1
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Fu X, Suo H, Zhang J, Chen D. Machine-learning-guided Directed Evolution for AAV Capsid Engineering. Curr Pharm Des 2024; 30:811-824. [PMID: 38445704 DOI: 10.2174/0113816128286593240226060318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
Target gene delivery is crucial to gene therapy. Adeno-associated virus (AAV) has emerged as a primary gene therapy vector due to its broad host range, long-term expression, and low pathogenicity. However, AAV vectors have some limitations, such as immunogenicity and insufficient targeting. Designing or modifying capsids is a potential method of improving the efficacy of gene delivery, but hindered by weak biological basis of AAV, complexity of the capsids, and limitations of current screening methods. Artificial intelligence (AI), especially machine learning (ML), has great potential to accelerate and improve the optimization of capsid properties as well as decrease their development time and manufacturing costs. This review introduces the traditional methods of designing AAV capsids and the general steps of building a sequence-function ML model, highlights the applications of ML in the development workflow, and summarizes its advantages and challenges.
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Affiliation(s)
- Xianrong Fu
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Hairui Suo
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Jiachen Zhang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Dongmei Chen
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
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2
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Sasaki N, Kok CY, Westhaus A, Alexander IE, Lisowski L, Kizana E. In Search of Adeno-Associated Virus Vectors With Enhanced Cardiac Tropism for Gene Therapy. Heart Lung Circ 2023; 32:816-824. [PMID: 37451880 DOI: 10.1016/j.hlc.2023.06.704] [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] [Received: 05/08/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
Globally, adeno-associated virus (AAV) vectors have been increasingly used for clinical gene therapy trials. In Australia, AAV-based gene therapy is available for hereditary diseases such as retinal dystrophy or spinal muscular atrophy 1 (SMA1). Many preclinical studies have used AAV vectors for gene therapy in models of cardiac disease with outcomes of varying translational potential. However, major barriers to effective and safe therapeutic gene delivery to the human heart remain to be overcome. These include tropism, efficient gene transfer, mitigating off-target gene delivery and avoidance of the host immune response. Developing such an enhanced AAV vector for cardiac gene therapy is of great interest to the field of advanced cardiac therapeutics. In this review, we provide an overview of the approaches currently being employed in the search for cardiac cell-specific AAV capsids, ranging from natural AAVs selected as a result of infection and latency in the heart, to the use of cutting-edge molecular techniques to engineer and select AAVs specific for cardiac cells with the use of high-throughput methods.
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Affiliation(s)
- Natsuki Sasaki
- The Centre for Heart Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Cindy Y Kok
- The Centre for Heart Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia; Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Adrian Westhaus
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland
| | - Eddy Kizana
- The Centre for Heart Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia; Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Cardiology, Westmead Hospital, Sydney, NSW, Australia.
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3
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Bravo A, Fernández-García L, Ibarra-Karmy R, Mardones GA, Mercado L, Bustos FJ, Gifford RJ, Arriagada G. Antiviral Activity of an Endogenous Parvoviral Element. Viruses 2023; 15:1420. [PMID: 37515112 PMCID: PMC10384997 DOI: 10.3390/v15071420] [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: 06/07/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Endogenous viral elements (EVEs) are genomic DNA sequences derived from viruses. Some EVEs have open reading frames (ORFs) that can express proteins with physiological roles in their host. Furthermore, some EVEs exhibit a protective role against exogenous viral infection in their host. Endogenous parvoviral elements (EPVs) are highly represented in mammalian genomes, and although some of them contain ORFs, their function is unknown. We have shown that the locus EPV-Dependo.43-ODegus, an EPV with an intact ORF, is transcribed in Octodon degus (degu). Here we examine the antiviral activity of the protein encoded in this EPV, named DeRep. DeRep was produced in bacteria and used to generate antibodies that recognize DeRep in western blots of degu tissue. To test if DeRep could protect against exogenous parvovirus, we challenged cells with the minute virus of mice (MVM), a model autonomous parvovirus. We observed that MVM protein expression, DNA damage induced by replication, viral DNA, and cytopathic effects are reduced when DeRep is expressed in cells. The results of this study demonstrate that DeRep is expressed in degu and can inhibit parvovirus replication. This is the first time that an EPV has been shown to have antiviral activity against an exogenous virus.
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Affiliation(s)
- Angelica Bravo
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370071, Chile
| | - Leandro Fernández-García
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370071, Chile
| | - Rodrigo Ibarra-Karmy
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370071, Chile
| | - Gonzalo A Mardones
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia 5110466, Chile
| | - Luis Mercado
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Fernando J Bustos
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370071, Chile
| | - Robert J Gifford
- Centre for Virus Research, MRC-University of Glasgow, 464 Bearsden Rd, Bearsden, Glasgow G61 1QH, UK
| | - Gloria Arriagada
- Instituto de Ciencias Biomedicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370071, Chile
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4
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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: 0] [Impact Index Per Article: 0] [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.
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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:
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Jäschke N, Büning H. Adeno-Associated Virus Vector Design-Moving the Adeno-Associated Virus to a Bioengineered Therapeutic Nanoparticle. Hematol Oncol Clin North Am 2022; 36:667-685. [PMID: 35778330 DOI: 10.1016/j.hoc.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Although the number of market-approved gene therapies is still low, this new class of therapeutics has become an integral part of modern medicine. The success and safety of gene therapy depend on the vectors used to deliver the therapeutic material. Adeno-associated virus (AAV) vectors have emerged as the most frequently used delivery system for in vivo gene therapy. This success was achieved with first-generation vectors, using capsids derived from natural AAV serotypes. Their broad tropism, the high seroprevalence for many of the AAV serotypes in the human population, and the high vector doses needed to transduce a sufficient number of therapy-relevant target cells are challenges that are addressed by engineering the capsid and the vector genome, improving the efficacy of these biological nanoparticles.
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Affiliation(s)
- Nico Jäschke
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str.1, Hannover 30625, Germany
| | - Hildegard Büning
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str.1, Hannover 30625, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, Carl-Neuberg-Str.1, Hannover 30625, Germany; German Center for Infection Research, Partner Site Hannover-Braunschweig.
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6
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Watson-Levings RS, Palmer GD, Levings PP, Dacanay EA, Evans CH, Ghivizzani SC. Gene Therapy in Orthopaedics: Progress and Challenges in Pre-Clinical Development and Translation. Front Bioeng Biotechnol 2022; 10:901317. [PMID: 35837555 PMCID: PMC9274665 DOI: 10.3389/fbioe.2022.901317] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
In orthopaedics, gene-based treatment approaches are being investigated for an array of common -yet medically challenging- pathologic conditions of the skeletal connective tissues and structures (bone, cartilage, ligament, tendon, joints, intervertebral discs etc.). As the skeletal system protects the vital organs and provides weight-bearing structural support, the various tissues are principally composed of dense extracellular matrix (ECM), often with minimal cellularity and vasculature. Due to their functional roles, composition, and distribution throughout the body the skeletal tissues are prone to traumatic injury, and/or structural failure from chronic inflammation and matrix degradation. Due to a mixture of environment and endogenous factors repair processes are often slow and fail to restore the native quality of the ECM and its function. In other cases, large-scale lesions from severe trauma or tumor surgery, exceed the body’s healing and regenerative capacity. Although a wide range of exogenous gene products (proteins and RNAs) have the potential to enhance tissue repair/regeneration and inhibit degenerative disease their clinical use is hindered by the absence of practical methods for safe, effective delivery. Cumulatively, a large body of evidence demonstrates the capacity to transfer coding sequences for biologic agents to cells in the skeletal tissues to achieve prolonged delivery at functional levels to augment local repair or inhibit pathologic processes. With an eye toward clinical translation, we discuss the research progress in the primary injury and disease targets in orthopaedic gene therapy. Technical considerations important to the exploration and pre-clinical development are presented, with an emphasis on vector technologies and delivery strategies whose capacity to generate and sustain functional transgene expression in vivo is well-established.
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Affiliation(s)
- Rachael S. Watson-Levings
- Department of Orthopaedic Surgery and Sports Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Glyn D. Palmer
- Department of Orthopaedic Surgery and Sports Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Padraic P. Levings
- Department of Orthopaedic Surgery and Sports Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - E. Anthony Dacanay
- Department of Orthopaedic Surgery and Sports Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Christopher H. Evans
- Rehabilitation Medicine Research Center, Mayo Clinic, Rochester, MI, United States
| | - Steven C. Ghivizzani
- Department of Orthopaedic Surgery and Sports Medicine, University of Florida College of Medicine, Gainesville, FL, United States
- *Correspondence: Steven C. Ghivizzani,
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7
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Mitogenome of the extinct Desert 'rat-kangaroo' times the adaptation to aridity in macropodoids. Sci Rep 2022; 12:5829. [PMID: 35388060 PMCID: PMC8987032 DOI: 10.1038/s41598-022-09568-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/25/2022] [Indexed: 01/31/2023] Open
Abstract
The evolution of Australia's distinctive marsupial fauna has long been linked to the onset of continent-wide aridity. However, how this profound climate change event affected the diversification of extant lineages is still hotly debated. Here, we assemble a DNA sequence dataset of Macropodoidea-the clade comprising kangaroos and their relatives-that incorporates a complete mitogenome for the Desert 'rat-kangaroo', Caloprymnus campestris. This enigmatic species went extinct nearly 90 years ago and is known from a handful of museum specimens. Caloprymnus is significant because it was the only macropodoid restricted to extreme desert environments, and therefore calibrates the group's specialisation for increasingly arid conditions. Our robustly supported phylogenies nest Caloprymnus amongst the bettongs Aepyprymnus and Bettongia. Dated ancestral range estimations further reveal that the Caloprymnus-Bettongia lineage originated in nascent xeric settings during the middle to late Miocene, ~ 12 million years ago (Ma), but subsequently radiated into fragmenting mesic habitats after the Pliocene to mid-Pleistocene. This timeframe parallels the ancestral divergences of kangaroos in woodlands and forests, but predates their adaptive dispersal into proliferating dry shrublands and grasslands from the late Miocene to mid-Pleistocene, after ~ 7 Ma. We thus demonstrate that protracted changes in both climate and vegetation likely staged the emergence of modern arid zone macropodoids.
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8
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Zolotukhin S, Vandenberghe L. AAV capsid design: A Goldilocks challenge. Trends Mol Med 2022; 28:183-193. [DOI: 10.1016/j.molmed.2022.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/16/2022]
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9
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Scott S, Hallwirth CV, Hartkopf F, Grigson S, Jain Y, Alexander IE, Bauer DC, O W Wilson L. Isling: a tool for detecting integration of wild-type viruses and clinical vectors. J Mol Biol 2021; 434:167408. [PMID: 34929203 DOI: 10.1016/j.jmb.2021.167408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 10/19/2022]
Abstract
Detecting viral and vector integration events is a key step when investigating interactions between viral and host genomes. This is relevant in several fields, including virology, cancer research and gene therapy. For example, investigating integrations of wild-type viruses such as human papillomavirus and hepatitis B virus has proven to be crucial for understanding the role of these integrations in cancer. Furthermore, identifying the extent of vector integration is vital for determining the potential for genotoxicity in gene therapies. To address these questions, we developed isling, the first tool specifically designed for identifying viral integrations in both wild-type and vector from next-generation sequencing data. Isling addresses complexities in integration behaviour including integration of fragmented genomes and integration junctions with ambiguous locations in a host or vector genome, and can also flag possible vector recombinations. We show that isling is up to 1.6-fold faster and up to 170% more accurate than other viral integration tools, and performs well on both simulated and real datasets. Isling is therefore an efficient and application-agnostic tool that will enable a broad range of investigations into viral and vector integration. These include comparisons between integrations of wild-type viruses and gene therapy vectors, as well as assessing the genotoxicity of vectors and understanding the role of viruses in cancer.
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Affiliation(s)
- Suzanne Scott
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, North Ryde, Australia; Gene Therapy Research Unit, Children's Medical Research Institute, Westmead, Australia; The Sydney Children's Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute, Westmead, Australia; The Sydney Children's Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Felix Hartkopf
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Susanna Grigson
- College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Yatish Jain
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, North Ryde, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Westmead, Australia; The Sydney Children's Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia; Discipline of Child and Adolescent Health,Faculty of Medicine and Health,The University of Sydney, Sydney, New South Wales, Australia
| | - Denis C Bauer
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, North Ryde, Australia; Discipline of Child and Adolescent Health,Faculty of Medicine and Health,The University of Sydney, Sydney, New South Wales, Australia; Macquarie University, Department of Biomedical Sciences, Faculty of Medicine and Health Science, Macquarie Park, Australia.
| | - Laurence O W Wilson
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, North Ryde, Australia; Macquarie University, Applied BioSciences, Faculty of Science and Engineering, Macquarie Park, Australia.
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10
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Harding EF, Russo AG, Yan GJH, Waters PD, White PA. Ancient viral integrations in marsupials: a potential antiviral defence. Virus Evol 2021; 7:veab076. [PMID: 34548931 PMCID: PMC8449507 DOI: 10.1093/ve/veab076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 08/05/2021] [Accepted: 08/31/2021] [Indexed: 12/28/2022] Open
Abstract
Marsupial viruses are understudied compared to their eutherian mammal counterparts, although they may pose severe threats to vulnerable marsupial populations. Genomic viral integrations, termed 'endogenous viral elements' (EVEs), could protect the host from infection. It is widely known past viral infections and EVEs play an active role in antiviral defence in invertebrates and plants. This study aimed to characterise actively transcribed EVEs in Australian marsupial species, because they may play an integral role in cellular defence against viruses. This study screened publicly available RNA sequencing data sets (n = 35) and characterised 200 viral transcripts from thirteen Australian marsupial species. Of the 200 transcripts, 188 originated from either Bornaviridae, Filoviridae, or Parvoviridae EVEs. The other twelve transcripts were from putative active infections from members of the Herpesviridae and Anelloviridae, and Hepadnaviridae. EVE transcripts (n = 188) were mapped to marsupial genomes (where available, n = 5/13) to identify the genomic insertion sites. Of the 188 transcripts, 117 mapped to 39 EVEs within the koala, bare-nosed wombat, tammar wallaby, brushtail possum, and Tasmanian devil genomes. The remaining eight animals had no available genome (transcripts n = 71). Every marsupial has Bornaviridae, Filoviridae, and Parvoviridae EVEs, a trend widely observed in eutherian mammals. Whilst eutherian bornavirus EVEs are predominantly nucleoprotein-derived, marsupial bornavirus EVEs demonstrate a surprising replicase gene bias. We predicted these widely distributed EVEs were conserved within marsupials from ancient germline integrations, as many were over 65 million years old. One bornavirus replicase EVE, present in six marsupial genomes, was estimated to be 160 million years old, predating the American-Australian marsupial split. We considered transcription of these EVEs through small non-coding RNA as an ancient viral defence. Consistent with this, in koala small RNA sequence data sets, we detected Bornaviridae replicase and Filoviridae nucleoprotein produced small RNA. These were enriched in testis tissue, suggesting they could protect marsupials from vertically transmitted viral integrations.
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Affiliation(s)
| | - Alice G Russo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Grace J H Yan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, UNSW Sydney, Sydney, NSW 2052, Australia
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11
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Colón-Thillet R, Jerome KR, Stone D. Optimization of AAV vectors to target persistent viral reservoirs. Virol J 2021; 18:85. [PMID: 33892762 PMCID: PMC8067653 DOI: 10.1186/s12985-021-01555-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/14/2021] [Indexed: 12/18/2022] Open
Abstract
Gene delivery of antiviral therapeutics to anatomical sites where viruses accumulate and persist is a promising approach for the next generation of antiviral therapies. Recombinant adeno-associated viruses (AAV) are one of the leading vectors for gene therapy applications that deliver gene-editing enzymes, antibodies, and RNA interference molecules to eliminate viral reservoirs that fuel persistent infections. As long-lived viral DNA within specific cellular reservoirs is responsible for persistent hepatitis B virus, Herpes simplex virus, and human immunodeficiency virus infections, the discovery of AAV vectors with strong tropism for hepatocytes, sensory neurons and T cells, respectively, is of particular interest. Identification of natural isolates from various tissues in humans and non-human primates has generated an extensive catalog of AAV vectors with diverse tropisms and transduction efficiencies, which has been further expanded through molecular genetic approaches. The AAV capsid protein, which forms the virions' outer shell, is the primary determinant of tissue tropism, transduction efficiency, and immunogenicity. Thus, over the past few decades, extensive efforts to optimize AAV vectors for gene therapy applications have focused on capsid engineering with approaches such as directed evolution and rational design. These approaches are being used to identify variants with improved transduction efficiencies, alternate tropisms, reduced sequestration in non-target organs, and reduced immunogenicity, and have produced AAV capsids that are currently under evaluation in pre-clinical and clinical trials. This review will summarize the most recent strategies to identify AAV vectors with enhanced tropism and transduction in cell types that harbor viral reservoirs.
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Affiliation(s)
- Rossana Colón-Thillet
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA.
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12
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Peters CW, Maguire CA, Hanlon KS. Delivering AAV to the Central Nervous and Sensory Systems. Trends Pharmacol Sci 2021; 42:461-474. [PMID: 33863599 DOI: 10.1016/j.tips.2021.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022]
Abstract
As gene therapy enters mainstream medicine, it is more important than ever to have a grasp of exactly how to leverage it for maximum benefit. The development of new targeting strategies and tools makes treating patients with genetic diseases possible. Many Mendelian disorders are amenable to gene replacement or correction. These often affect post-mitotic tissues, meaning that a single stably expressing therapy can be applied. Recent years have seen the development of a large number of novel viral vectors for delivering specific therapies. These new vectors - predominately recombinant adeno-associated virus (AAV) variants - target nervous tissues with differing efficiencies. This review gives an overview of current gene therapies in the brain, ear, and eye, and describes the optimal approaches, depending on cell type and transgene. Overall, this work aims to serve as a primer for gene therapy in the central nervous and sensory systems.
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Affiliation(s)
- Cole W Peters
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Casey A Maguire
- Molecular Neurogenetics Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Killian S Hanlon
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA; Molecular Neurogenetics Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA.
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13
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Bulcha JT, Wang Y, Ma H, Tai PWL, Gao G. Viral vector platforms within the gene therapy landscape. Signal Transduct Target Ther 2021; 6:53. [PMID: 33558455 PMCID: PMC7868676 DOI: 10.1038/s41392-021-00487-6] [Citation(s) in RCA: 511] [Impact Index Per Article: 170.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/05/2020] [Accepted: 10/23/2020] [Indexed: 01/30/2023] Open
Abstract
Throughout its 40-year history, the field of gene therapy has been marked by many transitions. It has seen great strides in combating human disease, has given hope to patients and families with limited treatment options, but has also been subject to many setbacks. Treatment of patients with this class of investigational drugs has resulted in severe adverse effects and, even in rare cases, death. At the heart of this dichotomous field are the viral-based vectors, the delivery vehicles that have allowed researchers and clinicians to develop powerful drug platforms, and have radically changed the face of medicine. Within the past 5 years, the gene therapy field has seen a wave of drugs based on viral vectors that have gained regulatory approval that come in a variety of designs and purposes. These modalities range from vector-based cancer therapies, to treating monogenic diseases with life-altering outcomes. At present, the three key vector strategies are based on adenoviruses, adeno-associated viruses, and lentiviruses. They have led the way in preclinical and clinical successes in the past two decades. However, despite these successes, many challenges still limit these approaches from attaining their full potential. To review the viral vector-based gene therapy landscape, we focus on these three highly regarded vector platforms and describe mechanisms of action and their roles in treating human disease.
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Affiliation(s)
- Jote T Bulcha
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Yi Wang
- Department of Pathophysiology, West China College of Basic medical sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Hong Ma
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Phillip W L Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
- VIDE Program, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
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14
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Hacker UT, Bentler M, Kaniowska D, Morgan M, Büning H. Towards Clinical Implementation of Adeno-Associated Virus (AAV) Vectors for Cancer Gene Therapy: Current Status and Future Perspectives. Cancers (Basel) 2020; 12:E1889. [PMID: 32674264 PMCID: PMC7409174 DOI: 10.3390/cancers12071889] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023] Open
Abstract
Adeno-associated virus (AAV) vectors have gained tremendous attention as in vivo delivery systems in gene therapy for inherited monogenetic diseases. First market approvals, excellent safety data, availability of large-scale production protocols, and the possibility to tailor the vector towards optimized and cell-type specific gene transfer offers to move from (ultra) rare to common diseases. Cancer, a major health burden for which novel therapeutic options are urgently needed, represents such a target. We here provide an up-to-date overview of the strategies which are currently developed for the use of AAV vectors in cancer gene therapy and discuss the perspectives for the future translation of these pre-clinical approaches into the clinic.
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Affiliation(s)
- Ulrich T. Hacker
- Department of Oncology, Gastroenterology, Hepatology, Pulmonology, and Infectious Diseases, University Cancer Center Leipzig (UCCL), Leipzig University Medical Center, 04103 Leipzig, Germany;
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (M.B.); (M.M.)
| | - Martin Bentler
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (M.B.); (M.M.)
| | - Dorota Kaniowska
- Department of Oncology, Gastroenterology, Hepatology, Pulmonology, and Infectious Diseases, University Cancer Center Leipzig (UCCL), Leipzig University Medical Center, 04103 Leipzig, Germany;
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (M.B.); (M.M.)
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Hildegard Büning
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (M.B.); (M.M.)
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstraße 7, 38124 Braunschweig, Germany
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15
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Pierce GF. Uncertainty in an era of transformative therapy for haemophilia: Addressing the unknowns. Haemophilia 2020; 27 Suppl 3:103-113. [PMID: 32484283 DOI: 10.1111/hae.14023] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/24/2020] [Indexed: 12/12/2022]
Abstract
Haemophilia is at the dawn of a new era in therapeutic management, one that can generate greater protection from bleeding and a functional cure in some individuals. Prior advances in protein engineering and monoclonal antibody technology have facilitated therapeutic options to maintain decreased risk of bleeding and less burdensome treatment. The use of gene transfer, first proposed in 1971 for monogenic diseases, is emerging as an effective long-term treatment for a variety of diseases. Transfer of functional factor VIII (FVIII) and factor IX (FIX) genes has witnessed a series of advances and setbacks since the first non-clinical experiments in animals were initiated nearly 30 years ago. More recently, multiyear therapeutic levels of FVIII and FIX activity have been achieved in human clinical trials, translated into meaningful clinical benefit and a functional cure. While clinical progress has been definitive, many questions remain unanswered as prelicensure phase 3 clinical trials are underway. These unanswered questions translate into a state of uncertainty about the known unknowns and unknown unknowns intrinsic to any new therapeutic platform. Accepting this modality as a means to functionally cure haemophilia also means accepting the uncertainty regarding the biology of viral vector-mediated gene transfer, which remains inadequately understood. Gene therapy is a far more complex biological 'drug' than small molecule and protein drugs, where manufacturing processes and the drugs themselves are now well characterized. Extent of community acceptance of uncertainty and acknowledgement of the need for an uncompromising drive for answers to the unknowns will characterize the introduction of this first generation of gene therapy for haemophilia to the wider patient population in both resource-rich and resource-poor countries.
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16
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Hildebrandt E, Penzes JJ, Gifford RJ, Agbandje-Mckenna M, Kotin RM. Evolution of dependoparvoviruses across geological timescales-implications for design of AAV-based gene therapy vectors. Virus Evol 2020; 6:veaa043. [PMID: 32913662 PMCID: PMC7474932 DOI: 10.1093/ve/veaa043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Endogenous viral elements (EVEs) are genetic remnants of viruses that have integrated into host genomes millions of years ago and retained as heritable elements passed on to offspring until present-day. As a result, EVEs provide an opportunity to analyse the genomes of extinct viruses utilizing these genomic viral fossils to study evolution of viruses over large timescales. Analysis of sequences from near full-length EVEs of dependoparvoviral origin identified within three mammalian taxa, Whippomorpha (whales and hippos), Vespertilionidae (smooth-nosed bats), and Lagomorpha (rabbits, hares, and pikas), indicates that distinct ancestral dependoparvovirus species integrated into these host genomes approximately 77 to 23 million years ago. These ancestral viruses are unique relative to modern adeno-associated viruses (AAVs), and distinct from extant species of genus Dependoparvovirus. These EVE sequences show characteristics previously unseen in modern, mammalian AAVs, but instead appear more similar to the more primitive, autonomously replicating and pathogenic waterfowl dependoparvoviruses. Phylogeny reconstruction suggests that the whippomorph EVE orthologue derives from exogenous ancestors of autonomous and highly pathogenic dependoparvovirus lineages, believed to have uniquely co-evolved with waterfowl birds to present date. In contrast, ancestors of the two other mammalian orthologues (Lagomorpha and Vespertilionidae) likely shared the same lineage as all other known mammalian exogenous AAVs. Comparative in silico analysis of the EVE genomes revealed remarkable overall conservation of AAV rep and cap genes, despite millions of years of integration within the host germline. Modelling these proteins identified unexpected variety, even between orthologues, in previously defined capsid viral protein (VP) variable regions, especially in those related to the three- and fivefold symmetry axes of the capsid. Moreover, the normally well-conserved phospholipase A2 domain of the predicted minor VP1 also exhibited a high degree of sequence variance. These findings may indicate unique biological properties for these virus ‘fossils’ relative to extant dependoparvoviruses and suggest key regions to explore within capsid sequences that may confer novel properties for engineered gene therapy vectors based on paleovirology data.
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Affiliation(s)
- Evin Hildebrandt
- University of Massachusetts Medical School, Department of Microbiology and Physiological Systems, Gene Therapy Center, 55 Lake Ave. North, Worcester, MA 01655, USA
| | - Judit J Penzes
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, 1200 Newell Drive, Gainesville, Florida, 32610, USA
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, Genomics & Bioinformatics, Sir Michael Stoker Building Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, Scotland, UK
| | - Mavis Agbandje-Mckenna
- University of Florida, Department of Biochemistry and Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, 1200 Newell Drive, Gainesville, Florida, 32610, USA
| | - Robert M Kotin
- University of Massachusetts Medical School, Department of Microbiology and Physiological Systems, Gene Therapy Center, 55 Lake Ave. North, Worcester, MA 01655, USA
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17
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Wang D, Tai PWL, Gao G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat Rev Drug Discov 2019; 18:358-378. [PMID: 30710128 DOI: 10.1038/s41573-019-0012-9] [Citation(s) in RCA: 1204] [Impact Index Per Article: 240.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Adeno-associated virus (AAV) vectors are the leading platform for gene delivery for the treatment of a variety of human diseases. Recent advances in developing clinically desirable AAV capsids, optimizing genome designs and harnessing revolutionary biotechnologies have contributed substantially to the growth of the gene therapy field. Preclinical and clinical successes in AAV-mediated gene replacement, gene silencing and gene editing have helped AAV gain popularity as the ideal therapeutic vector, with two AAV-based therapeutics gaining regulatory approval in Europe or the United States. Continued study of AAV biology and increased understanding of the associated therapeutic challenges and limitations will build the foundation for future clinical success.
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Affiliation(s)
- Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Phillip W L Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA. .,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA. .,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
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18
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Saleeba C, Dempsey B, Le S, Goodchild A, McMullan S. A Student's Guide to Neural Circuit Tracing. Front Neurosci 2019; 13:897. [PMID: 31507369 PMCID: PMC6718611 DOI: 10.3389/fnins.2019.00897] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/12/2019] [Indexed: 12/17/2022] Open
Abstract
The mammalian nervous system is comprised of a seemingly infinitely complex network of specialized synaptic connections that coordinate the flow of information through it. The field of connectomics seeks to map the structure that underlies brain function at resolutions that range from the ultrastructural, which examines the organization of individual synapses that impinge upon a neuron, to the macroscopic, which examines gross connectivity between large brain regions. At the mesoscopic level, distant and local connections between neuronal populations are identified, providing insights into circuit-level architecture. Although neural tract tracing techniques have been available to experimental neuroscientists for many decades, considerable methodological advances have been made in the last 20 years due to synergies between the fields of molecular biology, virology, microscopy, computer science and genetics. As a consequence, investigators now enjoy an unprecedented toolbox of reagents that can be directed against selected subpopulations of neurons to identify their efferent and afferent connectomes. Unfortunately, the intersectional nature of this progress presents newcomers to the field with a daunting array of technologies that have emerged from disciplines they may not be familiar with. This review outlines the current state of mesoscale connectomic approaches, from data collection to analysis, written for the novice to this field. A brief history of neuroanatomy is followed by an assessment of the techniques used by contemporary neuroscientists to resolve mesoscale organization, such as conventional and viral tracers, and methods of selecting for sub-populations of neurons. We consider some weaknesses and bottlenecks of the most widely used approaches for the analysis and dissemination of tracing data and explore the trajectories that rapidly developing neuroanatomy technologies are likely to take.
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Affiliation(s)
- Christine Saleeba
- Neurobiology of Vital Systems Node, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
- The School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Bowen Dempsey
- CNRS, Hindbrain Integrative Neurobiology Laboratory, Neuroscience Paris-Saclay Institute (Neuro-PSI), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Sheng Le
- Neurobiology of Vital Systems Node, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ann Goodchild
- Neurobiology of Vital Systems Node, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Simon McMullan
- Neurobiology of Vital Systems Node, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
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19
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Xu M, Li J, Xie J, He R, Su Q, Gao G, Tai PW. High-Throughput Quantification of In Vivo Adeno-Associated Virus Transduction with Barcoded Non-Coding RNAs. Hum Gene Ther 2019; 30:946-956. [PMID: 31072208 PMCID: PMC6703241 DOI: 10.1089/hum.2018.253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/12/2019] [Indexed: 02/06/2023] Open
Abstract
Recombinant adeno-associated viruses (rAAVs) have become favorable gene delivery vehicles for expressing therapeutic transgenes. Capsid engineering efforts to produce novel AAVs with improved transduction efficiencies, unique tissue specificities, and reduced host immunities are a direct response to the high demand for treatment needs that preexisting rAAVs cannot currently fulfill. New AAV capsids discovered by directed evolution methods, in silico design, or from natural proviral sequences ultimately require extensive characterization in relevant in vivo models. Consequently, quantitative screening of candidate capsid libraries now requires reliable high-throughput sequencing approaches. In this study, we have developed a vector/transgene tracking system that employs the indexing of a non-coding RNA. Specifically, a barcoded Tough Decoy (bcTuD) that express highly stable RNA transcripts that can be used as readouts for transduction efficiency. The pseudo-hairpin structure of the bcTuD contains a variable region that is amenable to barcode insertion, which can be detected by target amplicon sequencing. The described approach, named AAV-bcTuD screening, offers a new alternative for in vivo assessment of rAAV that can accurately quantify vector genomes and transcript abundances in tissues, as exampled by the demonstration in liver and brain infections. Proof-of-concept is provided to show that vector genome and transcript detection in tissues with this method is accurate and consistent for a vector dose range of upwards to four logs in a mixed vector injection, showing that this technique is robust, sensitive, and applicable for multiplexed screening of capsid performance in vivo.
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Affiliation(s)
- Meiyu Xu
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jia Li
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Jun Xie
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
- Viral Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Ran He
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
- Viral Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Qin Su
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
- Viral Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
- Viral Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Phillip W.L. Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts
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20
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Chen MY, Butler SS, Chen W, Suh J. Physical, chemical, and synthetic virology: Reprogramming viruses as controllable nanodevices. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 11:e1545. [PMID: 30411529 PMCID: PMC6461522 DOI: 10.1002/wnan.1545] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/03/2018] [Accepted: 10/04/2018] [Indexed: 01/24/2023]
Abstract
The fields of physical, chemical, and synthetic virology work in partnership to reprogram viruses as controllable nanodevices. Physical virology provides the fundamental biophysical understanding of how virus capsids assemble, disassemble, display metastability, and assume various configurations. Chemical virology considers the virus capsid as a chemically addressable structure, providing chemical pathways to modify the capsid exterior, interior, and subunit interfaces. Synthetic virology takes an engineering approach, modifying the virus capsid through rational, combinatorial, and bioinformatics-driven design strategies. Advances in these three subfields of virology aim to develop virus-based materials and tools that can be applied to solve critical problems in biomedicine and biotechnology, including applications in gene therapy and drug delivery, diagnostics, and immunotherapy. Examples discussed include mammalian viruses, such as adeno-associated virus (AAV), plant viruses, such as cowpea mosaic virus (CPMV), and bacterial viruses, such as Qβ bacteriophage. Importantly, research efforts in physical, chemical, and synthetic virology have further unraveled the design principles foundational to the form and function of viruses. This article is categorized under: Diagnostic Tools > Diagnostic Nanodevices Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
| | - Susan S Butler
- Department of Bioengineering, Rice University, Houston, Texas
| | - Weitong Chen
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas
| | - Junghae Suh
- Department of Bioengineering, Rice University, Houston, Texas
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, Texas
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21
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Callaway HM, Subramanian S, Urbina CA, Barnard KN, Dick RA, Bator CM, Hafenstein SL, Gifford RJ, Parrish CR. Examination and Reconstruction of Three Ancient Endogenous Parvovirus Capsid Protein Gene Remnants Found in Rodent Genomes. J Virol 2019; 93:e01542-18. [PMID: 30626673 PMCID: PMC6401472 DOI: 10.1128/jvi.01542-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 12/24/2018] [Indexed: 11/20/2022] Open
Abstract
Parvovirus-derived endogenous viral elements (EVEs) have been found in the genomes of many different animal species, resulting from integration events that may have occurred from more than 50 million years ago to much more recently. Here, we further investigate the properties of autonomous parvovirus EVEs and describe their relationships to contemporary viruses. While we did not find any intact capsid protein open reading frames in the integrated viral sequences, we examined three EVEs that were repaired to form full-length sequences with relatively few changes. These sequences were found in the genomes of Rattus norvegicus (brown rat), Mus spretus (Algerian mouse), and Apodemus sylvaticus (wood mouse). The R. norvegicus sequence was not present in the genomes of the closely related species R. rattus, R. tanezumi, R. exulans, and R. everetti, indicating that it was less than 2 million years old, and the M. spretus and A. sylvaticus sequences were not found in the published genomes of other mouse species, also indicating relatively recent insertions. The M. spretus VP2 sequence assembled into capsids, which had high thermal stability, bound the sialic acid N-acetylneuraminic acid, and entered murine L cells. The 3.89-Å structure of the M. spretus virus-like particles (VLPs), determined using cryo-electron microscopy, showed similarities to rodent and porcine parvovirus capsids. The repaired VP2 sequences from R. norvegicus and A. sylvaticus did not assemble as first prepared, but chimeras combining capsid surface loops from R. norvegicus with canine parvovirus assembled, allowing some of that capsid's structures and functions to be examined.IMPORTANCE Parvovirus endogenous viral elements (EVEs) that have been incorporated into the genomes of different animals represent remnants of the DNA sequences of ancient viruses that infected the ancestors of those animals millions of years ago, but we know little about their properties or how they differ from currently circulating parvoviruses. By expressing the capsid proteins of different parvovirus EVEs that were found integrated into the genomes of three different rodents, we can examine their structures and functions. A VP2 (major capsid protein) EVE sequence from a mouse genome assembled into capsids that had a similar structure and biophysical properties to extant parvoviruses and also bound sialic acids and entered rodent cells. Chimeras formed from combinations of canine parvovirus and portions of the parvovirus sequences from the brown rat genome allowed us to examine the structures and functions of the surface loops of that EVE capsid.
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Affiliation(s)
- Heather M Callaway
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Suriyasri Subramanian
- Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Christian A Urbina
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Karen N Barnard
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Robert A Dick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Carol M Bator
- Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Susan L Hafenstein
- Department of Medicine, Penn State University College of Medicine, Hershey, Pennsylvania, USA
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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22
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Cabanes-Creus M, Ginn SL, Amaya AK, Liao SHY, Westhaus A, Hallwirth CV, Wilmott P, Ward J, Dilworth KL, Santilli G, Rybicki A, Nakai H, Thrasher AJ, Filip AC, Alexander IE, Lisowski L. Codon-Optimization of Wild-Type Adeno-Associated Virus Capsid Sequences Enhances DNA Family Shuffling while Conserving Functionality. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 12:71-84. [PMID: 30534580 PMCID: PMC6279885 DOI: 10.1016/j.omtm.2018.10.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/29/2018] [Indexed: 12/22/2022]
Abstract
Adeno-associated virus (AAV) vectors have become one of the most widely used gene transfer tools in human gene therapy. Considerable effort is currently being focused on AAV capsid engineering strategies with the aim of developing novel variants with enhanced tropism for specific human cell types, decreased human seroreactivity, and increased manufacturability. Selection strategies based on directed evolution rely on the generation of highly variable AAV capsid libraries using methods such as DNA-family shuffling, a technique reliant on stretches of high DNA sequence identity between input parental capsid sequences. This identity dependence for reassembly of shuffled capsids is inherently limiting and results in decreased shuffling efficiency as the phylogenetic distance between parental AAV capsids increases. To overcome this limitation, we have developed a novel codon-optimization algorithm that exploits evolutionarily defined codon usage at each amino acid residue in the parental sequences. This method increases average sequence identity between capsids, while enhancing the probability of retaining capsid functionality, and facilitates incorporation of phylogenetically distant serotypes into the DNA-shuffled libraries. This technology will help accelerate the discovery of an increasingly powerful repertoire of AAV capsid variants for cell-type and disease-specific applications.
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Affiliation(s)
- Marti Cabanes-Creus
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Samantha L Ginn
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Sydney, NSW 2006, Australia
| | - Anais K Amaya
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Sydney, NSW 2006, Australia
| | - Sophia H Y Liao
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Sydney, NSW 2006, Australia
| | - Adrian Westhaus
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Sydney, NSW 2006, Australia
| | - Patrick Wilmott
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jason Ward
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Kimberley L Dilworth
- Vector and Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Giorgia Santilli
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Arkadiusz Rybicki
- Vector and Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Hiroyuki Nakai
- Oregon Health & Science University, Portland, OR 97239, USA
| | - Adrian J Thrasher
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Adrian C Filip
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Sydney, NSW 2006, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2145, Australia
| | - Leszek Lisowski
- Translational Vectorology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,Vector and Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,Military Institute of Hygiene and Epidemiology, The Biological Threats Identification and Countermeasure Centre, 24-100 Puławy, Poland
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23
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Mukai Y, Horie M, Tomonaga K. Systematic estimation of insertion dates of endogenous bornavirus-like elements in vesper bats. J Vet Med Sci 2018; 80:1356-1363. [PMID: 29973433 PMCID: PMC6115245 DOI: 10.1292/jvms.18-0211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Endogenous bornavirus-like elements (EBLs) are sequences derived from bornaviruses (the
family Bornaviridae) that are integrated into animal genomes. They are
formed through germline insertions of segments of bornaviral transcripts into animal
genomes. Because EBLs are molecular fossils of bornaviruses, they serve as precious
sources of information to understand the evolutionary history of bornaviruses. Previous
studies revealed the presence of many EBLs in bat genomes, especially in vesper bats, and
suggested the long-term association between bats and bornaviruses. However, insertion
dates of EBLs are largely unknown because of the limitations of available bat genome
sequences in the public database. In this study, through a combination of database
searches, PCR, and sequencing approaches, we systematically determined the gene
orthologies of 13 lineages of EBLs in bats of the genus Myotis and
Eptesicus and family Vespertilionidae. Using the above data, we
estimated their insertion dates: the EBLs in vesper bats were inserted approximately 14.2
to 53 million years ago. These results suggest that vesper bats have been repeatedly
infected by bornaviruses at different points in time during evolution. This study provides
novel insights into the evolutionary history of bornaviruses and demonstrates the
robustness of combining database searches, PCR, and sequencing approaches to estimate
insertion dates of bornaviruses.
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Affiliation(s)
- Yahiro Mukai
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences (InFRONT), Kyoto University, Kyoto 606-8507, Japan.,Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Masayuki Horie
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences (InFRONT), Kyoto University, Kyoto 606-8507, Japan.,Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences (InFRONT), Kyoto University, Kyoto 606-8507, Japan.,Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan.,Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
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24
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Pénzes JJ, Marsile-Medun S, Agbandje-McKenna M, Gifford RJ. Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses. Virus Evol 2018; 4:vey026. [PMID: 30443409 PMCID: PMC6232428 DOI: 10.1093/ve/vey026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Amdoparvoviruses (family Parvoviridae: genus Amdoparvovirus) infect carnivores, and are a major cause of morbidity and mortality in farmed animals. In this study, we systematically screened animal genomes to identify endogenous parvoviral elements (EPVs) disclosing a high degree of similarity to amdoparvoviruses, and investigated their genomic, phylogenetic and protein structural features. We report the first examples of full-length, amdoparvovirus-derived EPVs in the genome of the Transcaucasian mole vole (Ellobius lutescens). We also identify four EPVs in mammal and reptile genomes that are intermediate between amdoparvoviruses and their sister genus (Protoparvovirus) in terms of their phylogenetic placement and genomic features. In particular, we identify a genome-length EPV in the genome of a pit viper (Protobothrops mucrosquamatus) that is more similar to a protoparvovirus than an amdoparvovirus in terms of its phylogenetic placement and the structural features of its capsid protein (as revealed by homology modeling), yet exhibits characteristically amdoparvovirus-like genome features including: (1) a putative middle ORF gene; (2) a capsid gene that lacks a phospholipase A2 domain; (3) a genome structure consistent with an amdoparvovirus-like mechanism of capsid gene expression. Our findings indicate that amdoparvovirus host range extends to rodents, and that parvovirus lineages possessing a mixture of proto- and amdoparvovirus-like characteristics have circulated in the past. In addition, we show that EPV sequences in the mole vole and pit viper encode intact, expressible replicase genes that have potentially been co-opted or exapted in these host species.
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Affiliation(s)
- Judit J Pénzes
- University of Florida McKnight Brain Institute, 1149 Newell Dr, Gainesville, USA
| | - Soledad Marsile-Medun
- Agrocampus Ouest, 65 Rue de Saint-Brieuc, Rennes, France
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, UK
| | | | - Robert James Gifford
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, UK
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25
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Pierce GF, Iorio A. Past, present and future of haemophilia gene therapy: From vectors and transgenes to known and unknown outcomes. Haemophilia 2018; 24 Suppl 6:60-67. [DOI: 10.1111/hae.13489] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2018] [Indexed: 01/19/2023]
Affiliation(s)
- G. F. Pierce
- World Federation of Hemophilia; Montreal QC Canada
- World Federation of Hemophilia; Third Rock Ventures; San Francisco CA USA
| | - A. Iorio
- McMaster University; Hamilton ON Canada
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26
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Horie M, Tomonaga K. Paleovirology of bornaviruses: What can be learned from molecular fossils of bornaviruses. Virus Res 2018; 262:2-9. [PMID: 29630909 DOI: 10.1016/j.virusres.2018.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/05/2018] [Accepted: 04/05/2018] [Indexed: 02/05/2023]
Abstract
Endogenous viral elements (EVEs) are virus-derived sequences embedded in eukaryotic genomes formed by germline integration of viral sequences. As many EVEs were integrated into eukaryotic genomes millions of years ago, EVEs are considered molecular fossils of viruses. EVEs can be valuable informational sources about ancient viruses, including their time scale, geographical distribution, genetic information, and hosts. Although integration of viral sequences is not required for replications of viruses other than retroviruses, many non-retroviral EVEs have been reported to exist in eukaryotes. Investigation of these EVEs has expanded our knowledge regarding virus-host interactions, as well as provided information on ancient viruses. Among them, EVEs derived from bornaviruses, non-retroviral RNA viruses, have been relatively well studied. Bornavirus-derived EVEs are widely distributed in animal genomes, including the human genome, and the history of bornaviruses can be dated back to more than 65 million years. Although there are several reports focusing on the biological significance of bornavirus-derived sequences in mammals, paleovirology of bornaviruses has not yet been well described and summarized. In this paper, we describe what can be learned about bornaviruses from endogenous bornavirus-like elements from the view of paleovirology using published results and our novel data.
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Affiliation(s)
- Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan; Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| | - Keizo Tomonaga
- Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan; Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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27
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Tijssen P, Pénzes JJ, Yu Q, Pham HT, Bergoin M. Reprint of: Diversity of small, single-stranded DNA viruses of invertebrates and their chaotic evolutionary past. J Invertebr Pathol 2017; 147:23-36. [PMID: 32781498 DOI: 10.1016/j.jip.2017.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 11/25/2022]
Abstract
A wide spectrum of invertebrates is susceptible to various single-stranded DNA viruses. Their relative simplicity of replication and dependence on actively dividing cells makes them highly pathogenic for many invertebrates (Hexapoda, Decapoda, etc.). We present their taxonomical classification and describe the evolutionary relationships between various groups of invertebrate-infecting viruses, their high degree of recombination, and their relationship to viruses infecting mammals or other vertebrates. They share characteristics of the viruses within the various families, including structure of the virus particle, genome properties, and gene expression strategy.
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Affiliation(s)
- Peter Tijssen
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Judit J Pénzes
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Qian Yu
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Hanh T Pham
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Max Bergoin
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada; Laboratoire de Pathologie Comparée, Faculté des Sciences, Université Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
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28
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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: 2.3] [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.
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29
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Tijssen P, Pénzes JJ, Yu Q, Pham HT, Bergoin M. Diversity of small, single-stranded DNA viruses of invertebrates and their chaotic evolutionary past. J Invertebr Pathol 2016; 140:83-96. [PMID: 27663091 DOI: 10.1016/j.jip.2016.09.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 11/19/2022]
Abstract
A wide spectrum of invertebrates is susceptible to various single-stranded DNA viruses. Their relative simplicity of replication and dependence on actively dividing cells makes them highly pathogenic for many invertebrates (Hexapoda, Decapoda, etc.). We present their taxonomical classification and describe the evolutionary relationships between various groups of invertebrate-infecting viruses, their high degree of recombination, and their relationship to viruses infecting mammals or other vertebrates. They share characteristics of the viruses within the various families, including structure of the virus particle, genome properties, and gene expression strategy.
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Affiliation(s)
- Peter Tijssen
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Judit J Pénzes
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Qian Yu
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Hanh T Pham
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Max Bergoin
- Laboratoire de Virologie (Bldg 18), Institut National de Recherche Scientifique-Institut Armand-Frappier, 531 Boul. des Prairies, Laval, QC, H7V 1B7, Canada; Laboratoire de Pathologie Comparée, Faculté des Sciences, Université Montpellier, Place Eugène Bataillon, 34095 Montpellier, France
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