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Wu X, Jiang B, Zhang Y, Wang Q, Ma Y. Identification and genomic analysis of a pathogenic circovirus associated with maricultured Scophthalmus maximus L. in China. Virus Res 2024; 347:199428. [PMID: 38942295 PMCID: PMC11292549 DOI: 10.1016/j.virusres.2024.199428] [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: 05/10/2024] [Revised: 06/23/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
In China, a novel pathogen within the genus Circovirus has been identified as a causative agent of the 'novel acute hemorrhage syndrome' (NAHS) in aquacultured populations of turbot (Scophthalmus maximus L.). Histopathological examination using light microscopy revealed extensive necrosis within the cardiac, splenic, and renal tissues of the afflicted fish. Utilizing transmission electron microscopy (TEM), we detected the presence of circovirus particles within the cytoplasm of these cells, with the virions consistently exhibiting a spherical morphology of 20-40 nm in diameter. TEM inspections confirmed the predominance of these virions in the heart, spleen, and kidney. Subsequent molecular characterization through polymerase chain reaction (PCR) analysis corroborated the TEM findings, with positive signals in the aforementioned tissues, in stark contrast to the lack of detection in gill, fin, liver, and intestinal tissues. The TEM observations, supported by PCR electrophoresis data, strongly suggest that the spleen and kidney are the primary targets of the viral infection. Further characterization using biophysical, biochemical assays, and genomic sequencing confirmed the viral classification within the genus Circovirus, resulting in the nomenclature of turbot circovirus (TurCV). The current research endeavors to shed light on the pathogenesis of this pathogen, offering insights into the infection mechanisms of TurCV in this novel piscine host, thereby contributing to the broader understanding of its impact on turbot health and aquaculture.
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Affiliation(s)
- Xiao Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Boyin Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yuanxing Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China; Laboratory of Aquatic Animal Diseases of MOA, Shanghai 200237, China
| | - Yue Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China; Laboratory of Aquatic Animal Diseases of MOA, Shanghai 200237, China.
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2
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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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3
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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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4
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Boros Á, Pankovics P, László Z, Urbán P, Herczeg R, Gáspár G, Tóth F, Reuter G. The genomic and epidemiological investigations of enteric viruses of domestic caprine ( Capra hircus) revealed the presence of multiple novel viruses related to known strains of humans and ruminant livestock species. Microbiol Spectr 2023; 11:e0253323. [PMID: 37823638 PMCID: PMC10714811 DOI: 10.1128/spectrum.02533-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/04/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Compared with other domestic animals, the virome and viral diversity of small ruminants especially in caprine are less studied even of its zoonotic potential. In this study, the enteric virome of caprine was investigated in detail using next-generation sequencing and reverse transcription PCR techniques. The complete or nearly complete genomes of seven novel viruses were determined which show a close phylogenetic relationship to known human and ruminant viruses. The high similarity between the identified caprine tusavirus (family Parvoviridae) and an unassigned CRESS DNA virus with closely related human strains could indicate the (reverse) zoonotic potential of these viruses. Others, like astroviruses (family Astroviridae), enteroviruses, or novel caripiviruses (named after the term caprine picornavirus) of family Picornaviridae found mostly in multiple co-infections in caprine and ovine, could indicate the cross-species transmission capabilities of these viruses between small ruminants.
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Affiliation(s)
- Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Zoltán László
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Urbán
- János Szentágothai Research Centre of the University of Pécs, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Pécs, Hungary
| | - Róbert Herczeg
- János Szentágothai Research Centre of the University of Pécs, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Pécs, Hungary
| | - Gábor Gáspár
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Fruzsina Tóth
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
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5
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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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6
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Orf GS, Olivo A, Harris B, Weiss SL, Achari A, Yu G, Federman S, Mbanya D, James L, Mampunza S, Chiu CY, Rodgers MA, Cloherty GA, Berg MG. Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance. Viruses 2023; 15:v15041022. [PMID: 37113001 PMCID: PMC10145552 DOI: 10.3390/v15041022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has enabled the high-throughput multiplexed identification of sequences from microbes of potential medical relevance. This approach has become indispensable for viral pathogen discovery and broad-based surveillance of emerging or re-emerging pathogens. From 2015 to 2019, plasma was collected from 9586 individuals in Cameroon and the Democratic Republic of the Congo enrolled in a combined hepatitis virus and retrovirus surveillance program. A subset (n = 726) of the patient specimens was analyzed by mNGS to identify viral co-infections. While co-infections from known blood-borne viruses were detected, divergent sequences from nine poorly characterized or previously uncharacterized viruses were also identified in two individuals. These were assigned to the following groups by genomic and phylogenetic analyses: densovirus, nodavirus, jingmenvirus, bastrovirus, dicistrovirus, picornavirus, and cyclovirus. Although of unclear pathogenicity, these viruses were found circulating at high enough concentrations in plasma for genomes to be assembled and were most closely related to those previously associated with bird or bat excrement. Phylogenetic analyses and in silico host predictions suggested that these are invertebrate viruses likely transmitted through feces containing consumed insects or through contaminated shellfish. This study highlights the power of metagenomics and in silico host prediction in characterizing novel viral infections in susceptible individuals, including those who are immunocompromised from hepatitis viruses and retroviruses, or potentially exposed to zoonotic viruses from animal reservoir species.
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Affiliation(s)
- Gregory S Orf
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Ana Olivo
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Barbara Harris
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Sonja L Weiss
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Asmeeta Achari
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Guixia Yu
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Scot Federman
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Dora Mbanya
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé P.O. Box 1364, Cameroon
| | - Linda James
- School of Medicine, Université Protestante au Congo, Kinshasa P.O. Box 4745, Democratic Republic of the Congo
| | - Samuel Mampunza
- School of Medicine, Université Protestante au Congo, Kinshasa P.O. Box 4745, Democratic Republic of the Congo
| | - Charles Y Chiu
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
- Department of Laboratory Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
- Department of Medicine, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Mary A Rodgers
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Gavin A Cloherty
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
| | - Michael G Berg
- Infectious Disease Research, Abbott Diagnostics, Abbott Park, IL 60004, USA
- Abbott Pandemic Defense Coalition, Abbott Park, IL 60004, USA
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7
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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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8
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Zhang D, Wang Y, He Y, Ji L, Zhao K, Yang S, Zhang W. Identification of avihepadnaviruses and circoviruses in an unexplained death event in farmed ducks. Arch Virol 2023; 168:85. [PMID: 36763177 DOI: 10.1007/s00705-023-05719-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023]
Abstract
Research into disease pathogens can greatly benefit from viral metagenomics technology. Using this technique, we investigated potential disease pathogens that resulted in the death of many ducks on a duck farm. Two duck circoviruses (DuCV) and one duck hepatitis B virus (DHBV) were detected and identified, and all three strains were closely related to avian-associated viruses. Two duck circoviruses had 81.64%-97.65% genome-wide sequence identity to some reference strains, and duck hepatitis B virus shared 75.85%-98.92% identity with other strains. Clinical characteristics of the diseased ducks, including ruffled feathers, lethargy, and weight loss, were comparable to those observed in cases of DuCV infection. Further research is needed to determine whether coinfection with DHBV leads to liver damage and exacerbation of the disease.
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Affiliation(s)
- Dianqi Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yan Wang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yumin He
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Likai Ji
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Kai Zhao
- Department of Clinical Laboratory, Yishui County People's Hospital, Linyi, 276499, Shandong, China.
| | - Shixing Yang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
| | - Wen Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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9
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Zhang LH, Wang TX, Fu PF, Zhao YY, Li HX, Wang DM, Ma SJ, Chen HY, Zheng LL. First Molecular Detection and Genetic Analysis of a Novel Porcine Circovirus (Porcine Circovirus 4) in Dogs in the World. Microbiol Spectr 2023; 11:e0433322. [PMID: 36728419 PMCID: PMC10100769 DOI: 10.1128/spectrum.04333-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023] Open
Abstract
A novel circovirus species was identified in farmed pigs and designated porcine circovirus 4 (PCV4); it has recently been proved to be pathogenic to piglets. However, little is known about its cross-species transmission, and there is no evidence of PCV4 in dogs. A total of 217 fecal samples were collected from diarrheal dogs in Henan Province, China, and tested for the presence of PCV4 using a real-time PCR assay. Among the 217 samples, the total positivity rate for PCV4 was 5.99% (13/217 samples), with rates of 7.44% and 4.17% in 2020 and 2021, respectively. PCV4 was detected in dogs in 6 of 10 cities, demonstrating that PCV4 could be detected in dogs in Henan Province, China. One PCV4 strain (HN-Dog) was sequenced in this study and shared high levels of identity (97.9% to 99.6%) with reference strains at the genome level. Phylogenetic analysis based on complete genome sequences of HN-Dog and 42 reference strains showed that the HN-Dog strain was closely related to 3 PCV4 reference strains (from pig, raccoon dog, and fox) but differed genetically from other viruses in the genus Circovirus. Three genotypes, i.e., PCV4a, PCV4b, and PCV4c, were confirmed by phylogenetic analysis of complete genome sequences of 42 PCV4 strains, and one amino acid variation in Rep protein (V239L) and three amino acid variations in Cap protein (N27S, R28G, and M212L) were considered conserved genotype-specific molecular markers. In conclusion, the present study is the first to report the discovery of the PCV4 genome in dogs, and the association between PCV4 infection and diarrhea warrants further study. IMPORTANCE This study is the first to report the presence of PCV4 in dogs worldwide, and the first complete genome sequence was obtained from a dog affected with diarrhea. Three genotypes of PCV4 strains (PCV4a, PCV4b, and PCV4c) were determined, as supported by specific amino acid markers (V239L for open reading frame 1 [ORF1] and N27S R28G and M212L for ORF2). These findings help us understand the current status of intestinal infections in pet dogs in Henan Province, China, and also prompted us to accelerate research on the pathogenesis, epidemiology, and cross-species transmission of PCV4.
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Affiliation(s)
- Liu-Hui Zhang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
| | - Tong-Xuan Wang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
| | - Peng-Fei Fu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan Province, People’s Republic of China
| | - You-Yi Zhao
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
| | - Hong-Xuan Li
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
| | - Dong-Mei Wang
- Lushan Dabei Agriculture and Animal Husbandry Food Co., Ltd., Lushan, Henan Province, People’s Republic of China
| | - Shi-Jie Ma
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
| | - Hong-Ying Chen
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
| | - Lan-Lan Zheng
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province, People’s Republic of China
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Ji C, Zeng M, Wei Y, Lv X, Sun Y, Ma J. Genetic characterization of four strains porcine circovirus-like viruses in pigs with diarrhea in Hunan Province of China. Front Microbiol 2023; 14:1126707. [PMID: 36937298 PMCID: PMC10014920 DOI: 10.3389/fmicb.2023.1126707] [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: 12/18/2022] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
In this study, we detected a circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus [named Po-Circo-like (PCL) virus] in intestinal tissue and fecal samples of pigs. PCL virus contains a single-stranded DNA genome, and ORF1 encodes the Rep and not the typical capsid protein encoded in PCV. The Rep protein may be responsible for viral genome replication. In addition, PCL virus may be one of the pathogens causing diarrhea symptoms in pigs. We identified four strains of PCL virus in two different pig farms with severe diarrhea outbreaks in Hunan Province, China. The strains in this study share 85.7-99.7% nucleic acid identity and 84.7-100% amino acid identity with Rep of the reference strains. A multiple sequence alignment of these PCL viruses and Bo-Circo-like CH showed a identity of 93.2% for the Rep protein, and the nucleotide identity was 86.7-89.3%. Moreover, Bo-Circo-like CH and HN75, HN39-01, HN39-02 had similar stem-loop sequences. In conclusion, the present study is the first detailed report of the PCL virus in Hunan provinces, which is a potential new virus in pigs that might be involved in cross-species transmission. Further investigation is needed to determine the pathogenesis of this virus and its epidemiologic impact.
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Affiliation(s)
- Chihai Ji
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Meng Zeng
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yingfang Wei
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiaocheng Lv
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yuan Sun
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, College of Animal Science, South China Agricultural University, Guangzhou, China
- Yuan Sun,
| | - Jingyun Ma
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, College of Animal Science, South China Agricultural University, Guangzhou, China
- *Correspondence: Jingyun Ma,
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11
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Zhu J, Xiao Q, Wen L, Yin L, Zhang F, Li T, Banma Z, He K, Suolang S. First detection and complete genome analysis of porcine circovirus-like virus P1 and porcine circovirus-2 in yak in China. Vet Med Sci 2022; 8:2553-2561. [PMID: 36049138 PMCID: PMC9677406 DOI: 10.1002/vms3.911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023] Open
Abstract
Porcine circovirus-like virus P1, like porcine circovirus type 2 (PCV2), is a potential pathogen of post-weaning multisystemic wasting syndrome in swine. Yaks are a valuable species and an iconic symbol of the Tibet Plateau which is the highest and largest plateau in the world. In this study, a total of 105 yak diarrheal samples, collected from 13 farms in Linzhi in the Tibet Plateau from January 2019 to December 2021, that were screened for P1 and PCV2 by polymerase chain reaction, 10.48% (n = 11) were positive for P1, 4.76% (n = 5) for PCV2, and 5.71% (n = 6) were positive for coinfection of P1 and PCV2. In addition, the whole genomes of eight P1 strains and eight PCV2 strains were sequenced. Alignment of deduced amino acid sequences of P1 ORF1 and PCV2 ORF2 gene revealed that ON012566 had one unique amino acid mutation at residues 137 (T to P). This mutation has important implication for the study of virus virulence, tissue tropism, and immune response. Phylogenetic analysis shows that the yak-origin P1 strains in this study with cattle-origin P1 reference strains were grouped into one cluster. The yak-origin PCV2 (ON012566) and a buffalo-origin PCV2 (KM116514) reference strain clustered in the same branch in the PCV2b regions. Meanwhile, the remaining PCV2 strains and buffalo-origin PCV2 reference strain (ON012565) clustered in the PCV2d regions. To summarize, to our knowledge, this is the first report on the molecular prevalence and genome characteristics of P1 and PCV2 in yaks in the world and will contribute to further study of the molecular epidemiology, source, and evolution of P1 and PCV2 strains.
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Affiliation(s)
- Jiaping Zhu
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and TechnologyMinistry of Agriculture and Rural AffairsNanjingChina
- College of Animal ScienceTibet Agricultural and Animal Husbandry University, Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease ResearchLinZhiChina
| | - Qi Xiao
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and TechnologyMinistry of Agriculture and Rural AffairsNanjingChina
- Jiangsu Co‐innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou UniversityYangzhouChina
- Jiangsu Key Laboratory for Food Quality and Safety—State Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
| | - Libin Wen
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and TechnologyMinistry of Agriculture and Rural AffairsNanjingChina
- Jiangsu Co‐innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou UniversityYangzhouChina
- Jiangsu Key Laboratory for Food Quality and Safety—State Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
| | - Lihong Yin
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and TechnologyMinistry of Agriculture and Rural AffairsNanjingChina
- College of Animal ScienceTibet Agricultural and Animal Husbandry University, Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease ResearchLinZhiChina
| | - Fengxi Zhang
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and TechnologyMinistry of Agriculture and Rural AffairsNanjingChina
- College of Animal ScienceTibet Agricultural and Animal Husbandry University, Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease ResearchLinZhiChina
| | - Tianjiao Li
- College of Animal ScienceTibet Agricultural and Animal Husbandry University, Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease ResearchLinZhiChina
| | - Zelang Banma
- College of Animal ScienceTibet Agricultural and Animal Husbandry University, Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease ResearchLinZhiChina
| | - Kongwang He
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and TechnologyMinistry of Agriculture and Rural AffairsNanjingChina
- Jiangsu Co‐innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou UniversityYangzhouChina
- Jiangsu Key Laboratory for Food Quality and Safety—State Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
| | - Sizhu Suolang
- College of Animal ScienceTibet Agricultural and Animal Husbandry University, Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease ResearchLinZhiChina
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Barrón-Rodríguez RJ, Parra-Laca R, Rojas-Anaya E, Romero-Espinoza JÁI, Ayala-Sumuano JT, Vázquez-Pérez JA, García-Espinosa G, Loza-Rubio E. Evidence of Viral Communities in Three Species of Bats from Rural Environment in Mexico. ACTA CHIROPTEROLOGICA 2022. [DOI: 10.3161/15081109acc2022.24.1.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Rodrigo J. Barrón-Rodríguez
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal (CENID-Microbiología), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Carretera Federal México-Toluca km 15.5, Colonia Palo Alto, Cuajimalpa, Ciu
| | - Rocío Parra-Laca
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal (CENID-Microbiología), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Carretera Federal México-Toluca km 15.5, Colonia Palo Alto, Cuajimalpa, Ciu
| | - Edith Rojas-Anaya
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, Ciudad de México, CP 04510, México
| | - José Á. I. Romero-Espinoza
- Laboratorio de Virología, Instituto Nacional de Enfermedades Respiratorias (INER), Calzada de Tlalpan 4502, Del. Tlalpan, Colonia Sección XVI, Tlalpan, Ciudad de México, C.P. 14080, México
| | - Jorge T. Ayala-Sumuano
- Idix S.A. de C.V., Sonterra 3035 Interior 26, Fraccionamiento Sonterra, Santiago de Querétaro, Querétaro México, C.P. 76230, México
| | - Joel A. Vázquez-Pérez
- Laboratorio de Virología, Instituto Nacional de Enfermedades Respiratorias (INER), Calzada de Tlalpan 4502, Del. Tlalpan, Colonia Sección XVI, Tlalpan, Ciudad de México, C.P. 14080, México
| | - Gary García-Espinosa
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 3000, Colonia Ciudad Universitaria, Coyoacán, Ciudad de México, CP 04510, México
| | - Elizabeth Loza-Rubio
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal (CENID-Microbiología), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), Carretera Federal México-Toluca km 15.5, Colonia Palo Alto, Cuajimalpa, Ciu
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13
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Xu T, Chen XM, Fu Y, Ai Y, Wang DM, Wei ZY, Li XS, Zheng LL, Chen HY. Cross-species transmission of an emerging porcine circovirus (PCV4): First molecular detection and retrospective investigation in dairy cows. Vet Microbiol 2022; 273:109528. [PMID: 35944390 DOI: 10.1016/j.vetmic.2022.109528] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/23/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022]
Abstract
Porcine circovirus 4 (PCV4), a novel porcine circovirus identified in pigs, has recently been proved to be pathogenic to piglets. However, little is known about its cross-species transmission, and demonstration of PCV4 in dairy cows is lacking. To explore whether the PCV4 genome exists in dairy cows, 1170 fecal samples were collected from dairy farms in 7 cities in Henan Province of China during 2012-2021, and screened by qPCR for the presence of PCVs (PCV2-PCV4). The detection results showed that the positive rate of PCV4 in dairy cows was 2.22 % (26/1170), but all fecal samples were negative for PCV2 and PCV3. Three full-length and five partial genomes of PCV4 strains were acquired, of which two PCV4 strains (NY2012-DC and XC2013-DC) were achieved from 2012 and 2013, indicating that PCV4 has been circulating in dairy cows in Henan Province of China for at least 10 years. The three PCV4 strains sequenced in this study shared high identity (97.5-99.5 %) with reference strains at the genome level. In phylogenetic analysis, three genotypes (PCV4a, PCV4b and PCV4c) were temporarily confirmed by analyzing 44 strains, and one amino acid variation in Rep (V239L) and three amino acid variations in Cap (N27S, R28G and M212L) were considered as a conserved genotype specific molecular marker. Analyzed from three perspectives (cross-time, cross-species and transboundary), the high nucleotide homology of PCV4 strains indicated the PCV4 evolutionary rate might be slow. Overall, this study was the first to report the detection of PCV4 in dairy cows and conducted a long-term retrospective investigation of PCV4 in Henan Province of China, which has important implications for understanding the genetic diversity and cross-species transmission of the ongoing PCV4 cases.
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Affiliation(s)
- Tong Xu
- 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
| | - Yin Fu
- 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
| | - Yi Ai
- 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
| | - Dong-Mei Wang
- Lushan Dabei Agriculture and Animal Husbandry Food Co., Ltd., Lushan 467300, Henan Province, People's Republic of China
| | - Zhan-Yong Wei
- 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
| | - Xin-Sheng 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
| | - 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.
| | - 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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14
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Diversity of CRESS DNA Viruses in Squamates Recapitulates Hosts Dietary and Environmental Sources of Exposure. Microbiol Spectr 2022; 10:e0078022. [PMID: 35616383 PMCID: PMC9241739 DOI: 10.1128/spectrum.00780-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses comprise viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, and are considered the smallest known autonomously replicating, capsid-encoding animal pathogens. CRESS DNA viruses (phylum Cressdnaviricota) encompass several viral families including Circoviridae. Circoviruses are classified into two genera, Circovirus and Cyclovirus, and they are known to cause fatal diseases in birds and pigs. Circoviruses have also been identified in human stools, blood, and cerebrospinal fluid (CSF), as well as in various wild and domestic vertebrates, including reptiles. The synanthropic presence of Squamata reptiles has increased in the last century due to the anthropic pressure, which has shifted forested animal behavior to an urban and peri-urban adaptation. In this paper, we explored the diversity of CRESS DNA viruses in Squamata reptiles from different Italian areas representative of the Mediterranean basin. CRESS DNA viruses were detected in 31.7% (33/104) of sampled lizards and geckoes. Different CRESS DNA viruses likely reflected dietary composition or environmental contamination and included avian-like (n = 3), dog (n = 4), bat-like (n = 1), goat-like (n = 1), rodent-like (n = 4), and insect-like (n = 2) viruses. Rep sequences of at least two types of human-associated cycloviruses (CyV) were identified consistently, regardless of geographic location, namely, TN9-like (n = 11) and TN12-like (n = 6). A third human-associated CyV, TN25-like, was detected in a single sample. The complete genome of human-like CyVs, of a rodent-like, insect-like, and of a bat-like virus were generated. Collectively, the results recapitulate hosts dietary and environmental sources of exposure and may suggest unexpected ecological niches for some CRESS DNA viruses. IMPORTANCE CRESS DNA viruses are significant pathogens of birds and pigs and have been detected repeatedly in human samples (stools, serum, and cerebrospinal fluid), both from healthy individuals and from patients with neurological disease, eliciting in 2013 a risk assessment by the European Centre for Disease Prevention and Control (ECDC). Sequences of CRESS DNA viruses previously reported in humans (TN9, TN12, and TN25), and detected in different animal species (e.g., birds, dogs, and bats) were herein detected in fecal samples of synanthropic squamates (geckos and lizards). The complete genome sequence of six viruses was generated. This study extends the information on the genetic diversity and ecology of CRESS DNA viruses. Because geckos and lizards are synanthropic animals, a role in sustaining CRESS DNA virus circulation and increasing viral pressure in the environment is postulated.
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Turlewicz-Podbielska H, Augustyniak A, Pomorska-Mól M. Novel Porcine Circoviruses in View of Lessons Learned from Porcine Circovirus Type 2-Epidemiology and Threat to Pigs and Other Species. Viruses 2022; 14:v14020261. [PMID: 35215854 PMCID: PMC8877176 DOI: 10.3390/v14020261] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 01/20/2023] Open
Abstract
Porcine circovirus type 2 (PCV2) plays a key role in PCV2-associated disease (PCVAD) etiology and has yielded significant losses in the pig husbandry in the last 20 years. However, the impact of two recently described species of porcine circoviruses, PCV3 and PCV4, on the pork industry remains unknown. The presence of PCV3 has been associated with several clinical presentations in pigs. Reproductive failure and multisystemic inflammation have been reported most consistently. The clinical symptoms, anatomopathological changes and interaction with other pathogens during PCV3 infection in pigs indicate that PCV3 might be pathogenic for these animals and can cause economic losses in the swine industry similar to PCV2, which makes PCV3 worth including in the differential list as a cause of clinical disorders in reproductive swine herds. Moreover, subsequent studies indicate interspecies transmission and worldwide spreading of PCV3. To date, research related to PCV3 and PCV4 vaccine design is at early stage, and numerous aspects regarding immune response and virus characteristics remain unknown.
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Harding C, Larsen BB, Gryseels S, Otto HW, Suazo C, Kraberger S, Upham NS, Worobey M, Van Doorslaer K, Varsani A. Discovery of three cycloviruses in fecal samples from silver-haired bats (Lasionycteris noctivagans) in Arizona (USA). Arch Virol 2022; 167:2771-2775. [PMID: 36045303 PMCID: PMC9432798 DOI: 10.1007/s00705-022-05574-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
Bats harbour a diverse array of viruses, some of which are zoonotic, and are one of the most speciose groups of mammals on earth. As part of an ongoing bat-associated viral diversity research project, we identified three cycloviruses (family Circoviridae) in fecal samples of silver-haired bats (Lasionycteris noctivagans) caught in Cave Creek Canyon of Arizona (USA). Two of the three identified genomes represent two new species in the genus Cyclovirus. Cycloviruses have been found in a wide range of environments and hosts; however, little is known about their biology. These new genomes of cycloviruses are the first from silver-haired bats, adding to the broader knowledge of cyclovirus diversity. With continuing studies, it is likely that additional viruses of the family Circoviridae will be identified in Arizona bat populations.
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Affiliation(s)
- Ciara Harding
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, 85287-5001, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, 85287-5001, Tempe, AZ, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, 85721, Tucson, Arizona, USA
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 98102, Seattle, WA, USA
| | - Sophie Gryseels
- Department of Ecology and Evolutionary Biology, University of Arizona, 85721, Tucson, Arizona, USA
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium
- Department of Biology, University of Antwerp, 2000, Antwerp, Belgium
| | - Hans W Otto
- Department of Ecology and Evolutionary Biology, University of Arizona, 85721, Tucson, Arizona, USA
| | - Crystal Suazo
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, 85287-5001, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, 85287-5001, Tempe, AZ, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, 85287-5001, Tempe, AZ, USA
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, 85287-5001, Tempe, AZ, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, 85721, Tucson, Arizona, 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, 85724, Tucson, AZ, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, 85287-5001, Tempe, AZ, USA.
- School of Life Sciences, Arizona State University, 85287-5001, Tempe, AZ, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7701, Observatory, Cape Town, South Africa.
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Tarasova E, Okimoto N, Feng S, Nerukh D, Khayat R, Taiji M. Constant pH molecular dynamics of porcine circovirus 2 capsid protein reveals a mechanism for capsid assembly. Phys Chem Chem Phys 2021; 23:24617-24626. [PMID: 34726674 PMCID: PMC8705882 DOI: 10.1039/d1cp02874j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Spatiotemporal regulation of viral capsid assembly ensures the selection of the viral genome for encapsidation. The porcine circovirus 2 is the smallest autonomously replicating pathogenic virus, yet how PCV2 capsid assembly is regulated to occur within the nucleus remains unknown. We report that pure PCV2 capsid proteins, in the absence of nucleic acids, require acidic conditions to assemble into empty capsids in vitro. By employing constant pH replica exchange molecular dynamics, we unveil the atomistic mechanism of pH-dependency for capsid assembly. The results show that an appropriate protonation configuration for a cluster of acidic amino acids is necessary to appropriately position the GH-loop for driving the capsid assembly. We demonstrate that assembly is prohibited at neutral pH because deprotonation of these residues results in their electrostatic repulsion, shifting the GH-loop to a position incompatible with capsid assembly. We propose that encapsulation of nucleic acids overcomes this repulsion to suitably position the GH-loop. Our findings provide the first atomic resolution mechanism of capsid assembly regulation. These findings are useful for the development of therapeutics that inhibit PCV2 self-assembly.
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Affiliation(s)
- Elvira Tarasova
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA.
| | - Noriaki Okimoto
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Shanshan Feng
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA.
| | - Dmitry Nerukh
- Department of Mathematics, Aston University, Birmingham, UK
| | - Reza Khayat
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA.
| | - Makoto Taiji
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
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18
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Detection and Complete Genome Analysis of Circoviruses and Cycloviruses in the Small Indian Mongoose ( Urva auropunctata): Identification of Novel Species. Viruses 2021; 13:v13091700. [PMID: 34578282 PMCID: PMC8471302 DOI: 10.3390/v13091700] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/06/2023] Open
Abstract
Fecal samples from 76 of 83 apparently healthy small Indian mongooses (Urva auropunctata) were PCR positive with circovirus/cyclovirus pan-rep (replicase gene) primers. In this case, 30 samples yielded high quality partial rep sequences (~400 bp), of which 26 sequences shared maximum homology with cycloviruses from an arthropod, bats, humans or a sheep. Three sequences exhibited maximum identities with a bat circovirus, whilst a single sequence could not be assigned to either genus. Using inverse nested PCRs, the complete genomes of mongoose associated circoviruses (Mon-1, -29 and -66) and cycloviruses (Mon-20, -24, -32, -58, -60 and -62) were determined. Mon-1, -20, -24, -29, -32 and -66 shared <80% maximum genome-wide pairwise nucleotide sequence identities with circoviruses/cycloviruses from other animals/sources, and were assigned to novel circovirus, or cyclovirus species. Mon-58, -60 and -62 shared maximum pairwise identities of 79.90–80.20% with human and bat cycloviruses, which were borderline to the cut-off identity value for assigning novel cycloviral species. Despite high genetic diversity, the mongoose associated circoviruses/cycloviruses retained the various features that are conserved among members of the family Circoviridae, such as presence of the putative origin of replication (ori) in the 5′-intergenic region, conserved motifs in the putative replication-associated protein and an arginine rich region in the amino terminus of the putative capsid protein. Since only fecal samples were tested, and mongooses are polyphagous predators, we could not determine whether the mongoose associated circoviruses/cycloviruses were of dietary origin, or actually infected the host. To our knowledge, this is the first report on detection and complete genome analysis of circoviruses/cycloviruses in the small Indian mongoose, warranting further studies in other species of mongooses.
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19
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Detection of bat-associated circoviruses in Korean bats. Arch Virol 2021; 166:3013-3021. [PMID: 34402973 DOI: 10.1007/s00705-021-05202-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/14/2021] [Indexed: 10/20/2022]
Abstract
In recent years, several novel circular single-stranded DNA viruses have been detected in various mammals, birds, insects, and environmental samples using metagenomic and high-throughput sequencing approaches. In this study, we tested for the presence of circoviruses in 243 bat fecal samples collected between 2018 and 2019 from 48 sampling sites across Korea. To detect circoviruses, nested PCR was performed with degenerate primers targeting a conserved replication-associated protein (rep) gene of circovirus/cyclovirus. Among 243 samples tested, a total of 37 fecal samples from 14 sampling sites were PCR-positive for circoviruses at a frequency rate of 15.23%. We obtained 36 partial rep gene sequences of circoviruses and one complete genome sequence of bat-associated circovirus 12, encompassing a genome size of 2097 nt containing two inversely arranged open reading frames and a conserved nonamer sequence in the apex of a stem-loop structure. In addition, we found four bat species that were harboring circoviruses in Korea based on species identification PCR of circovirus-positive bat fecal samples. Detailed sequence analysis indicated that the bat-associated circovirus sequences identified in this study were related to those of known bat and avian groups of circoviruses. Herein, we report evidence for the presence of bat-associated circoviruses in Korean bats.
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20
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Prades Y, Pizarro R, Ruiz M, Moreno C, Avendaño LF, Luchsinger V. Cyclovirus detection in Chilean adults with and without community-acquired pneumonia. J Med Virol 2021; 93:4786-4793. [PMID: 34080215 DOI: 10.1002/jmv.27080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/15/2021] [Accepted: 05/07/2021] [Indexed: 12/27/2022]
Abstract
Cycloviruses (CyV) (genus Cyclovirus, family Circoviridae) are nonenveloped DNA viruses. The first report in humans was in 2010 and research has focused only on disease-associated human sample detection. The only HuACyV (CyCV-ChileNPA1, HuACyV10) reported in the Chilean population was in children (3.3%) with an acute respiratory infection. Its detection in respiratory samples from adults, with/without respiratory disease remains unknown. The aim of this study was to detect HuACyV10 in adults with and without respiratory disease. HuACyV10 was studied in nasopharyngeal swabs from 105 hospitalized adults with community-acquired pneumonia (CAP) and 104 adults without respiratory symptoms. Total nucleic acids were extracted, and viral rep and cp gene fragments were amplified by real-time polymerase chain reaction. HuACyV10 was detected in 19.05% adults with CAP and in 0.96% asymptomatic adults, being significantly higher in adult CAP than asymptomatic (n = 1) ones (p = 0.0001). C t values were between 26.7 and 39.6, and the median was 34.1 for rep and 33.8 for the CAP in adults CAP (p = 0.68), and 35.7 and 36.0, respectively, in the asymptomatic case. HuACyV10 detection in CAP adults concentrated in the Autumn-Winter season of the Southern hemisphere. The only asymptomatic adult with HuACyV10 was detected in the Spring-Summer period. In this first report of HuACyV10 in respiratory samples from adults, detection was significantly higher in CAP than in asymptomatic adults. As the sensitivity of both rep and cp genes was similar, both can be applied for detecting HuACyV10. It would be advisable to investigate the pathogenic role of HuACyV10 in adult respiratory infections. .
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Affiliation(s)
- Yara Prades
- Programa de Virología, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Rolando Pizarro
- Servicio Clínico, Hospital de Enfermedades Infecciosas Dr. L. Córdova, Santiago, Chile
| | - Mauricio Ruiz
- Departamento de Medicina Norte, Hospital Clínico Universidad de Chile, Santiago, Chile
| | - Cristian Moreno
- Programa de Virología, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Luis F Avendaño
- Programa de Virología, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Vivian Luchsinger
- Programa de Virología, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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21
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Abade Dos Santos FA, Portela SJ, Nogueira T, Carvalho CL, de Sousa R, Duarte MD. Harmless or Threatening? Interpreting the Results of Molecular Diagnosis in the Context of Virus-Host Relationships. Front Microbiol 2021; 12:647730. [PMID: 34093464 PMCID: PMC8175621 DOI: 10.3389/fmicb.2021.647730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/27/2021] [Indexed: 01/15/2023] Open
Abstract
Molecular methods, established in the 1980s, expanded and delivered tools for the detection of vestigial quantities of nucleic acids in biological samples. Nucleotide sequencing of these molecules reveals the identity of the organism it belongs to. However, the implications of such detection are often misinterpreted as pathogenic, even in the absence of corroborating clinical evidence. This is particularly significant in the field of virology where the concepts of commensalism, and other benign or neutral relationships, are still very new. In this manuscript, we review some fundamental microbiological concepts including commensalism, mutualism, pathogenicity, and infection, giving special emphasis to their application in virology, in order to clarify the difference between detection and infection. We also propose a system for the correct attribution of terminology in this context.
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Affiliation(s)
- Fábio A Abade Dos Santos
- National Institute for Agrarian and Veterinary Research, Oeiras, Portugal.,Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Sara J Portela
- Harrogate District Hospital NHS Foundation Trust, Harrogate, United Kingdom
| | - Teresa Nogueira
- National Institute for Agrarian and Veterinary Research, Oeiras, Portugal.,Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Carina L Carvalho
- National Institute for Agrarian and Veterinary Research, Oeiras, Portugal
| | - Rita de Sousa
- National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Margarida D Duarte
- National Institute for Agrarian and Veterinary Research, Oeiras, Portugal.,Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
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22
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Canova R, Budaszewski RF, Weber MN, da Silva MS, Puhl DE, Battisti LO, Soares JF, Wagner PG, Varela APM, Mayer FQ, Canal CW. Spleen and lung virome analysis of South American fur seals (Arctocephalus australis) collected on the southern Brazilian coast. INFECTION GENETICS AND EVOLUTION 2021; 92:104862. [PMID: 33848685 DOI: 10.1016/j.meegid.2021.104862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/17/2021] [Accepted: 04/08/2021] [Indexed: 01/23/2023]
Abstract
South American fur seals (Arctocephalus australis) are believed to reach the coast of Rio Grande do Sul (RS) through sea currents. They live in colonies and are frequently found resting on the beach. However, it is also common to find dead pinnipeds on beaches, sharing the environment with humans, domestic animals and other wild species on the coast and facilitating the transmission of pathogens. In the present study, a metagenomic approach was applied to evaluate the viral diversity in organs of fur seals found deceased along the coast of the state of RS, southern Brazil. The lungs and spleens of 29 animals were collected, macerated individually, pooled separately (one pool for lungs and another for spleens) and sequenced using the Illumina MiSeq platform. Sequences more closely related to members of the Anelloviridae and Circoviridae families were detected. Nine putative new species of anellovirus and one putative new genus, named Nitorquevirus, were described. Additionally, the circovirus sequences found in the lungs of A. australis have a common ancestor with PCV3, a proposed swine pathogen. Our study expanded the knowledge about viral communities in pinnipeds and could be useful for monitoring new viruses and potential viral sharing among wildlife, domestic animals, and humans.
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Affiliation(s)
- R Canova
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - R F Budaszewski
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - M N Weber
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - M S da Silva
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - D E Puhl
- Laboratório de Virologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Brazil
| | - L O Battisti
- Laboratório Protozoologia e Riquettsioses Vetoriais, Faculdade de Veterinária, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - J F Soares
- Laboratório Protozoologia e Riquettsioses Vetoriais, Faculdade de Veterinária, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - P G Wagner
- Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis (IBAMA), Brazil
| | - A P M Varela
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Secretaria da Agricultura, Pecuária e Irrigação do Rio Grande do Sul (SEAPI-RS), Eldorado do Sul, Rio Grande do Sul, Brazil
| | - F Q Mayer
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Secretaria da Agricultura, Pecuária e Irrigação do Rio Grande do Sul (SEAPI-RS), Eldorado do Sul, Rio Grande do Sul, Brazil
| | - C W Canal
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
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23
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Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission. Viruses 2021; 13:v13040533. [PMID: 33804837 PMCID: PMC8063800 DOI: 10.3390/v13040533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 01/06/2023] Open
Abstract
Redondoviridae is a recently discovered DNA virus family consisting of two species, vientovirus and brisavirus. Here we used PCR amplification and sequencing to characterize redondoviruses in nasal/throat swabs collected longitudinally from a cohort of 58 individuals working with animals in Vietnam. We additionally analyzed samples from animals to which redondovirus DNA-positive participants were exposed. Redondoviruses were detected in approximately 60% of study participants, including 33% (30/91) of samples collected during episodes of acute respiratory disease and in 50% (29/58) of baseline samples (with no respiratory symptoms). Vientovirus (73%; 24/33) was detected more frequently in samples than brisaviruses (27%; 9/33). In the 23 participants with at least 2 redondovirus-positive samples among their longitudinal samples, 10 (43.5%) had identical redondovirus replication-gene sequences detected (sampling duration: 35–132 days). We found no identical redondovirus replication genes in samples from different participants, and no redondoviruses were detected in 53 pooled nasal/throat swabs collected from domestic animals. Phylogenetic analysis described no large-scale geographical clustering between viruses from Vietnam, the US, Spain, and China, indicating that redondoviruses are highly genetically diverse and have a wide geographical distribution. Collectively, our study provides novel insights into the Redondoviridae family in humans, describing a high prevalence, potentially associated with chronic shedding in the respiratory tract with lack of evidence of zoonotic transmission from close animal contacts. The tropism and potential pathogenicity of this viral family remain to be determined.
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24
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Detection and genetic characterization of porcine circovirus 4 (PCV4) in Guangxi, China. Gene 2020; 773:145384. [PMID: 33383119 DOI: 10.1016/j.gene.2020.145384] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022]
Abstract
Porcine circovirus type 4 (PCV4), a novel circovirus, was identified in pigs with serious symptoms, including porcine dermatitis and nephropathy syndrome (PDNS)-like signs, in China in 2019. This study investigated the prevalence and genome diversity of PCV4 in pigs from Guangxi Province, China, between 2015 and 2019. Thirteen of 257 (5.1%) samples were positive for PCV4, 9 of these (69.2%) PCV4-positive samples were coinfected with PCV2 or PCV3, and one PCV4-positive sample was coinfected with both PCV2 and PCV3. Three complete PCV4 genomes shared 36.9-73.8% nucleotide similarity with other representative circovirus genomes. Phylogenetic analysis indicated that PCV4 was most closely related to bat-associated circovirus and mink circovirus. In summary, this is the first epidemiological investigation and evolutionary analysis of PCV4 in Guangxi Province, China, and the results provide insight into the molecular epidemiology of PCV4.
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25
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Ekine-Afolabi BA, Njan AA, Rotimi SO, R. I. A, Elbehi AM, Cash E, Adeyeye A. The Impact of Diet on the Involvement of Non-Coding RNAs, Extracellular Vesicles, and Gut Microbiome-Virome in Colorectal Cancer Initiation and Progression. Front Oncol 2020; 10:583372. [PMID: 33381452 PMCID: PMC7769005 DOI: 10.3389/fonc.2020.583372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/22/2020] [Indexed: 02/05/2023] Open
Abstract
Cancer is the major cause of morbidity and mortality in the world today. The third most common cancer and which is most diet related is colorectal cancer (CRC). Although there is complexity and limited understanding in the link between diet and CRC, the advancement in research methods have demonstrated the involvement of non-coding RNAs (ncRNAs) as key regulators of gene expression. MicroRNAs (miRNAs) which are a class of ncRNAs are key players in cancer related pathways in the context of dietary modulation. The involvement of ncRNA in cancer progression has recently been clarified throughout the last decade. ncRNAs are involved in biological processes relating to tumor onset and progression. The advances in research have given insights into cell to cell communication, by highlighting the pivotal involvement of extracellular vesicle (EV) associated-ncRNAs in tumorigenesis. The abundance and stability of EV associated ncRNAs act as a new diagnostic and therapeutic target for cancer. The understanding of the deranging of these molecules in cancer can give access to modulating the expression of the ncRNAs, thereby influencing the cancer phenotype. Food derived exosomes/vesicles (FDE) are gaining interest in the implication of exosomes in cell-cell communication with little or no understanding to date on the role FDE plays. There are resident microbiota in the colon; to which the imbalance in the normal intestinal occurrence leads to chronic inflammation and the production of carcinogenic metabolites that lead to neoplasm. Limited studies have shown the implication of various types of microbiome in CRC incidence, without particular emphasis on fungi and protozoa. This review discusses important dietary factors in relation to the expression of EV-associated ncRNAs in CRC, the impact of diet on the colon ecosystem with particular emphasis on molecular mechanisms of interactions in the ecosystem, the influence of homeostasis regulators such as glutathione, and its conjugating enzyme-glutathione S-transferase (GST) polymorphism on intestinal ecosystem, oxidative stress response, and its relationship to DNA adduct fighting enzyme-0-6-methylguanine-DNA methyltransferase. The understanding of the molecular mechanisms and interaction in the intestinal ecosystem will inform on the diagnostic, preventive and prognosis as well as treatment of CRC.
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Affiliation(s)
- Bene A. Ekine-Afolabi
- ZEAB Therapeutic, London, United Kingdom
- Cancer Biology and Therapeutics, High Impact Cancer Research Postgraduate Certificate Program, Harvard Medical School, Boston, MA, United States
| | - Anoka A. Njan
- Department of Pharmacology and Therapeutics, Faculty of Basic Medical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
| | | | - Anu R. I.
- Cancer Biology and Therapeutics, High Impact Cancer Research Postgraduate Certificate Program, Harvard Medical School, Boston, MA, United States
- Department of Clinical Biochemistry, MVR Cancer Centre and Research Institute, Calicut, India
| | - Attia M. Elbehi
- Cancer Biology and Therapeutics, High Impact Cancer Research Postgraduate Certificate Program, Harvard Medical School, Boston, MA, United States
- School of Care and Health Sciences, University of South Wales, Cardif, United Kingdom
| | - Elizabeth Cash
- Cancer Biology and Therapeutics, High Impact Cancer Research Postgraduate Certificate Program, Harvard Medical School, Boston, MA, United States
- Department of Otolaryngology-Head and Neck Surgery and Communicative Disorders, University of Louisville School of Medicine, Louisville, KY, United States
| | - Ademola Adeyeye
- Department of Surgery, University of Ilorin Teaching Hospital, Ilorin, Nigeria
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26
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Yan T, Li G, Zhou D, Yang X, Hu L, Cheng Z. Novel Cyclovirus Identified in Broiler Chickens With Transmissible Viral Proventriculitis in China. Front Vet Sci 2020; 7:569098. [PMID: 33134354 PMCID: PMC7550471 DOI: 10.3389/fvets.2020.569098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/18/2020] [Indexed: 11/30/2022] Open
Abstract
In October 2018, an outbreak of transmissible viral proventriculitis (TVP) occurred in 30-day-old commercial broiler chickens on a farm in Weifang, China. TVP, an infectious viral disease characterized by runting and stunting, is associated with many viruses, and has a significant economic impact on the global poultry industry. TVP is diagnosed according to clinical symptoms, gross and histological lesions, and negative PCR results for pathogenic bacteria, avian leukosis virus subgroup J, Marek's disease virus, reticuloendotheliosis virus, infectious bursa disease virus, avian reovirus, chicken anemia virus, infectious bronchitis virus, chicken proventricular necrosis virus, gyrovirus 3 and chicken circovirus. To further detect the possible causative pathogens of TVP, we used PacBio third-generation sequencing to examine proventricular samples. A dominant abundance of the novel cyclovirus (CyCV), chCyCV-SDAU-1, was identified in broilers with TVP. The complete chCyCV-SDAU-1 genome was verified via inverse PCR, was 1936 bp long, and consisted of Rep, Cp, and two intergenic regions. Phylogenetic tree analysis showed that chCyCV-SDAU-1 formed an independent branch with other cycloviruses. The homology of chCyCV-SDAU-1 with 20 others known cycloviruses was < 40%. Retrospective investigation showed that the CyCV infection rate in the broilers with TVP was 80% (16/20), while no CyCV was found in healthy chickens. In conclusion, a novel CyCV was identified in chickens with TVP, though its role in this disease is unclear.
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Affiliation(s)
- Tianxing Yan
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Gen Li
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China.,College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Defang Zhou
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Xiaoxia Yang
- Hospital of Shandong Agricultural University, Tai'an, China
| | - Liping Hu
- Animal Epidemic Prevention and Control Center of Shandong Province, Jinan, China
| | - Ziqiang Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
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27
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Sun W, Wang W, Cao L, Zheng M, Zhuang X, Zhang H, Yu N, Tian M, Lu H, Jin N. Genetic characterization of three porcine circovirus-like viruses in pigs with diarrhoea in China. Transbound Emerg Dis 2020; 68:289-295. [PMID: 32657534 DOI: 10.1111/tbed.13731] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 12/18/2022]
Abstract
In this study, we detected a circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus (named Po-Circo-like (PCL) virus) in intestinal tissue samples of pigs, and the complete genome sequences of three strains (named PCL viruses GX14, GX15 and GX19) were obtained. Unlike PCL virus strains 21 and 22, whose genome sequences have 3,912 and 3,923 nucleotides (nt), respectively, the strains revealed in this study have a circular genome with 3,944 nt and five major open reading frames (ORFs). Among these ORFs, ORF1 encodes the Rep and not the typical capsid protein encoded in PCV. Furthermore, the strains in this study share 79.2%-96.0% nucleic acid identity and 83.0%-98.1% amino acid identity with ORF1 of the reference strains. Moreover, the Rep of the PCL virus in this study shared 19.9%-22.2% (<30%) identity of its amino acid sequence with PCV but shared 34.9%-94.8% (>30%) identity of its amino acid sequence with sequences of five proteins that are expressed by the family Kirkoviridae. [Correction added on 24 December 2020 after first online publication: The preceding sentence has been corrected in this version.] Interestingly, the stem loop of the PCL virus has one nucleotide substitution, T1328G. The Bo-Circo-like CH strain shares high nucleic acid and amino acid similarity (>80%) with the PCL virus. Moreover, Bo-Circo-like CH and GX-19 had similar stem-loop sequences. The PCL virus might therefore be transmitted to non-porcine hosts by cross-species transmission routes. Phylogenetic analysis classified the PCL virus into the new family Kirkoviridae and indicated its close relationship with the Bo-Circo-like virus. A phylogenetic divergence analysis based on the rep gene classified all PCL virus strains into two genotypes (PCLa and PCLb). In conclusion, the present study is the first detailed report of the PCL virus, which is a potential new virus in pigs that might be involved in cross-species transmission. Further investigation is needed to determine the pathogenesis of this virus and its epidemiologic impact.
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Affiliation(s)
- Wenchao Sun
- Institute of Virology, Wenzhou University, Wenzhou, China.,Institute of Military Veterinary Medicine, Academy of Military Sciences, Changchun, China
| | - Wei Wang
- Institute of Military Veterinary Medicine, Academy of Military Sciences, Changchun, China.,College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Liang Cao
- College of Laboratory, Jilin Medical University, Jilin, China
| | - Min Zheng
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Xingyu Zhuang
- Institute of Military Veterinary Medicine, Academy of Military Sciences, Changchun, China
| | - He Zhang
- Institute of Military Veterinary Medicine, Academy of Military Sciences, Changchun, China
| | - Ning Yu
- Institute of Military Veterinary Medicine, Academy of Military Sciences, Changchun, China
| | - Minyao Tian
- Institute of Military Veterinary Medicine, Academy of Military Sciences, Changchun, China
| | - Huijun Lu
- Institute of Military Veterinary Medicine, Academy of Military Sciences, Changchun, China
| | - Ningyi Jin
- Institute of Virology, Wenzhou University, Wenzhou, China.,Institute of Military Veterinary Medicine, Academy of Military Sciences, Changchun, China.,College of Animal Science and Technology, Guangxi University, Nanning, China
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28
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Fur Seal Feces-Associated Circular DNA Virus Identified in Pigs in Anhui, China. Virol Sin 2020; 36:25-32. [PMID: 32488409 PMCID: PMC7973343 DOI: 10.1007/s12250-020-00232-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/07/2020] [Indexed: 11/08/2022] Open
Abstract
Fur seal feces-associated circular DNA virus (FSfaCV) is an unclassified circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA virus that has been detected in mammals (fur seals and pigs). The biology and epidemiology of the virus remain largely unknown. To investigate the virus diversity among pigs in Anhui Province, China, we pooled 600 nasal samples in 2017 and detected viruses using viral metagenomic methods. From the assembled contigs, 12 showed notably high nucleotide acid sequence similarities to the genome sequences of FSfaCVs. Based on these sequences, a full-length genome sequence of the virus was then obtained using overlapping PCR and sequencing, and the virus was designated as FSfaCV-CHN (GenBank No. MK462122). This virus shared 91.3% and 90.9% genome-wide nucleotide sequence similarities with the New Zealand fur seal strain FSfaCV-as50 and the Japanese pig strain FSfaCV-JPN1, respectively. It also clustered with the two previously identified FSfaCVs in a unique branch in the phylogenetic tree based on the open reading frame 2 (ORF2), Rep-coding gene, and the genome of the reference CRESS DNA viruses. Further epidemiological investigation using samples collected in 2018 showed that the overall positive rate for the virus was 56.4% (111/197) in Anhui Province. This is the first report of FSfaCVs identified in pigs in China, and further epidemiological studies are warranted to evaluate the influence of the virus on pigs.
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Kaszab E, Lengyel G, Marton S, Dán Á, Bányai K, Fehér E. Occurrence and genetic diversity of CRESS DNA viruses in wild birds: a Hungarian study. Sci Rep 2020; 10:7036. [PMID: 32341382 PMCID: PMC7184566 DOI: 10.1038/s41598-020-63795-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 04/03/2020] [Indexed: 12/11/2022] Open
Abstract
Circoviruses, cycloviruses and other circular, replication-associated protein-encoding single stranded (CRESS) DNA viruses have been detected in a variety of animal taxa. In this study, cloacal swab samples (n = 90) were examined for CRESS DNA viruses from 31 wild bird species living at various aquatic sites in Hungary to identify possible reservoirs of viruses pathogenic to domestic poultry. A total of 30 (33.3%) specimens tested positive with pan-CRESS DNA virus specific PCR. Goose circovirus (GoCV), Duck associated cyclovirus 1 (DuACyV-1) and Garrulus glandarius associated circular virus 1 (GgaCV-1) were detected in nine, three and two different bird species, respectively. Selected specimens were subjected to whole genome sequencing. The obtained sequence data revealed conserved gene structure within the identified virus species and detected homologous (within GoCV) and possible heterologous recombination (within DuACyV-1) events. Results presented here provide new information on the genomic diversity and evolution of selected CRESS DNA viruses.
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Affiliation(s)
- Eszter Kaszab
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - György Lengyel
- Hungarian Defence Forces Military Medical Centre, Budapest, Hungary
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Ádám Dán
- University of Veterinary Medicine, Budapest, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Enikő Fehér
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary.
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Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics. Viruses 2019; 11:v11121092. [PMID: 31775324 PMCID: PMC6950620 DOI: 10.3390/v11121092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/22/2019] [Accepted: 11/23/2019] [Indexed: 12/16/2022] Open
Abstract
DNA viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA viruses from invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA viruses, and herein we used this methodology to identify actively transcribing DNA viruses in meta-transcriptomic libraries of diverse invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nudiviridae, Polyomaviridae, and Herpesviridae, for which few invertebrate viruses have been identified to date. By incorporating the sequence of a "blank" experimental control we also highlight the importance of reagent contamination in metagenomic studies. In sum, this work expands our knowledge of the diversity and evolution of DNA viruses and illustrates the utility of meta-transcriptomic data in identifying organisms with DNA genomes.
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Kaján GL, Doszpoly A, Tarján ZL, Vidovszky MZ, Papp T. Virus-Host Coevolution with a Focus on Animal and Human DNA Viruses. J Mol Evol 2019; 88:41-56. [PMID: 31599342 PMCID: PMC6943099 DOI: 10.1007/s00239-019-09913-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/23/2019] [Indexed: 01/21/2023]
Abstract
Viruses have been infecting their host cells since the dawn of life, and this extremely long-term coevolution gave rise to some surprising consequences for the entire tree of life. It is hypothesised that viruses might have contributed to the formation of the first cellular life form, or that even the eukaryotic cell nucleus originates from an infection by a coated virus. The continuous struggle between viruses and their hosts to maintain at least a constant fitness level led to the development of an unceasing arms race, where weapons are often shuttled between the participants. In this literature review we try to give a short insight into some general consequences or traits of virus–host coevolution, and after this we zoom in to the viral clades of adenoviruses, herpesviruses, nucleo-cytoplasmic large DNA viruses, polyomaviruses and, finally, circoviruses.
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Affiliation(s)
- Győző L Kaján
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary.
| | - Andor Doszpoly
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
| | - Zoltán László Tarján
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
| | - Márton Z Vidovszky
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
| | - Tibor Papp
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
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Zhai SL, Lu SS, Wei WK, Lv DH, Wen XH, Zhai Q, Chen QL, Sun YW, Xi Y. Reservoirs of Porcine Circoviruses: A Mini Review. Front Vet Sci 2019; 6:319. [PMID: 31616677 PMCID: PMC6763682 DOI: 10.3389/fvets.2019.00319] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 09/05/2019] [Indexed: 01/01/2023] Open
Abstract
Porcine circovirus (PCV) is one of the smallest known DNA viruses in mammals. At present, PCVs are divided into three species, PCV1, PCV2, and PCV3. PCV1 and PCV2 were found in the 1970s and the 1990s, respectively, whereas PCV3 was discovered recently in 2016. PCV1 does not cause diseases in pigs. However, PCV3, similar to PCV2, is reported to be associated with several swine diseases, including porcine dermatitis and nephropathy syndrome (PDNS) and reproductive failure. PCVs are very common in domestic pigs as well as wild boars. However, PCVs have been occasionally isolated from non-porcine animals, including ruminants (such as cattle, goats, wild chamois, and roe deers), rodents (such as NMRI mice, BALB/c mice, Black C57 mice, ICR mice, Mus musculus, and Rattus rattus), canines (such as dogs, minks, foxes, and raccoon dogs), insects (such as flies, mosquitoes, and ticks), and shellfish. Moreover, PCVs are frequently reported in biological products, including human vaccines, animal vaccines, porcine-derived commercial pepsin products, and many cell lines. PCVs are also abundant in the environment, including water samples and air samples. Interestingly, PCV1 and/or PCV2 antibody or antigen has also been detected in sera, stool samples and respiratory swab samples of human, revealing zoonotic potential of PCVs. Thus, PCVs inhabit many types of reservoirs. In this review, we summarize the reservoirs of PCVs, and this information would be helpful in understanding the natural circulating status and possible cross-species transmission of PCVs.
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Affiliation(s)
- Shao-Lun Zhai
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Shou-Sheng Lu
- Guangdong Center for Animal Disease Prevention and Control, Guangzhou, China
| | - Wen-Kang Wei
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Dian-Hong Lv
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Xiao-Hui Wen
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Qi Zhai
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Qin-Ling Chen
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Yan-Wei Sun
- Guangdong Center for Animal Disease Prevention and Control, Guangzhou, China
| | - Yun Xi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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Li G, Yuan S, Yan T, Shan H, Cheng Z. Identification and characterization of chicken circovirus from commercial broiler chickens in China. Transbound Emerg Dis 2019; 67:6-10. [PMID: 31411792 DOI: 10.1111/tbed.13331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/09/2019] [Accepted: 08/04/2019] [Indexed: 01/19/2023]
Abstract
Circoviruses are found in many species, including mammals, birds, lower vertebrates and invertebrates. To date, there are no reports of circovirus-induced diseases in chickens. In this study, we identified a new strain of chicken circovirus (CCV) by PacBio third-generation sequencing samples from chickens with acute gastroenteritis in a Shandong commercial broiler farm in China. The complete genome of CCV was verified by inverse PCR. Genomic analysis revealed that CCV codes two inverse open reading frames (ORFs), and a potential stem-loop structure was present at the 5' end with a structure typical of a circular virus. Phylogenetic tree analysis showed that CCV formed an independent branch between mammalian and avian circovirus, and homology analysis indicated that the homology of CCV with 21 other known circoviruses was less than 40%. Thus, this CCV strain represents a new species in the genus Circovirus. The infection rate of CCV in 12 chickens with diarrhoea was 100%, but no CCV was found in healthy chickens, thereby indicating that the novel CCV strain is highly associated with acute infectious gastroenteritis in chickens. The emergence of a novel CCV in commercial broiler chickens is highly concerning for the broiler industry.
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Affiliation(s)
- Gen Li
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China.,College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Shiyu Yuan
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Tianxing Yan
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
| | - Hu Shan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Ziqiang Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, China
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Sun W, Wang W, Xin J, Cao L, Zhuang X, Zhang C, Zhu Y, Zhang H, Qin Y, Du Q, Han Z, Lu H, Zheng M, Jin N. An epidemiological investigation of porcine circovirus 3 infection in dogs in the Guangxi Province from 2015 to 2017, China. Virus Res 2019; 270:197663. [PMID: 31301332 PMCID: PMC7114628 DOI: 10.1016/j.virusres.2019.197663] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 01/03/2023]
Abstract
This study was the first seroprevalence and genetic investigation of PCV3 in dogs in the Guangxi province, China. This work is the first in the world to obtain the complete genome of dog PCV3. These PCV3 strains from the Guangxi province help to determine that PCV3 from dog origin and pig origin are from different branches.
Porcine circovirus type 3 (PCV3) is an emerging circovirus species associated with several diseases. The study aimed to investigate the frequency of porcine circovirus 3 (PCV3) and its coinfection with canine parvovirus type 2 (CPV-2) in dogs in the Guangxi province from 2015 to 2017, China, and to examine the genome diversity of PCV3. Using polymerase chain reaction (PCR) amplification and sequencing, 96 of 406 (23.6%)samples were positive for PCV3, 38 out of 406 (9.4%) samples were coinfected with both PCV3 and CPV-2. The CPV-positive rate was significantly higher in the PCV3-positive samples than in the non-PCV3 samples, and the difference was extremely significant (P < 0.01). The complete genome (n=4) and ten capsid genes (n=10) of PCV3 were sequenced. Multiple sequence alignment results showed that these sequences shared 98.5–100% nucleotide similarity with the reference genome sequence and 97.5–100% nucleotide similarity with the reference capsid gene sequence. PCV3 was classified into two different genotypes, according to phylogenetic analysis based on the whole genome. These strains were clustered in PCV3a, showing a close relationship with PCV3-US/SD2016. Surprisingly, we separately analyzed these PCV3 strains from the Guangxi province and found that the dog and pig PCV3 are from different branches. In summary, this was the first seroprevalence and genetic investigation of PCV3 in dogs in the Guangxi province, China, and the first complete genome PCV3 from dogs obtained in the world. The results provide insights into the epidemiology and pathogenesis of this important virus.
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Affiliation(s)
- Wenchao Sun
- Institute of Virology, Wenzhou University, Wenzhou, China; Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - Wei Wang
- College of Animal Science and Technology, Guangxi University, Nanning, China; Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - Jialiang Xin
- College of Animal Science and Technology, Guangxi University, Nanning, China; Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Liang Cao
- Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - Xinyu Zhuang
- Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - Cong Zhang
- University of Science and Technology of China, Hefei, China
| | - Yilong Zhu
- Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - He Zhang
- Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China
| | - Yuhao Qin
- Peking Union Medical College, Tsinghua University, Beijing, China
| | - Qian Du
- College of Animal Science and Technology, Guangxi University, Nanning, China; Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Zhixiao Han
- College of Animal Science and Technology, Guangxi University, Nanning, China; Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Huijun Lu
- Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.
| | - Min Zheng
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China.
| | - Ningyi Jin
- Institute of Virology, Wenzhou University, Wenzhou, China; College of Animal Science and Technology, Guangxi University, Nanning, China; Institute of Military Veterinary Medicine, Academy of Military Medical Sciences, Changchun, China.
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Deim Z, Dencső L, Erdélyi I, Valappil SK, Varga C, Pósa A, Makrai L, Rákhely G. Porcine circovirus type 3 detection in a Hungarian pig farm experiencing reproductive failures. Vet Rec 2019; 185:84. [PMID: 31177090 DOI: 10.1136/vr.104784] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/01/2019] [Accepted: 05/15/2019] [Indexed: 02/05/2023]
Abstract
Porcine circovirus 3 (PCV3) infection has been reported in piglets and sows with porcine dermatitis and nephropathy syndrome, reproductive failure, and cardiac and multisystemic inflammation. Few studies linked PCV3 infection to increased incidence of abortion and weak-born piglets. This is the first report of a detection of PCV3 Hungarian strain in several organs of aborted and weak-born piglets, including the thymus, lymph node, placenta, spleen, kidney and the liver. The tissue tropism of PCV3 in affected litters was analysed using real-time quantitative PCR, and the result showed the highest load of viral DNA in the thymus and lymph nodes. The ORF2 of Hungarian PCV3 strains was 524 nucleotides in length, and the sequence identity to GenBank sequences ranged from 98.5 per cent to 99.2 per cent. The results suggest that PCV3 may have a relevant role in reproductive failure in gilts.
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Affiliation(s)
- Zoltán Deim
- Interdisciplinary Excellence Centre, Department of Biotechnology, Szegedi Tudomanyegyetem, Szeged, Hungary
| | - László Dencső
- Department of Biotechnology, Szegedi Tudomanyegyetem, Szeged, Hungary
| | - Ildikó Erdélyi
- Pathology, Allatorvostudomanyi Egyetem, Budapest, Hungary
| | | | - Csaba Varga
- Department of Physiology, Anatomy and Neuroscience, Szegedi Tudomanyegyetem, Szeged, Hungary
| | - Anikó Pósa
- Interdisciplinary Excellence Centre, Department of Physiology, Anatomy and Neuroscience, Szegedi Tudomanyegyetem, Szeged, Hungary
| | - László Makrai
- Department of Microbiology and Infectious Diseases, Allatorvostudomanyi Egyetem, Budapest, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, Szegedi Tudomanyegyetem, Szeged, Hungary
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36
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Song T, Hao J, Zhang R, Tang M, Li W, Hui W, Fu Q, Wang C, Xin S, Zhang S, Rui P, Ren H, Ma Z. First detection and phylogenetic analysis of porcine circovirus type 2 in raccoon dogs. BMC Vet Res 2019; 15:107. [PMID: 30961660 PMCID: PMC6454600 DOI: 10.1186/s12917-019-1856-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 03/28/2019] [Indexed: 11/25/2022] Open
Abstract
Background Porcine circovirus type 2 (PCV2) is a major emerging virus of porcine circovirus-associated disease (PCVAD), which has brought huge economic losses to the global pig industry. Pigs are well known as the natural reservoir of PCV2. Recently, many researchers have revealed PCV2 could infect many other mammals like mice, calves, minks, dogs and goats. In 2018, our laboratory has admitted six cases of raccoon dogs from Qinhuangdao city of China, which were characterized by inappetence, lethargy, depression, abortion, and sterility. Results At last, six raccoon dog-origin PCV2 strains were isolated in this study. Pairwise-sequence comparisons demonstrated that the six raccoon dog-origin PCV2 strains shared a nucleotide similarity of 92.1–99.8% among 40 PCV2 representative strains. Phylogenetic analysis indicated these PCV2 isolates belonged to Chinese epidemic genotypes PCV2b and PCV2d. And aborted or sterile symptom was significantly associated with PCV2 infection in raccoon dogs by the chi-square test (χ2 = 87.3, p < 0.001). The retrospective study revealed that raccoon dog-origin PCV2 strains shared 100% sequence similarity with the PCV2 stains isolated from pig farms around these raccoon dog farms, respectively. Conclusion In this study, the first supported evidence of PCV2 prevalence in raccoon dog farms of China was documented. PCV2 may be one of the most significant causative agents resulting in the reproductive failure of farmed raccoon dogs, implying that PCV2 could transmit from pigs to raccoon dogs. That indicated that PCV2 cross-species transmission will be a serious threat to China’s fur animal farming industry.
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Affiliation(s)
- Tao Song
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Jianxiang Hao
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Ran Zhang
- College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Menghu Tang
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Wenao Li
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Weirong Hui
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Qiyuan Fu
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Chunfang Wang
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Shuyang Xin
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Shoucong Zhang
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Ping Rui
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Hai Ren
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China
| | - Zengjun Ma
- Hebei Key Laboratory of Preventive Veterinary Medicine, College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, 066004, China.
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Abstract
Viruses, which are the most abundant biological entities on the planet, have been regarded as the "dark matter" of biology in the sense that despite their ubiquity and frequent presence in large numbers, their detection and analysis are not always straightforward. The majority of them are very small (falling under the limit of 0.5 μm), and collectively, they are extraordinarily diverse. In fact, the majority of the genetic diversity on the planet is found in the so-called virosphere, or the world of viruses. Furthermore, the most frequent viral agents of disease in humans display an RNA genome, and frequently evolve very fast, due to the fact that most of their polymerases are devoid of proofreading activity. Therefore, their detection, genetic characterization, and epidemiological surveillance are rather challenging. This review (part of the Curated Collection on Advances in Molecular Epidemiology of Infectious Diseases) describes many of the methods that, throughout the last few decades, have been used for viral detection and analysis. Despite the challenge of having to deal with high genetic diversity, the majority of these methods still depend on the amplification of viral genomic sequences, using sequence-specific or sequence-independent approaches, exploring thermal profiles or a single nucleic acid amplification temperature. Furthermore, viral populations, and especially those with RNA genomes, are not usually genetically uniform but encompass swarms of genetically related, though distinct, viral genomes known as viral quasispecies. Therefore, sequence analysis of viral amplicons needs to take this fact into consideration, as it constitutes a potential analytic problem. Possible technical approaches to deal with it are also described here. *This article is part of a curated collection.
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Affiliation(s)
- Yashpal Singh Malik
- ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Uttar Pradesh India
| | - Raj Kumar Singh
- ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Uttar Pradesh India
| | - Mahendra Pal Yadav
- ICAR-Indian Veterinary Research Institute (ICAR-IVRI), Izatnagar, Uttar Pradesh, India, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, India
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Song T, Zhang S, Hao J, Xin S, Hui W, Tang M, Li W, Tian R, Liu X, Rui P, Ren H, Wang C, Fu Q, Ma Z. First detection and genetic analysis of fox-origin porcine circovirus type 2. Transbound Emerg Dis 2018; 66:1-6. [PMID: 30153367 DOI: 10.1111/tbed.13004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/16/2018] [Accepted: 08/18/2018] [Indexed: 02/01/2023]
Abstract
Porcine circovirus type 2 (PCV2) is a causative agent of porcine circovirus-associated disease (PCVAD), which is a serious problem in the swine industry worldwide. In recent years, nonporcine-origin PCV2 has attracted more and more attention of the researchers. This study reported on the first identification of PCV2 in farmed foxes with reproductive failure. Three fox-origin PCV2 strains were successfully isolated, sequenced, and designated as FoxHB1, FoxHB2, and FoxHB3 respectively. Pairwise-sequence comparisons of the complete genomes revealed that three fox-origin PCV2 strains had nucleotide identities varied from 91.9% to 99.7% with representative strains of PCV2 different genotypes. Meanwhile, phylogenetic analysis based on complete genomes of 44 PCV2 strains indicated that the fox-origin PCV2 strains belonged to Chinese epidemic genotypes PCV2b and PCV2d. These results provided the first supported evidence that PCV2 could infect foxes, implying that the cross-species transmission of PCV2 would be a big threat to Chinese fur animal-bearing industry.
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Affiliation(s)
- Tao Song
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China.,Animal Disease Diagnosis & Testing Center, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Shoucong Zhang
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China.,Animal Disease Diagnosis & Testing Center, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jianxiang Hao
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China.,Animal Disease Diagnosis & Testing Center, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Shuyang Xin
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China.,Animal Disease Diagnosis & Testing Center, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Weirong Hui
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China
| | - Menghu Tang
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China
| | - Wenao Li
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China
| | - Rui Tian
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China
| | - Xuanfu Liu
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China
| | - Ping Rui
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China.,Animal Disease Diagnosis & Testing Center, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Hai Ren
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China
| | - Chunfang Wang
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China
| | - Qiyuan Fu
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China
| | - Zengjun Ma
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.,Key Laboratory of Preventive Veterinary Medicine of Hebei, Qinhuangdao, China.,Animal Disease Diagnosis & Testing Center, Hebei Normal University of Science and Technology, Qinhuangdao, China
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40
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Klaumann F, Correa-Fiz F, Franzo G, Sibila M, Núñez JI, Segalés J. Current Knowledge on Porcine circovirus 3 (PCV-3): A Novel Virus With a Yet Unknown Impact on the Swine Industry. Front Vet Sci 2018; 5:315. [PMID: 30631769 PMCID: PMC6315159 DOI: 10.3389/fvets.2018.00315] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/28/2018] [Indexed: 12/21/2022] Open
Abstract
Porcine circovirus 3 (PCV-3) is a recently described virus belonging to the family Circoviridae. It represents the third member of genus Circovirus able to infect swine, together with PCV-1, considered non-pathogenic, and PCV-2, one of the most economically relevant viruses for the swine worldwide industry. PCV-3 was originally found by metagenomics analyses in 2015 in tissues of pigs suffering from porcine dermatitis and nephropathy syndrome, reproductive failure, myocarditis and multisystemic inflammation. The lack of other common pathogens as potential infectious agents of these conditions prompted the suspicion that PCV-3 might etiologically be involved in disease occurrence. Subsequently, viral genome was detected in apparently healthy pigs, and retrospective studies indicated that PCV-3 was already present in pigs by early 1990s. In fact, current evidence suggests that PCV-3 is a rather widespread virus worldwide. Recently, the virus DNA has also been found in wild boar, expanding the scope of infection susceptibility among the Suidae family; also, the potential reservoir role of this species for the domestic pig has been proposed. Phylogenetic studies with available PCV-3 partial and complete sequences from around the world have revealed high nucleotide identity (>96%), although two main groups and several subclusters have been described as well. Moreover, it has been proposed the existence of a most common ancestor dated around 50 years ago. Taking into account the economic importance and the well-known effects of PCV-2 on the swine industry, a new member of the same family like PCV-3 should not be neglected. Studies on epidemiology, pathogenesis, immunity and diagnosis are guaranteed in the next few years. Therefore, the present review will update the current knowledge and future trends of research on PCV-3.
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Affiliation(s)
- Francini Klaumann
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil.,IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Florencia Correa-Fiz
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Padua, Italy
| | - Marina Sibila
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - José I Núñez
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Joaquim Segalés
- UAB, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Barcelona, Spain
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41
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Lima DA, Cibulski SP, Tochetto C, Varela APM, Finkler F, Teixeira TF, Loiko MR, Cerva C, Junqueira DM, Mayer FQ, Roehe PM. The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics. Virus Res 2018; 261:9-20. [PMID: 30543873 DOI: 10.1016/j.virusres.2018.12.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/06/2018] [Accepted: 12/08/2018] [Indexed: 01/19/2023]
Abstract
Malabsorption syndrome (MAS) is an economically important disease of young, commercially reared broilers, characterized by growth retardation, defective feather development and diarrheic faeces. Several viruses have been tentatively associated to such syndrome. Here, in order to examine potential associations between enteric viruses and MAS, the faecal viromes of 70 stool samples collected from diseased (n = 35) and healthy (n = 35) chickens from seven flocks were characterized and compared. Following high-throughput sequencing, a total of 8,347,319 paired end reads, with an average of 231 nt, were generated. Through analysis of de novo assembled contigs, 144 contigs > 1000 nt were identified with hits to eukaryotic viral sequences, as determined by GenBank database. A number of known and unknown representatives of Adenoviridae, Anelloviridae, Astroviridae, Caliciviridae, Circoviridae, Parvoviridae, Picobirnaviridae, Picornaviridae and Reoviridae, as well as novel uncharacterized CRESS-DNA viruses, were identified. However, the distribution of sequence reads of viral genomes identified in diseased or healthy birds revealed no statistically significant differences. These findings indicate no association between the occurrence of MAS and enteric viruses. The viral genomes reported in the present study, including a variety of novel viruses, seem part of the normal intestinal microbiota of chickens.
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Affiliation(s)
- Diane A Lima
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
| | - Samuel P Cibulski
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Caroline Tochetto
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Ana Paula M Varela
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Fabrine Finkler
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Thais F Teixeira
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Márcia R Loiko
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Cristine Cerva
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Eldorado do Sul, RS, Brazil
| | - Dennis M Junqueira
- Centro Universitário Ritter dos Reis - UniRitter, Health Science Department, Porto Alegre, RS, Brazil
| | - Fabiana Q Mayer
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Eldorado do Sul, RS, Brazil
| | - Paulo M Roehe
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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42
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Zhao L, Rosario K, Breitbart M, Duffy S. Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range. Adv Virus Res 2018; 103:71-133. [PMID: 30635078 DOI: 10.1016/bs.aivir.2018.10.001] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
While single-stranded DNA (ssDNA) was once thought to be a relatively rare genomic architecture for viruses, modern metagenomics sequencing has revealed circular ssDNA viruses in most environments and in association with diverse hosts. In particular, circular ssDNA viruses encoding a homologous replication-associated protein (Rep) have been identified in the majority of eukaryotic supergroups, generating interest in the ecological effects and evolutionary history of circular Rep-encoding ssDNA viruses (CRESS DNA) viruses. This review surveys the explosion of sequence diversity and expansion of eukaryotic CRESS DNA taxonomic groups over the last decade, highlights similarities between the well-studied geminiviruses and circoviruses with newly identified groups known only through their genome sequences, discusses the ecology and evolution of eukaryotic CRESS DNA viruses, and speculates on future research horizons.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States
| | - Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, the State University of New Jersey, New Brunswick, NJ, United States.
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43
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Nishizawa T, Sugimoto Y, Takeda T, Kodera Y, Hatano Y, Takahashi M, Okamoto H. Identification and full-genome characterization of novel circoviruses in masked palm civets (Paguma larvata). Virus Res 2018; 258:50-54. [DOI: 10.1016/j.virusres.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 10/04/2018] [Accepted: 10/04/2018] [Indexed: 01/28/2023]
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44
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Abstract
The red-crowned crane is one of the rarest crane species, and its population is decreasing due to loss of habitat, poisoning, and infections. Using a viral metagenomics approach, we analyzed the virome of feces from wild and captive red-crowned cranes, which were pooled separately. Vertebrate viruses belonging to the families Picornaviridae, Parvoviridae, Circoviridae, and Caliciviridae were detected. Among the members of the family Picornaviridae, we found three that appear to represent new genera. Six nearly complete genomes from members of the family Parvoviridae were also obtained, including four new members of the proposed genus “Chapparvovirus”, and two members of the genus Aveparvovirus. Six small circular DNA genomes were also characterized. One nearly complete genome showing a low level of sequence identity to caliciviruses was also characterized. Numerous viruses believed to infect insects, plants, and crustaceans were also identified, which were probably derived from the diet of red-crowned cranes. This study increases our understanding of the enteric virome of red-crowned cranes and provides a baseline for comparison to those of other birds or following disease outbreaks.
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45
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Guo Z, He Q, Tang C, Zhang B, Yue H. Identification and genomic characterization of a novel CRESS DNA virus from a calf with severe hemorrhagic enteritis in China. Virus Res 2018; 255:141-146. [PMID: 30040978 PMCID: PMC7114660 DOI: 10.1016/j.virusres.2018.07.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/20/2018] [Accepted: 07/20/2018] [Indexed: 01/16/2023]
Abstract
In this study, a novel circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA virus was discovered in diarrheic sample of a calf with severe hemorrhagic enteritis. The virus, named Bo-Circo-like virus CH, has a circular genome with 3909 nucleotides (nt). Six putative open reading frames (ORFs) were identified, including Rep, capsid (Cap) and four proteins of unknown function. Both the genome size and the number as well as the organization of encoded ORFs, Bo-Circo-like virus CH is most closely related to Po-Circo-like virus 21 detected in pig faeces. A preliminary survey using specific primers for the Rep region showed that 5.3% (4/75) of diarrheic samples were positive for Bo-Circo-like virus, and all 42 healthy samples were negative. In conclusion, our results indicate that Bo-Circo-like virus CH may represent a new virus in bovine. Further investigation is needed to determine the relationship between the virus infection and diarrhea.
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Affiliation(s)
- Zijing Guo
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
| | - Qifu He
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
| | - Cheng Tang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
| | - Bin Zhang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China
| | - Hua Yue
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu, China.
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46
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Karuppannan AK, Opriessnig T. Possible risks posed by single-stranded DNA viruses of pigs associated with xenotransplantation. Xenotransplantation 2018; 25:e12453. [PMID: 30264878 PMCID: PMC6120555 DOI: 10.1111/xen.12453] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/12/2018] [Accepted: 07/20/2018] [Indexed: 12/11/2022]
Abstract
Routine large-scale xenotransplantation from pigs to humans is getting closer to clinical reality owing to several state-of-the-art technologies, especially the ability to rapidly engineer genetically defined pigs. However, using pig organs in humans poses risks including unwanted cross-species transfer of viruses and adaption of these pig viruses to the human organ recipient. Recent developments in the field of virology, including the advent of metagenomic techniques to characterize entire viromes, have led to the identification of a plethora of viruses in many niches. Single-stranded DNA (ssDNA) viruses are the largest group prevalent in virome studies in mammals. Specifically, the ssDNA viral genomes are characterized by a high rate of nucleotide substitution, which confers a proclivity to adapt to new hosts and cross-species barriers. Pig-associated ssDNA viruses include torque teno sus viruses (TTSuV) in the Anelloviridae family, porcine parvoviruses (PPV), and porcine bocaviruses (PBoV) both in the family of Parvoviridae, and porcine circoviruses (PCV) in the Circoviridae family, some of which have been confirmed to be pathogenic to pigs. The risks of these viruses for the human recipient during xenotransplantation procedures are relatively unknown. Based on the scant knowledge available on the prevalence, predilection, and pathogenicity of pig-associated ssDNA viruses, careful screening and monitoring are required. In the case of positive identification, risk assessments and strategies to eliminate these viruses in xenotransplantation pig stock may be needed.
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Affiliation(s)
- Anbu K. Karuppannan
- Department of Veterinary Diagnostic and Production Animal MedicineCollege of Veterinary MedicineIowa State UniversityAmesIowa
| | - Tanja Opriessnig
- Department of Veterinary Diagnostic and Production Animal MedicineCollege of Veterinary MedicineIowa State UniversityAmesIowa
- The Roslin Institute and The Royal (Dick) School of Veterinary StudiesUniversity of EdinburghRoslinMidlothianUK
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47
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Ye X, Berg M, Fossum C, Wallgren P, Blomström AL. Detection and genetic characterisation of porcine circovirus 3 from pigs in Sweden. Virus Genes 2018; 54:466-469. [PMID: 29564688 PMCID: PMC5951868 DOI: 10.1007/s11262-018-1553-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/10/2018] [Indexed: 01/27/2023]
Abstract
Porcine circovirus 3 (PCV3) is a newly detected circovirus belonging to the family Circoviridae with a circular ssDNA genome of 2000 bp that encodes two proteins-the replicase protein and the capsid protein. PCV3 was discovered for the first time in the US in 2016. After this initial discovery, PCV3 was detected in other parts of the world such as in China, South Korea, Italy and Poland. In this study, 49 tissue samples from Swedish pig herds were screened for PCV3 using PCR and 10 samples were positive and one was uncertain. The entire PCV3 genome and a mini PCV-like virus (MPCLV) were obtained from one of these samples. These two viruses showed a high sequence identity to PCV3 viruses from other countries as well as to MPCLV from the US. However, the sequence identity to PCV1 and 2 was only 31-48% on amino acid level. This is the first detection and complete genetic characterisation of PCV3 in Swedish pigs. It is also interesting to note that one of the positive samples was collected in 1993, showing that PCV3 has been present for a long time.
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Affiliation(s)
- Xingyu Ye
- Guangyuan Center for Animal Disease Control and Prevention, Guangyuan, 628017, China
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden
| | - Mikael Berg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden
| | - Caroline Fossum
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden
| | - Per Wallgren
- National veterinary institute (SVA), 751 89, Uppsala, Sweden
| | - Anne-Lie Blomström
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden.
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48
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Sun J, Wei L, Lu Z, Mi S, Bao F, Guo H, Tu C, Zhu Y, Gong W. Retrospective study of porcine circovirus 3 infection in China. Transbound Emerg Dis 2018. [PMID: 29521007 DOI: 10.1111/tbed.12853] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PCV3 is an emerging swine virus associated with porcine dermatitis and nephropathy syndrome (PDNS), reproductive failure, respiratory diseases and systematic inflammation. Although first identified in 2015, the earliest case has been traced back to 2009 in the United States. In China, PCV3 infection was first detected in 2015, but little information has been available about its occurrence and prevalence there before 2015. In this study, 200 porcine clinical samples collected from 20 provinces, five autonomous regions and four municipalities between 1990 and 1999 were analysed for PCV3 infection by PCR. Results showed that 6.5% of the porcine samples collected from eight provinces and one autonomous region were PCV3 positive, with the earliest cases occurring in 1996. Nucleotide sequence analysis showed that PCV3 strains obtained in this study shared 96.6%-99.7% and 97.1%-99.4% sequence identity at the ORF2 gene and genome levels with all available reference strains from China and other countries, indicating the high genetic stability of PCV3 over the past 20 years.
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Affiliation(s)
- J Sun
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Academy of Military Sciences, Changchun, China
| | - L Wei
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Z Lu
- College of Life Sciences and Engineering, Foshan University, Foshan, China
| | - S Mi
- Institute of Military Veterinary, Academy of Military Medical Sciences, Academy of Military Sciences, Changchun, China
| | - F Bao
- Institute of Military Veterinary, Academy of Military Medical Sciences, Academy of Military Sciences, Changchun, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - H Guo
- Institute of Military Veterinary, Academy of Military Medical Sciences, Academy of Military Sciences, Changchun, China
| | - C Tu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Academy of Military Sciences, Changchun, China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, China
| | - Y Zhu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - W Gong
- Institute of Military Veterinary, Academy of Military Medical Sciences, Academy of Military Sciences, Changchun, China
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49
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Evolutionary analysis of Porcine circovirus 3 (PCV3) indicates an ancient origin for its current strains and a worldwide dispersion. Virus Genes 2018; 54:376-384. [DOI: 10.1007/s11262-018-1545-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 03/01/2018] [Indexed: 11/27/2022]
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50
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Moens MAJ, Pérez-Tris J, Cortey M, Benítez L. Identification of two novel CRESS DNA viruses associated with an Avipoxvirus lesion of a blue-and-gray Tanager (Thraupis episcopus). INFECTION GENETICS AND EVOLUTION 2018; 60:89-96. [PMID: 29454113 DOI: 10.1016/j.meegid.2018.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/11/2018] [Accepted: 02/12/2018] [Indexed: 12/24/2022]
Abstract
The discovery of circular rep-encoding single stranded (CRESS) DNA viruses has increased spectacularly over the past decade. They represent the smallest animal viruses known worldwide infecting a wide variety of invertebrates and vertebrates in different natural and human-made environments. The extremely low similarity of nucleotide and protein sequences among different CRESS DNA genomes has challenged their classification. Moreover, the existence of capsid proteins (Cp) remains difficult to demonstrate which is crucial to understand the structural properties of these viruses. Here we describe two unclassified CRESS DNA viruses isolated from a cutaneous lesion, caused by a strain of Avipoxvirus, from a blue-and-gray tanager (Thraupis episcopus) in Southern Ecuador. Both viruses present replication-associated proteins (Rep) and one to two open reading frames (ORF), one of which represents a putative Cp. The two new Rep are long proteins characterized by the existence of the several highly conserved amino acid residues characteristic of rolling circle replication. Within the putative Cp we detected intrinsically disordered regions (IDR), potential protein and DNA binding regions, and nuclear localization signals (NLS), providing further evidence of presumed Cp. Despite being found on the same host lesion, both viruses show low similarity between each other (<60%) and other known CRESS DNA viruses. Furthermore, we analyze the evolutionary relationships within the CRESS DNA diversity. Additional sampling is needed to explore the possible pathogenic effects, prevalence and diversity (both phylogenetical and structural) of these viruses in wild bird populations.
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Affiliation(s)
- Michaël A J Moens
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University of Madrid. Calle José Antonio Nováis 12, 28040 Madrid, Spain; Jocotoco Foundation, Lizardo García E9-104 y Andrés Xaura, Quito, Ecuador.
| | - Javier Pérez-Tris
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University of Madrid. Calle José Antonio Nováis 12, 28040 Madrid, Spain.
| | - Martí Cortey
- Departament de Sanitat i d'Anatomia Animals, Universitat Autònoma de Barcelona. 08193 Cerdanyola del Vallès, Spain.
| | - Laura Benítez
- Department of Physiology, Genetics and Microbiology, Faculty of Biology, Complutense University of Madrid. Calle José Antonio Nováis 12, 28040,Madrid, Spain.
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