endangered. The speciation of lemurs, which are endemic to the island of Madagascar, occurred in geographic isolation apart from that of continental African primates. Although evidence of endogenized viruses in lemur genomes exists, no exogenous viruses of lemurs have been described to date. Here we identified two novel picornaviruses in fecal specimens of ring-tailed lemurs (Lemur catta) and black-and-white ruffed lemurs (Varecia variegata). We found that the viruses were transmitted in a species-specific manner (lesavirus 1 was detected only in ring-tailed lemurs, while lesavirus 2 was detected only in black-and-white ruffed lemurs). Longitudinal sampling over a 1-year interval demonstrated ongoing infection in the collection. This was supported by evidence of viral clearance in some animals and new infections in previously uninfected animals, including a set of newly born triplets that acquired the infection. While the two virus strains were found to be cocirculating in a mixed-species exhibit of ring-tailed lemurs, black-and-white ruffed lemurs, and black lemurs, there was no evidence of cross-species transmission. This suggests that despite high-intensity contact, host species barriers can prevent cross-species transmissions of these viruses. IMPORTANCE Up to 75% of emerging infectious diseases in humans today are the result of zoonotic transmission. However, a challenge in understanding transmission dynamics has been the limited models of cross-species transmission. Zoos provide a unique opportunity to explore parameters defining viral transmission. We demonstrated that ongoing virus transmission in a mixed lemur species exhibit was species specific. This suggests that despite high contact intensity, host species barriers contribute to protection from cross-species transmission of these viruses. While the combinations of species might differ, most zoological parks worldwide commonly feature mixed-species exhibits. Collectively, this report demonstrates a widely applicable approach toward understanding infectious disease transmission.
Collapse
|
42
|
Kaufer BB, Flamand L. Chromosomally integrated HHV-6: impact on virus, cell and organismal biology. Curr Opin Virol 2014; 9:111-8. [PMID: 25462442 DOI: 10.1016/j.coviro.2014.09.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 11/16/2022]
Abstract
HHV-6 integrates its genome into telomeres of human chromosomes. Integration can occur in somatic cells or gametes, the latter leading to individuals harboring the HHV-6 genome in every cell. This condition is transmitted to descendants and referred to as inherited chromosomally integrated human herpesvirus 6 (iciHHV-6). Although integration can occur in different chromosomes, it invariably takes place in the telomere region. This integration mechanism represents a way to maintain the virus genome during latency, which is so far unique amongst human herpesviruses. Recent work provides evidence that the integrated HHV-6 genome can be mobilized from the host chromosome, resulting in the onset of disease. Details on required structural determinants, putative integration mechanisms and biological and medical consequences of iciHHV-6 are discussed.
Collapse
Affiliation(s)
| | - Louis Flamand
- Division of Infectious and Immune Diseases, CHU de Quebec, Research Center and Department of Microbiology-Infectious Diseases and Immunology, Université Laval, Quebec, Canada.
| |
Collapse
|