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Buhlheller C, Sagmeister T, Grininger C, Gubensäk N, Sleytr UB, Usón I, Pavkov-Keller T. SymProFold: Structural prediction of symmetrical biological assemblies. Nat Commun 2024; 15:8152. [PMID: 39294115 PMCID: PMC11410804 DOI: 10.1038/s41467-024-52138-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 08/28/2024] [Indexed: 09/20/2024] Open
Abstract
Symmetry in nature often emerges from self-assembly processes and serves a wide range of functions. Cell surface layers (S-layers) form symmetrical lattices on many bacterial and archaeal cells, playing essential roles such as facilitating cell adhesion, evading the immune system, and protecting against environmental stress. However, the experimental structural characterization of these S-layers is challenging due to their self-assembly properties and high sequence variability. In this study, we introduce the SymProFold pipeline, which utilizes the high accuracy of AlphaFold-Multimer predictions to derive symmetrical assemblies from protein sequences, specifically focusing on two-dimensional S-layer arrays and spherical viral capsids. The pipeline tests all known symmetry operations observed in these systems (p1, p2, p3, p4, and p6) and identifies the most likely symmetry for the assembly. The predicted models were validated using available experimental data at the cellular level, and additional crystal structures were obtained to confirm the symmetry and interfaces of several SymProFold assemblies. Overall, the SymProFold pipeline enables the determination of symmetric protein assemblies linked to critical functions, thereby opening possibilities for exploring functionalities and designing targeted applications in diverse fields such as nanotechnology, biotechnology, medicine, and materials and environmental sciences.
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Affiliation(s)
- Christoph Buhlheller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Medical University of Graz, Graz, Austria
| | - Theo Sagmeister
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Nina Gubensäk
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Uwe B Sleytr
- Institute of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Isabel Usón
- Structural Biology Unit, Institute of Molecular Biology of Barcelona, Spanish National Research Council, Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.
- Field of Excellence BioHealth, University of Graz, Graz, Austria.
- BioTechMed-Graz, University of Graz, Graz, Austria.
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2
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Timm FCB, Campos FS, Janssen L, Dos Santos RN, Paredes-Galarza B, Stone NV, Oliveira MT, Gasparetto R, Müller NFD, Melgarejo ADS, Corrêa ML, Lozano LMV, Salvato RS, Godinho FMDS, Barcellos RB, Teixeira MADS, Riet-Correa G, Cerqueira VD, Bezerra Júnior PS, Franco AC, Roehe PM. The virome of bubaline (Bubalus bubalis) tonsils reveals an unreported bubaline polyomavirus. Braz J Microbiol 2024; 55:2893-2900. [PMID: 39014291 PMCID: PMC11405355 DOI: 10.1007/s42770-024-01449-0] [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: 12/26/2023] [Accepted: 06/17/2024] [Indexed: 07/18/2024] Open
Abstract
Water buffalo (Bubalus bubalis) farming is increasing in many regions of the world due to the species' ability to thrive in environments where bovine cattle would struggle. Despite water buffaloes being known for their resistance to diseases, there is a lack of data about the diversity of the microbiome of the species. In this study, we examined the virome diversity in palatine tonsils collected from animals from the island of Marajó, northern Pará state, Brazil, which harbors the largest bubaline flock in the country. Tonsil fragments from 60 clinically healthy bubalines were randomly selected from a sample of 293 animals. The samples were purified, extracted, and randomly amplified with phi29 DNA polymerase. After amplification, the products were purified and sequenced. Circular DNA viruses were predominant in the tonsils' virome. Sequences of genome segments representative of members of the genera Alphapolyomavirus (including a previously unreported bubaline polyomavirus genome) and Gemycircularvirus were identified, along with other not yet classified circular virus genomes. As the animals were clinically healthy at the time of sampling, such viruses likely constitute part of the normal tonsillar virome of water buffaloes inhabiting the Ilha do Marajó biome.
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Affiliation(s)
- Francine C B Timm
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Fabrício Souza Campos
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil.
| | - Luis Janssen
- Laboratório de Baculovírus, Instituto de Ciências Biológicas, Universidade de Brasília (UnB), Brasília, Brasil
| | - Raíssa Nunes Dos Santos
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Bruna Paredes-Galarza
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Nicole Vieira Stone
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Martha Trindade Oliveira
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Raíssa Gasparetto
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Nicolas Felipe Drum Müller
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Alanis da Silva Melgarejo
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Miguel Leonetti Corrêa
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Lina Marcela Violet Lozano
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Richard Steiner Salvato
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Centro Estadual de Vigilância em Saúde (CEVS) da Secretaria Estadual da Saúde do Rio Grande do Sul (SESRS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Fernanda Marques de Souza Godinho
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Centro Estadual de Vigilância em Saúde (CEVS) da Secretaria Estadual da Saúde do Rio Grande do Sul (SESRS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Regina Bones Barcellos
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Centro Estadual de Vigilância em Saúde (CEVS) da Secretaria Estadual da Saúde do Rio Grande do Sul (SESRS), Porto Alegre, Rio Grande do Sul, Brasil
| | | | - Gabriela Riet-Correa
- Laboratório de Patologia Animal, Instituto de Medicina Veterinária, Universidade Federal do Pará (UFPA), Castanhal, Pará, Brasil
| | - Valíria Duarte Cerqueira
- Laboratório de Patologia Animal, Instituto de Medicina Veterinária, Universidade Federal do Pará (UFPA), Castanhal, Pará, Brasil
| | - Pedro Soares Bezerra Júnior
- Laboratório de Patologia Animal, Instituto de Medicina Veterinária, Universidade Federal do Pará (UFPA), Castanhal, Pará, Brasil
| | - Ana Cláudia Franco
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Paulo Michel Roehe
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil.
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3
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Varsani A, Krupovic M. 2024 Smacoviridae family update: 59 new species in seven genera. Arch Virol 2024; 169:184. [PMID: 39167240 DOI: 10.1007/s00705-024-06116-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Family Smacoviridae (order Cremevirales, class Arfiviricetes, phylum Cressdnaviricota) comprises viruses with small circular genomes of ~2300-3000 nt in length that encode at least two proteins, the rolling-circle replication associated protein (Rep) and the capsid protein (CP). Smacovirids have been discovered in fecal samples of various animals and display remarkable sequence diversity. Here, we provide an overview of the genomic properties of classified smacovirids and report on the latest taxonomy update in the family Smacoviridae. The family has been expanded by 59 new species in the genera Porprismacovirus (n = 25), Inpeasmacovirus (n = 1), Felismacovirus (n = 22), Drosmacovirus (n = 4), Dragsmacovirus (n = 2), Bovismacovirus (n = 4), and Bonzesmacovirus (n = 1) and currently includes 12 genera with 143 species officially recognized by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, Tempe, AZ, 85287-5001, USA.
- Structural Biology Research Unit, Department of Integrative, Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, 25 rue du Dr Roux, 75015, Paris, France.
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4
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Varsani A, Harrach B, Roumagnac P, Benkő M, Breitbart M, Delwart E, Franzo G, Kazlauskas D, Rosario K, Segalés J, Dunay E, Rukundo J, Goldberg TL, Fehér E, Kaszab E, Bányai K, Krupovic M. 2024 taxonomy update for the family Circoviridae. Arch Virol 2024; 169:176. [PMID: 39143430 DOI: 10.1007/s00705-024-06107-2] [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: 08/16/2024]
Abstract
Circovirids have a circular single-stranded DNA genome packed into a small icosahedral capsid. They are classified within two genera, Circovirus and Cyclovirus, in the family Circoviridae (phylum Cressdnaviricota, class Arfiviricetes, order Cirlivirales). Over the last five years, a number of new circovirids have been identified, and, as a result, 54 new species have been created for their classification based on the previously established species demarcation criterion, namely, that viruses classified into different species share less than 80% genome-wide pairwise sequence identity. Of note, one of the newly created species includes a circovirus that was identified in human hepatocytes and suspected of causing liver damage. Furthermore, to comply with binomial species nomenclature, all new and previously recognized species have been (re)named in binomial format with a freeform epithet. Here, we provide a summary of the properties of circovirid genomes and their classification as of June 2024 (65 species in the genus Circovirus and 90 species in the genus Cyclovirus). Finally, we provide reference datasets of the nucleotide and amino acid sequences representing each of the officially recognized circovirid species to facilitate further classification of newly discovered members of the Circoviridae.
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Affiliation(s)
- Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA.
- Structural Biology Research Unit, Department of Integrative, Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa.
| | - Balázs Harrach
- HUN-REN Veterinary Medical Research Institute, Budapest, 1143, Hungary
| | - Philippe Roumagnac
- CIRAD-UMR PHIM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Mária Benkő
- HUN-REN Veterinary Medical Research Institute, Budapest, 1143, Hungary
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, 33701, USA
| | - Eric Delwart
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94118, USA
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), Università di Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, 33701, USA
| | - Joaquim Segalés
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
| | - Emily Dunay
- Department of Pathobiological Sciences, University of Wisconsin-Madison School of Veterinary Medicine, Madison, WI, USA
| | - Joshua Rukundo
- Ngamba Island Chimpanzee Sanctuary/Chimpanzee Trust, Entebbe, Uganda
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison School of Veterinary Medicine, Madison, WI, USA
| | - Enikő Fehér
- HUN-REN Veterinary Medical Research Institute, Budapest, 1143, Hungary
| | - Eszter Kaszab
- HUN-REN Veterinary Medical Research Institute, Budapest, 1143, Hungary
| | - Krisztián Bányai
- HUN-REN Veterinary Medical Research Institute, Budapest, 1143, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, 1078, Budapest, Hungary
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, 25 rue du Dr Roux, 75015, Paris, France.
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5
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Paietta EN, Kraberger S, Custer JM, Vargas KL, Ehmke E, Yoder AD, Varsani A. Metagenome-assembled microvirus and cressdnavirus genomes from fecal samples of house mice ( Mus musculus). Microbiol Resour Announc 2024; 13:e0033124. [PMID: 38975773 PMCID: PMC11320919 DOI: 10.1128/mra.00331-24] [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: 04/02/2024] [Accepted: 06/20/2024] [Indexed: 07/09/2024] Open
Abstract
House mice, Mus musculus, are highly adapted to anthropogenic spaces. Fecal samples were collected from house mice entering primate enclosure areas at the Duke Lemur Center (Durham, NC, USA). We identified 14 cressdnavirus and 59 microvirus genomes in these mouse feces.
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Affiliation(s)
- Elise N. Paietta
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Joy M. Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Karla L. Vargas
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Erin Ehmke
- Duke Lemur Center, Durham, North Carolina, USA
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
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6
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Smiley AT, Babilonia-Díaz N, Krueger AJ, Aihara H, Tompkins KJ, Lemmex ACD, Gordon WR. Sequence-Directed Covalent Protein-RNA Linkages in a Single Step Using Engineered HUH-Tags. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.13.607811. [PMID: 39185166 PMCID: PMC11343116 DOI: 10.1101/2024.08.13.607811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Replication-initiating HUH-endonucleases (Reps) are enzymes that form covalent bonds with single-stranded DNA (ssDNA) in a sequence specific manner to initiate rolling circle replication. These nucleases have been co-opted for use in biotechnology as sequence specific protein-ssDNA bioconjugation fusion partners dubbed 'HUH-tags'. Here, we describe the engineering and in vitro characterization of a series of laboratory evolved HUH-tags capable of forming robust sequence-directed covalent bonds with unmodified RNA substrates. We show that promiscuous Rep-RNA interaction can be enhanced through directed evolution from nearly undetectable levels in wildtype enzymes to robust reactivity in final engineered iterations. Taken together, these engineered HUH-tags represent a promising platform for enabling site-specific protein-RNA covalent bioconjugation in vitro, potentially mediating a host of new applications and offering a valuable addition to the HUH-tag repertoire.
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Affiliation(s)
- Adam T Smiley
- University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics
| | | | - August J Krueger
- University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics
| | - Hideki Aihara
- University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics
| | - Kassidy J Tompkins
- University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics
| | - Andrew C D Lemmex
- University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics
| | - Wendy R Gordon
- University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics
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Castro-Scholten S, Vasinioti VI, Caballero-Gómez J, García-Bocanegra I, Pellegrini F, Salvaggiulo A, Odigie AE, Diakoudi G, Camero M, Decaro N, Martella V, Lanave G. Identification and characterization of a novel circovirus in Iberian lynx in Spain. Res Vet Sci 2024; 176:105336. [PMID: 38880017 DOI: 10.1016/j.rvsc.2024.105336] [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: 04/03/2024] [Revised: 05/31/2024] [Accepted: 06/09/2024] [Indexed: 06/18/2024]
Abstract
Circoviruses cause severe disease in pigs and birds. Canine circovirus has thus far only been associated with respiratory and gastrointestinal disorders and systemic disease in dogs. The Iberian lynx (Lynx pardinus) is one of the most endangered carnivores in Europe and the most endangered felid worldwide. Exploring the virome of these animals may be important in terms of virus discovery and assessing the interspecies-circulation of viruses from related carnivores. In this study, 162 spleen samples from Iberian lynx were screened for CRESS DNA viruses. Overall, 11 (6.8%) of 162 samples tested positive using a consensus PCR. Partial rep sequences were tightly related to each other (96.6-100%). Specific molecular protocols were designed on the partial rep sequences of the novel virus, Iberian lynx-associated circovirus-1 (ILCV-1). By screening a subset of 45 spleen samples, the infection rate of ILCV-1 in Iberian lynxes was 57.8% (26/45). ILCV-1 strains formed a separate cluster intermingled with bat, rodent, mongoose, and felid circoviruses. The genome of the novel virus displayed the highest nucleotide identity (64.3-65.3%) to mongoose circoviruses, thus representing a novel candidate circovirus species. The detection of these viruses in the spleen tissues could suggest systemic infection in the animal host. Overall, these findings suggest that this novel circovirus is common in the Iberian lynx. Further studies are warranted to assess the possible health implications of ILCV-1 in this endangered species.
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Affiliation(s)
- Sabrina Castro-Scholten
- Animal Health and Zoonosis Research Group (GISAZ), Department of Animal Health, University of Córdoba, Córdoba, Spain
| | | | - Javier Caballero-Gómez
- Animal Health and Zoonosis Research Group (GISAZ), Department of Animal Health, University of Córdoba, Córdoba, Spain; Infectious Diseases Unit, Maimonides Institute for Biomedical Research (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Córdoba, Spain; CIBERINFEC, ISCIII - CIBER Infectious Diseases, Health Institute Carlos III, Madrid, Spain
| | - Ignacio García-Bocanegra
- Animal Health and Zoonosis Research Group (GISAZ), Department of Animal Health, University of Córdoba, Córdoba, Spain; CIBERINFEC, ISCIII - CIBER Infectious Diseases, Health Institute Carlos III, Madrid, Spain
| | - Francesco Pellegrini
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Bari, Italy
| | - Anna Salvaggiulo
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Bari, Italy
| | | | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Bari, Italy
| | - Michele Camero
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Bari, Italy
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Bari, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Bari, Italy; Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary
| | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Bari, Italy.
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8
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Mohebbi A, Kiani SJ, Khanaliha K, Donyavi T, Emtiazi N, Sharifian K, Mohebbi M, Gholami A, Behnezhad F, Abbasi-Kolli M, Dehghani-Dehej F, Bokharaei-Salim F. Dental complications as a potential indicator of Redondovirus infection: a cross-sectional study. BMC Infect Dis 2024; 24:673. [PMID: 38969993 PMCID: PMC11225247 DOI: 10.1186/s12879-024-09523-6] [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: 03/22/2024] [Accepted: 06/17/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND Redondoviridae is a newly discovered virus family linked to oral and respiratory conditions in people, while there is still debate about whether it is also coinfected with other respiratory viruses. This study aimed to determine the frequency of Redondovirus (ReDoV) in nasopharyngeal samples and to investigate any possible links to SARS-CoV-2 infections. METHODS A polymerase chain reaction (PCR) test was conducted on 731 nasopharyngeal samples from individuals referred to medical centers in Tehran, Iran, for SARS-CoV-2 testing to investigate the prevalence of ReDoV. An oral interview was performed to complete information on dental issues and the individuals' demographics, symptoms, and vaccination history. RESULTS The prevalence of ReDoV was 25.99%, and 15.26% had a coinfection with SARS-CoV-2. No notable correlation was found regarding ReDoVs and SARS-CoV-2 infections (p > 0.05). Women had a higher ReDoV positivity rate of 18.47% compared to men at 7.52% (p = 0.12), and there was no significant correlation between age groups and ReDoV presence. Nonetheless, a significant association was noted between ReDoVs and dental/gum issues (p < 0.0001, OR: 13.0326). A phylogenetic analysis showed that ReDoVs originated from various human-related clusters. CONCLUSIONS These results highlight the potential for detecting ReDoVs in nasopharyngeal samples of people with gum or dental issues. Additionally, conducting more ReDoV epidemiological research and proposing oral health as a possible marker for ReDoV infections is important.
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Affiliation(s)
- Alireza Mohebbi
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Vista Aria Rena Gene, Inc, Gorgan, Golestan Province, Iran
| | - Seyed Jalal Kiani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Khanaliha
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Tahereh Donyavi
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Nikoo Emtiazi
- Department of Pathology, Iran University of Medical Sciences, Tehran, Iran
| | - Kimia Sharifian
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Mohebbi
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Amytis Gholami
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farzane Behnezhad
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Abbasi-Kolli
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farzaneh Dehghani-Dehej
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farah Bokharaei-Salim
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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9
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Ramos EDSF, Tozetto-Mendoza TR, Bortoletto P, Ferreira NE, Honorato L, Barbosa EMG, Luchs A, Linhares IM, Spandorfer SD, Leal E, da Costa AC, Witkin SS, Mendes-Correa MC. Characterization of CRESS-DNA viruses in human vaginal secretions: An exploratory metagenomic investigation. J Med Virol 2024; 96:e29750. [PMID: 38953413 DOI: 10.1002/jmv.29750] [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: 04/01/2024] [Revised: 05/16/2024] [Accepted: 06/09/2024] [Indexed: 07/04/2024]
Abstract
The Phylum Cressdnaviricota consists of a large number of circular Rep-encoding single-stranded (CRESS)-DNA viruses. Recently, metagenomic analyzes revealed their ubiquitous distribution in a diverse range of eukaryotes. Data relating to CRESS-DNA viruses in humans remains scarce. Our study investigated the presence and genetic diversity of CRESS-DNA viruses in human vaginal secretions. Vaginal swabs were collected from 28 women between 29 and 43 years old attending a fertility clinic in New York City. An exploratory metagenomic analysis was performed and detection of CRESS-DNA viruses was confirmed through analysis of near full-length sequences of the viral isolates. A phylogenetic tree was based on the REP open reading frame sequences of the CRESS-DNA virus genome. Eleven nearly complete CRESS-DNA viral genomes were identified in 16 (57.1%) women. There were no associations between the presence of these viruses and any demographic or clinical parameters. Phylogenetic analysis indicated that one of the sequences belonged to the genus Gemycircularvirus within the Genomoviridae family, while ten sequences represented previously unclassified species of CRESS-DNA viruses. Novel species of CRESS-DNA viruses are present in the vaginal tract of adult women. Although they be transient commensal agents, the potential clinical implications for their presence at this site cannot be dismissed.
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Affiliation(s)
- Endrya do Socorro Foro Ramos
- Laboratório de diversidade Viral, Instituto de Ciências Biológicas, Departamento de Virologia, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Tania Regina Tozetto-Mendoza
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Pietro Bortoletto
- Fertility department, Boston IVF-The Eugin Group, Waltham, Massachusetts, USA
- Medicine department, Harvard Medical School, Boston, Massachusetts, USA
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Noely Evangelista Ferreira
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Layla Honorato
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Erick Matheus Garcia Barbosa
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Adriana Luchs
- Virology department, Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, Sao Paulo, Brazil
| | - Iara M Linhares
- Department of Gynecology and Obstetrics, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Steven D Spandorfer
- Department of Gynecology and Obstetrics, Center for Reproductive Medicine and Infertility, Weill Cornell Medicine, New York City, New York, USA
| | - Elcio Leal
- Laboratório de diversidade Viral, Instituto de Ciências Biológicas, Departamento de Virologia, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Antonio Charlys da Costa
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Steven S Witkin
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York City, New York, USA
| | - Maria Cassia Mendes-Correa
- Laboratório de Investigação Médica em Virologia (LIM52), Department of Infectology and Tropical Medicine, Instituto de Medicina Tropical de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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10
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Smiley AT, Babilonia-Díaz NS, Hughes AJ, Lemmex ACD, Anderson MJM, Tompkins KJ, Gordon WR. HUHgle: An Interactive Substrate Design Tool for Covalent Protein-ssDNA Labeling Using HUH-Tags. ACS Synth Biol 2024; 13:1669-1678. [PMID: 38820192 DOI: 10.1021/acssynbio.4c00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
HUH-tags have emerged as versatile fusion partners that mediate sequence specific protein-ssDNA bioconjugation through a simple and efficient reaction. Here we present HUHgle, a python-based interactive tool for the visualization, design, and optimization of substrates for HUH-tag mediated covalent labeling of proteins of interest with ssDNA substrates of interest. HUHgle streamlines design processes by integrating an intuitive plotting interface with a search function capable of predicting and displaying protein-ssDNA bioconjugate formation efficiency and specificity in proposed HUH-tag/ssDNA sequence combinations. Validation demonstrates that HUHgle accurately predicts product formation of HUH-tag mediated bioconjugation for single- and orthogonal-labeling reactions. In order to maximize the accessibility and utility of HUHgle, we have implemented it as a user-friendly Google Colab notebook which facilitates broad use of this tool, regardless of coding expertise.
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Affiliation(s)
- Adam T Smiley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Natalia S Babilonia-Díaz
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Aspen J Hughes
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Andrew C D Lemmex
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Michael J M Anderson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kassidy J Tompkins
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Wendy R Gordon
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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11
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Kandathil AJ, Thomas DL. The Blood Virome: A new frontier in biomedical science. Biomed Pharmacother 2024; 175:116608. [PMID: 38703502 PMCID: PMC11184943 DOI: 10.1016/j.biopha.2024.116608] [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: 01/08/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
Recent advances in metagenomic testing opened a new window into the mammalian blood virome. Comprised of well-known viruses like human immunodeficiency virus, hepatitis C virus, and hepatitis B virus, the virome also includes many other eukaryotic viruses and phages whose medical significance, lifecycle, epidemiology, and impact on human health are less well known and thus regarded as commensals. This review synthesizes available information for the so-called commensal virome members that circulate in the blood of humans considering their restriction to and interaction with the human host, their natural history, and their impact on human health and physiology.
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Affiliation(s)
- Abraham J Kandathil
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David L Thomas
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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12
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Cao X, Tang L, Song J. Circular Single-Stranded DNA: Discovery, Biological Effects, and Applications. ACS Synth Biol 2024; 13:1038-1058. [PMID: 38501391 DOI: 10.1021/acssynbio.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The field of nucleic acid therapeutics has witnessed a significant surge in recent times, as evidenced by the increasing number of approved genetic drugs. However, current platform technologies containing plasmids, lipid nanoparticle-mRNAs, and adeno-associated virus vectors encounter various limitations and challenges. Thus, we are devoted to finding a novel nucleic acid vector and have directed our efforts toward investigating circular single-stranded DNA (CssDNA), an ancient form of nucleic acid. CssDNAs are ubiquitous, but generally ignored. Accumulating evidence suggests that CssDNAs possess exceptional properties as nucleic acid vectors, exhibiting great potential for clinical applications in genetic disorders, gene editing, and immune cell therapy. Here, we comprehensively review the discovery and biological effects of CssDNAs as well as their applications in the field of biomedical research for the first time. Undoubtedly, as an ancient form of DNA, CssDNA holds immense potential and promises novel insights for biomedical research.
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Affiliation(s)
- Xisen Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
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13
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Yu M, Zhang M, Zeng R, Cheng R, Zhang R, Hou Y, Kuang F, Feng X, Dong X, Li Y, Shao Z, Jin M. Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments. Nat Commun 2024; 15:3228. [PMID: 38622147 PMCID: PMC11018836 DOI: 10.1038/s41467-024-47600-1] [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: 10/18/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Seamounts are globally distributed across the oceans and form one of the major oceanic biomes. Here, we utilized combined analyses of bulk metagenome and virome to study viral communities in seamount sediments in the western Pacific Ocean. Phylogenetic analyses and the protein-sharing network demonstrate extensive diversity and previously unknown viral clades. Inference of virus-host linkages uncovers extensive interactions between viruses and dominant prokaryote lineages, and suggests that viruses play significant roles in carbon, sulfur, and nitrogen cycling by compensating or augmenting host metabolisms. Moreover, temperate viruses are predicted to be prevalent in seamount sediments, which tend to carry auxiliary metabolic genes for host survivability. Intriguingly, the geographical features of seamounts likely compromise the connectivity of viral communities and thus contribute to the high divergence of viral genetic spaces and populations across seamounts. Altogether, these findings provides knowledge essential for understanding the biogeography and ecological roles of viruses in globally widespread seamounts.
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Affiliation(s)
- Meishun Yu
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Menghui Zhang
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Ruolin Cheng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Yanping Hou
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Fangfang Kuang
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Xuejin Feng
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Xiyang Dong
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Yinfang Li
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China
| | - Zongze Shao
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China.
| | - Min Jin
- State Key Laboratory Breeding Base of Marine Genetic Resource and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361000, China.
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14
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Bandoo RA, Kraberger S, Varsani A. Two Novel Geminiviruses Identified in Bees ( Apis mellifera and Nomia sp.). Viruses 2024; 16:602. [PMID: 38675943 PMCID: PMC11053556 DOI: 10.3390/v16040602] [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: 03/30/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Members of the Geminviridae family are circular single-stranded DNA plant-infecting viruses, some of which impact global food production. Geminiviruses are vectored by sap-feeding insects such as leafhoppers, treehoppers, aphids, and whiteflies. Additionally, geminivirus sequences have also been identified in other insects such as dragonflies, mosquitoes, and stingless bees. As part of a viral metagenomics study on honeybees and solitary bees (Nomia sp.), two geminivirus genomes were identified. These represent a novel citlodavirus (from honeybees collected from Westmoreland, Jamaica) and a mastrevirus-like genome (from a solitary bee collected from Tempe, Arizona, USA). The novel honeybee-derived citlodavirus genome shares ~61 to 69% genome-wide nucleotide pairwise identity with other citlodavirus genome sequences and is most closely related to the passion fruit chlorotic mottle virus identified in Brazil. Whereas the novel solitary bee-derived mastrevirus-like genome shares ~55 to 61% genome-wide nucleotide identity with other mastreviruses and is most closely related to tobacco yellow dwarf virus identified in Australia, based on pairwise identity scores of the full genome, replication-associated protein, and capsid protein sequences. Previously, two geminiviruses in the Begomovirus genus were identified in samples of stingless bee (Trigona spp.) samples. Here, we identify viruses that represent two new species of geminiviruses from a honeybee and a solitary bee, which continues to demonstrate that plant pollinators can be utilized for the identification of plant-infecting DNA viruses in ecosystems.
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Affiliation(s)
- Rohan Antonio Bandoo
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa
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15
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Buck CB, Welch N, Belford AK, Varsani A, Pastrana DV, Tisza MJ, Starrett GJ. Widespread Horizontal Gene Transfer Among Animal Viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586562. [PMID: 38712252 PMCID: PMC11071296 DOI: 10.1101/2024.03.25.586562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The initial objective of this study was to shed light on the evolution of small DNA tumor viruses by analyzing de novo assemblies of publicly available deep sequencing datasets. The survey generated a searchable database of contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened the search to include an increasingly wide range of other virus families. The analysis revealed a surprisingly diverse range of chimeras involving different virus groups. In some instances, genes resembling known DNA-replication modules or known virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel virion architectures. Discrete clades of an emerging group called adintoviruses were discovered in datasets representing humans and other primates. As a proof of concept, we show that the contig database is also useful for discovering RNA viruses and candidate archaeal phages. The ancillary searches revealed additional examples of chimerization between different virus groups. The observations support a gene-centric taxonomic framework that should be useful for future virus-hunting efforts.
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Affiliation(s)
| | - Nicole Welch
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: L.E.K. Consulting, Boston, MA, USA
| | - Anna K. Belford
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: University of Pittsburgh, Pittsburgh, PA, USA
| | - Arvind Varsani
- Arizona State University, Tempe, AZ, USA
- University of Cape Town, South Africa
| | | | - Michael J. Tisza
- National Cancer Institute, Bethesda, MD, USA
- current affiliation: Baylor College of Medicine, Houston, TX, USA
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16
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Yadhav Y, Selvaraj K, Ramasamy S, Venkataraman S. Computational studies on rep and capsid proteins of CRESS DNA viruses. Virusdisease 2024; 35:17-26. [PMID: 38817400 PMCID: PMC11133267 DOI: 10.1007/s13337-024-00858-x] [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: 11/20/2023] [Accepted: 01/29/2024] [Indexed: 06/01/2024] Open
Abstract
The circular rep-encoding single-stranded DNA viruses (CRESS DNA viruses) are among the smallest, with 2-6 kb ssDNA genomes that encode for a coat protein (C) and a replication protein (R). To comprehend the complexity and divergence of the C and R proteins, we have created predictive structural models of representative viruses infecting unique hosts from each family using the neural network-based method AlphaFold2 and carried out molecular dynamic simulations to assess their stability. The structural characteristics indicate that differences in loops and amino-terminus may play a significant role in facilitating adaptations to multiple hosts and vectors. In comparison to the C, the Rs show a high degree of conservation and structural mimicry of the nuclease-helicase domains of plasmids. A phylogenetic analysis based on the structures and sequences of the C and R proteins reveals evolutionary variances. Our study also highlights the conservation of structural components involved in the interaction of R with the conserved intergenic region of the genome. Further, we envisage that the adaptability of R's central linker may be crucial for establishing interactions with multiple protein partners, including C. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-024-00858-x.
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Affiliation(s)
- Yagavi Yadhav
- Department of Biotechnology, Anna University, Guindy, Chennai, 600025 India
| | - Karthiga Selvaraj
- Department of Biotechnology, Anna University, Guindy, Chennai, 600025 India
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17
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Opriessnig T, Xiao CT, Mueller NJ, Denner J. Emergence of novel circoviruses in humans and pigs and their possible importance for xenotransplantation and blood transfusions. Xenotransplantation 2024; 31:e12842. [PMID: 38501706 DOI: 10.1111/xen.12842] [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: 11/17/2023] [Accepted: 12/19/2023] [Indexed: 03/20/2024]
Abstract
BACKGROUND As sequencing is becoming more broadly available, virus discovery continues. Small DNA viruses contribute to up to 60% of the overall virus load in pigs. Porcine circoviruses (PCVs) are small DNA viruses with a single-stranded circular genome. They are common in pig breeds and have not been properly addressed for their potential risk in xenotransplantation. Whereas PCV1 is non-pathogenic in pigs, PCV2 has been associated with various disease manifestations. Recently two new circoviruses have been described, PCV3 and PCV4. While PCV4 is currently present mainly in Asia, PCV3 is widely distributed, and has been identified in commercial pigs, wild boars, and pigs generated for xenotransplantation. In one case PCV3 was transmitted by pigs to baboons via heart transplantation. PCV3 pathogenicity in pigs was controversial initially, however, the virus was found to be associated with porcine dermatitis and nephropathy syndrome (PDNS), reproductive failure, and multisystemic inflammation. Inoculation studies with PCV3 infectious clones confirmed that PCV3 is pathogenic. Most importantly, recently discovered human circoviruses (CV) are closely related to PCV3. METHODS Literature was evaluated and summarized. A dendrogram of existing circoviruses in pigs, humans, and other animal species was created and assessed at the species level. RESULTS We found that human circoviruses can be divided into three species, human CV1, CV2, and CV3. Human CV2 and CV3 are closest to PCV3. CONCLUSIONS Circoviruses are ubiquitous. This communication should create awareness of PCV3 and the newly discovered human circoviruses, which may be a problem for blood transfusions and xenotransplantation in immune suppressed individuals.
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Affiliation(s)
- Tanja Opriessnig
- Vaccines and Diagnostics Department, Moredun Research Institute, Penicuik, UK
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Chao-Ting Xiao
- Institute of Pathogen Biology and Immunology, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, China
| | - Nicolas J Mueller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University Zurich, Zurich, Switzerland
| | - Joachim Denner
- Institute of Virology, Free University Berlin, Berlin, Germany
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18
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Nweze JE, Schweichhart JS, Angel R. Viral communities in millipede guts: Insights into the diversity and potential role in modulating the microbiome. Environ Microbiol 2024; 26:e16586. [PMID: 38356108 DOI: 10.1111/1462-2920.16586] [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: 09/08/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Millipedes are important detritivores harbouring a diverse microbiome. Previous research focused on bacterial and archaeal diversity, while the virome remained neglected. We elucidated the DNA and RNA viral diversity in the hindguts of two model millipede species with distinct microbiomes: the tropical Epibolus pulchripes (methanogenic, dominated by Bacillota) and the temperate Glomeris connexa (non-methanogenic, dominated by Pseudomonadota). Based on metagenomic and metatranscriptomic assembled viral genomes, the viral communities differed markedly and preferentially infected the most abundant prokaryotic taxa. The majority of DNA viruses were Caudoviricetes (dsDNA), Cirlivirales (ssDNA) and Microviridae (ssDNA), while RNA viruses consisted of Leviviricetes (ssRNA), Potyviridae (ssRNA) and Eukaryotic viruses. A high abundance of subtypes I-C, I-B and II-C CRISPR-Cas systems was found, primarily from Pseudomonadota, Bacteroidota and Bacillota. In addition, auxiliary metabolic genes that modulate chitin degradation, vitamins and amino acid biosynthesis and sulphur metabolism were also detected. Lastly, we found low virus-to-microbe-ratios and a prevalence of lysogenic viruses, supporting a Piggyback-the-Winner dynamic in both hosts.
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Affiliation(s)
- Julius Eyiuche Nweze
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Johannes Sergej Schweichhart
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Roey Angel
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
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19
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Zhu P, Liu C, Liu GF, Liu H, Xie KM, Zhang HS, Xu X, Xiao J, Jiang JZ. Unveiling CRESS DNA Virus Diversity in Oysters by Virome. Viruses 2024; 16:228. [PMID: 38400004 PMCID: PMC10892194 DOI: 10.3390/v16020228] [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: 01/02/2024] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Oysters that filter feed can accumulate numerous pathogens, including viruses, which can serve as a valuable viral repository. As oyster farming becomes more prevalent, concerns are mounting about diseases that can harm both cultivated and wild oysters. Unfortunately, there is a lack of research on the viruses and other factors that can cause illness in shellfish. This means that it is harder to find ways to prevent these diseases and protect the oysters. This is part of a previously started project, the Dataset of Oyster Virome, in which we further study 30 almost complete genomes of oyster-associated CRESS DNA viruses. The replication-associated proteins and capsid proteins found in CRESS DNA viruses display varying evolutionary rates and frequently undergo recombination. Additionally, some CRESS DNA viruses have the capability for cross-species transmission. A plethora of unclassified CRESS DNA viruses are detectable in transcriptome libraries, exhibiting higher levels of transcriptional activity than those found in metagenome libraries. The study significantly enhances our understanding of the diversity of oyster-associated CRESS DNA viruses, emphasizing the widespread presence of CRESS DNA viruses in the natural environment and the substantial portion of CRESS DNA viruses that remain unidentified. This study's findings provide a basis for further research on the biological and ecological roles of viruses in oysters and their environment.
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Affiliation(s)
- Peng Zhu
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
- Animal and Plant Inspection and Quarantine Technology Centre, Shenzhen Customs, Shenzhen 518000, China
| | - Chang Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-sen University, Zhuhai 519000, China
| | - Guang-Feng Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
| | - Hong Liu
- Animal and Plant Inspection and Quarantine Technology Centre, Shenzhen Customs, Shenzhen 518000, China
| | - Ke-Ming Xie
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
- School of Life Science and Biopharmacy, Guangdong Pharmaceutical University, Guangzhou 510000, China
| | - Hong-Sai Zhang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
| | - Xin Xu
- Livestock, Aquaculture and Technology Promotion and Service Center of Conghua District, Guangzhou 510000, China
| | - Jian Xiao
- Livestock, Aquaculture and Technology Promotion and Service Center of Conghua District, Guangzhou 510000, China
| | - Jing-Zhe Jiang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510000, China
- School of Life Science and Biopharmacy, Guangdong Pharmaceutical University, Guangzhou 510000, China
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20
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Olivo D, Khalifeh A, Custer JM, Kraberger S, Varsani A. Diverse Small Circular DNA Viruses Identified in an American Wigeon Fecal Sample. Microorganisms 2024; 12:196. [PMID: 38258021 PMCID: PMC10821283 DOI: 10.3390/microorganisms12010196] [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: 12/24/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
American wigeons (Mareca americana) are waterfowls that are widely distributed throughout North America. Research of viruses associated with American wigeons has been limited to orthomyxoviruses, coronaviruses, and circoviruses. To address this poor knowledge of viruses associated with American wigeons, we undertook a pilot study to identify small circular DNA viruses in a fecal sample collected in January 2021 in the city of Tempe, Arizona (USA). We identified 64 diverse circular DNA viral genomes using a viral metagenomic workflow biased towards circular DNA viruses. Of these, 45 belong to the phylum Cressdnaviricota based on their replication-associated protein sequence, with 3 from the Genomoviridae family and the remaining 42 which currently cannot be assigned to any established virus group. It is most likely that these 45 viruses infect various organisms that are associated with their diet or environment. The remaining 19 virus genomes are part of the Microviridae family and likely associated with the gut enterobacteria of American wigeons.
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Affiliation(s)
- Diego Olivo
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Anthony Khalifeh
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Joy M. Custer
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Simona Kraberger
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
| | - Arvind Varsani
- Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85042, USA; (D.O.)
- Structural Biology Research Unit, Department of Integrative, Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa
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21
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Kaszab E, Bali K, Marton S, Ursu K, Farkas SL, Fehér E, Domán M, Martella V, Bányai K. Metagenomic Identification of Novel Eukaryotic Viruses with Small DNA Genomes in Pheasants. Animals (Basel) 2024; 14:237. [PMID: 38254406 PMCID: PMC10812470 DOI: 10.3390/ani14020237] [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: 11/22/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
A panel of intestinal samples collected from common pheasants (Phasianus colchicus) between 2008 and 2017 was used for metagenomic investigation using an unbiased enrichment protocol and different bioinformatic pipelines. The number of sequence reads in the metagenomic analysis ranged from 1,419,265 to 17,507,704 with a viral sequence read rate ranging from 0.01% to 59%. When considering the sequence reads of eukaryotic viruses, RNA and DNA viruses were identified in the samples, including but not limited to coronaviruses, reoviruses, parvoviruses, and CRESS DNA viruses (i.e., circular Rep-encoding single-stranded DNA viruses). Partial or nearly complete genome sequences were reconstructed of at least three different parvoviruses (dependoparvovirus, aveparvovirus and chaphamaparvovirus), as well as gyroviruses and diverse CRESS DNA viruses. Generating information of virus diversity will serve as a basis for developing specific diagnostic tools and for structured epidemiological investigations, useful to assess the impact of these novel viruses on animal health.
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Affiliation(s)
- Eszter Kaszab
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
- One Health Institute, Faculty of Health Sciences, University of Debrecen, 4032 Debrecen, Hungary
| | - Krisztina Bali
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
| | - Szilvia Marton
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
| | - Krisztina Ursu
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, 1143 Budapest, Hungary;
| | - Szilvia L. Farkas
- Department of Obstetrics and Food Animal Medicine Clinic, University of Veterinary Medicine, 1078 Budapest, Hungary;
| | - Enikő Fehér
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
| | - Marianna Domán
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy;
| | - Krisztián Bányai
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, 1078 Budapest, Hungary
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22
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Rodríguez-Negrete EA, Grande-Pérez A. Quantification of Virion-Sense and Complementary-Sense DNA Strands of Circular Single-Stranded DNA Viruses. Methods Mol Biol 2024; 2724:93-109. [PMID: 37987901 DOI: 10.1007/978-1-0716-3485-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Circular ssDNA viruses are ubiquitous and can be found in both prokaryotes and eukaryotes. To understand the interaction of ssDNA viruses with their hosts, it is important to characterize the dynamics of viral sense (VS) and complementary-sense (CS) viral strands during the infection process. Here, we present a simple and rapid protocol that allows sensitive and accurate determination of the VS and CS strands generated during viral infection.The method consists of a two-step qPCR in which the first step uses a strand-specific (CS or VS) labeled primer and T4 DNA polymerase that lacks strand displacement activity and makes a single copy per VS or CS strand. Next, the T4 DNA polymerase and unincorporated oligonucleotides are removed by a silica membrane spin column. Finally, the purified VS or CS strands are quantified by qPCR in a second step in which amplification uses a tag primer and a specific primer. Absolute quantification of VS and CS strands is obtained by extrapolating the Cq data to a standard curve of ssDNA, which can be generated by phagemid expression. Quantification of VS and CS strands of two geminiviruses in infections of Solanum lycopersicum (tomato) and Nicotiana benthamiana plants using this method is shown.
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Affiliation(s)
- Edgar A Rodríguez-Negrete
- Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa, Mexico
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain.
- Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain.
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23
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da Silva JPH, Zerbini FM. Taxonomic Classification of Geminiviruses Based on Pairwise Sequence Comparisons. Methods Mol Biol 2024; 2724:21-31. [PMID: 37987895 DOI: 10.1007/978-1-0716-3485-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Geminiviridae is the largest and one of the most diverse families of plant viruses, comprising 14 genera demarcated based on host range, type of insect vector, and phylogenetic relationships. The use of unbiased, whole-genome multiple displacement amplification techniques coupled with high-throughput sequencing has greatly expanded our knowledge of geminivirus diversity over the last two decades. As a result, a large number of new species have been described in recent years. Species demarcation criteria in the family are entirely based on sequence comparisons, but the specific cutoff values vary for each genus. The purpose of this chapter is to provide a step-by-step pipeline to classify new species in the family Geminiviridae.
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Affiliation(s)
| | - F Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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24
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Hess SC, Weiss KCB, Custer JM, Lewis JS, Kraberger S, Varsani A. Identification of small circular DNA viruses in coyote fecal samples from Arizona (USA). Arch Virol 2023; 169:12. [PMID: 38151635 DOI: 10.1007/s00705-023-05937-w] [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: 10/26/2023] [Accepted: 11/22/2023] [Indexed: 12/29/2023]
Abstract
Coyotes (Canis latrans) have a broad geographic distribution across North and Central America. Despite their widespread presence in urban environments in the USA, there is limited information regarding viruses associated with coyotes in the USA and in particular the state of Arizona. To explore viruses associated with coyotes, particularly small DNA viruses, 44 scat samples were collected (April-June 2021 and November 2021-January 2022) along the Salt River near Phoenix, Arizona (USA), along 43 transects (500 m). From these samples, we identified 11 viral genomes: two novel circoviruses, six unclassified cressdnaviruses, and two anelloviruses. One of the circoviruses is most closely related to a circovirus sequence identified from an aerosolized dust sample in Arizona, USA. The second circovirus is most closely related to a rodent-associated circovirus and canine circovirus. Of the unclassified cressdnaviruses, three encode replication-associated proteins that are similar to those found in protists (Histomonas meleagridis and Monocercomonoides exilis), implying an evolutionary relationship with or a connection to similar unidentified protist hosts. The two anelloviruses are most closely related to those found in rodents, and this suggests a diet-related identification.
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Affiliation(s)
- Savage C Hess
- The School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, 85281, USA
| | - Katherine C B Weiss
- The School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, 85281, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287, USA
| | - Jesse S Lewis
- College of Integrative Sciences and Arts, Arizona State University, Polytechnic Campus, 6073 South Backus Mall, Mesa, AZ, 85212, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- The School of Life Sciences, Arizona State University, 427 E Tyler Mall, Tempe, AZ, 85281, USA.
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ, 85287, USA.
- Center of Evolution and Medicine, Arizona State University, 427 E Tyler Mall, Tempe, AZ, 85281, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa.
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25
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Ruiz-Padilla A, Turina M, Ayllón MA. Molecular characterization of a tetra segmented ssDNA virus infecting Botrytis cinerea worldwide. Virol J 2023; 20:306. [PMID: 38114992 PMCID: PMC10731770 DOI: 10.1186/s12985-023-02256-z] [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: 07/25/2023] [Accepted: 12/02/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Family Genomoviridae was recently established, and only a few mycoviruses have been described and characterized, and almost all of them (Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1, Fusarium graminearum gemyptripvirus 1 and Botrytis cinerea gemydayirivirus 1) induced hypovirulence in their host. Botrytis cinerea ssDNA virus 1 (BcssDV1), a tetrasegmented single-stranded DNA virus infecting the fungus Botrytis cinerea, has been molecularly characterized in this work. METHODS BcssDV1 was detected in Spanish and Italian B. cinerea field isolates obtained from grapevine. BcssDV1 variants genomes were molecularly characterized via NGS and Sanger sequencing. Nucleotide and amino acid sequences were used for diversity and phylogenetic analysis. Prediction of protein tertiary structures and putative associated functions were performed by AlphaFold2 and DALI. RESULTS BcssDV1 is a tetrasegmented single-stranded DNA virus. The mycovirus was composed by four genomic segments of approximately 1.7 Kb each, which are DNA-A, DNA-B, and DNA-C and DNA-D, that coded, respectively, for the rolling-circle replication initiation protein (Rep), capsid protein (CP) and two hypothetical proteins. BcssDV1 was present in several Italian and Spanish regions with high incidence and low variability among the different viral variants. DNA-A and DNA-D were found to be the more conserved genomic segments among variants, while DNA-B and DNA-C segments were shown to be the most variable ones. Tertiary structures of the proteins encoded by each segment suggested specific functions associated with each of them. CONCLUSIONS This study presented the first complete sequencing and characterization of a tetrasegmented ssDNA mycovirus, its incidence in Spain and Italy, its presence in other countries and its high conservation among regions.
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Affiliation(s)
- Ana Ruiz-Padilla
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (UPM-INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, Italy
| | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (UPM-INIA/CSIC), Pozuelo de Alarcón, Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
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26
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Shafiq M, Ondrasek G, Al-Sadi AM, Shahid MS. Molecular Signature of a Novel Alternanthera Yellow Vein Virus Variant Infecting the Ageratum conyzoides Weed in Oman. Viruses 2023; 15:2381. [PMID: 38140622 PMCID: PMC10747960 DOI: 10.3390/v15122381] [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: 10/15/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Alternanthera yellow vein virus (AlYVV), a monopartite begomovirus, has been identified infecting a diverse range of crops and native plants in Pakistan, India, and China. However, distinctive yellow vein symptoms, characteristic of begomovirus infection, were observed on the Ageratum conyzoides weed in Oman, prompting a thorough genomic characterization in this study. The results unveiled a complete genome sequence of 2745 base pairs and an associated betasatellite spanning 1345 base pairs. In addition, Sequence Demarcation Tool analyses indicated the highest nucleotide identity of 92.8% with a previously reported AlYVV-[IN_abalpur_A_17:LC316182] strain, whereas the betasatellite exhibited a 99.8% nucleotide identity with isolates of tomato leaf curl betasatellite. Thus, our findings propose a novel AlYVV Oman virus (AlYVV-OM) variant, emphasizing the need for additional epidemiological surveillance to understand its prevalence and significance in Oman and the broader region. To effectively manage the spread of AlYVV-OM and minimize its potential harm to (agro)ecosystems, future research should focus on elucidating the genetic diversity of AlYVV-OM and its interactions with other begomoviruses.
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Affiliation(s)
- Muhammad Shafiq
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud, Muscat 123, Oman
| | - Gabrijel Ondrasek
- Faculty of Agriculture, University of Zagreb, Svetosimunska Cesta 25, 10000 Zagreb, Croatia
| | - Abdullah Mohammed Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud, Muscat 123, Oman
| | - Muhammad Shafiq Shahid
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud, Muscat 123, Oman
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27
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Rosani U, Corinaldesi C, Luongo G, Sollitto M, Dal Monego S, Licastro D, Bongiorni L, Venier P, Pallavicini A, Dell’Anno A. Viral Diversity in Benthic Abyssal Ecosystems: Ecological and Methodological Considerations. Viruses 2023; 15:2282. [PMID: 38140524 PMCID: PMC10747316 DOI: 10.3390/v15122282] [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: 10/10/2023] [Revised: 11/13/2023] [Accepted: 11/18/2023] [Indexed: 12/24/2023] Open
Abstract
Viruses are the most abundant 'biological entities' in the world's oceans. However, technical and methodological constraints limit our understanding of their diversity, particularly in benthic abyssal ecosystems (>4000 m depth). To verify advantages and limitations of analyzing virome DNA subjected either to random amplification or unamplified, we applied shotgun sequencing-by-synthesis to two sample pairs obtained from benthic abyssal sites located in the North-eastern Atlantic Ocean at ca. 4700 m depth. One amplified DNA sample was also subjected to single-molecule long-read sequencing for comparative purposes. Overall, we identified 24,828 viral Operational Taxonomic Units (vOTUs), belonging to 22 viral families. Viral reads were more abundant in the amplified DNA samples (38.5-49.9%) compared to the unamplified ones (4.4-5.8%), with the latter showing a greater viral diversity and 11-16% of dsDNA viruses almost undetectable in the amplified samples. From a procedural point of view, the viromes obtained by direct sequencing (without amplification step) provided a broader overview of both ss and dsDNA viral diversity. Nevertheless, our results suggest that the contextual use of random amplification of the same sample and long-read technology can improve the assessment of viral assemblages by reducing off-target reads.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padova, Italy;
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
| | - Gabriella Luongo
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
| | - Marco Sollitto
- Department of Life Sciences, University of Trieste, Via Licio Giorgeri 5, 34127 Trieste, Italy; (M.S.); (A.P.)
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, 6000 Koper, Slovenia
| | - Simeone Dal Monego
- Laboratorio di Genomica ed Epigenomica, AREA Scienze Park, Padriciano 99, 34149 Trieste, Italy; (S.D.M.); (D.L.)
| | - Danilo Licastro
- Laboratorio di Genomica ed Epigenomica, AREA Scienze Park, Padriciano 99, 34149 Trieste, Italy; (S.D.M.); (D.L.)
| | - Lucia Bongiorni
- Consiglio Nazionale delle Ricerche, Istituto di Scienze Marine, Tesa 104–Arsenale, Castello 2737/F, 30122 Venezia, Italy;
| | - Paola Venier
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121 Padova, Italy;
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Licio Giorgeri 5, 34127 Trieste, Italy; (M.S.); (A.P.)
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy;
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28
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Medvedeva S, Borrel G, Krupovic M, Gribaldo S. A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment. Nat Microbiol 2023; 8:2170-2182. [PMID: 37749252 DOI: 10.1038/s41564-023-01485-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/30/2023] [Indexed: 09/27/2023]
Abstract
Methanogenic archaea are major producers of methane, a potent greenhouse gas and biofuel, and are widespread in diverse environments, including the animal gut. The ecophysiology of methanogens is likely impacted by viruses, which remain, however, largely uncharacterized. Here we carried out a global investigation of viruses associated with all current diversity of methanogens by assembling an extensive CRISPR database consisting of 156,000 spacers. We report 282 high-quality (pro)viral and 205 virus-like/plasmid sequences assigned to hosts belonging to ten main orders of methanogenic archaea. Viruses of methanogens can be classified into 87 families, underscoring a still largely undiscovered genetic diversity. Viruses infecting gut-associated archaea provide evidence of convergence in adaptation with viruses infecting gut-associated bacteria. These viruses contain a large repertoire of lysin proteins that cleave archaeal pseudomurein and are enriched in glycan-binding domains (Ig-like/Flg_new) and diversity-generating retroelements. The characterization of this vast repertoire of viruses paves the way towards a better understanding of their role in regulating methanogen communities globally, as well as the development of much-needed genetic tools.
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Affiliation(s)
- Sofia Medvedeva
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Unit Archaeal Virology, Paris, France.
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France.
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29
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Gomes RAL, Zerbini FM. ConCreT, a 2D convolutional neural network for taxonomic classification applied to viruses in the phylum Cressdnaviricota. J Virol Methods 2023; 320:114789. [PMID: 37536450 DOI: 10.1016/j.jviromet.2023.114789] [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: 05/03/2023] [Revised: 07/19/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Taxonomic assignments allow scientists to communicate better with each other. In virology, taxonomy is continually improving towards a more precise and comprehensive framework. With the huge numbers of new viruses being described in metagenomic studies, automated taxonomy tools are urgently needed. A number of such tools have been proposed, and those applying machine learning (ML), mainly in the deep learning branch, stand out with accurate results. Still, there is a demand for tools that are less computationally intensive and that can classify viruses down to the ranks of genus and species. Cressdnaviruses are good subjects for testing such tools, due to their small, circular genomes and the existence of several families and genera with a highly imbalanced number of species. We developed a 2D convolutional neural network for virus taxonomy and tested it for classification of viruses from the phylum Cressdnaviricota. We obtained >98 % accuracy in the final pipeline tested, which we named ConCreT (Convolutional Neural Network for Cressdnavirus Taxonomy). The mixture of augmentation for more imbalanced groups with no augmentation for more balanced ones achieved the best score in the final test.
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Affiliation(s)
- Ruither A L Gomes
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil; National Institute for Science and Technology on Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - F Murilo Zerbini
- Dep. de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil; National Institute for Science and Technology on Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
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30
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Abstract
Two decades of metagenomic analyses have revealed that in many environments, small (∼5 kb), single-stranded DNA phages of the family Microviridae dominate the virome. Although the emblematic microvirus phiX174 is ubiquitous in the laboratory, most other microviruses, particularly those of the gokushovirus and amoyvirus lineages, have proven to be much more elusive. This puzzling lack of representative isolates has hindered insights into microviral biology. Furthermore, the idiosyncratic size and nature of their genomes have resulted in considerable misjudgments of their actual abundance in nature. Fortunately, recent successes in microvirus isolation and improved metagenomic methodologies can now provide us with more accurate appraisals of their abundance, their hosts, and their interactions. The emerging picture is that phiX174 and its relatives are rather rare and atypical microviruses, and that a tremendous diversity of other microviruses is ready for exploration.
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Affiliation(s)
- Paul C Kirchberger
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA;
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
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31
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Shakir S, Mubin M, Nahid N, Serfraz S, Qureshi MA, Lee TK, Liaqat I, Lee S, Nawaz-ul-Rehman MS. REPercussions: how geminiviruses recruit host factors for replication. Front Microbiol 2023; 14:1224221. [PMID: 37799604 PMCID: PMC10548238 DOI: 10.3389/fmicb.2023.1224221] [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: 05/22/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023] Open
Abstract
Circular single-stranded DNA viruses of the family Geminiviridae encode replication-associated protein (Rep), which is a multifunctional protein involved in virus DNA replication, transcription of virus genes, and suppression of host defense responses. Geminivirus genomes are replicated through the interaction between virus Rep and several host proteins. The Rep also interacts with itself and the virus replication enhancer protein (REn), which is another essential component of the geminivirus replicase complex that interacts with host DNA polymerases α and δ. Recent studies revealed the structural and functional complexities of geminivirus Rep, which is believed to have evolved from plasmids containing a signature domain (HUH) for single-stranded DNA binding with nuclease activity. The Rep coding sequence encompasses the entire coding sequence for AC4, which is intricately embedded within it, and performs several overlapping functions like Rep, supporting virus infection. This review investigated the structural and functional diversity of the geminivirus Rep.
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Affiliation(s)
- Sara Shakir
- Plant Genetics Lab, Gembloux Agro-Bio Tech, University of Liѐge, Gembloux, Belgium
| | - Muhammad Mubin
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, Pakistan
| | - Nazia Nahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Saad Serfraz
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, Pakistan
| | - Muhammad Amir Qureshi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Taek-Kyun Lee
- Risk Assessment Research Center, Korea Institute of Ocean Science and Technology, Geoje, Republic of Korea
| | - Iram Liaqat
- Microbiology Lab, Department of Zoology, Government College University, Lahore, Pakistan
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Muhammad Shah Nawaz-ul-Rehman
- Virology Lab, Center for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, Pakistan
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van der Loos LM, De Coninck L, Zell R, Lequime S, Willems A, De Clerck O, Matthijnssens J. Highly divergent CRESS DNA and picorna-like viruses associated with bleached thalli of the green seaweed Ulva. Microbiol Spectr 2023; 11:e0025523. [PMID: 37724866 PMCID: PMC10581178 DOI: 10.1128/spectrum.00255-23] [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: 01/16/2023] [Accepted: 07/19/2023] [Indexed: 09/21/2023] Open
Abstract
Marine macroalgae (seaweeds) are important primary producers and foundation species in coastal ecosystems around the world. Seaweeds currently contribute to an estimated 51% of the global mariculture production, with a long-term growth rate of 6% per year, and an estimated market value of more than US$11.3 billion. Viral infections could have a substantial impact on the ecology and aquaculture of seaweeds, but surprisingly little is known about virus diversity in macroalgal hosts. Using metagenomic sequencing, we characterized viral communities associated with healthy and bleached specimens of the commercially important green seaweed Ulva. We identified 20 putative new and divergent viruses, of which the majority belonged to the Circular Rep-Encoding Single-Stranded (CRESS) DNA viruses [single-stranded (ss)DNA genomes], Durnavirales [double-stranded (ds)RNA], and Picornavirales (ssRNA). Other newly identified RNA viruses were related to the Ghabrivirales, the Mitoviridae, and the Tombusviridae. Bleached Ulva samples contained particularly high viral read numbers. While reads matching assembled CRESS DNA viruses and picorna-like viruses were nearly absent from the healthy Ulva samples (confirmed by qPCR), they were very abundant in the bleached specimens. Therefore, bleaching in Ulva could be caused by one or a combination of the identified viruses but may also be the result of another causative agent or abiotic stress, with the viruses simply proliferating in already unhealthy seaweed tissue. This study highlights how little we know about the diversity and ecology of seaweed viruses, especially in relation to the health and diseases of the algal host, and emphasizes the need to better characterize the algal virosphere. IMPORTANCE Green seaweeds of the genus Ulva are considered a model system to study microbial interactions with the algal host. Remarkably little is known, however, about viral communities associated with green seaweeds, especially in relation to the health of the host. In this study, we characterized the viral communities associated with healthy and bleached Ulva. Our findings revealed the presence of 20 putative novel viruses associated with Ulva, encompassing both DNA and RNA viruses. The majority of these viruses were found to be especially abundant in bleached Ulva specimens. This is the first step toward understanding the role of viruses in the ecology and aquaculture of this green seaweed.
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Affiliation(s)
- Luna M. van der Loos
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Lander De Coninck
- Laboratory of Clinical and Epidemiological Virology, Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Roland Zell
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Sebastian Lequime
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Anne Willems
- Laboratory of Microbiology, Department Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Ghent, Belgium
| | - Jelle Matthijnssens
- Laboratory of Clinical and Epidemiological Virology, Laboratory of Viral Metagenomics, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
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Vidovszky MZ, Kapitány S, Gellért Á, Harrach B, Görföl T, Boldogh SA, Kohl C, Wibbelt G, Mühldorfer K, Kemenesi G, Gembu GC, Hassanin A, Tu VT, Estók P, Horváth A, Kaján GL. Detection and genetic characterization of circoviruses in more than 80 bat species from eight countries on four continents. Vet Res Commun 2023; 47:1561-1573. [PMID: 37002455 PMCID: PMC10066014 DOI: 10.1007/s11259-023-10111-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/19/2023] [Indexed: 04/03/2023]
Abstract
Several bat-associated circoviruses and circular rep-encoding single-stranded DNA (CRESS DNA) viruses have been described, but the exact diversity and host species of these viruses are often unknown. Our goal was to describe the diversity of bat-associated circoviruses and cirliviruses, thus, 424 bat samples from more than 80 species were collected on four continents. The samples were screened for circoviruses using PCR and the resulting amino acid sequences were subjected to phylogenetic analysis. The majority of bat strains were classified in the genus Circovirus and some strains in the genus Cyclovirus and the clades CRESS1 and CRESS3. Some strains, however, could only be classified at the taxonomic level of the order and were not classified in any of the accepted or proposed clades. In the family Circoviridae, 71 new species have been predicted. This screening of bat samples revealed a great diversity of circoviruses and cirliviruses. These studies underline the importance of the discovery and description of new cirliviruses and the need to establish new species and families in the order Cirlivirales.
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Affiliation(s)
| | | | - Ákos Gellért
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Balázs Harrach
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Tamás Görföl
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
| | | | - Claudia Kohl
- Centre for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin, Germany
| | - Gudrun Wibbelt
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Kristin Mühldorfer
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Gábor Kemenesi
- National Laboratory of Virology, University of Pécs, Pécs, Hungary
| | - Guy-Crispin Gembu
- Faculté des Sciences, Université de Kisangani, Kisangani, République Démocratique du Congo
| | - Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Péter Estók
- Department of Zoology, Eszterházy Károly Catholic University, Eger, Hungary
| | - Anna Horváth
- QUIRÓN, Center for Equine Assisted Interventions and Training for Well-Being and Sustainability, Comitán de Domínguez, Mexico
| | - Győző L. Kaján
- Veterinary Medical Research Institute, Budapest, Hungary
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Paietta EN, Kraberger S, Custer JM, Vargas KL, Espy C, Ehmke E, Yoder AD, Varsani A. Characterization of Diverse Anelloviruses, Cressdnaviruses, and Bacteriophages in the Human Oral DNA Virome from North Carolina (USA). Viruses 2023; 15:1821. [PMID: 37766228 PMCID: PMC10537320 DOI: 10.3390/v15091821] [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: 07/08/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
The diversity of viruses identified from the various niches of the human oral cavity-from saliva to dental plaques to the surface of the tongue-has accelerated in the age of metagenomics. This rapid expansion demonstrates that our understanding of oral viral diversity is incomplete, with only a few studies utilizing passive drool collection in conjunction with metagenomic sequencing methods. For this pilot study, we obtained 14 samples from healthy staff members working at the Duke Lemur Center (Durham, NC, USA) to determine the viral diversity that can be identified in passive drool samples from humans. The complete genomes of 3 anelloviruses, 9 cressdnaviruses, 4 Caudoviricetes large bacteriophages, 29 microviruses, and 19 inoviruses were identified in this study using high-throughput sequencing and viral metagenomic workflows. The results presented here expand our understanding of the vertebrate-infecting and microbe-infecting viral diversity of the human oral virome in North Carolina (USA).
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Affiliation(s)
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M. Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Karla L. Vargas
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Claudia Espy
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Erin Ehmke
- Duke Lemur Center, Duke University, Durham, NC 27705, USA;
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
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da Silva JPH, de Resende FMP, da Silva JCF, de Breuil S, Nome C, Bejerman N, Zerbini FM. Amesuviridae: a new family of plant-infecting viruses in the phylum Cressdnaviricota, realm Monodnaviria. Arch Virol 2023; 168:223. [PMID: 37561218 DOI: 10.1007/s00705-023-05852-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
The phylum Cressdnaviricota comprises viruses with single-stranded, circular DNA genomes that encode an HUH-type endonuclease (known as Rep). The phylum includes two classes, eight orders, and 11 families. Here, we report the creation of a twelfth family in the order Mulpavirales, class Arfiviricetes of the phylum Cressdnaviricota. The family Amesuviridae comprises viruses that infect plants and is divided into two genera: Temfrudevirus, including the species Temfrudevirus temperatum (with temperate fruit decay-associated virus as a member), and Yermavirus, including the species Yermavirus ilicis (with yerba mate-associated circular DNA virus as a member). Both viruses encode Rep proteins with HUH endonuclease and SH3 superfamily helicase domains. Phylogenetic analysis indicates that the replicative module of amesuviruses constitutes a well-supported monophyletic clade related to Rep proteins from viruses in the order Mulpavirales. Furthermore, both viruses encode a single capsid protein (CP) related to geminivirus CPs. Phylogenetic incongruence between the replicative and structural modules of amesuviruses suggests a chimeric origin resulting from remote recombination events between ancestral mulpavirales and geminivirids. The creation of the family Amesuviridae has been ratified by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
| | | | | | - Soledad de Breuil
- Instituto de Patología Vegetal, Centro de Investigaciones, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5.5, X5020ICA, Agropecuarias, Córdoba, Argentina
| | - Claudia Nome
- Instituto de Patología Vegetal, Centro de Investigaciones, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5.5, X5020ICA, Agropecuarias, Córdoba, Argentina
| | - Nicolas Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5.5, X5020ICA, Agropecuarias, Córdoba, Argentina
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Vasinioti VI, Pellegrini F, Buonavoglia A, Capozza P, Cardone R, Diakoudi G, Desario C, Catella C, Vicenza T, Lucente MS, Di Martino B, Camero M, Elia G, Decaro N, Martella V, Lanave G. Investigating the genetic diversity of CRESS DNA viruses in cats identifies a novel feline circovirus and unveils exposure of cats to canine circovirus. Res Vet Sci 2023; 161:86-95. [PMID: 37327693 DOI: 10.1016/j.rvsc.2023.06.011] [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: 04/12/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA viruses include Circoviruses which have been found in several animal species and in human specimens. Circoviruses are associated with severe disease in pigs and birds and with respiratory and gastrointestinal disorders and systemic disease in dogs. In cats there are only a few anecdotical studies reporting CRESS DNA viruses. In this study, a total of 530 samples (361 sera, 131 stools, and 38 respiratory swabs) from cats, were screened for the presence of CRESS DNA viruses. Overall, 48 (9.0%) of 530 samples tested positive using a pan-Rep PCR. A total of 30 Rep sequences were obtained. Ten sequences of fecal origin were tightly related to each other (82.4-100% nt identity) and more distantly related to mongoose circoviruses (68.3 to 77.2% nt identity). At genome level these circoviruses displayed the highest nt identity (74.3-78.7%) to mongoose circoviruses thus representing a novel circovirus species. Circoviruses from different animal hosts (n = 12) and from humans (n = 8) were also identified. However, six Rep sequences were obtained from serum samples, including canine circoviruses, a human cyclovirus and human and fish-associated CRESS DNA viruses. The presence of these viruses in the sera would imply, to various extent, virus replication in the animal host, able to sustain viremia. Overall, these findings indicate a wide genetic diversity of CRESS DNA viruses in cats and warrant further investigations.
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Affiliation(s)
- Violetta Iris Vasinioti
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Francesco Pellegrini
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Alessio Buonavoglia
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Paolo Capozza
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Roberta Cardone
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Costantina Desario
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Cristiana Catella
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Teresa Vicenza
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Maria Stella Lucente
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Barbara Di Martino
- Department of Veterinary Medicine, Università degli Studi di Teramo, SP18, 64100 Teramo, Italy
| | - Michele Camero
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Gabriella Elia
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy
| | - Gianvito Lanave
- Department of Veterinary Medicine, University of Bari Aldo Moro, S.p. per Casamassima Km 3, Valenzano, 70010 Bari, Italy.
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37
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Dunay E, Rukundo J, Atencia R, Cole MF, Cantwell A, Emery Thompson M, Rosati AG, Goldberg TL. Viruses in saliva from sanctuary chimpanzees (Pan troglodytes) in Republic of Congo and Uganda. PLoS One 2023; 18:e0288007. [PMID: 37384730 PMCID: PMC10310015 DOI: 10.1371/journal.pone.0288007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
Pathogen surveillance for great ape health monitoring has typically been performed on non-invasive samples, primarily feces, in wild apes and blood in sanctuary-housed apes. However, many important primate pathogens, including known zoonoses, are shed in saliva and transmitted via oral fluids. Using metagenomic methods, we identified viruses in saliva samples from 46 wild-born, sanctuary-housed chimpanzees at two African sanctuaries in Republic of Congo and Uganda. In total, we identified 20 viruses. All but one, an unclassified CRESS DNA virus, are classified in five families: Circoviridae, Herpesviridae, Papillomaviridae, Picobirnaviridae, and Retroviridae. Overall, viral prevalence ranged from 4.2% to 87.5%. Many of these viruses are ubiquitous in primates and known to replicate in the oral cavity (simian foamy viruses, Retroviridae; a cytomegalovirus and lymphocryptovirus; Herpesviridae; and alpha and gamma papillomaviruses, Papillomaviridae). None of the viruses identified have been shown to cause disease in chimpanzees or, to our knowledge, in humans. These data suggest that the risk of zoonotic viral disease from chimpanzee oral fluids in sanctuaries may be lower than commonly assumed.
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Affiliation(s)
- Emily Dunay
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Joshua Rukundo
- Ngamba Island Chimpanzee Sanctuary / Chimpanzee Trust, Entebbe, Uganda
| | - Rebeca Atencia
- Jane Goodall Institute Congo, Pointe-Noire, Republic of Congo
| | - Megan F. Cole
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Averill Cantwell
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Melissa Emery Thompson
- Department of Anthropology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Alexandra G. Rosati
- Department of Psychology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Anthropology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Lund MC, Larsen BB, Rowsey DM, Otto HW, Gryseels S, Kraberger S, Custer JM, Steger L, Yule KM, Harris RE, Worobey M, Van Doorslaer K, Upham NS, Varsani A. Using archived and biocollection samples towards deciphering the DNA virus diversity associated with rodent species in the families cricetidae and heteromyidae. Virology 2023; 585:42-60. [PMID: 37276766 DOI: 10.1016/j.virol.2023.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Abstract
Rodentia is the most speciose order of mammals, and they are known to harbor a wide range of viruses. Although there has been significant research on zoonotic viruses in rodents, research on the diversity of other viruses has been limited, especially for rodents in the families Cricetidae and Heteromyidae. In fecal and liver samples of nine species of rodents, we identify 346 distinct circular DNA viral genomes. Of these, a large portion are circular, single-stranded DNA viruses in the families Anelloviridae (n = 3), Circoviridae (n = 5), Genomoviridae (n = 7), Microviridae (n = 297), Naryaviridae (n = 4), Vilyaviridae (n = 15) and in the phylum Cressdnaviricota (n = 13) that cannot be assigned established families. We also identified two large bacteriophages of 36 and 50 kb that are part of the class Caudoviricetes. Some of these viruses are clearly those that infect rodents, however, most of these likely infect various organisms associated with rodents, their environment or their diet.
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Affiliation(s)
- Michael C Lund
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98102, USA
| | - Dakota M Rowsey
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Hans W Otto
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Sophie Gryseels
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium; Department of Biology, University of Antwerp, 2000, Antwerp, Belgium; OD Taxonomy and Phylogeny, Royal Belgian Museum of Natural Sciences, 1000, Brussels, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Laura Steger
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Kelsey M Yule
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Robin E Harris
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, AZ, 85724, USA
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7701, South Africa.
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Krupovic M, Dolja VV, Koonin EV. The virome of the last eukaryotic common ancestor and eukaryogenesis. Nat Microbiol 2023; 8:1008-1017. [PMID: 37127702 PMCID: PMC11130978 DOI: 10.1038/s41564-023-01378-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/29/2023] [Indexed: 05/03/2023]
Abstract
All extant eukaryotes descend from the last eukaryotic common ancestor (LECA), which is thought to have featured complex cellular organization. To gain insight into LECA biology and eukaryogenesis-the origin of the eukaryotic cell, which remains poorly understood-we reconstructed the LECA virus repertoire. We compiled an inventory of eukaryotic hosts of all major virus taxa and reconstructed the LECA virome by inferring the origins of these groups of viruses. The origin of the LECA virome can be traced back to a small set of bacterial-not archaeal-viruses. This provenance of the LECA virome is probably due to the bacterial origin of eukaryotic membranes, which is most compatible with two endosymbiosis events in a syntrophic model of eukaryogenesis. In the first endosymbiosis, a bacterial host engulfed an Asgard archaeon, preventing archaeal viruses from entry owing to a lack of archaeal virus receptors on the external membranes.
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Affiliation(s)
- Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France.
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA.
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40
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Butkovic A, Kraberger S, Smeele Z, Martin DP, Schmidlin K, Fontenele RS, Shero MR, Beltran RS, Kirkham AL, Aleamotu’a M, Burns JM, Koonin EV, Varsani A, Krupovic M. Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein. Virus Evol 2023; 9:vead035. [PMID: 37325085 PMCID: PMC10266747 DOI: 10.1093/ve/vead035] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Anelloviruses are highly prevalent in diverse mammals, including humans, but so far have not been linked to any disease and are considered to be part of the 'healthy virome'. These viruses have small circular single-stranded DNA (ssDNA) genomes and encode several proteins with no detectable sequence similarity to proteins of other known viruses. Thus, anelloviruses are the only family of eukaryotic ssDNA viruses currently not included in the realm Monodnaviria. To gain insights into the provenance of these enigmatic viruses, we sequenced more than 250 complete genomes of anelloviruses from nasal and vaginal swab samples of Weddell seal (Leptonychotes weddellii) from Antarctica and a fecal sample of grizzly bear (Ursus arctos horribilis) from the USA and performed a comprehensive family-wide analysis of the signature anellovirus protein ORF1. Using state-of-the-art remote sequence similarity detection approaches and structural modeling with AlphaFold2, we show that ORF1 orthologs from all Anelloviridae genera adopt a jelly-roll fold typical of viral capsid proteins (CPs), establishing an evolutionary link to other eukaryotic ssDNA viruses, specifically, circoviruses. However, unlike CPs of other ssDNA viruses, ORF1 encoded by anelloviruses from different genera display remarkable variation in size, due to insertions into the jelly-roll domain. In particular, the insertion between β-strands H and I forms a projection domain predicted to face away from the capsid surface and function at the interface of virus-host interactions. Consistent with this prediction and supported by recent experimental evidence, the outermost region of the projection domain is a mutational hotspot, where rapid evolution was likely precipitated by the host immune system. Collectively, our findings further expand the known diversity of anelloviruses and explain how anellovirus ORF1 proteins likely diverged from canonical jelly-roll CPs through gradual augmentation of the projection domain. We suggest assigning Anelloviridae to a new phylum, 'Commensaviricota', and including it into the kingdom Shotokuvirae (realm Monodnaviria), alongside Cressdnaviricota and Cossaviricota.
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Affiliation(s)
- Anamarija Butkovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, Paris 75015, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Zoe Smeele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Darren P Martin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Michelle R Shero
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543, USA
| | - Roxanne S Beltran
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Amy L Kirkham
- U.S. Fish and Wildlife Service, Marine Mammals Management, 1011 E, Tudor Road, Anchorage, AK 99503, USA
| | - Maketalena Aleamotu’a
- School of Environmental and Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Jennifer M Burns
- Department of Biological Sciences, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, 1 Anzio Road, Cape Town 7925, South Africa
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, Paris 75015, France
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Atabekova AK, Solovieva AD, Chergintsev DA, Solovyev AG, Morozov SY. Role of Plant Virus Movement Proteins in Suppression of Host RNAi Defense. Int J Mol Sci 2023; 24:ijms24109049. [PMID: 37240394 DOI: 10.3390/ijms24109049] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
One of the systems of plant defense against viral infection is RNA silencing, or RNA interference (RNAi), in which small RNAs derived from viral genomic RNAs and/or mRNAs serve as guides to target an Argonaute nuclease (AGO) to virus-specific RNAs. Complementary base pairing between the small interfering RNA incorporated into the AGO-based protein complex and viral RNA results in the target cleavage or translational repression. As a counter-defensive strategy, viruses have evolved to acquire viral silencing suppressors (VSRs) to inhibit the host plant RNAi pathway. Plant virus VSR proteins use multiple mechanisms to inhibit silencing. VSRs are often multifunctional proteins that perform additional functions in the virus infection cycle, particularly, cell-to-cell movement, genome encapsidation, or replication. This paper summarizes the available data on the proteins with dual VSR/movement protein activity used by plant viruses of nine orders to override the protective silencing response and reviews the different molecular mechanisms employed by these proteins to suppress RNAi.
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Affiliation(s)
- Anastasia K Atabekova
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
| | - Anna D Solovieva
- Department of Virology, Biological Faculty, Moscow State University, 119234 Moscow, Russia
| | - Denis A Chergintsev
- Department of Virology, Biological Faculty, Moscow State University, 119234 Moscow, Russia
| | - Andrey G Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
- Department of Virology, Biological Faculty, Moscow State University, 119234 Moscow, Russia
| | - Sergey Y Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
- Department of Virology, Biological Faculty, Moscow State University, 119234 Moscow, Russia
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42
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König MT, Frölich K, Jandowsky A, Knauf-Witzens T, Langner C, Dietrich R, Märtlbauer E, Didier A. First Insights into the Occurrence of Circular Single-Stranded DNA Genomes in Asian and African Cattle. Animals (Basel) 2023; 13:ani13091492. [PMID: 37174530 PMCID: PMC10177065 DOI: 10.3390/ani13091492] [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: 03/17/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Circular replicase-encoding single-stranded (CRESS) DNA viruses and other circular DNA agents are increasingly found in various samples and animals. A specific class of these agents-termed bovine meat and milk factors (BMMF)-has been supposed to act as a factor in indirect carcinogenesis in humans. Initial observations attributed the BMMF to European cattle breeds and foodstuffs produced thereof. In the present study, blood and fecal samples from African and Asian cattle were examined. BMMF molecules and genomoviruses were detected in all bovids under study. The majority (79%) of the 29 circular elements could be assigned to BMMF groups 1 and 2, whereas CRESS viruses of the family Genomoviridae accounted for the smaller part (21%). Two genomoviruses belong to the genus Gemykibivirus and one to the genus Gemykrogvirus. The remaining three might be considered as novel species within the genus Gemycircularvirus. The majority of all isolated molecules originated from fecal samples, whereas only three derived from blood. The results from this study expand our knowledge on the diversity and presence of circular DNA in different ruminants that serve for food production in many countries over the world.
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Affiliation(s)
- Marie-Thérèse König
- Department of Veterinary Sciences, Institute of Food Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstraße 8, 85764 Oberschleißheim, Germany
| | - Kai Frölich
- Tierpark Arche Warder, Zentrum für Seltene Nutztierrassen e. V., Langwedeler Weg 11, 24646 Warder, Germany
| | - Anabell Jandowsky
- Tierpark Arche Warder, Zentrum für Seltene Nutztierrassen e. V., Langwedeler Weg 11, 24646 Warder, Germany
| | - Tobias Knauf-Witzens
- Wilhelma Zoological-Botanical Gardens Stuttgart, Wilhelma 13, 70376 Stuttgart, Germany
| | - Christoph Langner
- Stralsund Zoological Garden, Grünhufer Bogen 2, 18437 Stralsund, Germany
| | - Richard Dietrich
- Department of Veterinary Sciences, Institute of Food Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstraße 8, 85764 Oberschleißheim, Germany
| | - Erwin Märtlbauer
- Department of Veterinary Sciences, Institute of Food Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstraße 8, 85764 Oberschleißheim, Germany
| | - Andrea Didier
- Department of Veterinary Sciences, Institute of Food Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstraße 8, 85764 Oberschleißheim, Germany
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Gainor K, Stewart KM, Picknell A, Russ M, Makela N, Watson K, Mancuso DM, Malik YS, Ghosh S. First Report on Detection and Complete Genomic Analysis of a Novel CRESS DNA Virus from Sea Turtles. Pathogens 2023; 12:pathogens12040601. [PMID: 37111487 PMCID: PMC10142553 DOI: 10.3390/pathogens12040601] [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: 03/13/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
To date, only a handful of viruses have been identified in sea turtles. Although eukaryotic circular Rep (replication initiation protein)-encoding single-stranded DNA (CRESS DNA) viruses have been reported from a wide variety of terrestrial species, and some of these viruses have been associated with clinical conditions in certain animals, limited information is available on CRESS DNA viruses from marine life. The present study aimed to investigate the presence of CRESS DNA viruses in sea turtles. In the present study, two (samples T3 and T33) of the 34 cloacal samples from 31 sea turtles (found in ocean waters around the Caribbean Islands of St. Kitts and Nevis) tested positive for CRESS DNA viruses by a pan-rep nested PCR assay. The partial Rep sequence of T3 shared 75.78% of a deduced amino acid (aa) identity with that of a CRESS DNA virus (classified under family Circoviridae) from a mollusk. On the other hand, the complete genome (2428 bp) of T33 was determined by an inverse nested PCR assay. The genomic organization of T33 mirrored those of type II CRESS DNA viral genomes of cycloviruses, characterized by the putative "origin of replication" in the 5'-intergenic region, and the putative Capsid (Cap)- and Rep-encoding open reading frame on the virion-sense- and antisense-strand, respectively. The putative Rep (322 aa) of T33 retained the conserved "HUH endonuclease" and the "super 3 family helicase" domains and shared pairwise aa identities of ~57% with unclassified CRESS DNA viruses from benthic sediment and mollusks. Phylogenetically, the T33 Rep formed a distinct branch within an isolated cluster of unclassified CRESS DNA viruses. The putative Cap (370 aa) of T33 shared maximum pairwise aa identity of 30.51% with an unclassified CRESS DNA virus from a capybara. Except for a blood sample from T33 that tested negative for CRESS DNA viruses, other tissue samples were not available from the sea turtles. Therefore, we could not establish whether the T3 and T33 viral strains infected the sea turtles or were of dietary origin. To our knowledge, this is the first report on the detection of CRESS DNA viruses from sea turtles, adding yet another animal species to the rapidly expanding host range of these viruses. Complete genome analysis of T33 identified a novel, unclassified CRESS DNA virus, providing insights into the high genetic diversity between viruses within the phylum Cressdnaviricota. Considering that sea turtles are an at-risk species, extensive studies on virus discovery, surveillance, and pathogenesis in these marine animals are of the utmost importance.
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Affiliation(s)
- Kerry Gainor
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
| | - Kimberly M Stewart
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
- St. Kitts Sea Turtle Monitoring Network, Basseterre P.O. Box 2298, Saint Kitts and Nevis
| | - Angela Picknell
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
- St. Kitts Sea Turtle Monitoring Network, Basseterre P.O. Box 2298, Saint Kitts and Nevis
| | - Morgan Russ
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
- St. Kitts Sea Turtle Monitoring Network, Basseterre P.O. Box 2298, Saint Kitts and Nevis
| | - Noah Makela
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
- St. Kitts Sea Turtle Monitoring Network, Basseterre P.O. Box 2298, Saint Kitts and Nevis
| | - Kierra Watson
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
- St. Kitts Sea Turtle Monitoring Network, Basseterre P.O. Box 2298, Saint Kitts and Nevis
| | - Diana M Mancuso
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
| | - Yashpal Singh Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana 141012, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
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Makoa-Meng M, Semmar R, Antezack A, Penant G, La Scola B, Monnet-Corti V, Colson P. Correlation of Redondovirus and Entamoeba gingivalis Detections in the Human Oral Cavity Suggests That This Amoeba Is Possibly the Redondovirus Host. Int J Mol Sci 2023; 24:ijms24076303. [PMID: 37047275 PMCID: PMC10094137 DOI: 10.3390/ijms24076303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
The virome of the human oral cavity and the relationships between viruses and diseases such as periodontitis are scarcely deciphered. Redondoviruses were reported in the human oral cavity in 2019, including in periodontitis patients. Here, we aimed at detecting redondoviruses and at searching for a potential viral host in human saliva. Non-stimulated saliva was collected between December 2020 and June 2021. These samples were tested using real-time PCR regarding the presence of redondovirus and Entamoeba gingivalis DNA. Similarity searches were performed using BLAST against eukaryotic and prokaryotic sequences from GenBank. The redondovirus DNA was detected in 46% of the 28 human saliva samples. In addition, short fragments of redondovirus genomes were detected in silico within Entamoeba sequences. Finally, Entamoeba gingivalis DNA was detected in 46% of the 28 saliva samples, with a strong correlation between redondovirus DNA and E. gingivalis DNA detections, in 93% of the cases. Regarded together, these findings and previous ones strongly support the presence of redondoviruses in the human oral cavity and their association to E. gingivalis as their likely host.
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Melnik BC, Stadler R, Weiskirchen R, Leitzmann C, Schmitz G. Potential Pathogenic Impact of Cow’s Milk Consumption and Bovine Milk-Derived Exosomal MicroRNAs in Diffuse Large B-Cell Lymphoma. Int J Mol Sci 2023; 24:ijms24076102. [PMID: 37047075 PMCID: PMC10094152 DOI: 10.3390/ijms24076102] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/05/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Epidemiological evidence supports an association between cow’s milk consumption and the risk of diffuse large B-cell lymphoma (DLBCL), the most common non-Hodgkin lymphoma worldwide. This narrative review intends to elucidate the potential impact of milk-related agents, predominantly milk-derived exosomes (MDEs) and their microRNAs (miRs) in lymphomagenesis. Upregulation of PI3K-AKT-mTORC1 signaling is a common feature of DLBCL. Increased expression of B cell lymphoma 6 (BCL6) and suppression of B lymphocyte-induced maturation protein 1 (BLIMP1)/PR domain-containing protein 1 (PRDM1) are crucial pathological deviations in DLBCL. Translational evidence indicates that during the breastfeeding period, human MDE miRs support B cell proliferation via epigenetic upregulation of BCL6 (via miR-148a-3p-mediated suppression of DNA methyltransferase 1 (DNMT1) and miR-155-5p/miR-29b-5p-mediated suppression of activation-induced cytidine deaminase (AICDA) and suppression of BLIMP1 (via MDE let-7-5p/miR-125b-5p-targeting of PRDM1). After weaning with the physiological termination of MDE miR signaling, the infant’s BCL6 expression and B cell proliferation declines, whereas BLIMP1-mediated B cell maturation for adequate own antibody production rises. Because human and bovine MDE miRs share identical nucleotide sequences, the consumption of pasteurized cow’s milk in adults with the continued transfer of bioactive bovine MDE miRs may de-differentiate B cells back to the neonatal “proliferation-dominated” B cell phenotype maintaining an increased BLC6/BLIMP1 ratio. Persistent milk-induced epigenetic dysregulation of BCL6 and BLIMP1 expression may thus represent a novel driving mechanism in B cell lymphomagenesis. Bovine MDEs and their miR cargo have to be considered potential pathogens that should be removed from the human food chain.
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Harding C, Larsen BB, Otto HW, Potticary AL, Kraberger S, Custer JM, Suazo C, Upham NS, Worobey M, Van Doorslaer K, Varsani A. Diverse DNA virus genomes identified in fecal samples of Mexican free-tailed bats (Tadarida brasiliensis) captured in Chiricahua Mountains of southeast Arizona (USA). Virology 2023; 580:98-111. [PMID: 36801670 DOI: 10.1016/j.virol.2023.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
Bats (order Chiroptera) are some of the most abundant mammals on earth and their species ecology strongly influences zoonotic potential. While substantial research has been conducted on bat-associated viruses, particularly on those that can cause disease in humans and/or livestock, globally, limited research has focused on endemic bats in the USA. The southwest region of the US is of particular interest because of its high diversity of bat species. We identified 39 single-stranded DNA virus genomes in the feces of Mexican free-tailed bats (Tadarida brasiliensis) sampled in the Rucker Canyon (Chiricahua Mountains) of southeast Arizona (USA). Twenty-eight of these belong to the virus families Circoviridae (n = 6), Genomoviridae (n = 17), and Microviridae (n = 5). Eleven viruses cluster with other unclassified cressdnaviruses. Most of the viruses identified represent new species. Further research on identification of novel bat-associated cressdnaviruses and microviruses is needed to provide greater insights regarding their co-evolution and ecology relative to bats.
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Affiliation(s)
- Ciara Harding
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Howard Hughes Medical Institute, Seattle, WA, 98109, USA
| | - Hans W Otto
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Ahva L Potticary
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; University of Georgia in the Department of Entomology, Athens, GA, 30602, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA
| | - Crystal Suazo
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, Genetics Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, AZ, 85724, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7701, South Africa.
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Lee BD, Neri U, Roux S, Wolf YI, Camargo AP, Krupovic M, Simmonds P, Kyrpides N, Gophna U, Dolja VV, Koonin EV. Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs. Cell 2023; 186:646-661.e4. [PMID: 36696902 PMCID: PMC9911046 DOI: 10.1016/j.cell.2022.12.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/11/2022] [Accepted: 12/20/2022] [Indexed: 01/26/2023]
Abstract
Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters, a 5-fold increase compared to the previously identified viroid-like elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is far broader than currently known, and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes.
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Affiliation(s)
- Benjamin D Lee
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Uri Neri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Antonio Pedro Camargo
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015 Paris, France
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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Zhang LH, Wang LQ, Li HX, Zhang HL, Zheng LL, Chen XM, Chen HY. Detection and genetic analysis of porcine circovirus-like virus in pigs with diarrhea between 2016 and 2021 in Henan and Shanxi provinces of China. Arch Virol 2023; 168:76. [PMID: 36709234 DOI: 10.1007/s00705-023-05701-0] [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: 09/01/2022] [Accepted: 12/06/2022] [Indexed: 01/29/2023]
Abstract
Porcine circovirus-like virus (PCLV) is a recently discovered virus that may be associated with diarrhea in pigs. To investigate the epidemic profile and genetic characteristics of this virus, 175 clinical samples (141 intestinal samples, 17 blood samples, and 17 fecal samples) were collected from diseased piglets during outbreaks of diarrhea from 33 pig farms in 19 cities of Henan and Shanxi provinces of China between 2016 and 2021 and were screened by PCR for the presence of PCLV. The results showed that the positive rate for PCLV was 32% (56/175) at the sample level, 60.6% (20/33) at the farm level, and 57.9% (11/19) at the city level, which varied from 5.88% to 44.12% between 2016 and 2021. It was also found that PCLV occurred in coinfections with porcine circovirus type 2 (PCV2), PCV3, PCV4, porcine epidemic diarrhea virus, and porcine reproductive and respiratory syndrome virus, but no nucleic acids were detected for transmissible gastroenteritis virus, porcine deltacoronavirus, or porcine rotavirus in piglets with diarrhea. Notably, PCLV was detected in 13 diarrheal piglets from four different farms that were negative for the other porcine viruses. These findings suggest that PCLV may be associated with porcine diarrhea and that it has been circulating in piglets in Henan and Shanxi provinces of China. In addition, the complete genomes of 13 PCLV strains were sequenced and found to share 35.4%-91.0% nucleotide sequence identity with sequences available in the GenBank database. Phylogenetic analysis based on Rep amino acid sequences revealed that the 13 PCLV strains from this study clustered in group 1 and were closely related to eight Chinese PCLV strains, Bo-Circo-like virus CH, American strains 21 and 22, and Hungarian strains 288_4 and 302_4, but they differed genetically from seven other foreign PCLV strains. The whole genome and rep gene of 13 PCLV strains in this study were 72.2%-82% and 83.8%-89.7% identical, respectively, to those of Bo-Circo-like virus strain CH, indicating that PCLV is a novel virus in pigs that may be involved in cross-species transmission. Evidence of a recombination event was found in the rep region of the 13 PCLV strains sequenced. This study enriches the epidemiological data on PCLV infection in pigs in China and lays a foundation for further study on the pathogenesis of PCLV.
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Affiliation(s)
- Liu-Hui Zhang
- Zhengzhou Major Pig Disease Prevention and Control Laboratory, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China
| | - Lin-Qing Wang
- Zhengzhou Major Pig Disease Prevention and Control Laboratory, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China
- Department of Life Science, Zhengzhou Normal University, Zhengzhou, 450044, Henan Province, People's Republic of China
| | - Hong-Xuan Li
- Zhengzhou Major Pig Disease Prevention and Control Laboratory, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China
| | - Hong-Lei Zhang
- Zhengzhou Major Pig Disease Prevention and Control Laboratory, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China
| | - Lan-Lan Zheng
- Zhengzhou Major Pig Disease Prevention and Control Laboratory, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China
| | - Xi-Meng Chen
- Zhengzhou Major Pig Disease Prevention and Control Laboratory, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China.
| | - Hong-Ying Chen
- Zhengzhou Major Pig Disease Prevention and Control Laboratory, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China.
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Moonen JP, Schinkel M, van der Most T, Miesen P, van Rij RP. Composition and global distribution of the mosquito virome - A comprehensive database of insect-specific viruses. One Health 2023; 16:100490. [PMID: 36817977 PMCID: PMC9929601 DOI: 10.1016/j.onehlt.2023.100490] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Mosquitoes are vectors for emerging and re-emerging infectious viral diseases of humans, livestock and other animals. In addition to these arthropod-borne (arbo)viruses, mosquitoes are host to an array of insect-specific viruses, collectively referred to as the mosquito virome. Mapping the mosquito virome and understanding if and how its composition modulates arbovirus transmission is critical to understand arboviral disease emergence and outbreak dynamics. In recent years, next-generation sequencing as well as PCR and culture-based methods have been extensively used to identify mosquito-associated viruses, providing insights into virus ecology and evolution. Until now, the large amount of mosquito virome data, specifically those acquired by metagenomic sequencing, has not been comprehensively integrated. We have constructed a searchable database of insect-specific viruses associated with vector mosquitoes from 175 studies, published between October 2000 and February 2022. We identify the most frequently detected and widespread viruses of the Culex, Aedes and Anopheles mosquito genera and report their global distribution. In addition, we highlight the challenges of extracting and integrating published virome data and we propose that a standardized reporting format will facilitate data interpretation and re-use by other scientists. We expect our comprehensive database, summarizing mosquito virome data collected over 20 years, to be a useful resource for future studies.
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Sun Y, Sun L, Sun S, Tu Z, Liu Y, Yi L, Tu C, He B. Virome Profiling of an Eastern Roe Deer Reveals Spillover of Viruses from Domestic Animals to Wildlife. Pathogens 2023; 12:pathogens12020156. [PMID: 36839428 PMCID: PMC9959412 DOI: 10.3390/pathogens12020156] [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: 12/27/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Eastern roe deer (Capreolus pygargus) is a small ruminant and is widespread across China. This creature plays an important role in our ecological system. Although a few studies have been conducted to investigate pathogens harbored by this species, our knowledge of the virus diversity is still very sparse. In this study, we conducted the whole virome profiling of a rescue-failed roe deer, which revealed a kobuvirus (KoV), a bocaparvovirus (BoV), and multiple circular single-stranded viruses. These viruses were mainly recovered from the rectum, but PCR detection showed systematic infection of the KoV. Particularly, the KoV and BoV exhibited closely genetic relationships with bovine and canine viruses, respectively, highly suggesting the spillover of viruses from domestic animals to wildlife. Although these viruses were unlikely to have been responsible for the death of the animal, they provide additional data to understand the virus spectrum harbored by roe deer. The transmission of viruses between domestic animals and wildlife highlights the need for extensive investigation of wildlife viruses.
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Affiliation(s)
- Yue Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Lanshun Sun
- Provincial Wildlife Disease Monitoring Station of Shuanghe, Xunke 164400, China
| | - Sheng Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Zhongzhong Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Yang Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Le Yi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China
- Correspondence: (C.T.); (B.H.)
| | - Biao He
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China
- Correspondence: (C.T.); (B.H.)
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