1
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Wang J, Li W, Gong X, Wang Z, Wang Y, Ling J, Jiang Z, Zhu G, Li Y. Recombination and amino acid point mutations in VP3 exhibit a synergistic effect on increased virulence of rMDPV. Virulence 2024; 15:2366874. [PMID: 38869140 PMCID: PMC11178272 DOI: 10.1080/21505594.2024.2366874] [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: 03/15/2024] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Recombinant Muscovy duck parvovirus (rMDPV) is a product of genetic recombination between classical Muscovy duck parvovirus (MDPV) and goose parvovirus (GPV). The recombination event took place within a 1.1-kb DNA segment located in the middle of the VP3 gene, and a 187-bp sequence extending from the P9 promoter to the 5' initiation region of the Rep1 ORF. This resulted in the alteration of five amino acids within VP3. Despite these genetic changes, the precise influence of recombination and amino acid mutations on the pathogenicity of rMDPV remains ambiguous. In this study, based on the rMDPV strain ZW and the classical MDPV strain YY, three chimeric viruses (rZW-mP9, rZW-mPR187, and rYY-rVP3) and the five amino acid mutations-introduced mutants (rZW-g5aa and rYY-5aa(ZW)) were generated using reverse genetic technology. When compared to the parental virus rZW, rZW-g5aa exhibited a prolonged mean death time (MDT) and a decreased median lethal dose (ELD50) in embryonated duck eggs. In contrast, rYY-5aa(ZW) did not display significant differences in MDT and ELD50 compared to rYY. In 2-day-old Muscovy ducklings, infection with rZW-g5aa and rYY-5aa(ZW) resulted in mortality rates of only 20% and 10%, respectively, while infections with the three chimeric viruses (rZW-mP9, rZW-mPR187, rYY-rVP3) and rZW still led to 100% mortality. Notably, rYY-rVP3, containing the VP3 region from strain ZW, exhibited 50% mortality in 6-day-old Muscovy ducklings and demonstrated significant horizontal transmission. Collectively, our findings indicate that recombination and consequent amino acid changes in VP3 have a synergistic impact on the heightened virulence of rMDPV in Muscovy ducklings.
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Affiliation(s)
- Jianye Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Department of Preventive Veterinary Medicine, Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonosis, Yangzhou, Jiangsu, China
| | - Wanmei Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Department of Preventive Veterinary Medicine, Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonosis, Yangzhou, Jiangsu, China
| | - Xiaoyan Gong
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Department of Preventive Veterinary Medicine, Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonosis, Yangzhou, Jiangsu, China
| | - Zhixian Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Department of Preventive Veterinary Medicine, Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonosis, Yangzhou, Jiangsu, China
| | - Yu Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Department of Preventive Veterinary Medicine, Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonosis, Yangzhou, Jiangsu, China
| | - Jueyi Ling
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Department of Preventive Veterinary Medicine, Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonosis, Yangzhou, Jiangsu, China
| | - Zhiwei Jiang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Department of Preventive Veterinary Medicine, Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonosis, Yangzhou, Jiangsu, China
| | - Guoqiang Zhu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Department of Preventive Veterinary Medicine, Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonosis, Yangzhou, Jiangsu, China
| | - Yufeng Li
- Shandong Academy of Agricultural Sciences, Institute of Poultry Science, Jinan, Shandong, China
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2
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Matsuzaka Y, Yashiro R. Therapeutic Application and Structural Features of Adeno-Associated Virus Vector. Curr Issues Mol Biol 2024; 46:8464-8498. [PMID: 39194716 DOI: 10.3390/cimb46080499] [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: 06/10/2024] [Revised: 07/02/2024] [Accepted: 07/12/2024] [Indexed: 08/29/2024] Open
Abstract
Adeno-associated virus (AAV) is characterized by non-pathogenicity, long-term infection, and broad tropism and is actively developed as a vector virus for gene therapy products. AAV is classified into more than 100 serotypes based on differences in the amino acid sequence of the capsid protein. Endocytosis involves the uptake of viral particles by AAV and accessory receptors during AAV infection. After entry into the cell, they are transported to the nucleus through the nuclear pore complex. AAVs mainly use proteoglycans as receptors to enter cells, but the types of sugar chains in proteoglycans that have binding ability are different. Therefore, it is necessary to properly evaluate the primary structure of receptor proteins, such as amino acid sequences and post-translational modifications, including glycosylation, and the higher-order structure of proteins, such as the folding of the entire capsid structure and the three-dimensional (3D) structure of functional domains, to ensure the efficacy and safety of biopharmaceuticals. To further enhance safety, it is necessary to further improve the efficiency of gene transfer into target cells, reduce the amount of vector administered, and prevent infection of non-target cells.
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Affiliation(s)
- Yasunari Matsuzaka
- Division of Molecular and Medical Genetics, Center for Gene and Cell Therapy, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
- Administrative Section of Radiation Protection, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira 187-8551, Japan
| | - Ryu Yashiro
- Administrative Section of Radiation Protection, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira 187-8551, Japan
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
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3
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Mietzsch M, Kailasan S, Bennett A, Chipman P, Fane B, Huiskonen JT, Clarke IN, McKenna R. The Structure of Spiroplasma Virus 4: Exploring the Capsid Diversity of the Microviridae. Viruses 2024; 16:1103. [PMID: 39066266 PMCID: PMC11281519 DOI: 10.3390/v16071103] [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: 06/11/2024] [Revised: 07/02/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Spiroplasma virus 4 (SpV4) is a bacteriophage of the Microviridae, which packages circular ssDNA within non-enveloped T = 1 icosahedral capsids. It infects spiroplasmas, which are known pathogens of honeybees. Here, the structure of the SpV4 virion is determined using cryo-electron microscopy to a resolution of 2.5 Å. A striking feature of the SpV4 capsid is the mushroom-like protrusions at the 3-fold axes, which is common among all members of the subfamily Gokushovirinae. While the function of the protrusion is currently unknown, this feature varies widely in this subfamily and is therefore possibly an adaptation for host recognition. Furthermore, on the interior of the SpV4 capsid, the location of DNA-binding protein VP8 was identified and shown to have low structural conservation to the capsids of other viruses in the family. The structural characterization of SpV4 will aid future studies analyzing the virus-host interaction, to understand disease mechanisms at a molecular level. Furthermore, the structural comparisons in this study, including a low-resolution structure of the chlamydia phage 2, provide an overview of the structural repertoire of the viruses in this family that infect various bacterial hosts, which in turn infect a wide range of animals and plants.
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Affiliation(s)
- Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA (A.B.)
| | - Shweta Kailasan
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA (A.B.)
| | - Antonette Bennett
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA (A.B.)
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA (A.B.)
| | - Bentley Fane
- The BIO5 Institute, Keating Building, University of Arizona, Tucson, AZ 85721, USA
| | - Juha T. Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, 00014 Helsinki, Finland
| | - Ian N. Clarke
- Molecular Microbiology Group, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA (A.B.)
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4
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Prosdocimi F, de Farias ST. Major evolutionary transitions before cells: A journey from molecules to organisms. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 191:11-24. [PMID: 38971326 DOI: 10.1016/j.pbiomolbio.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/25/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Basing on logical assumptions and necessary steps of complexification along biological evolution, we propose here an evolutionary path from molecules to cells presenting four ages and three major transitions. At the first age, the basic biomolecules were formed and become abundant. The first transition happened with the event of a chemical symbiosis between nucleic acids and peptides worlds, which marked the emergence of both life and the process of organic encoding. FUCA, the first living process, was composed of self-replicating RNAs linked to amino acids and capable to catalyze their binding. The second transition, from the age of FUCA to the age of progenotes, involved the duplication and recombination of proto-genomes, leading to specialization in protein production and the exploration of protein to metabolite interactions in the prebiotic soup. Enzymes and metabolic pathways were incorporated into biology from protobiotic reactions that occurred without chemical catalysts, step by step. Then, the fourth age brought origin of organisms and lineages, occurring when specific proteins capable to stackle together facilitated the formation of peptidic capsids. LUCA was constituted as a progenote capable to operate the basic metabolic functions of a cell, but still unable to interact with lipid molecules. We present evidence that the evolution of lipid interaction pathways occurred at least twice, with the development of bacterial-like and archaeal-like membranes. Also, data in literature suggest at least two paths for the emergence of DNA biosynthesis, allowing the stabilization of early life strategies in viruses, archaeas and bacterias. Two billion years later, the eukaryotes arouse, and after 1,5 billion years of evolution, they finally learn how to evolve multicellularity via tissue specialization.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminski, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds, LS7 3RB, UK
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5
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Luo S, Jiang H, Li Q, Qin Y, Yang S, Li J, Xu L, Gou Y, Zhang Y, Liu F, Ke X, Zheng Q, Sun X. An adeno-associated virus variant enabling efficient ocular-directed gene delivery across species. Nat Commun 2024; 15:3780. [PMID: 38710714 DOI: 10.1038/s41467-024-48221-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 04/24/2024] [Indexed: 05/08/2024] Open
Abstract
Recombinant adeno-associated viruses (rAAVs) have emerged as promising gene therapy vectors due to their proven efficacy and safety in clinical applications. In non-human primates (NHPs), rAAVs are administered via suprachoroidal injection at a higher dose. However, high doses of rAAVs tend to increase additional safety risks. Here, we present a novel AAV capsid (AAVv128), which exhibits significantly enhanced transduction efficiency for photoreceptors and retinal pigment epithelial (RPE) cells, along with a broader distribution across the layers of retinal tissues in different animal models (mice, rabbits, and NHPs) following intraocular injection. Notably, the suprachoroidal delivery of AAVv128-anti-VEGF vector completely suppresses the Grade IV lesions in a laser-induced choroidal neovascularization (CNV) NHP model for neovascular age-related macular degeneration (nAMD). Furthermore, cryo-EM analysis at 2.1 Å resolution reveals that the critical residues of AAVv128 exhibit a more robust advantage in AAV binding, the nuclear uptake and endosome escaping. Collectively, our findings highlight the potential of AAVv128 as a next generation ocular gene therapy vector, particularly using the suprachoroidal delivery route.
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Affiliation(s)
- Shuang Luo
- Chengdu Origen Biotechnology Co. Ltd, Chengdu, 610036, China
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
- Sichuan Provincial Key Laboratory of Innovative Biomedicine, Chengdu, 610036, China
| | - Hao Jiang
- Chengdu Origen Biotechnology Co. Ltd, Chengdu, 610036, China
- Sichuan Provincial Key Laboratory of Innovative Biomedicine, Chengdu, 610036, China
| | - Qingwei Li
- Chengdu Origen Biotechnology Co. Ltd, Chengdu, 610036, China
- Sichuan Provincial Key Laboratory of Innovative Biomedicine, Chengdu, 610036, China
| | - Yingfei Qin
- Chengdu Origen Biotechnology Co. Ltd, Chengdu, 610036, China
| | - Shiping Yang
- Chengdu Origen Biotechnology Co. Ltd, Chengdu, 610036, China
| | - Jing Li
- Chengdu Origen Biotechnology Co. Ltd, Chengdu, 610036, China
| | - Lingli Xu
- Chengdu Origen Biotechnology Co. Ltd, Chengdu, 610036, China
| | - Yan Gou
- Chengdu Origen Biotechnology Co. Ltd, Chengdu, 610036, China
| | - Yafei Zhang
- Chengdu Origen Biotechnology Co. Ltd, Chengdu, 610036, China
| | - Fengjiang Liu
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, 510005, China
| | - Xiao Ke
- Chengdu Origen Biotechnology Co. Ltd, Chengdu, 610036, China.
- Chengdu Kanghong Pharmaceuticals Group Co Ltd, Chengdu, 610036, China.
| | - Qiang Zheng
- Chengdu Origen Biotechnology Co. Ltd, Chengdu, 610036, China.
- Sichuan Provincial Key Laboratory of Innovative Biomedicine, Chengdu, 610036, China.
| | - Xun Sun
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
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6
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Mietzsch M, Nelson AR, Hsi J, Zachary J, Potts L, Chipman P, Ghanem M, Khandekar N, Alexander IE, Logan GJ, Huiskonen JT, McKenna R. Structural characterization of antibody-responses from Zolgensma treatment provides the blueprint for the engineering of an AAV capsid suitable for redosing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.590489. [PMID: 38746165 PMCID: PMC11092599 DOI: 10.1101/2024.05.01.590489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Monoclonal antibodies (mAbs) are useful tools to dissect the neutralizing antibody response against the adeno-associated virus (AAV) capsids used as gene therapy delivery vectors. This study structurally characterizes the interactions of 21 human-derived antibodies from patients treated with the AAV9 vector, Zolgensma ® , utilizing high-resolution cryo-electron microscopy. The majority of the bound antibodies do not conform to the icosahedral symmetry of the capsid, thus requiring localized reconstructions. These complex structures provide unprecedented details of the mAbs binding interfaces, with some antibodies inducing structural perturbations of the capsid upon binding. Key surface capsid amino acid residues were identified facilitating the design of capsid variants with an antibody escape phenotype, with the potential to expand the patient cohort treatable with AAV9 vectors to include those that were previously excluded due to their pre-existing neutralizing antibodies, and possibly also to those requiring redosing.
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7
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Chukwudozie KI, Wang H, Wang X, Lu C, Xue J, Zhang W, Shan T. Viral metagenomic analysis reveals diverse viruses and a novel bocaparvovirus in the enteric virome of snow leopard ( Panthera uncia). Heliyon 2024; 10:e29799. [PMID: 38681641 PMCID: PMC11053277 DOI: 10.1016/j.heliyon.2024.e29799] [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: 09/23/2023] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/01/2024] Open
Abstract
The enteric virome, comprising a complex community of viruses inhabiting the gastrointestinal tract, plays a significant role in health and disease dynamics. In this study, the fecal sample of a wild snow leopard was subjected to viral metagenomic analysis using a double barcode Illumina MiSeq platform. The resulting reads were de novo assembled into contigs with SOAPdenovo2 version r240. Additional bioinformatic analysis of the assembled genome and genome annotation was done using the Geneious prime software (version 2022.0.2). Following viral metagenomic analysis and bioinformatic analysis, a total of 7 viral families and a novel specie of bocaparvovirus tentatively named Panthera uncia bocaparvovirus (PuBOV) with GenBank accession number OQ627713 were identified. The complete genome of PuBOV was predicted to contain 3 open reading frames (ORFs), contains 5433 nucleotides and has a G + C content of 47.40 %. BLASTx analysis and pairwise sequence comparison indicated the novel virus genome was a new species in the genus Bocaparvovirus based on the species demarcation criteria of the International Committee on the Taxonomy of Viruses. This study provides valuable insights into the diversity and composition of the enteric virome in wild endangered snow leopards. The identification and characterization of viruses in wildlife is crucial for developing effective strategies to manage and mitigate potential zoonotic and other viral disease threats to human and animal health.
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Affiliation(s)
- Kingsley Ikechukwu Chukwudozie
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang. Zip code: 212300, PR China
- Department of Microbiology, University of Nigeria, Zip code: 410001, PR China
| | - Haoning Wang
- Heilongjiang cold Region Wetland Ecology and Environment Research key laboratory, school of geography and tourism, Harbin university, 109 zhongxing Road, Harbin, 150086, Heilongjiang province, PR China
- School of Geography and Tourism, Harbin University, Harbin 150086, Heilongjiang province, PR China
| | - Xiaolong Wang
- The Key Laboratory of Wildlife Diseases and Biosecurity Management of Heilongjiang Province. Zip code: 154100, PR China
| | - Chunying Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang. Zip code: 212300, PR China
| | - Jiaxin Xue
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang. Zip code: 212300, PR China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang. Zip code: 212300, PR China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, PR China
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8
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Ikeda T, Yamaguchi Y, Oyama H, Matsushita A, Tsunaka Y, Fukuhara M, Torisu T, Uchiyama S. Higher-Order Structure of Adeno-Associated Virus Serotype 8 by Hydrogen/Deuterium Exchange Mass Spectrometry. Viruses 2024; 16:585. [PMID: 38675928 PMCID: PMC11053801 DOI: 10.3390/v16040585] [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: 03/04/2024] [Revised: 03/29/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
The higher-order structure (HOS) is a critical quality attribute of recombinant adeno-associated viruses (rAAVs). Evaluating the HOS of the entire rAAV capsid is challenging because of the flexibility and/or less folded nature of the VP1 unique (VP1u) and VP1/VP2 common regions, which are structural features essential for these regions to exert their functions following viral infection. In this study, hydrogen/deuterium exchange mass spectrometry (HDX-MS) was used for the structural analysis of full and empty rAAV8 capsids. We obtained 486 peptides representing 85% sequence coverage. Surprisingly, the VP1u region showed rapid deuterium uptake even though this region contains the phospholipase A2 domain composed primarily of α-helices. The comparison of deuterium uptake between full and empty capsids showed significant protection from hydrogen/deuterium exchange in the full capsid at the channel structure of the 5-fold symmetry axis. This corresponds to cryo-electron microscopy studies in which the extended densities were observed only in the full capsid. In addition, deuterium uptake was reduced in the VP1u region of the full capsid, suggesting the folding and/or interaction of this region with the encapsidated genome. This study demonstrated HDX-MS as a powerful method for probing the structure of the entire rAAV capsid.
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Affiliation(s)
- Tomohiko Ikeda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Yuki Yamaguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Hiroaki Oyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Aoba Matsushita
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Yasuo Tsunaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Mitsuko Fukuhara
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Tetsuo Torisu
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan; (T.I.); (Y.Y.); (H.O.); (A.M.); (Y.T.); (M.F.); (T.T.)
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
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9
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Divekar G, Colmant AMG, Furlong MJ, Etebari K. Transcriptome Analysis Reveals a Diverse Range of Novel Viruses in Australian Sugarcane Soldier Fly ( Inopus flavus) Larvae. Viruses 2024; 16:516. [PMID: 38675859 PMCID: PMC11054854 DOI: 10.3390/v16040516] [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: 03/11/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
In Australia, Soldier flies (Inopus spp.) are economically significant pests of sugarcane that currently lack a viable management strategy. Despite various research efforts, the mechanisms underlying the damage caused by soldier fly larvae remain poorly understood. Our study aims to explore whether this damage is associated with the transmission of plant viruses during larval feeding. We also explore the larval transcriptome to identify any entomopathogenic viruses with the potential to be used as biocontrol agents in future pest management programs. Seven novel virus sequences are identified and characterised using de novo assembly of RNA-Seq data obtained from salivary glands of larvae. The novel virus sequences belong to different virus families and are tentatively named SF-associated anphevirus (SFaAV), SF-associated orthomyxo-like virus (SFaOV), SF-associated narna-like virus (SFaNV), SF-associated partiti-like virus (SFaPV), SF-associated toti-like virus (SFaTV-1 and SFaTV-2) and SF-associated densovirus (SFaDV). These newly identified viruses are more likely insect-associated viruses, as phylogenetic analyses show that they cluster with other insect-specific viruses. Small RNA analysis indicates prominent peaks at both 21 nt and 26-29 nt, suggesting the activation of host siRNA and piwiRNA pathways. Our study helps to improve understanding of the virome of soldier flies and could identify insect viruses for deployment in novel pest management strategies.
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Affiliation(s)
- Gayatri Divekar
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton 4343, Australia
| | - Agathe M. G. Colmant
- Unité des Virus Émergents (UVE: Aix-Marseille Univ, Università di Corsica, IRD 190, Inserm 1207, IRBA), 13005 Marseille, France
| | - Michael J. Furlong
- School of the Environment, The University of Queensland, Brisbane 4072, Australia
| | - Kayvan Etebari
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton 4343, Australia
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10
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Hoad M, Roby JA, Forwood JK. Structural basis for nuclear import of bat adeno-associated virus capsid protein. J Gen Virol 2024; 105:001960. [PMID: 38441555 PMCID: PMC10999750 DOI: 10.1099/jgv.0.001960] [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: 05/22/2023] [Accepted: 01/22/2024] [Indexed: 03/07/2024] Open
Abstract
Adeno-associated viruses (AAV) are one of the world's most promising gene therapy vectors and as a result, are one of the most intensively studied viral vectors. Despite a wealth of research into these vectors, the precise characterisation of AAVs to translocate into the host cell nucleus remains unclear. Recently we identified the nuclear localization signals of an AAV porcine strain and determined its mechanism of binding to host importin proteins. To expand our understanding of diverse AAV import mechanisms we sought to determine the mechanism in which the Cap protein from a bat-infecting AAV can interact with transport receptor importins for translocation into the nucleus. Using a high-resolution crystal structure and quantitative assays, we were able to not only determine the exact region and residues of the N-terminal domain of the Cap protein which constitute the functional NLS for binding with the importin alpha two protein, but also reveal the differences in binding affinity across the importin-alpha isoforms. Collectively our results allow for a detailed molecular view of the way AAV Cap proteins interact with host proteins for localization into the cell nucleus.
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Affiliation(s)
- Mikayla Hoad
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Justin A. Roby
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Jade K. Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
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11
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Lopes TS, Lunge VR, Streck AF. Antiviral alternatives against important members of the subfamily Parvovirinae: a review. Arch Virol 2024; 169:52. [PMID: 38378929 DOI: 10.1007/s00705-024-05995-8] [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: 09/15/2023] [Accepted: 01/04/2024] [Indexed: 02/22/2024]
Abstract
Parvoviruses are responsible for multiple diseases, and there is a critical need for effective antiviral therapies. Specific antiviral treatments for parvovirus infections are currently lacking, and the available options are mostly supportive and symptomatic. In recent years, significant research efforts have been directed toward understanding the molecular mechanisms of parvovirus replication and identifying potential targets for antiviral interventions. This review highlights the structure, pathogenesis, and treatment options for major viruses of the subfamily Parvovirinae, such as parvovirus B19 (B19V), canine parvovirus type 2 (CPV-2), and porcine parvovirus (PPV) and also describes different approaches in the development of antiviral alternatives against parvovirus, including drug repurposing, serendipity, and computational tools (molecular docking and artificial intelligence) in drug discovery. These advances greatly increase the likelihood of discoveries that will lead to potent antiviral strategies against different parvovirus infections.
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12
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Schieferecke AJ, Lee H, Chen A, Kilaru V, Krish Williams J, Schaffer DV. Evolving membrane-associated accessory protein variants for improved adeno-associated virus production. Mol Ther 2024; 32:340-351. [PMID: 38115579 PMCID: PMC10861973 DOI: 10.1016/j.ymthe.2023.12.015] [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: 06/23/2023] [Revised: 10/14/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023] Open
Abstract
Manufacturing sufficient adeno-associated virus (AAV) to meet current and projected clinical needs is a significant hurdle to the growing gene therapy industry. The recently discovered membrane-associated accessory protein (MAAP) is encoded by an alternative open reading frame in the AAV cap gene that is found in all presently reported natural serotypes. Recent evidence has emerged supporting a functional role of MAAP in AAV egress, although the underlying mechanisms of MAAP function remain unknown. Here, we show that inactivation of MAAP from AAV2 by a single point mutation that is silent in the VP1 open reading frame (ORF) (AAV2-ΔMAAP) decreased exosome-associated and secreted vector genome production. We hypothesized that novel MAAP variants could be evolved to increase AAV production and thus subjected a library encoding over 1 × 106 MAAP protein variants to five rounds of packaging selection into the AAV2-ΔMAAP capsid. Between each successive packaging round, we observed a progressive increase in both overall titer and ratio of secreted vector genomes conferred by the bulk-selected MAAP library population. Next-generation sequencing uncovered enriched mutational features, and a resulting selected MAAP variant containing missense mutations and a frameshifted C-terminal domain increased overall GFP transgene packaging in AAV2, AAV6, and AAV9 capsids.
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Affiliation(s)
- Adam J Schieferecke
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hyuncheol Lee
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Aleysha Chen
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Vindhya Kilaru
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Justin Krish Williams
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David V Schaffer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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13
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Basso CR, Cruz TF, Vieira LB, Pedrosa VDA, Possebon FS, Araujo Junior JP. Development of a Gold Nanoparticle-Based ELISA for Detection of PCV2. Pathogens 2024; 13:108. [PMID: 38392846 PMCID: PMC10893201 DOI: 10.3390/pathogens13020108] [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: 11/17/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024] Open
Abstract
In this new methodology, plasmonic ELISA (pELISA) was used to detect Circovirus porcine2 (PCV2) in serum samples without the need for plate reading equipment. This process occurs by adapting the conventional ELISA test with gold nanoparticles (AuNPs) to promote a color change on the plate and quickly identify this difference with the naked eye, generating a dark purple-gray hue when the samples are positive and red when the samples are negative. The technique demonstrated high efficiency in detecting samples with a viral load ≥ 5 log10 copies/mL. Plasmonic ELISA offers user-friendly, cost-effective, and reliable characteristics, making it a valuable tool for PCV2 diagnosis and potentially adaptable for other pathogen detection applications.
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Affiliation(s)
- Caroline Rodrigues Basso
- Biotechnology Institute, São Paulo State University, Botucatu 18607-440, SP, Brazil; (T.F.C.); (F.S.P.)
| | - Taís Fukuta Cruz
- Biotechnology Institute, São Paulo State University, Botucatu 18607-440, SP, Brazil; (T.F.C.); (F.S.P.)
- Chemical and Biological Sciences Department, Bioscience Institute, São Paulo State University, Botucatu 18618-000, SP, Brazil;
| | - Larissa Baldo Vieira
- Biotechnology Institute, São Paulo State University, Botucatu 18607-440, SP, Brazil; (T.F.C.); (F.S.P.)
| | - Valber de Albuquerque Pedrosa
- Chemical and Biological Sciences Department, Bioscience Institute, São Paulo State University, Botucatu 18618-000, SP, Brazil;
| | - Fábio Sossai Possebon
- Biotechnology Institute, São Paulo State University, Botucatu 18607-440, SP, Brazil; (T.F.C.); (F.S.P.)
| | - João Pessoa Araujo Junior
- Biotechnology Institute, São Paulo State University, Botucatu 18607-440, SP, Brazil; (T.F.C.); (F.S.P.)
- Chemical and Biological Sciences Department, Bioscience Institute, São Paulo State University, Botucatu 18618-000, SP, Brazil;
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14
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Xie Q, Sun Z, Xue X, Pan Y, Zhen S, Liu Y, Zhan J, Jiang L, Zhang J, Zhu H, Yu X, Zhang X. China-origin G1 group isolate FPV072 exhibits higher infectivity and pathogenicity than G2 group isolate FPV027. Front Vet Sci 2024; 11:1328244. [PMID: 38288138 PMCID: PMC10822907 DOI: 10.3389/fvets.2024.1328244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/02/2024] [Indexed: 01/31/2024] Open
Abstract
Introduction Feline parvovirus (FPV), a single-stranded DNA virus, is accountable for causing feline panleukopenia, a highly contagious and often lethal disease that primarily affects cats. The epidemiology prevalence and pathogenicity of FPV in certain regions of China, however, remains unclear. The aim of this research was to investigate the epidemiology of FPV in different regions of China in 2021 and compare its infectivity and pathogenicity. Methods In this research, a total of 36 FPV strains were obtained from diverse regions across China. Phylogenetic analysis was performed based on the VP2 and NS1 sequences, and two representative strains, FPV027 and FPV072, which belonged to different branches, were selected for comparative assessment of infectivity and pathogenicity. Results and discussion The results revealed that all strains were phylogenetically classified into two groups, G1 and G2, with a higher prevalence of G1 strains in China. Both in vitro and in vivo experiments demonstrated that FPV072 (G1 group) exhibited enhanced infectivity and pathogenicity compared to FPV027 (G2 Group). The structural alignment of the VP2 protein between the two viruses revealed mutations in residues 91, 232, and 300 that may contribute to differences in infectivity and pathogenicity. The findings from these observations will contribute significantly to the overall understanding of the molecular epidemiology of FPV in China and facilitate the development of an effective FPV vaccine.
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Affiliation(s)
- Qiaoqiao Xie
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Zhen Sun
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Xiu Xue
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Yajie Pan
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Shuye Zhen
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Yang Liu
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Jiuyu Zhan
- School of Life Sciences, Ludong University, Yantai, China
| | - Linlin Jiang
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Jianlong Zhang
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Hongwei Zhu
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Xin Yu
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
| | - Xingxiao Zhang
- School of Life Sciences, Ludong University, Yantai, China
- Collaborative Innovation Center for the Pet Infectious Diseases and Public Health in the Middle and Lower Stream Regions of the Yellow River, Yantai, China
- Provincial Engineering Research Center for Pet Animal Vaccines, Yantai, China
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15
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Vargas-Bermudez DS, Mogollon JD, Franco-Rodriguez C, Jaime J. The Novel Porcine Parvoviruses: Current State of Knowledge and Their Possible Implications in Clinical Syndromes in Pigs. Viruses 2023; 15:2398. [PMID: 38140639 PMCID: PMC10747800 DOI: 10.3390/v15122398] [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: 10/18/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 12/24/2023] Open
Abstract
Parvoviruses (PVs) affect various animal species causing different diseases. To date, eight different porcine parvoviruses (PPV1 through PPV8) are recognized in the swine population, all of which are distributed among subfamilies and genera of the Parvoviridae family. PPV1 is the oldest and is recognized as the primary agent of SMEDI, while the rest of the PPVs (PPV2 through PPV8) are called novel PPVs (nPPVs). The pathogenesis of nPPVs is still undefined, and whether these viruses are putative disease agents is unknown. Structurally, the PPVs are very similar; the differences occur mainly at the level of their genomes (ssDNA), where there is variation in the number and location of the coding genes. Additionally, it is considered that the genome of PVs has mutation rates similar to those of ssRNA viruses, that is, in the order of 10-5-10-4 nucleotide/substitution/year. These mutations manifest mainly in the VP protein, constituting the viral capsid, affecting virulence, tropism, and viral antigenicity. For nPPVs, mutation rates have already been established that are similar to those already described; however, within this group of viruses, the highest mutation rate has been reported for PPV7. In addition to the mutations, recombinations are also reported, mainly in PPV2, PPV3, and PPV7; these have been found between strains of domestic pigs and wild boars and in a more significant proportion in VP sequences. Regarding affinity for cell types, nPPVs have been detected with variable prevalence in different types of organs and tissues; this has led to the suggestion that they have a broad tropism, although proportionally more have been found in lung and lymphoid tissue such as spleen, tonsils, and lymph nodes. Regarding their epidemiology, nPPVs are present on all continents (except PPV8, only in Asia), and within pig farms, the highest prevalences detecting viral genomes have been seen in the fattener and finishing groups. The relationship between nPPVs and clinical manifestations has been complicated to establish. However, there is already some evidence that establishes associations. One of them is PPV2 with porcine respiratory disease complex (PRDC), where causality tests (PCR, ISH, and histopathology) lead to proposing the PPV2 virus as a possible agent involved in this syndrome. With the other nPPVs, there is still no clear association with any pathology. These have been detected in different systems (respiratory, reproductive, gastrointestinal, urinary, and nervous), and there is still insufficient evidence to classify them as disease-causing agents. In this regard, nPPVs (except PPV8) have been found to cause porcine reproductive failure (PRF), with the most prevalent being PPV4, PPV6, and PPV7. In the case of PRDC, nPPVs have also been detected, with PPV2 having the highest viral loads in the lungs of affected pigs. Regarding coinfections, nPPVs have been detected in concurrence in healthy and sick pigs, with primary PRDC and PRF viruses such as PCV2, PCV3, and PRRSV. The effect of these coinfections is not apparent; it is unknown whether they favor the replication of the primary agents, the severity of the clinical manifestations, or have no effect. The most significant limitation in the study of nPPVs is that their isolation has been impossible; therefore, there are no studies on their pathogenesis both in vitro and in vivo. For all of the above, it is necessary to propose basic and applied research on nPPVs to establish if they are putative disease agents, establish their effect on coinfections, and measure their impact on swine production.
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Affiliation(s)
| | | | | | - Jairo Jaime
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Medicina Veterinaria y de Zootecnia, Departamento de Salud Animal, Centro de Investigación en Infectología e Inmunología Veterinaria (CI3V), Carrera 30 No. 45-03, Bogotá 111321, CP, Colombia; (D.S.V.-B.); (J.D.M.); (C.F.-R.)
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16
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Grand RJ. Pathogenicity and virulence of human adenovirus F41: Possible links to severe hepatitis in children. Virulence 2023; 14:2242544. [PMID: 37543996 PMCID: PMC10405776 DOI: 10.1080/21505594.2023.2242544] [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: 05/16/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023] Open
Abstract
Over 100 human adenoviruses (HAdVs) have been isolated and allocated to seven species, A-G. Species F comprises two members-HAdV-F40 and HAdV-F41. As their primary site of infection is the gastrointestinal tract they have been termed, with species A, enteric adenoviruses. HAdV-F40 and HAdV-F41 are a common cause of gastroenteritis and diarrhoea in children. Partly because of difficulties in propagating the viruses in the laboratory, due to their restrictions on growth in many cell lines, our knowledge of the properties of individual viral proteins is limited. However, the structure of HAdV-F41 has recently been determined by cryo-electron microscopy. The overall structure is similar to those of HAdV-C5 and HAdV-D26 although with some differences. The sequence and arrangement of the hexon hypervariable region 1 (HVR1) and the arrangement of the C-terminal region of protein IX differ. Variations in the penton base and hexon HVR1 may play a role in facilitating infection of intestinal cells by HAdV-F41. A unique feature of HAdV-F40 and F41, among human adenoviruses, is the presence and expression of two fibre genes, giving long and short fibre proteins. This may also contribute to the tropism of these viruses. HAdV-F41 has been linked to a recent outbreak of severe acute hepatitis "of unknown origin" in young children. Further investigation has shown a very high prevalence of adeno-associated virus-2 in the liver and/or plasma of some cohorts of patients. These observations have proved controversial as HAdV-F41 had not been reported to infect the liver and AAV-2 has generally been considered harmless.
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Affiliation(s)
- Roger J. Grand
- Institute for Cancer and Genomic Science, the Medical School, University of Birmingham, Birmingham, UK
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17
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Li Y, Zheng L, He H, Xiong H, Chen J, Sun H, Chen C, Li Q, Fu J, Wu F, Gao Y, Xian J, Liang M, Xiao G, Chen Q. First detection of cutavirus DNA in stools of patients with rheumatic diseases in Guangzhou, China. Virol Sin 2023; 38:860-867. [PMID: 37839551 PMCID: PMC10786651 DOI: 10.1016/j.virs.2023.10.006] [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: 02/13/2023] [Accepted: 10/08/2023] [Indexed: 10/17/2023] Open
Abstract
Cutavirus (CuV) is a novel protoparvovirus possibly associated with diarrhea and cutaneous T-cell lymphomas. Patients with rheumatic disease are immunosuppressed and may be more vulnerable to pathogenic viruses. A descriptive study was conducted among hospitalized patients with rheumatic diseases and individuals undergoing medical health check-ups between June 2019 and June 2022 in Guangzhou, China. Stool samples of subjects were tested for CuV DNA. Demographic and fecal examination data of patients were obtained from electronic medical records. A total of 505 patients with rheumatic diseases and 244 individuals who underwent medical health check-ups were included in the study. Of the patients with rheumatic disease, 5.74% [95% confidence interval (CI): 4.03%-8.12%] were positive for CuV DNA, while no individual in the medical health check-up group was positive, indicating a close correlation between CuV and rheumatic disease. Men and patients with rheumatoid arthritis or ankylosing spondylitis, according to the disease classification, were more susceptible to being infected with CuV (P < 0.01). After adjustments, being male remained the only significant factor, with an adjusted odd ratio (OR) of 4.4 (95% CI: 1.7-11.4, P = 0.002). Phylogenetic analysis of the CuV VP2 sequences showed three diverse clades, one of which was segregated to be a single branching independent of previously known sequences, which is possible a new genotype.
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Affiliation(s)
- Yongzhi Li
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Liting Zheng
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Huan He
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Husheng Xiong
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jiaqi Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Hengbiao Sun
- Clinical Laboratory of Third Affiliated Hospital of Southern Medical University, Guangzhou, 510500, China
| | - Caiyun Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Qiushuang Li
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jiaqi Fu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Fei Wu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Yuhan Gao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Juxian Xian
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Minyi Liang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Gang Xiao
- Clinical Laboratory of Third Affiliated Hospital of Southern Medical University, Guangzhou, 510500, China.
| | - Qing Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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18
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Gonzalez TJ, Mitchell-Dick A, Blondel LO, Fanous MM, Hull JA, Oh DK, Moller-Tank S, Castellanos Rivera RM, Piedrahita JA, Asokan A. Structure-guided AAV capsid evolution strategies for enhanced CNS gene delivery. Nat Protoc 2023; 18:3413-3459. [PMID: 37735235 DOI: 10.1038/s41596-023-00875-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: 07/21/2022] [Accepted: 06/13/2023] [Indexed: 09/23/2023]
Abstract
Over the past 5 years, our laboratory has systematically developed a structure-guided library approach to evolve new adeno-associated virus (AAV) capsids with altered tissue tropism, higher transduction efficiency and the ability to evade pre-existing humoral immunity. Here, we provide a detailed protocol describing two distinct evolution strategies using structurally divergent AAV serotypes as templates, exemplified by improving CNS gene transfer efficiency in vivo. We outline four major components of our strategy: (i) structure-guided design of AAV capsid libraries, (ii) AAV library production, (iii) library cycling in single versus multiple animal models, followed by (iv) evaluation of lead AAV vector candidates in vivo. The protocol spans ~95 d, excluding gene expression analysis in vivo, and can vary depending on user experience, resources and experimental design. A distinguishing attribute of the current protocol is the focus on providing biomedical researchers with 3D structural information to guide evolution of precise 'hotspots' on AAV capsids. Furthermore, the protocol outlines two distinct methods for AAV library evolution consisting of adenovirus-enabled infectious cycling in a single species and noninfectious cycling in a cross-species manner. Notably, our workflow can be seamlessly merged with other RNA transcript-based library strategies and tailored for tissue-specific capsid selection. Overall, the procedures outlined herein can be adapted to expand the AAV vector toolkit for genetic manipulation of animal models and development of human gene therapies.
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Affiliation(s)
- Trevor J Gonzalez
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Leo O Blondel
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Marco M Fanous
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Joshua A Hull
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Daniel K Oh
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Sven Moller-Tank
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Jorge A Piedrahita
- North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Aravind Asokan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA.
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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19
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Hsi J, Mietzsch M, Chipman P, Afione S, Zeher A, Huang R, Chiorini J, McKenna R. Structural and antigenic characterization of the avian adeno-associated virus capsid. J Virol 2023; 97:e0078023. [PMID: 37702486 PMCID: PMC10617571 DOI: 10.1128/jvi.00780-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/19/2023] [Indexed: 09/14/2023] Open
Abstract
IMPORTANCE AAVs are extensively studied as promising therapeutic gene delivery vectors. In order to circumvent pre-existing antibodies targeting primate-based AAV capsids, the AAAV capsid was evaluated as an alternative to primate-based therapeutic vectors. Despite the high sequence diversity, the AAAV capsid was found to bind to a common glycan receptor, terminal galactose, which is also utilized by other AAVs already being utilized in gene therapy trials. However, contrary to the initial hypothesis, AAAV was recognized by approximately 30% of human sera tested. Structural and sequence comparisons point to conserved epitopes in the fivefold region of the capsid as the reason determinant for the observed cross-reactivity.
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Affiliation(s)
- Jane Hsi
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Sandra Afione
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland, USA
| | - Allison Zeher
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
- Department of Epidemiology, Bloomberg School for Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Rick Huang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - John Chiorini
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
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20
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Jiang X, Liu J, Xi Y, Zhang Q, Wang Y, Zhao M, Lu X, Wu H, Shan T, Ni B, Zhang W, Ma X. Virome of high-altitude canine digestive tract and genetic characterization of novel viruses potentially threatening human health. mSphere 2023; 8:e0034523. [PMID: 37724888 PMCID: PMC10597464 DOI: 10.1128/msphere.00345-23] [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: 06/25/2023] [Accepted: 07/25/2023] [Indexed: 09/21/2023] Open
Abstract
The majority of currently emerging infectious illnesses are zoonotic infections, which have caused serious public health and economic implications. The development of viral metagenomics has helped us to explore unknown viruses. We collected 1,970 canine feces from Yushu and Guoluo in the plateau region of China for this study to do a metagenomics analysis of the viral community of the canine digestive tract. Our analysis identified 203 novel viruses, classified into 11 known families and 2 unclassified groups. These viruses include the hepatitis E virus, first identified in dogs, and the astrovirus, coronavirus, polyomavirus, and others. The relationship between the newly identified canine viruses and known viruses was investigated through the use of phylogenetic analysis. Furthermore, we demonstrated the cross-species transmission of viruses and predicted new viruses that may cause diseases in both humans and animals, providing technical support for the prevention and control of diseases caused by environmental pollution viruses. IMPORTANCE Most emerging infectious diseases are due to zoonotic disease agents. Because of their effects on the security of human or animal life, agriculture production, and food safety, zoonotic illnesses and livestock diseases are of worldwide significance. Because dogs are closely related to humans and domestic animals, they serve as one of the important links in the transmission of zoonotic and livestock diseases. Canines can contaminate the environment in which humans live such as water and soil through secretions, potentially altering the human gut microbiota or causing diseases. Our study enriched the viral community in the digestive tract microbiome of dogs and found types of viruses that threaten human health, providing technical support for the prevention and control of early warning of diseases caused by environmental contaminant viruses.
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Affiliation(s)
- Xiaojie Jiang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jia Liu
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Yuan Xi
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qing Zhang
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Yongshun Wang
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Min Zhao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiang Lu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Haisheng Wu
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Bin Ni
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiao Ma
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai, China
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21
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Zhao Q, Zhao R, Sun Y, Ji L, Xi Y, Wang X, Shen Q, Ji L, Wang Y, You Z, Yang S, Zhang W. Identification of Multiple Novel Viruses in Fecal Samples of Black-Necked Cranes Using Viral Metagenomic Methods. Viruses 2023; 15:2068. [PMID: 37896845 PMCID: PMC10612090 DOI: 10.3390/v15102068] [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: 09/11/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
The black-necked crane is the only species of crane that lives in the high-altitude region of the Tibet Plateau. At present, there is little research on viral diseases of the black-necked crane (Grus nigricollis). In this study, a viral metagenomic approach was employed to investigate the fecal virome of black-necked cranes in Saga County, Shigatse City, Tibet, China. The identified virus families carried by black-necked cranes mainly include Genomoviridae, Parvoviridae, and Picornaviridae. The percentages of sequence reads belonging to these three virus families were 1.6%, 3.1%, and 93.7%, respectively. Among them, one genome was characterized as a novel species in the genus Grusopivirus of the family Picornaviridae, four new parvovirus genomes were obtained and classified into four different novel species within the genus Chaphamaparvovirus of the subfamily Hamaparvovirinae, and four novel genomovirus genomes were also acquired and identified as members of three different species, including Gemykroznavirus haeme1, Gemycircularvirus ptero6, and Gemycircularvirus ptero10. All of these viruses were firstly detected in fecal samples of black-necked cranes. This study provides valuable information for understanding the viral community composition in the digestive tract of black-necked cranes in Tibet, which can be used for monitoring, preventing, and treating potential viral diseases in black-necked cranes.
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Affiliation(s)
- Qifan Zhao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Ran Zhao
- Department of Prevention and Control, Xiamen Animal Disease Prevention and Control Center, Xiamen 361009, China;
| | - Yijie Sun
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Li Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Yuan Xi
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Yan Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Zhenqiang You
- School of Public Health, Hangzhou Medical College, Hangzhou 310013, China;
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
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22
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Li Y, Tang C, Zhang Y, Li Z, Wang G, Peng R, Huang Y, Hu X, Xin H, Feng B, Cao X, He Y, Guo T, He Y, Su H, Cui X, Niu L, Wu Z, Yang J, Yang F, Lu G, Gao L, Jin Q, Xiao M, Yin F, Du J. Diversity and independent evolutionary profiling of rodent-borne viruses in Hainan, a tropical island of China. Virol Sin 2023; 38:651-662. [PMID: 37572844 PMCID: PMC10590688 DOI: 10.1016/j.virs.2023.08.003] [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: 03/21/2023] [Accepted: 08/08/2023] [Indexed: 08/14/2023] Open
Abstract
The risk of emerging infectious diseases (EID) is increasing globally. More than 60% of EIDs worldwide are caused by animal-borne pathogens. This study aimed to characterize the virome, analyze the phylogenetic evolution, and determine the diversity of rodent-borne viruses in Hainan Province, China. We collected 682 anal and throat samples from rodents, combined them into 28 pools according to their species and location, and processed them for next-generation sequencing and bioinformatics analysis. The diverse viral contigs closely related to mammals were assigned to 22 viral families. Molecular clues of the important rodent-borne viruses were further identified by polymerase chain reaction for phylogenetic analysis and annotation of genetic characteristics such as arenavirus, coronavirus, astrovirus, pestivirus, parvovirus, and papillomavirus. We identified pestivirus and bocavirus in Leopoldoms edwardsi from Huangjinjiaoling, and bocavirus in Rattus andamanensis from the national nature reserves of Bangxi with low amino acid identity to known pathogens are proposed as the novel species, and their rodent hosts have not been previously reported to carry these viruses. These results expand our knowledge of viral classification and host range and suggest that there are highly diverse, undiscovered viruses that have evolved independently in their unique wildlife hosts in inaccessible areas.
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Affiliation(s)
- Youyou Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Chuanning Tang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Yun Zhang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Zihan Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Gaoyu Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Ruoyan Peng
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Yi Huang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Xiaoyuan Hu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Henan Xin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Boxuan Feng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xuefang Cao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yongpeng He
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Tonglei Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Yijun He
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Haoxiang Su
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xiuji Cui
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Lina Niu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Zhiqiang Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Gang Lu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China
| | - Lei Gao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Meifang Xiao
- Department of Clinical Laboratory, Center for Laboratory Medicine, Hainan Women and Children's Medical Center, Haikou, 571199, China.
| | - Feifei Yin
- Department of Clinical Laboratory, Center for Laboratory Medicine, Hainan Women and Children's Medical Center, Haikou, 571199, China; Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China; Department of Pathogen Biology, Hainan Medical University, Haikou, 571199, China.
| | - Jiang Du
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China; Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, 571199, China.
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23
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Früh SP, Adu OF, López-Astacio RA, Weichert WS, Wasik BR, Parrish CR. Isolation, cloning and analysis of parvovirus-specific canine antibodies from peripheral blood B cells. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104894. [PMID: 37467826 PMCID: PMC10542859 DOI: 10.1016/j.dci.2023.104894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/05/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
B-cell cloning methods enable the analysis of antibody responses against target antigens and can be used to reveal the host antibody repertoire, antigenic sites (epitopes), and details of protective immunity against pathogens. Here, we describe improved methods for isolation of canine peripheral blood B cells producing antibodies against canine parvovirus (CPV) capsids by fluorescence-activated cell sorting, followed by cell cloning. We cultured sorted B cells from an immunized dog in vitro and screened for CPV-specific antibody production. Updated canine-specific primer sets were used to amplify and clone the heavy and light chain immunoglobulin sequences directly from the B cells by reverse transcription and PCR. Monoclonal canine IgGs were produced by cloning heavy and light chain sequences into antibody expression vectors, which were screened for CPV binding. Three different canine monoclonal antibodies were analyzed, including two that shared the same heavy chain, and one that had distinct heavy and light chains. The antibodies showed broad binding to CPV variants, and epitopes were mapped to antigenic sites on the capsid. The methods described here are applicable for the isolation of canine B cells and monoclonal antibodies against many antigens.
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Affiliation(s)
- Simon P Früh
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA; Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Oluwafemi F Adu
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Robert A López-Astacio
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Wendy S Weichert
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Brian R Wasik
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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24
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Du C, Cleary SP, Kostelic MM, Jones BJ, Kafader JO, Wysocki VH. Combining Surface-Induced Dissociation and Charge Detection Mass Spectrometry to Reveal the Native Topology of Heterogeneous Protein Complexes. Anal Chem 2023; 95:13889-13896. [PMID: 37672632 PMCID: PMC10874503 DOI: 10.1021/acs.analchem.3c02185] [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] [Indexed: 09/08/2023]
Abstract
Charge detection mass spectrometry (CDMS) enables the direct mass measurement of heterogeneous samples on the megadalton scale, as the charge state for a single ion is determined simultaneously with the mass-to-charge ratio (m/z). Surface-induced dissociation (SID) is an effective activation method to dissociate non-intertwined, non-covalent protein complexes without extensive gas-phase restructuring, producing various subcomplexes reflective of the native protein topology. Here, we demonstrate that using CDMS after SID on an Orbitrap platform offers subunit connectivity, topology, proteoform information, and relative interfacial strengths of the intact macromolecular assemblies. SID dissects the capsids (∼3.7 MDa) of adeno-associated viruses (AAVs) into trimer-containing fragments (3mer, 6mer, 9mer, 15mer, etc.) that can be detected by the individual ion mass spectrometry (I2MS) approach on Orbitrap instruments. SID coupled to CDMS provides unique structural insights into heterogeneous assemblies that are not readily obtained by traditional MS measurements.
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Affiliation(s)
- Chen Du
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sean P Cleary
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Marius M Kostelic
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Benjamin J Jones
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jared O Kafader
- Departments of Chemistry, Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
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25
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Velez M, Mietzsch M, Hsi J, Bell L, Chipman P, Fu X, McKenna R. Structural Characterization of Canine Minute Virus, Rat and Porcine Bocavirus. Viruses 2023; 15:1799. [PMID: 37766206 PMCID: PMC10534443 DOI: 10.3390/v15091799] [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: 08/04/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
Bocaparvovirus is an expansive genus of the Parvovirinae, with a wide range of vertebrate hosts. This study investigates Canine minute virus (CnMV), Rat bocavirus (RBoV), and Porcine bocavirus 1 (PBoV1). Both CnMV and PBoV1 have been found in gastrointestinal infections in their respective hosts, with CnMV responsible for spontaneous abortions in dogs, while PBoV has been associated with encephalomyelitis in piglets. The pathogenicity of the recently identified RBoV is currently unknown. To initiate the characterization of these viruses, their capsids structures were determined by cryo-electron microscopy at resolutions ranging from 2.3 to 2.7 Å. Compared to other parvoviruses, the CnMV, PBoV1, and RBoV capsids showed conserved features, such as the channel at the fivefold symmetry axis. However, major differences were observed at the two- and threefold axes. While CnMV displays prominent threefold protrusions, the same region is more recessed in PBoV1 and RBoV. Furthermore, the typical twofold axis depression of parvoviral capsids is absent in CnMV or very small in PBoV and RBoV. These capsid structures extend the structural portfolio for the Bocaparvovirus genus and will allow future characterization of these pathogens on a molecular level. This is important, as no antivirals or vaccines exist for these viruses.
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Affiliation(s)
- Michael Velez
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Mario Mietzsch
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Jane Hsi
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Logan Bell
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Paul Chipman
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Xiaofeng Fu
- Biological Science Imaging Resource, Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Robert McKenna
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32610, USA
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26
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Casy W, Garza IT, Chen X, Dong T, Hu Y, Kanchwala M, Trygg CB, Shyng C, Xing C, Bunnell BA, Braun SE, Gray SJ. SMRT Sequencing Enables High-Throughput Identification of Novel AAVs from Capsid Shuffling and Directed Evolution. Genes (Basel) 2023; 14:1660. [PMID: 37628711 PMCID: PMC10454592 DOI: 10.3390/genes14081660] [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: 07/21/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
The use of AAV capsid libraries coupled with various selection strategies has proven to be a remarkable approach for generating novel AAVs with enhanced and desired features. The inability to reliably sequence the complete capsid gene in a high-throughput manner has been the bottleneck of capsid engineering. As a result, many library strategies are confined to localized and modest alterations in the capsid, such as peptide insertions or single variable region (VR) alterations. The caveat of short reads by means of next-generation sequencing (NGS) hinders the diversity of capsid library construction, shifting the field away from whole-capsid modifications. We generated AAV capsid shuffled libraries of naturally occurring AAVs and applied directed evolution in both mice and non-human primates (NHPs), with the goal of yielding AAVs that are compatible across both species for translational applications. We recovered DNA from the tissues of injected animal and used single molecule real-time (SMRT) sequencing to identify variants enriched in the central nervous system (CNS). We provide insights and considerations for variant identification by comparing bulk tissue sequencing to that of isolated nuclei. Our work highlights the potential advantages of whole-capsid engineering, as well as indispensable methodological improvements for the analysis of recovered capsids, including the nuclei-enrichment step and SMRT sequencing.
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Affiliation(s)
- Widler Casy
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA (I.T.G.); (X.C.); (Y.H.)
| | - Irvin T. Garza
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA (I.T.G.); (X.C.); (Y.H.)
- Graduate School of Basic Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xin Chen
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA (I.T.G.); (X.C.); (Y.H.)
| | - Thomas Dong
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA (I.T.G.); (X.C.); (Y.H.)
| | - Yuhui Hu
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA (I.T.G.); (X.C.); (Y.H.)
| | - Mohammed Kanchwala
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (M.K.)
| | - Cynthia B. Trygg
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433, USA (B.A.B.); (S.E.B.)
| | - Charles Shyng
- Gene Therapy Center, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; (M.K.)
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bruce A. Bunnell
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433, USA (B.A.B.); (S.E.B.)
| | - Stephen E. Braun
- Tulane National Primate Research Center, Tulane University School of Medicine, Covington, LA 70433, USA (B.A.B.); (S.E.B.)
| | - Steven J. Gray
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA (I.T.G.); (X.C.); (Y.H.)
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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López-Astacio RA, Adu OF, Lee H, Hafenstein SL, Parrish CR. The Structures and Functions of Parvovirus Capsids and Missing Pieces: the Viral DNA and Its Packaging, Asymmetrical Features, Nonprotein Components, and Receptor or Antibody Binding and Interactions. J Virol 2023; 97:e0016123. [PMID: 37367301 PMCID: PMC10373561 DOI: 10.1128/jvi.00161-23] [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] [Indexed: 06/28/2023] Open
Abstract
Parvoviruses are among the smallest and superficially simplest animal viruses, infecting a broad range of hosts, including humans, and causing some deadly infections. In 1990, the first atomic structure of the canine parvovirus (CPV) capsid revealed a 26-nm-diameter T=1 particle made up of two or three versions of a single protein, and packaging about 5,100 nucleotides of single-stranded DNA. Our structural and functional understanding of parvovirus capsids and their ligands has increased as imaging and molecular techniques have advanced, and capsid structures for most groups within the Parvoviridae family have now been determined. Despite those advances, significant questions remain unanswered about the functioning of those viral capsids and their roles in release, transmission, or cellular infection. In addition, the interactions of capsids with host receptors, antibodies, or other biological components are also still incompletely understood. The parvovirus capsid's apparent simplicity likely conceals important functions carried out by small, transient, or asymmetric structures. Here, we highlight some remaining open questions that may need to be answered to provide a more thorough understanding of how these viruses carry out their various functions. The many different members of the family Parvoviridae share a capsid architecture, and while many functions are likely similar, others may differ in detail. Many of those parvoviruses have not been experimentally examined in detail (or at all in some cases), so we, therefore, focus this minireview on the widely studied protoparvoviruses, as well as the most thoroughly investigated examples of adeno-associated viruses.
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Affiliation(s)
- Robert A. López-Astacio
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Oluwafemi F. Adu
- Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Hyunwook Lee
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Susan L. Hafenstein
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - 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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28
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Logan GJ, Mietzsch M, Khandekar N, D'Silva A, Anderson D, Mandwie M, Hsi J, Nelson AR, Chipman P, Jackson J, Schofield P, Christ D, Goodnow CC, Reed JH, Farrar MA, McKenna R, Alexander IE. Structural and functional characterization of capsid binding by anti-AAV9 monoclonal antibodies from infants after SMA gene therapy. Mol Ther 2023; 31:1979-1993. [PMID: 37012705 PMCID: PMC10362397 DOI: 10.1016/j.ymthe.2023.03.032] [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: 01/20/2023] [Revised: 03/02/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Success in the treatment of infants with spinal muscular atrophy (SMA) underscores the potential of vectors based on adeno-associated virus (AAV). However, a major obstacle to the full realization of this potential is pre-existing natural and therapy-induced anti-capsid humoral immunity. Structure-guided capsid engineering is one possible approach to surmounting this challenge but necessitates an understanding of capsid-antibody interactions at high molecular resolution. Currently, only mouse-derived monoclonal antibodies (mAbs) are available to structurally map these interactions, which presupposes that mouse and human-derived antibodies are functionally equivalent. In this study, we have characterized the polyclonal antibody responses of infants following AAV9-mediated gene therapy for SMA and recovered 35 anti-capsid mAbs from the abundance of switched-memory B (smB) cells present in these infants. For 21 of these mAbs, seven from each of three infants, we have undertaken functional and structural analysis measuring neutralization, affinities, and binding patterns by cryoelectron microscopy (cryo-EM). Four distinct patterns were observed akin to those reported for mouse-derived mAbs, but with early evidence of differing binding pattern preference and underlying molecular interactions. This is the first human and largest series of anti-capsid mAbs to have been comprehensively characterized and will prove to be powerful tools for basic discovery and applied purposes.
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Affiliation(s)
- Grant J Logan
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, Australia
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Neeta Khandekar
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, Australia
| | - Arlene D'Silva
- School of Women's and Children's Health, University of New South Wales Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Daniel Anderson
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, Australia
| | - Mawj Mandwie
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, Australia
| | - Jane Hsi
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Austin R Nelson
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Jennifer Jackson
- Garvan Institute of Medical Research, UNSW Sydney, Faculty of Medicine, Darlinghurst, NSW, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, UNSW Sydney, Faculty of Medicine, Darlinghurst, NSW, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, UNSW Sydney, Faculty of Medicine, Darlinghurst, NSW, Australia
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, UNSW Sydney, Faculty of Medicine, Darlinghurst, NSW, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst, NSW, Australia
| | - Joanne H Reed
- Westmead Institute for Medical Research, Centre for Immunology and Allergy Research, Westmead, NSW, Australia
| | - Michelle A Farrar
- School of Women's and Children's Health, University of New South Wales Medicine, UNSW Sydney, Sydney, NSW, Australia; Department of Neurology, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
| | - 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, Westmead, NSW, Australia; Discipline of Child and Adolescent Health, University of Sydney, Westmead, NSW, Australia.
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29
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He H, Li Y, Chen J, Xian J, Zheng L, Sun H, Fan S, Fu J, Li Q, Chen C, Liang M, Zhang M, Wu R, Xiao G, Chen Q. Identification and genetic characteristics of tusavirus in fecal samples of patients with chronic diseases in Guangzhou, China. Front Microbiol 2023; 14:1205134. [PMID: 37396384 PMCID: PMC10310535 DOI: 10.3389/fmicb.2023.1205134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/29/2023] [Indexed: 07/04/2023] Open
Abstract
Purpose The Tunisian stool-associated parvovirus [Tusavirus (TuV)] is a novel member of the genus Protoparvovirus, which may be linked to diarrhea. Herein, we investigated the prevalence of TuV in different populations and analyzed its genetic and bioinformatic characteristics. Methods This study was conducted in a tertiary hospital in Guangzhou (China) from February 2018 to July 2022. Demographic and clinical information and stool samples were collected from individuals who visited the hospital. ProtScale, SwissModel, Datamonkey, and other tools were used to analyze and predict the physicochemical parameters, tertiary structure, selection pressure, and B-cell epitopes of capsid viral protein 2 of TuV (VP2-TuV). Results A total of 3,837 participants were enrolled, among which two stool samples from patients with chronic illnesses were tested positive for TuV DNA. However, no positive sample was detected among patients with diarrhea. Two near-complete genome sequences were amplified. The genetic analysis revealed the presence of diversity among TuVs isolated from distinct host species. Bioinformatics analysis revealed that VP2-TuV exhibited hydrophilic properties and lacked transmembrane domains and signal peptides. The secondary structure of VP2-TuV was composed mainly of random coils and β-strands. Selective-pressure analysis of the VP2 region suggested that TuV primarily underwent negative selection during evolution. Negatively selected codon sites coincided with residues comprising of B-cell epitopes, suggesting minimal changes in the immunogenicity of TuV over time. Conclusion TuV was detected in patients with chronic diseases but not in patients with diarrhea. The putative roles of TuV in the pathogenicity of human diseases and zoonotic viruses must be determined by additional studies.
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Affiliation(s)
- Huan He
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yongzhi Li
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jiaqi Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Juxian Xian
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Liting Zheng
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Hengbiao Sun
- Clinical Laboratory, Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Shunchang Fan
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jiaqi Fu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Qiushuang Li
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Caiyun Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Minyi Liang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Minyi Zhang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Ruojun Wu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Gang Xiao
- Clinical Laboratory, Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Qing Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
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30
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Pénzes JJ, Pham HT, Chipman P, Smith EW, McKenna R, Tijssen P. Bipartite genome and structural organization of the parvovirus Acheta domesticus segmented densovirus. Nat Commun 2023; 14:3515. [PMID: 37316488 DOI: 10.1038/s41467-023-38875-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/17/2023] [Indexed: 06/16/2023] Open
Abstract
Parvoviruses (family Parvoviridae) are currently defined by a linear monopartite ssDNA genome, T = 1 icosahedral capsids, and distinct structural (VP) and non-structural (NS) protein expression cassettes within their genome. We report the discovery of a parvovirus with a bipartite genome, Acheta domesticus segmented densovirus (AdSDV), isolated from house crickets (Acheta domesticus), in which it is pathogenic. We found that the AdSDV harbors its NS and VP cassettes on two separate genome segments. Its vp segment acquired a phospholipase A2-encoding gene, vpORF3, via inter-subfamily recombination, coding for a non-structural protein. We showed that the AdSDV evolved a highly complex transcription profile in response to its multipartite replication strategy compared to its monopartite ancestors. Our structural and molecular examinations revealed that the AdSDV packages one genome segment per particle. The cryo-EM structures of two empty- and one full-capsid population (3.3, 3.1 and 2.3 Å resolution) reveal a genome packaging mechanism, which involves an elongated C-terminal tail of the VP, "pinning" the ssDNA genome to the capsid interior at the twofold symmetry axis. This mechanism fundamentally differs from the capsid-DNA interactions previously seen in parvoviruses. This study provides new insights on the mechanism behind ssDNA genome segmentation and on the plasticity of parvovirus biology.
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Affiliation(s)
- Judit J Pénzes
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, H7V 1B7, Canada.
- The McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
- Institute for Quantitative Biomedicine, Rutgers, the Sate University of New Jersey, Piscataway, NJ, 08854, USA.
| | - Hanh T Pham
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, H7V 1B7, Canada
- HTG Molecular Diagnostics, 3430 E Global Loop, Tucson, AZ, 85706, USA
| | - Paul Chipman
- The McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Emmanuel W Smith
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306, USA
- JEOL USA Inc., Peabody, MA, 01960, USA
| | - Robert McKenna
- The McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
| | - Peter Tijssen
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, H7V 1B7, Canada.
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31
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Mietzsch M, Liu W, Ma K, Bennett A, Nelson AR, Gliwa K, Chipman P, Fu X, Bechler S, McKenna R, Viner R. Production and characterization of an AAV1-VP3-only capsid: An analytical benchmark standard. Mol Ther Methods Clin Dev 2023; 29:460-472. [PMID: 37273903 PMCID: PMC10238842 DOI: 10.1016/j.omtm.2023.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/04/2023] [Indexed: 06/06/2023]
Abstract
Adeno-associated viruses (AAVs) are non-enveloped ssDNA icosahedral T = 1 viruses used as vectors for clinical gene delivery. Currently, there are over 200 AAV-related clinical trials and six approved biologics on the market. As such new analytical methods are continually being developed to characterize and monitor the quality and purity of manufactured AAV vectors, these include ion-exchange chromatography and Direct Mass Technology. However, these methods require homogeneous analytical standards with a high molecular weight standard comparable to the mass of an AAV capsid. Described here is the design, production, purification, characterization, and the cryo-electron microscopy structure of an AAV1-VP3-only capsid that fulfills this need as a calibrant to determine capsid mass, charge, homogeneity, and transgene packaging characteristics.
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Affiliation(s)
- Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Weijing Liu
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, CA 95134, USA
| | - Ke Ma
- Thermo Fisher Scientific, 490 Lakeside Dr., Sunnyvale, CA 94085, USA
| | - Antonette Bennett
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Austin R. Nelson
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Keely Gliwa
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Xiaofeng Fu
- Biological Science Imaging Resource, Department of Biological Sciences, Florida State University, Tallahassee, FL, USA
| | - Shane Bechler
- Thermo Fisher Scientific, 490 Lakeside Dr., Sunnyvale, CA 94085, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Rosa Viner
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, CA 95134, USA
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32
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Golm SK, Hübner W, Müller KM. Fluorescence Microscopy in Adeno-Associated Virus Research. Viruses 2023; 15:v15051174. [PMID: 37243260 DOI: 10.3390/v15051174] [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: 03/14/2023] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Research on adeno-associated virus (AAV) and its recombinant vectors as well as on fluorescence microscopy imaging is rapidly progressing driven by clinical applications and new technologies, respectively. The topics converge, since high and super-resolution microscopes facilitate the study of spatial and temporal aspects of cellular virus biology. Labeling methods also evolve and diversify. We review these interdisciplinary developments and provide information on the technologies used and the biological knowledge gained. The emphasis lies on the visualization of AAV proteins by chemical fluorophores, protein fusions and antibodies as well as on methods for the detection of adeno-associated viral DNA. We add a short overview of fluorescent microscope techniques and their advantages and challenges in detecting AAV.
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Affiliation(s)
- Susanne K Golm
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
| | - Wolfgang Hübner
- Biomolecular Photonics, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
| | - Kristian M Müller
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany
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33
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Fuertes MA, López Mateos D, Valiente L, Rodríguez Huete A, Valbuena A, Mateu MG. Electrostatic Screening, Acidic pH and Macromolecular Crowding Increase the Self-Assembly Efficiency of the Minute Virus of Mice Capsid In Vitro. Viruses 2023; 15:v15051054. [PMID: 37243141 DOI: 10.3390/v15051054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/14/2023] [Accepted: 04/22/2023] [Indexed: 05/28/2023] Open
Abstract
The hollow protein capsids from a number of different viruses are being considered for multiple biomedical or nanotechnological applications. In order to improve the applied potential of a given viral capsid as a nanocarrier or nanocontainer, specific conditions must be found for achieving its faithful and efficient assembly in vitro. The small size, adequate physical properties and specialized biological functions of the capsids of parvoviruses such as the minute virus of mice (MVM) make them excellent choices as nanocarriers and nanocontainers. In this study we analyzed the effects of protein concentration, macromolecular crowding, temperature, pH, ionic strength, or a combination of some of those variables on the fidelity and efficiency of self-assembly of the MVM capsid in vitro. The results revealed that the in vitro reassembly of the MVM capsid is an efficient and faithful process. Under some conditions, up to ~40% of the starting virus capsids were reassembled in vitro as free, non aggregated, correctly assembled particles. These results open up the possibility of encapsidating different compounds in VP2-only capsids of MVM during its reassembly in vitro, and encourage the use of virus-like particles of MVM as nanocontainers.
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Affiliation(s)
- Miguel Angel Fuertes
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Diego López Mateos
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Luis Valiente
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Alicia Rodríguez Huete
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Xie Q, Wang J, Gu C, Wu J, Liu W. Structure and function of the parvoviral NS1 protein: a review. Virus Genes 2023; 59:195-203. [PMID: 36253516 DOI: 10.1007/s11262-022-01944-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/07/2022] [Indexed: 10/24/2022]
Abstract
Parvoviruses possess a single-stranded DNA genome of about 5 kb, which contains two open reading frames (ORFs), one encoding nonstructural (NS) proteins, the other capsid proteins. The NS1 protein contains an N-terminal origin-binding domain, a helicase domain, and a C-terminal transactive domain, and is essential for effective viral replication and production of infectious virus. We first summarize the developments in the structure of NS1 protein, including the original binding domain and the helicase domain. We discuss the role of different DNA substrates in the oligomerization of these two domains of NS1. During the parvovirus life cycle, the NS1 protein is closely related to the viral gene expression, viral replication, and infection. We provide the current understanding of the impact of parvovirus NS1 protein mutations on its biological properties. Overall, in this review, we focus on the structure and function of the parvoviral NS1 protein.
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Affiliation(s)
- Qianqian Xie
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jigui Wang
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Chenchen Gu
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jing Wu
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Weiquan Liu
- State Key Laboratory of Agrobiotechnology, Department of Biochemistry and Molecular Biology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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35
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Zin EA, Ozturk BE, Dalkara D, Byrne LC. Developing New Vectors for Retinal Gene Therapy. Cold Spring Harb Perspect Med 2023; 13:a041291. [PMID: 36987583 PMCID: PMC10691475 DOI: 10.1101/cshperspect.a041291] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Since their discovery over 55 years ago, adeno-associated virus (AAV) vectors have become powerful tools for experimental and therapeutic in vivo gene delivery, particularly in the retina. Increasing knowledge of AAV structure and biology has propelled forward the development of engineered AAV vectors with improved abilities for gene delivery. However, major obstacles to safe and efficient therapeutic gene delivery remain, including tropism, inefficient and untargeted gene delivery, and limited carrying capacity. Additional improvements to AAV vectors will be required to achieve therapeutic benefit while avoiding safety issues. In this review, we provide an overview of recent methods for engineering-enhanced AAV capsids, as well as remaining challenges that must be overcome to achieve optimized therapeutic gene delivery in the eye.
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Affiliation(s)
- Emilia A Zin
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France
| | - Bilge E Ozturk
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Deniz Dalkara
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France
| | - Leah C Byrne
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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36
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Novel Chaphamaparvovirus in Insectivorous Molossus molossus Bats, from the Brazilian Amazon Region. Viruses 2023; 15:v15030606. [PMID: 36992315 PMCID: PMC10054343 DOI: 10.3390/v15030606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/17/2023] [Accepted: 02/18/2023] [Indexed: 02/25/2023] Open
Abstract
Chaphamaparvovirus (CHPV) is a recently characterized genus of the Parvoviridae family whose members can infect different hosts, including bats, which constitute the second most diverse order of mammals and are described worldwide as important transmitters of zoonotic diseases. In this study, we identified a new CHPV in bat samples from the municipality of Santarém (Pará state, North Brazil). A total of 18 Molossus molossus bats were analyzed using viral metagenomics. In five animals, we identified CHPVs. These CHPV sequences presented the genome with a size ranging from 3797 to 4284 bp. Phylogenetic analysis-based nucleotide and amino acid sequences of the VP1 and NS1 regions showed that all CHPV sequences are monophyletic. They are also closely related to CHPV sequences previously identified in bats in southern and southeast Brazil. According to the International Committee on Taxonomy of Viruses (ICTV) classification criteria for this species (the CHPV NS1 gene region must have 85% identity to be classified in the same species), our sequences are likely a new specie within the genus Chaphamaparvovirus, since they have less than 80% identity with other CHPV described earlier in bats. We also make some phylogenetic considerations about the interaction between CHPV and their host. We suggest a high level of specificity of CPHV and its hosts. Thus, the findings contribute to improving information about the viral diversity of parvoviruses and show the importance of better investigating bats, considering that they harbor a variety of viruses that may favor zoonotic events.
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37
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Hoad M, Cross EM, Donnelly CM, Sarker S, Roby JA, Forwood JK. Structural Characterization of Porcine Adeno-Associated Virus Capsid Protein with Nuclear Trafficking Protein Importin Alpha Reveals a Bipartite Nuclear Localization Signal. Viruses 2023; 15:v15020315. [PMID: 36851528 PMCID: PMC9964314 DOI: 10.3390/v15020315] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Adeno-associated viruses (AAV) are important vectors for gene therapy, and accordingly, many aspects of their cell transduction pathway have been well characterized. However, the specific mechanisms that AAV virions use to enter the host nucleus remain largely unresolved. We therefore aimed to reveal the interactions between the AAV Cap protein and the nuclear transport protein importin alpha (IMPα) at an atomic resolution. Herein we expanded upon our earlier research into the Cap nuclear localization signal (NLS) of a porcine AAV isolate, by examining the influence of upstream basic regions (BRs) towards IMPα binding. Using a high-resolution crystal structure, we identified that the IMPα binding determinants of the porcine AAV Cap comprise a bipartite NLS with an N-terminal BR binding at the minor site of IMPα, and the previously identified NLS motif binding at the major site. Quantitative assays showed a vast difference in binding affinity between the previously determined monopartite NLS, and bipartite NLS described in this study. Our results provide a detailed molecular view of the interaction between AAV capsids and the nuclear import receptor, and support the findings that AAV capsids enter the nucleus by binding the nuclear import adapter IMPα using the classical nuclear localization pathway.
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Affiliation(s)
- Mikayla Hoad
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Emily M. Cross
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Camilla M. Donnelly
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Subir Sarker
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, VIC 3086, Australia
| | - Justin A. Roby
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Jade K. Forwood
- School of Dentistry and Medical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Correspondence:
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38
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Dai Z, Wang H, Wu H, Zhang Q, Ji L, Wang X, Shen Q, Yang S, Ma X, Shan T, Zhang W. Parvovirus dark matter in the cloaca of wild birds. Gigascience 2022; 12:giad001. [PMID: 36734170 PMCID: PMC9896142 DOI: 10.1093/gigascience/giad001] [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: 09/28/2022] [Revised: 11/28/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
With the development of viral metagenomics and next-generation sequencing technology, more and more novel parvoviruses have been identified in recent years, including even entirely new lineages. The Parvoviridae family includes a different group of viruses that can infect a wide variety of animals. In this study, systematic analysis was performed to identify the "dark matter" (datasets that cannot be easily attributed to known viruses) of parvoviruses and to explore their genetic diversity from wild birds' cloacal swab samples. We have tentatively defined this parvovirus "dark matter" as a highly divergent lineage in the Parvoviridae family. All parvoviruses showed several characteristics, including 2 major protein-coding genes and similar genome lengths. Moreover, we observed that the novel parvo-like viruses share similar genome organizations to most viruses in Parvoviridae but could not clustered with the established subfamilies in phylogenetic analysis. We also found some new members associated with the Bidnaviridae family, which may be derived from parvovirus. This suggests that systematic analysis of domestic and wild animal samples is necessary to explore the genetic diversity of parvoviruses and to mine for more of this potential dark matter.
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Affiliation(s)
- Ziyuan Dai
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Nantong University, Yancheng Third People's Hospital, Yancheng, Jiangsu 224001, China
| | - Haoning Wang
- School of Geography and Tourism, Harbin University, Harbin, Heilongjiang 150076, China
| | - Haisheng Wu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai 810099, China
| | - Qing Zhang
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai 810099, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiao Ma
- Qinghai Institute of Endemic Disease Prevention and Control, Xining, Qinghai 810099, China
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 810099, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
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39
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A link between severe hepatitis in children and adenovirus 41 and adeno-associated virus 2 infections. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Over the past few months there have been reports of severe acute hepatitis in several hundred, otherwise healthy, immunocompetent young children. Several deaths have been recorded and a relatively large proportion of the patients have needed liver transplants. Most of the cases, so far, have been seen in the UK and in North America, but it has also been reported in many other European countries, the Middle East and Asia. Most common viruses have been ruled out as a causative agent; hepatitis A virus (HAV), hepatitis B virus (HBV) and hepatitis C virus (HCV) were not detected, nor were Epstein–Barr virus (EBV), cytomegalovirus (CMV) and human immunodeficiency virus (HIV) in many cases. A small proportion of the children had been infected with SARS-CoV-2 but these seem to be in a minority; similarly, almost none of the children had been vaccinated against COVID-19. Significantly, many of the patients were infected with adenovirus 41 (HAdV-F41). Previously, HAdV-41 had not been linked to hepatitis and is usually considered to cause gastroenteritis in both immunocompetent and immunocompromised patients. In two most recent studies, adeno-associated virus 2 (AAV2) was detected in almost all patients, together with species C and F HAdVs and human herpesvirus 6B (HHV6B). Here, I discuss the possibility that a change in tropism of HAdV-41 and changes in AAV2 may be responsible for their links to acute hepatitis.
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40
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Lakshmanan R, Mietzsch M, Jimenez Ybargollin A, Chipman P, Fu X, Qiu J, Söderlund-Venermo M, McKenna R. Capsid Structure of Aleutian Mink Disease Virus and Human Parvovirus 4: New Faces in the Parvovirus Family Portrait. Viruses 2022; 14:2219. [PMID: 36298773 PMCID: PMC9612331 DOI: 10.3390/v14102219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/07/2022] Open
Abstract
Parvoviruses are small, single-stranded DNA viruses with non-enveloped capsids. Determining the capsid structures provides a framework for annotating regions important to the viral life cycle. Aleutian mink disease virus (AMDV), a pathogen in minks, and human parvovirus 4 (PARV4), infecting humans, are parvoviruses belonging to the genera Amdoparvovirus and Tetraparvovirus, respectively. While Aleutian mink disease caused by AMDV is a major threat to mink farming, no clear clinical manifestations have been established following infection with PARV4 in humans. Here, the capsid structures of AMDV and PARV4 were determined via cryo-electron microscopy at 2.37 and 3.12 Å resolutions, respectively. Despite low amino acid sequence identities (10-30%) both viruses share the icosahedral nature of parvovirus capsids, with 60 viral proteins (VPs) assembling the capsid via two-, three-, and five-fold symmetry VP-related interactions, but display major structural variabilities in the surface loops when the capsid structures are superposed onto other parvoviruses. The capsid structures of AMDV and PARV4 will add to current knowledge of the structural platform for parvoviruses and permit future functional annotation of these viruses, which will help in understanding their infection mechanisms at a molecular level for the development of diagnostics and therapeutics.
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Affiliation(s)
- Renuk Lakshmanan
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Alberto Jimenez Ybargollin
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Paul Chipman
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - Xiaofeng Fu
- Biological Science Imaging Resource, Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Jianming Qiu
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | | | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32603, USA
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41
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Mattola S, Aho V, Bustamante‐Jaramillo LF, Pizzioli E, Kann M, Vihinen‐Ranta M. Nuclear entry and egress of parvoviruses. Mol Microbiol 2022; 118:295-308. [PMID: 35974704 PMCID: PMC9805091 DOI: 10.1111/mmi.14974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/10/2022] [Accepted: 08/13/2022] [Indexed: 01/09/2023]
Abstract
Parvoviruses are small non-enveloped single-stranded DNA viruses, which depend on host cell nuclear transcriptional and replication machinery. After endosomal exposure of nuclear localization sequence and a phospholipase A2 domain on the capsid surface, and escape into the cytosol, parvovirus capsids enter the nucleus. Due to the small capsid diameter of 18-26 nm, intact capsids can potentially pass into the nucleus through nuclear pore complexes (NPCs). This might be facilitated by active nuclear import, but capsids may also follow an alternative entry pathway that includes activation of mitotic factors and local transient disruption of the nuclear envelope. The nuclear entry is followed by currently undefined events of viral genome uncoating. After genome release, viral replication compartments are initiated and infection proceeds. Parvoviral genomes replicate during cellular S phase followed by nuclear capsid assembly during virus-induced S/G2 cell cycle arrest. Nuclear egress of capsids occurs upon nuclear envelope degradation during apoptosis and cell lysis. An alternative pathway for nuclear export has been described using active transport through the NPC mediated by the chromosome region maintenance 1 protein, CRM1, which is enhanced by phosphorylation of the N-terminal domain of VP2. However, other alternative but not yet uncharacterized nuclear export pathways cannot be excluded.
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Affiliation(s)
- Salla Mattola
- Department of Biological and Environmental ScienceUniversity of JyvaskylaJyvaskylaFinland
| | - Vesa Aho
- Department of Biological and Environmental ScienceUniversity of JyvaskylaJyvaskylaFinland
| | | | - Edoardo Pizzioli
- Department of Infectious Diseases, Institute of BiomedicineUniversity of GothenburgGothenburgSweden
| | - Michael Kann
- Department of Infectious Diseases, Institute of BiomedicineUniversity of GothenburgGothenburgSweden,Sahlgrenska AcademyGothenburgSweden,Department of Clinical MicrobiologyRegion Västra Götaland, Sahlgrenska University HospitalGothenburgSweden
| | - Maija Vihinen‐Ranta
- Department of Biological and Environmental ScienceUniversity of JyvaskylaJyvaskylaFinland
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42
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El Andari J, Renaud-Gabardos E, Tulalamba W, Weinmann J, Mangin L, Pham QH, Hille S, Bennett A, Attebi E, Bourges E, Leborgne C, Guerchet N, Fakhiri J, Krämer C, Wiedtke E, McKenna R, Guianvarc’h L, Toueille M, Ronzitti G, Hebben M, Mingozzi F, VandenDriessche T, Agbandje-McKenna M, Müller OJ, Chuah MK, Buj-Bello A, Grimm D. Semirational bioengineering of AAV vectors with increased potency and specificity for systemic gene therapy of muscle disorders. SCIENCE ADVANCES 2022; 8:eabn4704. [PMID: 36129972 PMCID: PMC9491714 DOI: 10.1126/sciadv.abn4704] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 08/03/2022] [Indexed: 05/31/2023]
Abstract
Bioengineering of viral vectors for therapeutic gene delivery is a pivotal strategy to reduce doses, facilitate manufacturing, and improve efficacy and patient safety. Here, we engineered myotropic adeno-associated viral (AAV) vectors via a semirational, combinatorial approach that merges AAV capsid and peptide library screens. We first identified shuffled AAVs with increased specificity in the murine skeletal muscle, diaphragm, and heart, concurrent with liver detargeting. Next, we boosted muscle specificity by displaying a myotropic peptide on the capsid surface. In a mouse model of X-linked myotubular myopathy, the best vectors-AAVMYO2 and AAVMYO3-prolonged survival, corrected growth, restored strength, and ameliorated muscle fiber size and centronucleation. In a mouse model of Duchenne muscular dystrophy, our lead capsid induced robust microdystrophin expression and improved muscle function. Our pipeline is compatible with complementary AAV genome bioengineering strategies, as demonstrated here with two promoters, and could benefit many clinical applications beyond muscle gene therapy.
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Affiliation(s)
- Jihad El Andari
- Medical Faculty, Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Edith Renaud-Gabardos
- Genethon, 91000 Evry, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Warut Tulalamba
- Department of Gene Therapy and Regenerative Medicine, Vrije Universiteit Brussel (VUB), Brussels 1090, Belgium
| | - Jonas Weinmann
- Medical Faculty, Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Louise Mangin
- Genethon, 91000 Evry, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Quang Hong Pham
- Department of Gene Therapy and Regenerative Medicine, Vrije Universiteit Brussel (VUB), Brussels 1090, Belgium
| | - Susanne Hille
- University Hospital Schleswig-Holstein, Campus Kiel, Innere Medizin III, 24105 Kiel, Germany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Antonette Bennett
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | | | | | - Christian Leborgne
- Genethon, 91000 Evry, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | | | - Julia Fakhiri
- Medical Faculty, Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Chiara Krämer
- Medical Faculty, Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ellen Wiedtke
- Medical Faculty, Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | | | | | - Giuseppe Ronzitti
- Genethon, 91000 Evry, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | | | - Federico Mingozzi
- Genethon, 91000 Evry, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Thierry VandenDriessche
- Department of Gene Therapy and Regenerative Medicine, Vrije Universiteit Brussel (VUB), Brussels 1090, Belgium
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | - Oliver J. Müller
- University Hospital Schleswig-Holstein, Campus Kiel, Innere Medizin III, 24105 Kiel, Germany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Marinee K. Chuah
- Department of Gene Therapy and Regenerative Medicine, Vrije Universiteit Brussel (VUB), Brussels 1090, Belgium
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Leuven 3000, Belgium
| | - Ana Buj-Bello
- Genethon, 91000 Evry, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000 Evry, France
| | - Dirk Grimm
- Medical Faculty, Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Cluster of Excellence CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
- German Center for Infection Research (DZIF) and German Center for Cardiovascular Research (DZHK), partner site Heidelberg, Heidelberg, Germany
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43
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Abstract
Adeno-associated virus (AAV) has a single-stranded DNA genome encapsidated in a small icosahedrally symmetric protein shell with 60 subunits. AAV is the leading delivery vector in emerging gene therapy treatments for inherited disorders, so its structure and molecular interactions with human hosts are of intense interest. A wide array of electron microscopic approaches have been used to visualize the virus and its complexes, depending on the scientific question, technology available, and amenability of the sample. Approaches range from subvolume tomographic analyses of complexes with large and flexible host proteins to detailed analysis of atomic interactions within the virus and with small ligands at resolutions as high as 1.6 Å. Analyses have led to the reclassification of glycan receptors as attachment factors, to structures with a new-found receptor protein, to identification of the epitopes of antibodies, and a new understanding of possible neutralization mechanisms. AAV is now well-enough characterized that it has also become a model system for EM methods development. Heralding a new era, cryo-EM is now also being deployed as an analytic tool in the process development and production quality control of high value pharmaceutical biologics, namely AAV vectors.
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Affiliation(s)
- Scott
M. Stagg
- Department
of Biological Sciences, Florida State University, Tallahassee, Florida 32306, United States
- Institute
of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States
| | - Craig Yoshioka
- Department
of Biomedical Engineering, Oregon Health
& Science University, Portland Oregon 97239, United States
| | - Omar Davulcu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Michael S. Chapman
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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44
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Jang S, Shen HK, Ding X, Miles TF, Gradinaru V. Structural basis of receptor usage by the engineered capsid AAV-PHP.eB. Mol Ther Methods Clin Dev 2022; 26:343-354. [PMID: 36034770 PMCID: PMC9382559 DOI: 10.1016/j.omtm.2022.07.011] [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: 04/29/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022]
Abstract
Adeno-associated virus serotype 9 (AAV9) is a promising gene therapy vector for treating neurodegenerative diseases due to its ability to penetrate the blood-brain barrier. PHP.eB was engineered from AAV9 by insertion of a 7-amino acid peptide and point mutation of neighboring residues, thereby enhancing potency in the central nervous system. Here, we report a 2.24-Å resolution cryo-electron microscopy structure of PHP.eB, revealing conformational differences from other 7-mer insertion capsid variants. In PHP.eB, the 7-mer loop adopts a bent conformation, mediated by an interaction between engineered lysine and aspartate residues. Further, we identify PKD2 as the main AAV receptor (AAVR) domain recognizing both AAV9 and PHP.eB and find that the PHP.eB 7-mer partially destabilizes this interaction. Analysis of previously reported AAV structures together with our pull-down data demonstrate that the 7-mer topology determined by the lysine-aspartate interaction dictates AAVR binding strength. Our results suggest that PHP.eB's altered tropism may arise from both an additional interaction with LY6A and weakening of its AAVR interaction. Changing the insertion length, but not sequence, modifies PKD2 binding affinity, suggesting that a steric clash impedes AAVR binding. This research suggests improved library designs for future AAV selections to identify non-LY6A-dependent vectors and modulate AAVR interaction strength.
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Affiliation(s)
- Seongmin Jang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hao K Shen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xiaozhe Ding
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Timothy F Miles
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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45
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Kostelic MM, Ryan JP, Brown LS, Jackson TW, Hsieh CC, Zak CK, Sanders HM, Liu Y, Chen VS, Byrne M, Aspinwall CA, Baker ES, Marty MT. Stability and Dissociation of Adeno-Associated Viral Capsids by Variable Temperature-Charge Detection-Mass Spectrometry. Anal Chem 2022; 94:11723-11727. [PMID: 35981215 DOI: 10.1021/acs.analchem.2c02378] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Adeno-associated viral (AAV) vectors have emerged as gene therapy and vaccine delivery systems. Differential scanning fluorimetry or differential scanning calorimetry is commonly used to measure the thermal stability of AAVs, but these global methods are unable to distinguish the stabilities of different AAV subpopulations in the same sample. To address this challenge, we combined charge detection-mass spectrometry (CD-MS) with a variable temperature (VT) electrospray source that controls the temperature of the solution prior to electrospray. Using VT-CD-MS, we measured the thermal stabilities of empty and filled capsids. We found that filled AAVs ejected their cargo first and formed intermediate empty capsids before completely dissociating. Finally, we observed that pH stress caused a major decrease in thermal stability. This new approach better characterizes the thermal dissociation of AAVs, providing the simultaneous measurement of the stabilities and dissociation pathways of different subpopulations.
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Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Jack P Ryan
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Levi S Brown
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Tyler W Jackson
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Chih-Chieh Hsieh
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Ciara K Zak
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Henry M Sanders
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Yang Liu
- REGENXBIO Inc., 9804 Medical Center Dr., Rockville, Maryland 20850, United States
| | - Victor Shugui Chen
- REGENXBIO Inc., 9804 Medical Center Dr., Rockville, Maryland 20850, United States
| | - Michael Byrne
- REGENXBIO Inc., 9804 Medical Center Dr., Rockville, Maryland 20850, United States
| | - Craig A Aspinwall
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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46
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Wang J, Chen X, Zhou Y, Yue H, Zhou N, Gong H, Tang C. Prevalence and characteristics of a feline parvovirus-like virus in dogs in China. Vet Microbiol 2022; 270:109473. [DOI: 10.1016/j.vetmic.2022.109473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 12/01/2022]
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47
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Canuti M, Pénzes JJ, Lang AS. A new perspective on the evolution and diversity of the genus Amdoparvovirus (family Parvoviridae) through genetic characterization, structural homology modeling, and phylogenetics. Virus Evol 2022; 8:veac056. [PMID: 35783582 PMCID: PMC9242002 DOI: 10.1093/ve/veac056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/13/2022] [Accepted: 06/13/2022] [Indexed: 12/11/2022] Open
Abstract
Amdoparvoviruses (genus Amdoparvovirus, family Parvoviridae) are primarily viruses of carnivorans, but recent studies have indicated that their host range might also extend to rodents and chiropterans. While their classification is based on the full sequence of the major nonstructural protein (NS1), several studies investigating amdoparvoviral diversity have been focused on partial sequences, leading to difficulties in accurately determining species demarcations and leaving several viruses unclassified. In this study, while reporting the complete genomic sequence of a novel amdoparvovirus identified in an American mink (British Columbia amdoparvovirus, BCAV), we studied the phylogenetic relationships of all amdoparvovirus-related sequences and provide a comprehensive reevaluation of their diversity and evolution. After excluding recombinant sequences, phylogenetic and pairwise sequence identity analyses allowed us to define fourteen different viruses, including the five currently classified species, BCAV, and four additional viruses that fulfill the International Committee on Taxonomy of Viruses criteria to be classified as species. We show that the group of viruses historically known as Aleutian mink disease virus (species Carnivore amdoparvovirus 1) should be considered as a cluster of at least four separate viral species that have been co-circulating in mink farms, facilitating the occurrence of inter-species recombination. Genome organization, splicing donor and acceptor sites, and protein sequence motifs were surprisingly conserved within the genus. The sequence of the major capsid protein virus protein 2 (VP2) was significantly more conserved between and within species compared to NS1, a phenomenon possibly linked to antibody-dependent enhancement (ADE). Homology models suggest a remarkably high degree of conservation of the spikes located near the icosahedral threefold axis of the capsid, comprising the surface region associated with ADE. A surprisingly high number of divergent amino acid positions were found in the luminal threefold and twofold axes of the capsid, regions of hitherto unknown function. We emphasize the importance of complete genome analyses and, given the marked phylogenetic inconsistencies across the genome, advise to obtain the complete coding sequences of divergent strains. Further studies on amdoparvovirus biology and structure as well as epidemiological and virus discovery investigations are required to better characterize the ecology and evolution of this important group of viruses.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 45 Arctic Ave., St. John’s NL A1C 5S7, Canada
| | - Judit J Pénzes
- Institute for Quantitative Biomedicine, Rutgers the State University of New Jersey, 174 Frelinghuysen Rd, Piscataway, NJ 08854, USA
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 45 Arctic Ave., St. John’s NL A1C 5S7, Canada
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Kostelic MM, Hsieh CC, Sanders HM, Zak CK, Ryan JP, Baker ES, Aspinwall CA, Marty MT. Surface Modified Nano-Electrospray Needles Improve Sensitivity for Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1031-1037. [PMID: 35588532 DOI: 10.1021/jasms.2c00087] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Native mass spectrometry (MS) and charge detection-mass spectrometry (CD-MS) have become versatile tools for characterizing a wide range of proteins and macromolecular complexes. Both commonly use nanoelectrospray ionization (nESI) from pulled borosilicate needles, but some analytes are known to nonspecifically adsorb to the glass, which may lower sensitivity and limit the quality of the data. To improve the sensitivity of native MS and CD-MS, we modified the surface of nESI needles with inert surface modifiers, including polyethylene-glycol. We found that the surface modification improved the signal intensity for native MS of proteins and for CD-MS of adeno-associated viral capsids. Based on mechanistic comparisons, we hypothesize that the improvement is more likely due to an increased flow rate with coated ESI needles rather than less nonspecific adsorption. In any case, these surface-modified needles provide a simple and inexpensive method for improving the sensitivity of challenging analytes.
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Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Chih-Chieh Hsieh
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Henry M Sanders
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Ciara K Zak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Jack P Ryan
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27659, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27659, United States
| | - Craig A Aspinwall
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
- Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
- Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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Basso CR, Yamakawa AC, Cruz TF, Pedrosa VA, Magro M, Vianello F, Araújo Júnior JP. Colorimetric Kit for Rapid Porcine Circovirus 2 (PCV-2) Diagnosis. Pathogens 2022; 11:570. [PMID: 35631091 PMCID: PMC9147935 DOI: 10.3390/pathogens11050570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 02/05/2023] Open
Abstract
The aim of the current study is to present a low-cost and easy-to-interpret colorimetric kit used to diagnose porcine circovirus 2 (PCV-2) to the naked eye, without any specific equipment. The aforementioned kit used as base hybrid nanoparticles resulting from the merge of surface active maghemite nanoparticles and gold nanoparticles, based on the deposition of specific PCV-2 antibodies on their surface through covalent bonds. In total, 10 negative and 40 positive samples (≥102 DNA copies/µL of serum) confirmed by qPCR technique were tested. PCV-1 virus, adenovirus, and parvovirus samples were tested as interferents to rule out likely false-positive results. Positive samples showed purple color when they were added to the complex, whereas negative samples showed red color; they were visible to the naked eye. The entire color-change process took place approximately 1 min after the analyzed samples were added to the complex. They were tested at different dilutions, namely pure, 1:10, 1:100, 1:1000, and 1:10,000. Localized surface plasmon resonance (LSPR) and transmission electron microscopy (TEM) images were generated to validate the experiment. This new real-time PCV-2 diagnostic methodology emerged as simple and economic alternative to traditional tests since the final price of the kit is USD 4.00.
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Affiliation(s)
- Caroline Rodrigues Basso
- Biotechnology Institute, São Paulo State University, Botucatu 18607-440, SP, Brazil; (A.C.Y.); (T.F.C.); (J.P.A.J.)
| | - Ana Carolina Yamakawa
- Biotechnology Institute, São Paulo State University, Botucatu 18607-440, SP, Brazil; (A.C.Y.); (T.F.C.); (J.P.A.J.)
| | - Taís Fukuta Cruz
- Biotechnology Institute, São Paulo State University, Botucatu 18607-440, SP, Brazil; (A.C.Y.); (T.F.C.); (J.P.A.J.)
- Chemical and Biological Sciences Department, Bioscience Institute, São Paulo State University, Botucatu 18618-000, SP, Brazil;
| | - Valber Albuquerque Pedrosa
- Chemical and Biological Sciences Department, Bioscience Institute, São Paulo State University, Botucatu 18618-000, SP, Brazil;
| | - Massimiliano Magro
- Comparative Biomedicine and Food Science Department, University of Padua, 35020 Legnaro, Italy; (M.M.); (F.V.)
| | - Fabio Vianello
- Comparative Biomedicine and Food Science Department, University of Padua, 35020 Legnaro, Italy; (M.M.); (F.V.)
| | - João Pessoa Araújo Júnior
- Biotechnology Institute, São Paulo State University, Botucatu 18607-440, SP, Brazil; (A.C.Y.); (T.F.C.); (J.P.A.J.)
- Chemical and Biological Sciences Department, Bioscience Institute, São Paulo State University, Botucatu 18618-000, SP, Brazil;
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Characterization of the Serpentine Adeno-Associated Virus (SAAV) Capsid Structure: Receptor Interactions and Antigenicity. J Virol 2022; 96:e0033522. [DOI: 10.1128/jvi.00335-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AAVs are widely studied therapeutic gene delivery vectors. However, preexisting antibodies and their detrimental effect on therapeutic efficacy are a primary challenge encountered during clinical trials.
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