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Sarchese V, Palombieri A, Prandi I, Robetto S, Bertolotti L, Capucchio MT, Orusa R, Mauthe von Degerfeld M, Quaranta G, Vacchetta M, Martella V, Di Martino B, Di Profio F. Molecular Surveillance for Bocaparvoviruses and Bufaviruses in the European Hedgehog ( Erinaceus europaeus). Microorganisms 2024; 12:189. [PMID: 38258015 PMCID: PMC10819369 DOI: 10.3390/microorganisms12010189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
The presence of bocaparvoviruses (BoVs) and bufaviruses (BuVs) in the European hedgehog (Erinaceus europaeus) was investigated by screening duodenal and liver samples collected from 183 carcasses, delivered to wildlife rescue centers located in northwestern Italy. BoV DNA was detected in 15 animals (8.2%), with prevalences of 7.1% (13/183) and 2.7% (5/183) in intestine and liver samples, respectively. Upon the sequence analyses of the NS1 gene, two highly divergent BoVs (65.5-67.8% nt identities) were identified. Fourteen strains showed the highest identity (98.3-99.4% nt) to the hedgehog BoV strains recently detected in China in Amur hedgehogs (Erinaceus amurensis), whilst four strains were genetically related (98.9-99.4% nt identities) to the porcine BoVs identified in pigs and classified in the species Bocaparvovirus ungulate 4, which included related viruses also found in rats, minks, shrews, and mice. BuV DNA was detected in the duodenal samples of two hedgehogs, with a prevalence rate of 1.1%. The nearly full-length genome of two BuV strains, Hedgehog/331DU-2022/ITA and Hedgehog/1278DU/2019/ITA, was reconstructed. Upon phylogenetic analysis based on the NS and VP aa sequences, the Italian hedgehog BuVs tightly clustered with the BuVs recently identified in the Chinese Amur hedgehogs, within a potential novel candidate species of the genus Protoparvovirus.
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Affiliation(s)
- Vittorio Sarchese
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, TE, Italy; (V.S.); (A.P.); (B.D.M.)
| | - Andrea Palombieri
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, TE, Italy; (V.S.); (A.P.); (B.D.M.)
| | - Ilaria Prandi
- Centro Animali Non Convenzionali (C.A.N.C.), Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, TO, Italy; (I.P.); (M.T.C.); (M.M.v.D.); (G.Q.)
| | - Serena Robetto
- Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), Istituto Zooprofilattico Sperimentale del Piemonte, della Liguria e della Valle d’Aosta, 11020 Quart, AO, Italy; (S.R.); (R.O.)
| | - Luigi Bertolotti
- Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, TO, Italy;
| | - Maria Teresa Capucchio
- Centro Animali Non Convenzionali (C.A.N.C.), Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, TO, Italy; (I.P.); (M.T.C.); (M.M.v.D.); (G.Q.)
| | - Riccardo Orusa
- Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), Istituto Zooprofilattico Sperimentale del Piemonte, della Liguria e della Valle d’Aosta, 11020 Quart, AO, Italy; (S.R.); (R.O.)
| | - Mitzy Mauthe von Degerfeld
- Centro Animali Non Convenzionali (C.A.N.C.), Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, TO, Italy; (I.P.); (M.T.C.); (M.M.v.D.); (G.Q.)
| | - Giuseppe Quaranta
- Centro Animali Non Convenzionali (C.A.N.C.), Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, TO, Italy; (I.P.); (M.T.C.); (M.M.v.D.); (G.Q.)
| | | | - Vito Martella
- Department of Veterinary Medicine, Università Aldo Moro di Bari, 70010 Valenzano, BA, Italy;
| | - Barbara Di Martino
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, TE, Italy; (V.S.); (A.P.); (B.D.M.)
| | - Federica Di Profio
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, TE, Italy; (V.S.); (A.P.); (B.D.M.)
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2
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Xin W, Guo Z, Wang L, Li Y, Shangguan H, Xue K, Chen H, Yang H, Zhao L, Ge J. Multiple genotypes infection and molecular characterization of Torque teno neovison virus: A novel Anelloviridae of mink in China. Res Vet Sci 2023; 161:145-155. [PMID: 37384973 DOI: 10.1016/j.rvsc.2023.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/01/2023]
Abstract
A novel Torque teno neovison virus (TTVs) was identified in specimens collected from dead mink during an outbreak of the Aleutian mink disease virus. Eighteen complete genomic sequences were obtained, ranging from 2109 to 2158 nucleotides in length and consisting of an untranslated region and three open reading frames. The genomic organization of mink TTVs is similar to previously reported anelloviruses. However, the deduced amino acid sequence of its ORF1 protein shows genetic diversity compared to related anelloviruses, suggesting that it represents a putative new species within the Anelloviridae family. This study provides a detailed molecular characterization of the novel mink anelloviruses, including its codon usage pattern, origin, and evolution. Analysis of the viral genomic sequences reveals the existence of multiple genotypes of co-infection. Principal component analysis and phylogenetic trees confirm the coexistence of multiple genotypes. Furthermore, the codon usage analyses indicate that mink TTVs have a genotype-specific codon usage pattern and show a low codon usage bias. Host-specific adaptation analysis suggests that TTVs are less adapted to mink. The possible origin and evolutionary history of mink TTVs were elucidated. Mink TTVs was genetically closely related to giant panda anellovirus, representing a new species. The observed incongruence between the phylogenetic history of TTVs and that of their hosts suggests that the evolution of anellovirus is largely determined by cross-species transmission. The study provides insights into the co-infection and genetic evolution of anellovirus in China.
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Affiliation(s)
- Weizhi Xin
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Zhiyuan Guo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Lin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Yifan Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Haikun Shangguan
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Kun Xue
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, PR China
| | - Hongliang Yang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Lili Zhao
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, PR China; College of Veterinary Medicine, Jilin University, 5333 Xian Road, Changchun 130062, China.
| | - Junwei Ge
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal, Pathogen Biology, Harbin 150030, China.
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Zhuang Z, Qian L, Lu J, Zhang X, Mahmood A, Cui L, Wang H, Wang X, Yang S, Ji L, Shan T, Shen Q, Zhang W. Comparison of viral communities in the blood, feces and various tissues of wild brown rats ( Rattus norvegicus). Heliyon 2023; 9:e17222. [PMID: 37389044 PMCID: PMC10300334 DOI: 10.1016/j.heliyon.2023.e17222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 07/01/2023] Open
Abstract
Viral diseases caused by new outbreaks of viral infections pose a serious threat to human health. Wild brown rats (Rattus norvegicus), considered one of the world's largest and most widely distributed rodents, are host to various zoonotic pathogens. To further understand the composition of the virus community in wild brown rats and explore new types of potentially pathogenic viruses, viral metagenomics was conducted to investigate blood, feces, and various tissues of wild brown rats captured from Zhenjiang, China. Results indicated that the composition of the virus community in different samples showed significant differences. In blood and tissue samples, members of the Parvoviridae and Anelloviridae form the main body of the virus community. Picornaviridae, Picobirnaviridae, and Astroviridae made up a large proportion of fecal samples. Several novel genome sequences from members of different families, including Anelloviridae, Parvoviridae, and CRESS DNA viruses, were detected in both blood and other samples, suggesting that they have the potential to spread across organs to cause viremia. These viruses included not only strains closely related to human viruses, but also a potential recombinant virus. Multiple dual-segment picornaviruses were obtained from fecal samples, as well as virus sequences from the Astroviridae and Picornaviridae. Phylogenetic analysis showed that these viruses belonged to different genera, with multiple viruses clustered with other animal viruses. Whether they have pathogenicity and the ability to spread across species needs further study.
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Affiliation(s)
- Zi Zhuang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Lingling Qian
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Juan Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Xiaodan Zhang
- Department of Clinical Laboratory, Zhenjiang Center for Disease Prevention and Control, Zhenjiang, 212002, China
| | - Asif Mahmood
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Lei Cui
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 200062, China
| | - Huiying Wang
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
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Capozza P, Buonavoglia A, Pratelli A, Martella V, Decaro N. Old and Novel Enteric Parvoviruses of Dogs. Pathogens 2023; 12:pathogens12050722. [PMID: 37242392 DOI: 10.3390/pathogens12050722] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Parvovirus infections have been well known for around 100 years in domestic carnivores. However, the use of molecular assays and metagenomic approaches for virus discovery and characterization has led to the detection of novel parvovirus species and/or variants in dogs. Although some evidence suggests that these emerging canine parvoviruses may act as primary causative agents or as synergistic pathogens in the diseases of domestic carnivores, several aspects regarding epidemiology and virus-host interaction remain to be elucidated.
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Affiliation(s)
- Paolo Capozza
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy
| | - Alessio Buonavoglia
- Department of Biomedical and Neuromotor Sciences, Dental School, Via Zamboni 33, 40126 Bologna, Italy
| | - Annamaria Pratelli
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy
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Pacini MI, Mazzei M, Sgorbini M, D’Alfonso R, Papini RA. A One-Year Retrospective Analysis of Viral and Parasitological Agents in Wildlife Animals Admitted to a First Aid Hospital. Animals (Basel) 2023; 13:ani13050931. [PMID: 36899788 PMCID: PMC10000059 DOI: 10.3390/ani13050931] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
This study aimed to provide information on the presence and frequency of viral and parasitic agents in wildlife presented to a Veterinary Teaching Hospital in 2020-2021. Serum and faecal samples were collected from 50 rescued animals (roe deer, fallow deer, foxes, badgers, pine martens, and porcupines) and examined by serological, molecular, and parasitological techniques. Transtracheal wash (TTW) was also collected post-mortem from roe deer. Overall, the results of the different techniques showed infections with the following viral and parasitic agents: Bovine Viral Diarrhea Virus, Small Ruminant Lentiviruses, Kobuvirus, Astrovirus, Canine Adenovirus 1, Bopivirus, gastrointestinal strongyles, Capillaria, Ancylostomatidae, Toxocara canis, Trichuris vulpis, Hymenolepis, Strongyloides, Eimeria, Isospora, Dictyocaulus, Angiostrongylus vasorum, Crenosoma, Dirofilaria immitis, Neospora caninum, Giardia duodenalis, and Cryptosporidium. Sequencing (Tpi locus) identified G. duodenalis sub-assemblages AI and BIV in one roe deer and one porcupine, respectively. Adult lungworms collected from the TTW were identified as Dictyocaulus capreolus (COX1 gene). This is the first molecular identification of G. duodenalis sub-assemblage AI and D. capreolus in roe deer in Italy. These results show a wide presence of pathogens in wild populations and provide an overview of environmental health surveillance.
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Affiliation(s)
- Maria Irene Pacini
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
- Correspondence:
| | - Maurizio Mazzei
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Micaela Sgorbini
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
| | - Rossella D’Alfonso
- Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Roberto Amerigo Papini
- Department of Veterinary Sciences, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy
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Miranda TDS, Schiffler FB, D'arc M, Moreira FRR, Cosentino MAC, Coimbra A, Mouta R, Medeiros G, Girardi DL, Wanderkoke V, Soares CFA, Francisco TM, Henry MD, Afonso BC, Soffiati FL, Ferreira SS, Ruiz-Miranda CR, Soares MA, Santos AFA. Metagenomic analysis reveals novel dietary-related viruses in the gut virome of marmosets hybrids (Callithrix jacchus x Callithrix penicillata), Brazil. Virus Res 2023; 325:199017. [PMID: 36565815 DOI: 10.1016/j.virusres.2022.199017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022]
Abstract
Viral metagenomics has contributed enormously to the characterization of a wide range of viruses infecting animals of all phyla in the last decades. Among Neotropical primates, especially those introduced, knowledge about viral diversity remains poorly studied. Therefore, using metagenomics based on virus enrichment, we explored the viral microbiota present in the feces of introduced common marmosets (Callithrix sp.) in three locations from the Silva Jardim region in the State of Rio de Janeiro, Brazil. Fecal samples were collected from nine marmosets, pooled into three sample pools, and sequenced on Illumina MiSeq platform. Sequence reads were analyzed using a viral metagenomic analysis pipeline and two novel insect viruses belonging to the Parvoviridae and Baculoviridae families were identified. The complete genome of a densovirus (Parvoviridae family) of 5,309 nucleotides (nt) was obtained. The NS1 and VP1 proteins share lower than 32% sequence identity with the corresponding proteins of known members of the subfamily Densovirinae. Phylogenetic analysis suggests that this virus represents a new genus, provisionally named Afoambidensovirus due to its discovery in the Brazilian Atlantic Forest. The novel species received the name Afoambidensovirus incertum 1. The complete circular genome of a baculovirus of 107,191 nt was also obtained, showing 60.8% sequence identity with the most closely related member of the Baculoviridae family. Phylogenetic analysis suggests that this virus represents a new species in the Betabaculovirus genus, provisionally named Betabaculovirus incertum 1. In addition, sequences from several families of arthropods in the three pools evaluated were characterized (contigs ranging from 244 to 6,750 nt), corroborating the presence of possible insect hosts with which these new viruses may be associated. Our study expands the knowledge about two viral families known to infect insects, an important component of the marmosets' diet. This identification in hosts' feces samples demonstrates one of the many uses of this type of data and could serve as a basis for future research characterizing viruses in wildlife using noninvasive samples.
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Affiliation(s)
- Thamiris Dos Santos Miranda
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Mirela D'arc
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | | | - Amanda Coimbra
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Ricardo Mouta
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Gabriel Medeiros
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Déa Luiza Girardi
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Victor Wanderkoke
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Caique Ferreira Amaral Soares
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Talitha Mayumi Francisco
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Malinda Dawn Henry
- Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Bianca Cardozo Afonso
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | | | | | - Carlos Ramon Ruiz-Miranda
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Marcelo Alves Soares
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - André Felipe Andrade Santos
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
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Abstract
Anelloviruses are small negative-sense single-stranded DNA viruses with genomes ranging in size from 1.6 to 3.9 kb. The family Anelloviridae comprised 14 genera before the present changes. However, in the last five years, a large number of diverse anelloviruses have been identified in various organisms. Here, we undertake a global analysis of mammalian anelloviruses whose full genome sequences have been determined and have an intact open reading frame 1 (ORF1). We established new criteria for the classification of anelloviruses, and, based on our analyses, we establish new genera and species to accommodate the unclassified anelloviruses. We also note that based on the updated species demarcation criteria, some previously assigned species (n = 10) merge with other species. Given the rate at which virus sequence data are accumulating, and with the identification of diverse anelloviruses, we acknowledge that the taxonomy will have to be dynamic and continuously evolve to accommodate new members.
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Abstract
The family Genomoviridae (phylum Cressdnaviricota, class Repensiviricetes, order Geplafuvirales) includes viruses with circular single-stranded DNA genomes encoding two proteins, the capsid protein and the rolling-circle replication initiation protein. The genomes of the vast majority of members in this family have been sequenced directly from diverse environmental or animal- and plant-associated samples, but two genomoviruses have been identified infecting fungi. Since the last taxonomic update of the Genomoviridae, a number of new members of this family have been sequenced. Here, we report on the most recent taxonomic update, including the creation of one new genus, Gemytripvirus, and classification of ~420 new genomoviruses into 164 new species. We also announce the adoption of the "Genus + freeform epithet" binomial system for the naming of all 236 officially recognized species in the family Genomoviridae. The updated taxonomy presented in this article has been accepted by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France.
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Khalifa ME, MacDiarmid RM. A Mechanically Transmitted DNA Mycovirus Is Targeted by the Defence Machinery of Its Host, Botrytis cinerea. Viruses 2021; 13:v13071315. [PMID: 34372522 PMCID: PMC8309985 DOI: 10.3390/v13071315] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/11/2022] Open
Abstract
Eukaryotic circular single-stranded DNA (ssDNA) viruses were known only to infect plants and vertebrates until the discovery of the isolated DNA mycovirus from the fungus Sclerotinia sclerotiorum. Similar viral sequences were reported from several other sources and classified in ten genera within the Genomoviridae family. The current study reports two circular ssDNA mycoviruses isolated from the phytopathogen Botrytis cinerea, and their assignment to a newly created genus tentatively named Gemydayirivirus. The mycoviruses, tentatively named botrytis gemydayirivirus 1 (BGDaV1) and BGDaV2, are 1701 and 1693 nt long and encode three and two open reading frames (ORFs), respectively. Of the predicted ORFs, only ORF I, which codes for a replication initiation protein (Rep), shared identity with other proteins in GenBank. BGDaV1 is infective as cell-free purified particles and confers hypovirulence on its natural host. Investigation revealed that BGDaV1 is a target for RNA silencing and genomic DNA methylation, keeping the virus at very low titre. The discovery of BGDaV1 expands our knowledge of the diversity of genomoviruses and their interaction with fungal hosts.
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Affiliation(s)
- Mahmoud E. Khalifa
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand;
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta 34517, Egypt
- Correspondence:
| | - Robin M. MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand;
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
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Emerging Parvoviruses in Domestic Cats. Viruses 2021; 13:v13061077. [PMID: 34200079 PMCID: PMC8229815 DOI: 10.3390/v13061077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
Parvovirus infections in cats have been well known for around 100 years. Recently, the use of molecular assays and metagenomic approaches for virus discovery and characterization has led to the detection of novel parvovirus lineages and/or species infecting the feline host. However, the involvement of emerging parvoviruses in the onset of gastroenteritis or other feline diseases is still uncertain.
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Bandoo RA, Bautista J, Lund M, Newkirk E, Squires J, Varsani A, Kraberger S. Identification of novel circovirus and anelloviruses from wolverines using a non-invasive faecal sampling approach. INFECTION GENETICS AND EVOLUTION 2021; 93:104914. [PMID: 33992814 DOI: 10.1016/j.meegid.2021.104914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/21/2021] [Accepted: 05/11/2021] [Indexed: 10/21/2022]
Abstract
Viruses in the families Circoviridae and Anelloviridae have circular single-stranded DNA genomes and have been identified in various animal species. Some members of the Circoviridae family such as beak and feather disease and porcine circovirus have been found to cause disease in their host animals. Anelloviruses on the other hand have not been identified to cause disease in their hosts but are highly prevalent in mammalian species. Using a non-invasive sampling approach, we identified novel circovirus and anelloviruses from faecal samples of wolverines dwelling in Montana, USA. Wolverines are forest carnivores that feed on a wide variety of carrion and other prey species, and they occupy diverse habitats across northern Europe to North America. Little is known about viruses associated with wild wolverines. Our investigation of the faecal samples resulted in the identification of a novel circovirus from three out of four wolverine samples, two collected in 2018 and one in 2019. Comparison with other circoviruses shows it is most closely related to a porcine circovirus 3, sharing ~69% identity. Additionally, three anellovirus genomes were recovered from two wolverine faecal samples which share 68--69% ORF1 nucleotide similarity with an anellovirus from another mustelid species, pine martens. Here we identify novel single-stranded DNA viruses associated with wolverine and open up new avenues for research.
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Affiliation(s)
- Rohan Antonio Bandoo
- 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
| | - Joshua Bautista
- 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
| | - Michael Lund
- 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
| | - Eric Newkirk
- Speedgoat Wildlife Solutions, Missoula, MT 59801, USA
| | - John Squires
- U.S. Forest Service, Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT 59801, USA
| | - 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, Rondebosch, 7700 Cape Town, South Africa.
| | - Simona Kraberger
- 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.
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12
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Canuti M, Todd M, Monteiro P, Van Osch K, Weir R, Schwantje H, Britton AP, Lang AS. Ecology and Infection Dynamics of Multi-Host Amdoparvoviral and Protoparvoviral Carnivore Pathogens. Pathogens 2020; 9:pathogens9020124. [PMID: 32075256 PMCID: PMC7168296 DOI: 10.3390/pathogens9020124] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/15/2022] Open
Abstract
Amdoparvovirus and Protoparvovirus are monophyletic viral genera that infect carnivores. We performed surveillance for and sequence analyses of parvoviruses in mustelids in insular British Columbia to investigate parvoviral maintenance and cross-species transmission among wildlife. Overall, 19.1% (49/256) of the tested animals were parvovirus-positive. Aleutian mink disease virus (AMDV) was more prevalent in mink (41.6%, 32/77) than martens (3.1%, 4/130), feline panleukopenia virus (FPV) was more prevalent in otters (27.3%, 6/22) than mink (5.2%, 4/77) or martens (2.3%, 3/130), and canine parvovirus 2 (CPV-2) was found in one mink, one otter, and zero ermines (N = 27). Viruses were endemic and bottleneck events, founder effects, and genetic drift generated regional lineages. We identified two local closely related AMDV lineages, one CPV-2 lineage, and five FPV lineages. Highly similar viruses were identified in different hosts, demonstrating cross-species transmission. The likelihood for cross-species transmission differed among viruses and some species likely represented dead-end spillover hosts. We suggest that there are principal maintenance hosts (otters for FPV, raccoons for CPV-2/FPV, mink for AMDV) that enable viral persistence and serve as sources for other susceptible species. In this multi-host system, viral and host factors affect viral persistence and distribution, shaping parvoviral ecology and evolution, with implications for insular carnivore conservation.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada
- Correspondence: (M.C.); (A.S.L.); Tel.: +1-709-864-8761 (M.C.); +1-709-864-7517 (A.S.L.)
| | - Melissa Todd
- British Columbia Ministry of Forests, Lands, Natural Resource Operations, and Rural Development, Coast Area Research Section, Suite 103-2100 Labieux Rd., Nanaimo, BC V9T 6E9, Canada; (M.T.); (P.M.); (K.V.O.)
| | - Paige Monteiro
- British Columbia Ministry of Forests, Lands, Natural Resource Operations, and Rural Development, Coast Area Research Section, Suite 103-2100 Labieux Rd., Nanaimo, BC V9T 6E9, Canada; (M.T.); (P.M.); (K.V.O.)
| | - Kalia Van Osch
- British Columbia Ministry of Forests, Lands, Natural Resource Operations, and Rural Development, Coast Area Research Section, Suite 103-2100 Labieux Rd., Nanaimo, BC V9T 6E9, Canada; (M.T.); (P.M.); (K.V.O.)
| | - Richard Weir
- British Columbia Ministry of Environment and Climate Change Strategy, PO Box 9338 STN Prov Govt, Victoria, BC V8W 9M2, Canada;
| | - Helen Schwantje
- British Columbia Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Wildlife Health Program, Wildlife and Habitat Branch, 2080 Labieux Rd., Nanaimo, BC V9T 6J9, Canada;
| | - Ann P. Britton
- Animal Health Center, British Columbia Ministry of Agriculture, 1767 Angus Campbell Rd., Abbotsford, BC V3G 2M3, Canada;
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada
- Correspondence: (M.C.); (A.S.L.); Tel.: +1-709-864-8761 (M.C.); +1-709-864-7517 (A.S.L.)
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Di Martino B, Di Profio F, Melegari I, Marsilio F. Feline Virome-A Review of Novel Enteric Viruses Detected in Cats. Viruses 2019; 11:v11100908. [PMID: 31575055 PMCID: PMC6832874 DOI: 10.3390/v11100908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/28/2019] [Accepted: 09/28/2019] [Indexed: 12/13/2022] Open
Abstract
Recent advances in the diagnostic and metagenomic investigations of the feline enteric environment have allowed the identification of several novel viruses that have been associated with gastroenteritis in cats. In the last few years, noroviruses, kobuviruses, and novel parvoviruses have been repetitively detected in diarrheic cats as alone or in mixed infections with other pathogens, raising a number of questions, with particular regards to their pathogenic attitude and clinical impact. In the present article, the current available literature on novel potential feline enteric viruses is reviewed, providing a meaningful update on the etiology, epidemiologic, pathogenetic, clinical, and diagnostic aspects of the infections caused by these pathogens.
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Affiliation(s)
- Barbara Di Martino
- Laboratory of Infectious Diseases, Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy.
| | - Federica Di Profio
- Laboratory of Infectious Diseases, Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy.
| | - Irene Melegari
- Laboratory of Infectious Diseases, Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy.
| | - Fulvio Marsilio
- Laboratory of Infectious Diseases, Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy.
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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: 123] [Impact Index Per Article: 20.5] [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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15
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Nishizawa T, Sugimoto Y, Takeda T, Kodera Y, Hatano Y, Takahashi M, Okamoto H. Identification and whole genome characterization of novel anelloviruses in masked palm civets (Paguma larvata): Segregation into four distinct clades. Virus Res 2018; 256:183-191. [PMID: 30149046 DOI: 10.1016/j.virusres.2018.08.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/16/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
The members of the family Anelloviridae are small and single-stranded DNA viruses with marked diversity in sequence and length, which ubiquitously infect many vertebrates, including mammals, birds and reptiles. The anelloviruses isolated from mammals are currently classified into 11 assigned and four proposed genera; some anelloviruses remain unassigned. The present study was conducted to identify anelloviruses in wild-caught masked palm civets (Paguma larvata) in Japan using a rolling-circle amplification method. Thirteen novel anellovirus strains were identified from 8 of 10 masked palm civets and their entire genomic sequences (2039-2535 nucleotides) were determined; they were classifiable into four distinct clades. Comparative analyses of all reported anelloviruses for which the entire or near-entire genomic sequences have been determined, including the 13 strains obtained in the present study, revealed that anelloviruses can provisionally be classified into 20 clades, which may correspond to 20 genera (including 11 assigned and four proposed genera) by a >70% amino acid sequence difference in open reading frame 1 (ORF1). This study suggested that novel anelloviruses of marked diversity are circulating in animals worldwide, and that the rolling-circle amplification method would be useful for identifying novel anelloviruses and other viruses with a circular DNA genome.
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Affiliation(s)
- Tsutomu Nishizawa
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
| | - Yuji Sugimoto
- Nikko Branch, Tochigi Hunter Association, Nikko, Tochigi, 321-2522, Japan
| | - Tsutomu Takeda
- Center for Weeds and Wildlife Management, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Yuuji Kodera
- Center for Weeds and Wildlife Management, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Yumi Hatano
- Sakakibara Heart Institute Clinic, Shinjuku-ku, Tokyo, 163-0804, Japan
| | - Masaharu Takahashi
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan.
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16
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Creasy A, Rosario K, Leigh BA, Dishaw LJ, Breitbart M. Unprecedented Diversity of ssDNA Phages from the Family Microviridae Detected within the Gut of a Protochordate Model Organism ( Ciona robusta). Viruses 2018; 10:v10080404. [PMID: 30065169 PMCID: PMC6116155 DOI: 10.3390/v10080404] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 07/23/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022] Open
Abstract
Phages (viruses that infect bacteria) play important roles in the gut ecosystem through infection of bacterial hosts, yet the gut virome remains poorly characterized. Mammalian gut viromes are dominated by double-stranded DNA (dsDNA) phages belonging to the order Caudovirales and single-stranded DNA (ssDNA) phages belonging to the family Microviridae. Since the relative proportion of each of these phage groups appears to correlate with age and health status in humans, it is critical to understand both ssDNA and dsDNA phages in the gut. Building upon prior research describing dsDNA viruses in the gut of Ciona robusta, a marine invertebrate model system used to study gut microbial interactions, this study investigated ssDNA phages found in the Ciona gut. We identified 258 Microviridae genomes, which were dominated by novel members of the Gokushovirinae subfamily, but also represented several proposed phylogenetic groups (Alpavirinae, Aravirinae, Group D, Parabacteroides prophages, and Pequeñovirus) and a novel group. Comparative analyses between Ciona specimens with full and cleared guts, as well as the surrounding water, indicated that Ciona retains a distinct and highly diverse community of ssDNA phages. This study significantly expands the known diversity within the Microviridae family and demonstrates the promise of Ciona as a model system for investigating their role in animal health.
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Affiliation(s)
- Alexandria Creasy
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Karyna Rosario
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Brittany A Leigh
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Larry J Dishaw
- Department of Pediatrics, Children's Research Institute, University of South Florida, St. Petersburg, FL 33701, USA.
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St. Petersburg, FL 33701, USA.
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Liu C, Liu F, Li Z, Qu L, Liu D. First report of feline bocavirus associated with severe enteritis of cat in Northeast China, 2015. J Vet Med Sci 2018; 80:731-735. [PMID: 29459503 PMCID: PMC5938208 DOI: 10.1292/jvms.17-0444] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Feline bocavirus (FBoV) is a newly identified bocavirus of cats in the family
Parvoviridae. A novel FBoV HRB2015-LDF was first identified from the cat
with severe enteritis in Northeast China, with an overall positive rate of 2.78% (1/36).
Phylogenetic and homologous analysis of the complete genome showed that FBoV HRB2015-LDF
was clustered into the FBoV branch and closely related to other FBoVs, with 68.7–97.5%
identities. And the genes of VP1, NPA and NS1 shared 70.7–97.6, 72.4–98.6 and 67.2–98.0%
nucleotide identities with other FBoVs, respectively. The results suggested that the FBoVs
could be divided into two distinct lineages, and the difference of nucleotide identities
was >20–30% between the lineages.
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Affiliation(s)
- Chunguo Liu
- State Key Lab of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Fei Liu
- Shanghai Hile Bio-Pharmaceutical Co., Ltd., Shanghai, 201403, China
| | - Zhigang Li
- Wendengying Veterinary Station, Weihai, Shandong 264413, China
| | - Liandong Qu
- State Key Lab of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Dafei Liu
- State Key Lab of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China.,College of Wildlife Resources, Northeast Forestry University, Harbin, Heilongjiang 150040, China
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18
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Zhang W, Yang S, Shan T, Hou R, Liu Z, Li W, Guo L, Wang Y, Chen P, Wang X, Feng F, Wang H, Chen C, Shen Q, Zhou C, Hua X, Cui L, Deng X, Zhang Z, Qi D, Delwart E. Virome comparisons in wild-diseased and healthy captive giant pandas. MICROBIOME 2017; 5:90. [PMID: 28780905 PMCID: PMC5545856 DOI: 10.1186/s40168-017-0308-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 07/13/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND The giant panda (Ailuropoda melanoleuca) is a vulnerable mammal herbivore living wild in central China. Viral infections have become a potential threat to the health of these endangered animals, but limited information related to these infections is available. METHODS Using a viral metagenomic approach, we surveyed viruses in the feces, nasopharyngeal secretions, blood, and different tissues from a wild giant panda that died from an unknown disease, a healthy wild giant panda, and 46 healthy captive animals. RESULTS The previously uncharacterized complete or near complete genomes of four viruses from three genera in Papillomaviridae family, six viruses in a proposed new Picornaviridae genus (Aimelvirus), two unclassified viruses related to posaviruses in Picornavirales order, 19 anelloviruses in four different clades of Anelloviridae family, four putative circoviruses, and 15 viruses belonging to the recently described Genomoviridae family were sequenced. Reflecting the diet of giant pandas, numerous insect virus sequences related to the families Iflaviridae, Dicistroviridae, Iridoviridae, Baculoviridae, Polydnaviridae, and subfamily Densovirinae and plant viruses sequences related to the families Tombusviridae, Partitiviridae, Secoviridae, Geminiviridae, Luteoviridae, Virgaviridae, and Rhabdoviridae; genus Umbravirus, Alphaflexiviridae, and Phycodnaviridae were also detected in fecal samples. A small number of insect virus sequences were also detected in the nasopharyngeal secretions of healthy giant pandas and lung tissues from the dead wild giant panda. Although the viral families present in the sick giant panda were also detected in the healthy ones, a higher proportion of papillomaviruses, picornaviruses, and anelloviruses reads were detected in the diseased panda. CONCLUSION This viral survey increases our understanding of eukaryotic viruses in giant pandas and provides a baseline for comparison to viruses detected in future infectious disease outbreaks. The similar viral families detected in sick and healthy giant pandas indicate that these viruses result in commensal infections in most immuno-competent animals.
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Affiliation(s)
- Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Zhijian Liu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Wang Li
- Department of Laboratory Medicine, Jiangsu Taizhou People’s Hospital, Taizhou, Jiangsu 225300 China
| | - Lianghua Guo
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Yan Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Peng Chen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Feifei Feng
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Hua Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Chao Chen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People’s Hospital, Taizhou, Jiangsu 225300 China
| | - Xiuguo Hua
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Li Cui
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Xutao Deng
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118 USA
| | - Zhihe Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Dunwu Qi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610000 China
| | - Eric Delwart
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118 USA
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Conceição‐Neto N, Godinho R, Álvares F, Yinda CK, Deboutte W, Zeller M, Laenen L, Heylen E, Roque S, Petrucci‐Fonseca F, Santos N, Van Ranst M, Mesquita JR, Matthijnssens J. Viral gut metagenomics of sympatric wild and domestic canids, and monitoring of viruses: Insights from an endangered wolf population. Ecol Evol 2017; 7:4135-4146. [PMID: 28649326 PMCID: PMC5478050 DOI: 10.1002/ece3.2991] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/15/2017] [Accepted: 03/21/2017] [Indexed: 12/13/2022] Open
Abstract
Animal host-microbe interactions are a relevant concern for wildlife conservation, particularly regarding generalist pathogens, where domestic host species can play a role in the transmission of infectious agents, such as viruses, to wild animals. Knowledge on viral circulation in wild host species is still scarce and can be improved by the recent advent of modern molecular approaches. We aimed to characterize the fecal virome and identify viruses of potential conservation relevance of diarrheic free-ranging wolves and sympatric domestic dogs from Central Portugal, where a small and threatened wolf population persists in a highly anthropogenically modified landscape. Using viral metagenomics, we screened diarrheic stools collected from wolves (n = 8), feral dogs (n = 4), and pet dogs (n = 6), all collected within wolf range. We detected novel highly divergent viruses as well as known viral pathogens with established effects on population dynamics, including canine distemper virus, a novel bocavirus, and canine minute virus. Furthermore, we performed a 4-year survey for the six wolf packs comprising this endangered wolf population, screening 93 fecal samples from 36 genetically identified wolves for canine distemper virus and the novel bocavirus, previously identified using our metagenomics approach. Our novel approach using metagenomics for viral screening in noninvasive samples of wolves and dogs has profound implications on the knowledge of both virology and wildlife diseases, establishing a complementary tool to traditional screening methods for the conservation of threatened species.
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Affiliation(s)
- Nádia Conceição‐Neto
- Department of Microbiology and ImmunologyLaboratory of Viral MetagenomicsRega Institute for Medical ResearchKU Leuven – University of LeuvenLeuvenBelgium
- Department of Microbiology and ImmunologyLaboratory of Clinical VirologyRega Institute for Medical ResearchKU Leuven – University of LeuvenLeuvenBelgium
| | - Raquel Godinho
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do PortoPortoPortugal
| | - Francisco Álvares
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Claude K. Yinda
- Department of Microbiology and ImmunologyLaboratory of Viral MetagenomicsRega Institute for Medical ResearchKU Leuven – University of LeuvenLeuvenBelgium
- Department of Microbiology and ImmunologyLaboratory of Clinical VirologyRega Institute for Medical ResearchKU Leuven – University of LeuvenLeuvenBelgium
| | - Ward Deboutte
- Department of Microbiology and ImmunologyLaboratory of Viral MetagenomicsRega Institute for Medical ResearchKU Leuven – University of LeuvenLeuvenBelgium
| | - Mark Zeller
- Department of Microbiology and ImmunologyLaboratory of Viral MetagenomicsRega Institute for Medical ResearchKU Leuven – University of LeuvenLeuvenBelgium
| | - Lies Laenen
- Department of Microbiology and ImmunologyLaboratory of Clinical VirologyRega Institute for Medical ResearchKU Leuven – University of LeuvenLeuvenBelgium
| | - Elisabeth Heylen
- Department of Microbiology and ImmunologyLaboratory of Viral MetagenomicsRega Institute for Medical ResearchKU Leuven – University of LeuvenLeuvenBelgium
| | - Sara Roque
- cE3c, Centre for Ecology, Evolution and Environmental ChangesFaculdade de Ciências da Universidade de LisboaLisbonPortugal
- Departamento de Biologia AnimalGrupo LoboFaculdade de Ciências da Universidade de LisboaLisbonPortugal
| | - Francisco Petrucci‐Fonseca
- cE3c, Centre for Ecology, Evolution and Environmental ChangesFaculdade de Ciências da Universidade de LisboaLisbonPortugal
- Departamento de Biologia AnimalGrupo LoboFaculdade de Ciências da Universidade de LisboaLisbonPortugal
| | - Nuno Santos
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
| | - Marc Van Ranst
- Department of Microbiology and ImmunologyLaboratory of Clinical VirologyRega Institute for Medical ResearchKU Leuven – University of LeuvenLeuvenBelgium
| | - João R. Mesquita
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- Department of Zootechnics, Rural Engineering and VeterinaryAgrarian Superior School of ViseuViseuPortugal
| | - Jelle Matthijnssens
- Department of Microbiology and ImmunologyLaboratory of Viral MetagenomicsRega Institute for Medical ResearchKU Leuven – University of LeuvenLeuvenBelgium
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20
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Moreno PS, Wagner J, Mansfield CS, Stevens M, Gilkerson JR, Kirkwood CD. Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics. PLoS One 2017; 12:e0178433. [PMID: 28570584 PMCID: PMC5453527 DOI: 10.1371/journal.pone.0178433] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/12/2017] [Indexed: 01/01/2023] Open
Abstract
The virome has been increasingly investigated in numerous animal species and in different sites of the body, facilitating the identification and discovery of a variety of viruses. In spite of this, the faecal virome of healthy dogs has not been investigated. In this study we describe the faecal virome of healthy dogs and dogs with acute diarrhoea in Australia, using a shotgun metagenomic approach. Viral sequences from a range of different virus families, including both RNA and DNA families, and known pathogens implicated in enteric disease were documented. Twelve viral families were identified, of which four were bacteriophages. Eight eukaryotic viral families were detected: Astroviridae, Coronaviridae, Reoviridae, Picornaviridae, Caliciviridae, Parvoviridae, Adenoviridae and Papillomaviridae. Families Astroviridae, Picornaviridae and Caliciviridae were found only in dogs with acute diarrhoea, with Astroviridae being the most common family identified in this group. Due to its prevalence, characterisation the complete genome of a canine astrovirus was performed. These studies indicate that metagenomic analyses are useful for the investigation of viral populations in the faeces of dogs. Further studies to elucidate the epidemiological and biological relevance of these findings are warranted.
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Affiliation(s)
- Paloma S. Moreno
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Translational Research and Animal Clinical Trial Study (TRACTS) group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- * E-mail:
| | - Josef Wagner
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Caroline S. Mansfield
- Translational Research and Animal Clinical Trial Study (TRACTS) group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Matthew Stevens
- Australian Genome Research Facility, Melbourne, Victoria, Australia
| | - James R. Gilkerson
- Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Carl D. Kirkwood
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
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21
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Cadar D, Lühken R, van der Jeugd H, Garigliany M, Ziegler U, Keller M, Lahoreau J, Lachmann L, Becker N, Kik M, Oude Munnink BB, Bosch S, Tannich E, Linden A, Schmidt V, Koopmans MP, Rijks J, Desmecht D, Groschup MH, Reusken C, Schmidt-Chanasit J. Widespread activity of multiple lineages of Usutu virus, western Europe, 2016. ACTA ACUST UNITED AC 2017; 22:30452. [PMID: 28181903 PMCID: PMC5388094 DOI: 10.2807/1560-7917.es.2017.22.4.30452] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/11/2017] [Indexed: 11/21/2022]
Abstract
In the summer of 2016, Belgium, France, Germany and the Netherlands reported widespread Usutu virus (USUV) activity based on live and dead bird surveillance. The causative USUV strains represented four lineages, of which two putative novel lineages were most likely recently introduced into Germany and spread to other western European countries. The spatial extent of the outbreak area corresponded with R0 values > 1. The occurrence of the outbreak, the largest USUV epizootic registered so far in Europe, allowed us to gain insight in how a recently introduced arbovirus with potential public health implications can spread and become a resident pathogen in a naïve environment. Understanding the ecological and epidemiological factors that drive the emergence or re-emergence of USUV is critical to develop and implement timely surveillance strategies for adequate preventive and control measures. Public health authorities, blood transfusion services and clinicians in countries where USUV was detected should be aware of the risk of possible USUV infection in humans, including in patients with unexplained encephalitis or other neurological impairments, especially during late summer when mosquito densities peak.
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Affiliation(s)
- Daniel Cadar
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany.,These authors contributed equally to this work
| | - Renke Lühken
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany.,These authors contributed equally to this work
| | - Henk van der Jeugd
- These authors contributed equally to this work.,Vogeltrekstation - Dutch Centre for Avian Migration and Demography (NIOO-KNAW), Wageningen, the Netherlands
| | - Mutien Garigliany
- These authors contributed equally to this work.,Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Ute Ziegler
- These authors contributed equally to this work.,Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Markus Keller
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | | | - Lars Lachmann
- Nature and Biodiversity Conservation Union (NABU), Berlin, Germany
| | - Norbert Becker
- German Mosquito Control Association (KABSeV), Speyer, Germany.,University of Heidelberg, Heidelberg, Germany
| | - Marja Kik
- Dutch Wildlife Health Centre, Utrecht University, Utrecht, The Netherlands
| | - Bas B Oude Munnink
- Erasmus MC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Rotterdam, The Netherlands
| | - Stefan Bosch
- Nature and Biodiversity Conservation Union (NABU), Stuttgart, Germany
| | - Egbert Tannich
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany.,German Centre for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel, Hamburg, Germany
| | - Annick Linden
- Belgian Wildlife Health Surveillance Network, Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Volker Schmidt
- Clinic for birds and reptiles, University Leipzig, Germany
| | - Marion P Koopmans
- Erasmus MC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Rotterdam, The Netherlands
| | - Jolianne Rijks
- These authors contributed equally to this work.,Dutch Wildlife Health Centre, Utrecht University, Utrecht, The Netherlands
| | - Daniel Desmecht
- These authors contributed equally to this work.,Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Martin H Groschup
- These authors contributed equally to this work.,Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Chantal Reusken
- These authors contributed equally to this work.,Erasmus MC, Department of Viroscience, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Rotterdam, The Netherlands
| | - Jonas Schmidt-Chanasit
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany.,These authors contributed equally to this work.,German Centre for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel, Hamburg, Germany
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22
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van Beurden SJ, IJsseldijk LL, van de Bildt MWG, Begeman L, Wellehan JFX, Waltzek TB, de Vrieze G, Gröne A, Kuiken T, Verheije MH, Penzes JJ. A novel cetacean adenovirus in stranded harbour porpoises from the North Sea: detection and molecular characterization. Arch Virol 2017; 162:2035-2040. [DOI: 10.1007/s00705-017-3310-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/28/2017] [Indexed: 10/20/2022]
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23
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ENDEMIC INFECTION OF STRANDED SOUTHERN SEA OTTERS (ENHYDRA LUTRIS NEREIS) WITH NOVEL PARVOVIRUS, POLYOMAVIRUS, AND ADENOVIRUS. J Wildl Dis 2017; 53:532-542. [PMID: 28192039 DOI: 10.7589/2016-04-082] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Over the past century, the southern sea otter (SSO; Enhydra lutris nereis) population has been slowly recovering from near extinction due to overharvest. The SSO is a threatened subspecies under federal law and a fully protected species under California law, US. Through a multiagency collaborative program, stranded animals are rehabilitated and released, while deceased animals are necropsied and tissues are cryopreserved to facilitate scientific study. Here, we processed archival tissues to enrich particle-associated viral nucleic acids, which we randomly amplified and deeply sequenced to identify viral genomes through sequence similarities. Anelloviruses and endogenous retroviral sequences made up over 50% of observed viral sequences. Polyomavirus, parvovirus, and adenovirus sequences made up most of the remaining reads. We characterized and phylogenetically analyzed the full genome of sea otter polyomavirus 1 and the complete coding sequence of sea otter parvovirus 1 and found that the closest known viruses infect primates and domestic pigs ( Sus scrofa domesticus), respectively. We tested archived tissues from 69 stranded SSO necropsied over 14 yr (2000-13) by PCR. Polyomavirus, parvovirus, and adenovirus infections were detected in 51, 61, and 29% of examined animals, respectively, with no significant increase in frequency over time, suggesting endemic infection. We found that 80% of tested SSO were infected with at least one of the three DNA viruses, whose tissue distribution we determined in 261 tissue samples. Parvovirus DNA was most frequently detected in mesenteric lymph node, polyomavirus DNA in spleen, and adenovirus DNA in multiple tissues (spleen, retropharyngeal and mesenteric lymph node, lung, and liver). This study describes the virome in tissues of a threatened species and shows that stranded SSO are frequently infected with multiple viruses, warranting future research to investigate associations between these infections and observed lesions.
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24
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Varsani A, Krupovic M. Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae. Virus Evol 2017; 3:vew037. [PMID: 28458911 PMCID: PMC5399927 DOI: 10.1093/ve/vew037] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
With the advent of metagenomics approaches, a large diversity of known and unknown viruses has been identified in various types of environmental, plant, and animal samples. One such widespread virus group is the recently established family Genomoviridae which includes viruses with small (∼2-2.4 kb), circular ssDNA genomes encoding rolling-circle replication initiation proteins (Rep) and unique capsid proteins. Here, we propose a sequence-based taxonomic framework for classification of 121 new virus genomes within this family. Genomoviruses display ∼47% sequence diversity, which is very similar to that within the well-established and extensively studied family Geminiviridae (46% diversity). Based on our analysis, we establish a 78% genome-wide pairwise identity as a species demarcation threshold. Furthermore, using a Rep sequence phylogeny-based analysis coupled with the current knowledge on the classification of geminiviruses, we establish nine genera within the Genomoviridae family. These are Gemycircularvirus (n = 73), Gemyduguivirus (n = 1), Gemygorvirus (n = 9), Gemykibivirus (n = 29), Gemykolovirus (n = 3), Gemykrogvirus (n = 3), Gemykroznavirus (n = 1), Gemytondvirus (n = 1), Gemyvongvirus (n = 1). The presented taxonomic framework offers rational classification of genomoviruses based on the sequence information alone and sets an example for future classification of other groups of uncultured viruses discovered using metagenomics approaches.
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Affiliation(s)
- Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory 7700, South Africa
| | - Mart Krupovic
- Unité Biologie moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France
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25
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da Silva Assis MR, Vieira CB, Fioretti JM, Rocha MS, de Almeida PIN, Miagostovich MP, Fumian TM. Detection and Molecular Characterization of Gemycircularvirus from Environmental Samples in Brazil. FOOD AND ENVIRONMENTAL VIROLOGY 2016; 8:305-309. [PMID: 27393014 DOI: 10.1007/s12560-016-9254-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/30/2016] [Indexed: 06/06/2023]
Abstract
Gemycircularvirus (GemyCV) is a group of viruses which has been recently proposed as a new viral genus detected in fecal and environmental samples around the world. GemyCVs have been detected in human blood, brain tissue, cerebrospinal fluid, and stool sample. In the present study, we demonstrate for the first time, through molecular detection and characterization, the presence of GemyCVs in environmental samples from Brazil. Our results show a percentage of positivity ranging from 69 (25/36) to 97 % (35/36) in river water samples collected in Manaus, Amazon region, and wastewater from a wastewater treatment plant located in Rio de Janeiro, respectively, revealing GemyCVs as an important environmental contaminant.
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Affiliation(s)
- Matheus Ribeiro da Silva Assis
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Avenida Brasil, 4365, 21040-360, Rio de Janeiro, Brazil
| | - Carmen Baur Vieira
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Avenida Brasil, 4365, 21040-360, Rio de Janeiro, Brazil
| | - Julia Monassa Fioretti
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Avenida Brasil, 4365, 21040-360, Rio de Janeiro, Brazil
| | - Mônica Simões Rocha
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Avenida Brasil, 4365, 21040-360, Rio de Janeiro, Brazil
| | - Pedro Ivo Neves de Almeida
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Avenida Brasil, 4365, 21040-360, Rio de Janeiro, Brazil
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Avenida Brasil, 4365, 21040-360, Rio de Janeiro, Brazil
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Avenida Brasil, 4365, 21040-360, Rio de Janeiro, Brazil.
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26
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Pearson VM, Caudle SB, Rokyta DR. Viral recombination blurs taxonomic lines: examination of single-stranded DNA viruses in a wastewater treatment plant. PeerJ 2016; 4:e2585. [PMID: 27781171 PMCID: PMC5075696 DOI: 10.7717/peerj.2585] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/19/2016] [Indexed: 12/26/2022] Open
Abstract
Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a broad range of hosts. To examine this complex collection of viruses, full-length genomes of circular ssDNA viruses were isolated from a wastewater treatment facility using a combination of sucrose-gradient size selection and rolling-circle amplification and sequenced on an Illumina MiSeq. Single-stranded DNA viruses are among the least understood groups of microbial pathogens due to genomic biases and culturing difficulties, particularly compared to the larger, more often studied dsDNA viruses. However, the group contains several notable well-studied examples, including agricultural pathogens which infect both livestock and crops (Circoviridae and Geminiviridae), and model organisms for genetics and evolution studies (Microviridae). Examination of the collected viral DNA provided evidence for 83 unique genotypic groupings, which were genetically dissimilar to known viral types and exhibited broad diversity within the community. Furthermore, although these genomes express similarities to known viral families, such as Circoviridae, Geminiviridae, and Microviridae, many are so divergent that they may represent new taxonomic groups. This study demonstrated the efficacy of the protocol for separating bacteria and large viruses from the sought after ssDNA viruses and the ability to use this protocol to obtain an in-depth analysis of the diversity within this group.
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Affiliation(s)
- Victoria M Pearson
- Department of Biological Science, Florida State University , Tallahassee , FL , USA
| | - S Brian Caudle
- Division of Food Safety, Florida Department of Agriculture and Consumer Services , Tallahassee , FL , USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University , Tallahassee , FL , USA
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27
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Zhang W, Wang H, Wang Y, Liu Z, Li J, Guo L, Yang S, Shen Q, Zhao X, Cui L, Hua X. Identification and genomic characterization of a novel species of feline anellovirus. Virol J 2016; 13:146. [PMID: 27568181 PMCID: PMC5002325 DOI: 10.1186/s12985-016-0601-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/15/2016] [Indexed: 01/30/2023] Open
Abstract
Here, a novel feline anellovirus strain (named FelineAV621 and GenBank no. KX262893) was detected in two cats with diarrhea. The complete genome of FelineAV621 is 2409 nt long with a G+C content of 56.67 %, including three open reading frames (ORFs). Phylogenetic analysis based on the amino acid sequence of the putative capsid protein (ORF1) indicated that FelineAV621 belonged to a novel anellovirus species inside a clade containing the seal anellovirus, canine TTVs, and porcine TTVs, but was distant from all the previous feline anelloviruses.
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Affiliation(s)
- Wen Zhang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Hua Wang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Yan Wang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Zhijian Liu
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Jingjiao Li
- School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Lianghua Guo
- School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Quan Shen
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Xiaoying Zhao
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Li Cui
- School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Xiuguo Hua
- School of Agriculture and Biology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
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28
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Genomoviridae: a new family of widespread single-stranded DNA viruses. Arch Virol 2016; 161:2633-43. [DOI: 10.1007/s00705-016-2943-3] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/17/2016] [Indexed: 11/26/2022]
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29
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Zhang W, Li L, Deng X, Blümel J, Nübling CM, Hunfeld A, Baylis SA, Delwart E. Viral nucleic acids in human plasma pools. Transfusion 2016; 56:2248-55. [PMID: 27306718 DOI: 10.1111/trf.13692] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/06/2016] [Accepted: 04/21/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND The identification of viruses in human blood is required for epidemiologic surveillance and to detect potentially emerging threats to blood transfusion safety. STUDY DESIGN AND METHODS Viral nucleic acids in plasma fractionation pools assembled from blood donors in the United States and Europe were analyzed by viral metagenomics. RESULTS Anelloviruses were detected in each of the 10 plasma pools. Human pegivirus A (HPgV; GB virus type C) sequences were identified in eight of the 10 pools, more than 90% of which belong to Genotype 2. The recently described human HPgV2 in Flaviviridae was not detected. A small number of sequence reads of human papillomavirus were also detected in three pools. In one pool, two different gemycircularvirus genomes were identified and fully sequenced. The capsid protein of one gemycircularvirus shared 83% to 84% identity to those of genomes from human serum and sewage. The presence of the gemycircularvirus genomes in the plasma pool was independently confirmed and the viral concentration estimated by digital PCR at more than 10(6) copies/mL assuming their origin from single donors. CONCLUSION Further research is required to elucidate whether gemycircularviruses can infect humans or are indicative of contamination occurring during phlebotomy, plasma pool processing, or ongoing donor fungal infections.
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Affiliation(s)
- Wen Zhang
- Blood Systems Research Institute, San Francisco, California.,Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | - Linlin Li
- Blood Systems Research Institute, San Francisco, California.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | | | | | | | | | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California. .,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California.
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30
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Lamers MM, Smits SL, Hundie GB, Provacia LB, Koopmans M, Osterhaus ADME, Haagmans BL, Raj VS. Naturally occurring recombination in ferret coronaviruses revealed by complete genome characterization. J Gen Virol 2016; 97:2180-2186. [PMID: 27283016 PMCID: PMC7079585 DOI: 10.1099/jgv.0.000520] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ferret coronaviruses (FRCoVs) exist as an enteric and a systemic pathotype, of which the latter is highly lethal to ferrets. To our knowledge, this study provides the first full genome sequence of a FRCoV, tentatively called FRCoV-NL-2010, which was detected in 2010 in ferrets in The Netherlands. Phylogenetic analysis showed that FRCoV-NL-2010 is most closely related to mink CoV, forming a separate clade of mustelid alphacoronavirus that split off early from other alphacoronaviruses. Based on sequence homology of the complete genome, we propose that these mustelid coronaviruses may be assigned to a new species. Comparison of FRCoV-NL-2010 with the partially sequenced ferret systemic coronavirus MSU-1 and ferret enteric coronavirus MSU-2 revealed that recombination in the spike, 3c and envelope genes occurred between different FRCoVs.
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Affiliation(s)
- Mart M Lamers
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Saskia L Smits
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Gadissa B Hundie
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | - Marion Koopmans
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Albert D M E Osterhaus
- Artemis One Health, Utrecht, The Netherlands.,Center for Infection Medicine and Zoonoses Research, University of Veterinary Medicine, Hannover, Germany
| | - Bart L Haagmans
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - V Stalin Raj
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
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31
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Steel O, Kraberger S, Sikorski A, Young LM, Catchpole RJ, Stevens AJ, Ladley JJ, Coray DS, Stainton D, Dayaram A, Julian L, van Bysterveldt K, Varsani A. Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand. INFECTION GENETICS AND EVOLUTION 2016; 43:151-64. [PMID: 27211884 DOI: 10.1016/j.meegid.2016.05.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/13/2022]
Abstract
In recent years, innovations in molecular techniques and sequencing technologies have resulted in a rapid expansion in the number of known viral sequences, in particular those with circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA genomes. CRESS DNA viruses are present in the virome of many ecosystems and are known to infect a wide range of organisms. A large number of the recently identified CRESS DNA viruses cannot be classified into any known viral families, indicating that the current view of CRESS DNA viral sequence space is greatly underestimated. Animal faecal matter has proven to be a particularly useful source for sampling CRESS DNA viruses in an ecosystem, as it is cost-effective and non-invasive. In this study a viral metagenomic approach was used to explore the diversity of CRESS DNA viruses present in the faeces of domesticated and wild animals in New Zealand. Thirty-eight complete CRESS DNA viral genomes and two circular molecules (that may be defective molecules or single components of multicomponent genomes) were identified from forty-nine individual animal faecal samples. Based on shared genome organisations and sequence similarities, eighteen of the isolates were classified as gemycircularviruses and twelve isolates were classified as smacoviruses. The remaining eight isolates lack significant sequence similarity with any members of known CRESS DNA virus groups. This research adds significantly to our knowledge of CRESS DNA viral diversity in New Zealand, emphasising the prevalence of CRESS DNA viruses in nature, and reinforcing the suggestion that a large proportion of CRESS DNA viruses are yet to be identified.
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Affiliation(s)
- Olivia Steel
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Alyssa Sikorski
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Laura M Young
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Ryan J Catchpole
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Aaron J Stevens
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Jenny J Ladley
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Dorien S Coray
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Daisy Stainton
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Anisha Dayaram
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Laurel Julian
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Katherine van Bysterveldt
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Structural Biology Research Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, USA.
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Discovery and complete genome sequence of a novel circovirus-like virus in the endangered rowi kiwi, Apteryx rowi. Virus Genes 2016; 52:727-31. [PMID: 27115421 DOI: 10.1007/s11262-016-1342-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 04/15/2016] [Indexed: 10/21/2022]
Abstract
Circoviruses are circular, non-enveloped, single-stranded DNA viruses around 2000 nucleotides (nt) in length and include the pathogenic species, Porcine circovirus 1 and Beak and feather disease virus, capable of causing significant morbidity and mortality. This group of viruses may be robust to degradation by external environments, and avian circoviruses are known to move between closely related hosts. Using a de novo metagenomic approach, followed by confirmatory PCR, we identify for the first time a circular Rep-encoding single-stranded (CRESS) DNA virus in New Zealand kiwi, Apteryx spp., derived from faecal matter of the rowi kiwi (A. rowi) showing signs of verminous dermatitis. The entire 2085 nt genome was cloned and sequenced and contains both capsid and replicase genes, as well as a conserved 9 nt motif. Phylogenetic analyses place it within Circoviridae, adjacent to other environmental CRESS-DNA viruses, and most closely related to badger circovirus-like virus (Meles meles circovirus-like virus). As the rowi is the most critically endangered kiwi, it is vital to understand the role of rowi kiwi circovirus-like virus as a possible pathogen and also any potential cross-species transmission.
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Bexton S, Wiersma LC, Getu S, van Run PR, Verjans GMGM, Schipper D, Schapendonk CME, Bodewes R, Oldroyd L, Haagmans BL, Koopmans MMP, Smits SL. Detection of Circovirus in Foxes with Meningoencephalitis, United Kingdom, 2009-2013. Emerg Infect Dis 2016; 21:1205-8. [PMID: 26079061 PMCID: PMC4480402 DOI: 10.3201/eid2107.150228] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A fox circovirus was identified in serum samples from foxes with unexplained neurologic signs by using viral metagenomics. Fox circovirus nucleic acid was localized in histological lesions of the cerebrum by in situ hybridization. Viruses from the family Circoviridae may have neurologic tropism more commonly than previously anticipated.
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Guo D, Wang Z, Yao S, Li C, Geng Y, Wang E, Zhao X, Su M, Wei S, Wang X, Feng L, Chang YF, Sun D. Epidemiological investigation reveals genetic diversity and high co-infection rate of canine bocavirus strains circulating in Heilongjiang province, Northeast China. Res Vet Sci 2016; 106:7-13. [PMID: 27234529 PMCID: PMC7111776 DOI: 10.1016/j.rvsc.2016.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 02/16/2016] [Accepted: 03/07/2016] [Indexed: 01/24/2023]
Abstract
To trace evolution of CBoV in Northeast China, 201 fecal samples from rectal swabs of diarrheic dogs collected from May 2014 to April 2015 were investigated using PCR targeting partial NS1 gene (440 bp). Furthermore, phylogenetic analysis of the identified CBoV strains was conducted using nucleotide sequences of the partial NS1 gene. The results indicated that 15 of 201 fecal samples (7.5%) were positive for CBoV; the partial NS1 genes of the 15 CBoV strains exhibited 83.1%–100% nucleotide identity, and 75.8%–100% amino acid identity; the entire VP2 gene of five selected CBoV strains exhibited 82.9%–96.8% nucleotide identity, and 90.4%–99.1% amino acid identity. The 15 CBoV strains exhibited high co-infection rates with CPV-2 (40%), CCoV (20%), and CaKV (26.67%). Phylogenetic analysis of the partial NS1 gene revealed that the 15 CBoV strains were divided into different subgroups of CBoV-2 when compared with CBoV-2 strains from South Korea, USA, Germany, and Hong Kong in China. Moreover, phylogenetic analysis of the VP2 gene indicated that five selected CBoV strains were divided into three different genetic groups of CBoV-2, involving in CBoV-2HK group, CBoV-2C group, and CBoV-2B group. The recombination analysis using the entire VP2 gene revealed three potential recombination events that occurred among five selected strains in our study. These data demonstrated that the CBoV strains circulating in Heilongjiang province, Northeast China showed genetic diversities, potential recombination events, and high co-infection rate. Further studies will be required to address the potential pathogenic role of these diverse CBoV strains. Canine bocavirus (CBoV) exhibits high prevalence in Northeast China from 2.8% to 20%. We revealed high co-infection of CBoV with canine parvovirus-2, canine coronavirus, and canine kobuvirus. The CBoV strains circulating in Northeast China show multiple genetic groups. Potential recombination events occur among the CBoV strains circulating in Northeast China.
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Affiliation(s)
- Donghua Guo
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, Sartu District, Daqing 163319, PR China
| | - Zhihui Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, Sartu District, Daqing 163319, PR China
| | - Shuang Yao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, Sartu District, Daqing 163319, PR China
| | - Chunqiu Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, Sartu District, Daqing 163319, PR China
| | - Yufei Geng
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, Sartu District, Daqing 163319, PR China
| | - Enyu Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, Sartu District, Daqing 163319, PR China
| | - Xiwen Zhao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, Sartu District, Daqing 163319, PR China
| | - Mingjun Su
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, Sartu District, Daqing 163319, PR China
| | - Shan Wei
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, Sartu District, Daqing 163319, PR China
| | - Xinyu Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, Sartu District, Daqing 163319, PR China
| | - Li Feng
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences, No. 427 Maduan Street, Nangang District, Harbin 150001, PR China
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary medicine, Cornell University, Ithaca, NY 14853, USA.
| | - Dongbo Sun
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 2 Xinyang Road, Sartu District, Daqing 163319, PR China.
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Male MF, Kraberger S, Stainton D, Kami V, Varsani A. Cycloviruses, gemycircularviruses and other novel replication-associated protein encoding circular viruses in Pacific flying fox (Pteropus tonganus) faeces. INFECTION GENETICS AND EVOLUTION 2016; 39:279-292. [PMID: 26873064 DOI: 10.1016/j.meegid.2016.02.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/27/2016] [Accepted: 02/06/2016] [Indexed: 12/13/2022]
Abstract
Viral metagenomic studies have demonstrated that animal faeces can be a good sampling source for exploring viral diversity associated with the host and its environment. As part of an continuing effort to identify novel circular replication-associated protein encoding single-stranded (CRESS) DNA viruses circulating in the Tongan archipelago, coupled with the fact that bats are a reservoir species of a large number of viruses, we used a metagenomic approach to investigate the CRESS DNA virus diversity in Pacific flying fox (Pteropus tonganus) faeces. Faecal matter from four roosting sites located in Ha'avakatolo, Kolovai, Ha'ateiho and Lapaha on Tongatapu Island was collected in April 2014 and January 2015. From these samples we identified five novel cycloviruses representing three putative species, 25 gemycircularviruses representing at least 14 putative species, 17 other CRESS DNA viruses (15 putative species), two circular DNA molecules and a putative novel multi-component virus for which we have identified three cognate molecules. This study demonstrates that there exists a large diversity of CRESS DNA viruses in Pacific flying fox faeces.
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Affiliation(s)
- Maketalena F Male
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Daisy Stainton
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | | | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Structural Biology Research Unit, Division of Medical Biochemistry, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory 7700, South Africa; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, USA.
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36
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van Elk C, van de Bildt M, van Run P, de Jong A, Getu S, Verjans G, Osterhaus A, Kuiken T. Central nervous system disease and genital disease in harbor porpoises (Phocoena phocoena) are associated with different herpesviruses. Vet Res 2016; 47:28. [PMID: 26861818 PMCID: PMC4748569 DOI: 10.1186/s13567-016-0310-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/07/2016] [Indexed: 11/20/2022] Open
Abstract
Herpesvirus infection causes disease of variable severity in many species, including cetaceans. However, little is known about herpesvirus infection in harbor porpoises (Phocoena phocoena), despite being widespread in temperate coastal waters of the Northern Hemisphere. Therefore, we examined harbor porpoises that stranded alive in the Netherlands, Belgium, and Germany between 2000 and 2014 for herpesvirus infection and associated disease. Porpoises that died or had to be euthanized were autopsied, and samples were collected for virological and pathological analyses. We found one known herpesvirus (Phocoena phocoena herpesvirus type 1, PPHV-1)—a gammaherpesvirus—and two novel herpesviruses (PPHV-2 and PPHV-3)—both alphaherpesviruses—in these porpoises. A genital plaque, in which PPHV-1 was detected, occurred in 1% (1/117) of porpoises. The plaque was characterized by epithelial hyperplasia and intranuclear inclusion bodies that contained herpesvirus-like particles, and that stained positive by a PPHV-1-specific in situ hybridization test. PPHV-2 occurred in the brain of 2% (1/74) of porpoises. This infection was associated with lymphocytic encephalitis, characterized by neuronal necrosis and intranuclear inclusion bodies containing herpesvirus-like particles. PPHV-3 had a prevalence of 5% (4/74) in brain tissue, 5% (2/43) in blowhole swabs, and 2% (1/43) in genital swabs, but was not associated with disease. Phylogenetically, PPHV-1 was identical to a previously reported herpesvirus from a harbor porpoise, PPHV-2 showed closest identity with two herpesviruses from dolphins, and PPHV-3 showed closest identity with a cervid herpesvirus. In conclusion, harbor porpoises may be infected with at least three different herpesviruses, one of which can cause clinically severe neurological disease.
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Affiliation(s)
- Cornelis van Elk
- Dolfinarium Harderwijk, Strandboulevard Oost 1, 3841 AB, Harderwijk, The Netherlands.
| | - Marco van de Bildt
- Department of Viroscience, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - Peter van Run
- Department of Viroscience, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - Anton de Jong
- Department of Pathology, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - Sarah Getu
- Department of Viroscience, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - Georges Verjans
- Department of Viroscience, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - Albert Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine, Bünteweg 2, 30559, Hannover, Germany.
| | - Thijs Kuiken
- Department of Viroscience, Erasmus Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
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Lojkić I, Biđin M, Prpić J, Šimić I, Krešić N, Bedeković T. Faecal virome of red foxes from peri-urban areas. Comp Immunol Microbiol Infect Dis 2016; 45:10-5. [PMID: 27012914 PMCID: PMC7112549 DOI: 10.1016/j.cimid.2016.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 01/05/2016] [Accepted: 01/23/2016] [Indexed: 12/27/2022]
Abstract
High-throughput sequencing and viral metagenomic analysis were performed on faecal samples of juvenile and adult foxes. Fox picobirnavirus was more closely related to the porcine and human picobirnaviruses than to fox picobirnavirus. New fox circovirus highly similar to dog circovirus of is de novo asembled from the high-throughput sequencing data.
Red foxes (Vulpes vulpes) are the most abundant carnivore species in the Northern Hemisphere. Since their populations are well established in peri-urban and urban areas, they represent a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. In this study, we evaluated the faecal virome of juvenile and adult foxes from peri-urban areas in central Croatia. The dominating mammalian viruses were fox picobirnavirus and parvovirus. The highest number of viral reads (N = 1412) was attributed to a new fox circovirus and complete viral genome was de novo assembled from the high-throughput sequencing data. Fox circovirus is highly similar to dog circoviruses identified in diseased dogs in USA and Italy, and to a recently discovered circovirus of foxes with neurologic disease from the United Kingdom. Our fox picobirnavirus was more closely related to the porcine and human picobirnaviruses than to known fox picobirnaviruses.
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Affiliation(s)
- Ivana Lojkić
- Department of Virology, Croatian Veterinary Institute, Zagreb, Croatia.
| | - Marina Biđin
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Jelena Prpić
- Department of Virology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Ivana Šimić
- Department of Virology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Nina Krešić
- Department of Virology, Croatian Veterinary Institute, Zagreb, Croatia
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Zhou C, Zhang S, Gong Q, Hao A. A novel gemycircularvirus in an unexplained case of child encephalitis. Virol J 2015; 12:197. [PMID: 26596706 PMCID: PMC4657213 DOI: 10.1186/s12985-015-0431-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 11/17/2015] [Indexed: 12/21/2022] Open
Abstract
Background Recently, a diverse group of viruses with circular, replication initiator protein(Rep) encoding, single stranded DNA (CRESS-DNA) genomes, were discovered from wide range of eukaryotic organisms ranging from mammals to fungi. Gemycircularvirus belongs to a distinct group of CRESS-DNA genomes and is classified under the genus name of Gemycircularvirus. Findings Here, a novel gemycircularvirus named GeTz1 from cerebrospinal fluid sample of a child with unexplainable encephalitis was characterized. The novel gemycircularvirus encodes two major proteins, including a capsid protein (Cap) and a replication-associated protein (Rep). Phylogenetic analysis based on the amino acid sequence of Rep indicated that GeTz1 clusters with one gemycircularvirus discovered from bird (KF371633), sharing 46.6 % amino acid sequence identity with each other. Conclusion A novel gemycircularvirus was discovered from cerebrospinal fluid sample of a child with unexplainable encephalitis. Further studies, such as testing human sera for specific antibodies, should be performed to investigate whether gemycircularvirus infects human and is associated with encephalitis.
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Affiliation(s)
- Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu, 225300, China.
| | - Shibing Zhang
- Department of Laboratory Medicine, the First People's Hospital of Suqian, Suqian, Jiangsu, 223800, China.
| | - Qin Gong
- Jiangsu Taizhou People's Hospital, Taizhou, Jiangsu, 225300, China.
| | - Aimin Hao
- Department of Laboratory Medicine, the Second People's Hospital of Wuxi, Wuxi, Jiangsu, 214002, China.
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Hrazdilová K, Slaninková E, Brožová K, Modrý D, Vodička R, Celer V. New species of Torque Teno miniviruses infecting gorillas and chimpanzees. Virology 2015; 487:207-14. [PMID: 26547037 DOI: 10.1016/j.virol.2015.10.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/12/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Anelloviridae family is comprised of small, non-enveloped viruses of various genome lengths, high sequence diversity, sharing the same genome organization. Infections and co-infections by different genotypes in humans are ubiquitous. Related viruses were described in number of mammalian hosts, but very limited data are available from the closest human relatives - great apes and non-human primates. Here we report the 100% prevalence determined by semi-nested PCR from fecal samples of 16 captive primate species. Only the Mandrillus sphinx, showed the prevalence only 8%. We describe three new species of gorillas׳ and four new species of chimpanzees׳ Betatorqueviruses and their co-infections in one individual. This study is also first report and analysis of nearly full length TTMV genomes infecting gorillas. Our attempts to sequence the complete genomes of anelloviruses from host feces invariably failed. Broader usage of blood /tissue material is necessary to understand the diversity and interspecies transmission of anelloviruses.
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Affiliation(s)
- Kristýna Hrazdilová
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic.
| | - Eva Slaninková
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic
| | - Kristýna Brožová
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic
| | - David Modrý
- CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Roman Vodička
- The Prague Zoological Garden, Prague 171 00, Czech Republic
| | - Vladimír Celer
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic
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40
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Li W, Gu Y, Shen Q, Yang S, Wang X, Wan Y, Zhang W. A novel gemycircularvirus from experimental rats. Virus Genes 2015; 51:302-5. [PMID: 26303898 DOI: 10.1007/s11262-015-1238-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/14/2015] [Indexed: 11/25/2022]
Abstract
Recently, gemycircularviruses have been found in humans and various species of animals. Here, a novel gemycircularvirus named Ch-zjrat-01 from blood samples of experimental rats was characterized. The novel gemycircularvirus encodes two major proteins, including a capsid protein (Cap) and a replication-associated protein (Rep). Phylogenetic analysis based on the amino acid sequence of Rep indicated that Ch-zjrat-01 clusters with two gemycircularviruses discovered from bird (KF371635) and mosquito (HQ335086), sharing 48.7 and 49.4 % sequence identities with them, respectively.
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Affiliation(s)
- Wang Li
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yu Gu
- Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yan Wan
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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41
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Rosario K, Schenck RO, Harbeitner RC, Lawler SN, Breitbart M. Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins. Front Microbiol 2015. [PMID: 26217327 PMCID: PMC4498126 DOI: 10.3389/fmicb.2015.00696] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA) viruses that encode a conserved replication initiator protein (Rep) in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA) viruses were originally thought to only infect plants and vertebrates, recent studies have identified these viruses in a number of invertebrates. To further explore CRESS-DNA viruses in the marine environment, this study surveyed CRESS-DNA viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported viruses, were recovered from 21 invertebrate species, mainly crustaceans. Phylogenetic analysis based on the Rep revealed a novel clade of CRESS-DNA viruses that included approximately one third of the marine invertebrate associated viruses identified here and whose members may represent a novel family. Investigation of putative capsid proteins (Cap) encoded within the eukaryotic CRESS-DNA viral genomes from this study and those in GenBank demonstrated conserved patterns of predicted intrinsically disordered regions (IDRs), which can be used to complement similarity-based searches to identify divergent structural proteins within novel genomes. Overall, this study expands our knowledge of CRESS-DNA viruses associated with invertebrates and explores a new tool to evaluate divergent structural proteins encoded by these viruses.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Ryan O Schenck
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Rachel C Harbeitner
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Stephanie N Lawler
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
| | - Mya Breitbart
- College of Marine Science, University of South Florida St. Petersburg, FL, USA
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42
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Moesker FM, van Kampen JJA, van der Eijk AA, van Rossum AMC, de Hoog M, Schutten M, Smits SL, Bodewes R, Osterhaus ADME, Fraaij PLA. Human bocavirus infection as a cause of severe acute respiratory tract infection in children. Clin Microbiol Infect 2015; 21:964.e1-8. [PMID: 26100374 PMCID: PMC7172568 DOI: 10.1016/j.cmi.2015.06.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 05/20/2015] [Accepted: 06/12/2015] [Indexed: 12/15/2022]
Abstract
In 2005 human bocavirus (HBoV) was discovered in respiratory tract samples of children. The role of HBoV as the single causative agent for respiratory tract infections remains unclear. Detection of HBoV in children with respiratory disease is frequently in combination with other viruses or bacteria. We set up an algorithm to study whether HBoV alone can cause severe acute respiratory tract infection (SARI) in children. The algorithm was developed to exclude cases with no other likely cause than HBoV for the need for admission to the paediatric intensive care unit (PICU) with SARI. We searched for other viruses by next-generation sequencing (NGS) in these cases and studied their HBoV viral loads. To benchmark our algorithm, the same was applied to respiratory syncytial virus (RSV)-positive patients. From our total group of 990 patients who tested positive for a respiratory virus by means of RT-PCR, HBoV and RSV were detected in 178 and 366 children admitted to our hospital. Forty-nine HBoV-positive patients and 72 RSV-positive patients were admitted to the PICU. We found seven single HBoV-infected cases with SARI admitted to PICU (7/49, 14%). They had no other detectable virus by NGS. They had much higher HBoV loads than other patients positive for HBoV. We identified 14 RSV-infected SARI patients with a single RSV infection (14/72, 19%). We conclude that our study provides strong support that HBoV can cause SARI in children in the absence of viral and bacterial co-infections.
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Affiliation(s)
- F M Moesker
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - J J A van Kampen
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - A A van der Eijk
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | - M de Hoog
- Department of Paediatrics, Paediatric Intensive Care Unit, Erasmus MC-Sophia, Rotterdam, The Netherlands
| | - M Schutten
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - S L Smits
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - R Bodewes
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - A D M E Osterhaus
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands; Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine, Hannover, Germany
| | - P L A Fraaij
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands; Department of Paediatrics, The Netherlands.
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Conceição-Neto N, Zeller M, Heylen E, Lefrère H, Mesquita JR, Matthijnssens J. Fecal virome analysis of three carnivores reveals a novel nodavirus and multiple gemycircularviruses. Virol J 2015; 12:79. [PMID: 25986582 PMCID: PMC4459443 DOI: 10.1186/s12985-015-0305-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/30/2015] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND More knowledge about viral populations in wild animals is needed in order to better understand and assess the risk of zoonotic diseases. In this study we performed viral metagenomic analysis of fecal samples from three healthy carnivores: a badger (Meles meles), a mongoose (Herpestes ichneumon) and an otter (Lutra lutra) from Portugal. RESULTS We detected the presence of novel highly divergent viruses in the fecal material of the carnivores analyzed, such as five gemycircularviruses. Four of these gemycircularviruses were found in the mongoose and one in the badger. In addition we also identified an RNA-dependent RNA polymerase gene from a putative novel member of the Nodaviridae family in the fecal material of the otter. CONCLUSIONS Together these results underline that many novel viruses are yet to be discovered and that fecal associated viruses are not always related to disease. Our study expands the knowledge of viral species present in the gut, although the interpretation of the true host species of such novel viruses needs to be reviewed with great caution.
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Affiliation(s)
- Nádia Conceição-Neto
- Laboratory of viral metagenomics, Rega Institute for Medical Research Leuven, Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, B-3000, Belgium.
| | - Mark Zeller
- Laboratory of viral metagenomics, Rega Institute for Medical Research Leuven, Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, B-3000, Belgium.
| | - Elisabeth Heylen
- Laboratory of viral metagenomics, Rega Institute for Medical Research Leuven, Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, B-3000, Belgium.
| | - Hanne Lefrère
- Laboratory of viral metagenomics, Rega Institute for Medical Research Leuven, Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, B-3000, Belgium.
| | - João Rodrigo Mesquita
- Polytechnic Institute of Viseu, Department of Animal Science, Rural Engineering and Veterinary, Viseu, Portugal.
| | - Jelle Matthijnssens
- Laboratory of viral metagenomics, Rega Institute for Medical Research Leuven, Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, B-3000, Belgium.
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Bodewes R, Contreras GJS, García AR, Hapsari R, van de Bildt MWG, Kuiken T, Osterhaus ADME. Identification of DNA sequences that imply a novel gammaherpesvirus in seals. J Gen Virol 2015; 96:1109-1114. [DOI: 10.1099/vir.0.000029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 12/07/2014] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rogier Bodewes
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | | | - Ana Rubio García
- Seal Rehabilitation and Research Centre, Pieterburen, the Netherlands
| | | | | | - Thijs Kuiken
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Albert D. M. E. Osterhaus
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
- Centre for Infection Medicine and Zoonoses Research, University of Veterinary Medicine, Hannover, Germany
- Artemis Research Institute for Wildlife Health, Utrecht, the Netherlands
- Viroclinics Biosciences BV, Rotterdam, the Netherlands
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Phan TG, Mori D, Deng X, Rajindrajith S, Ranawaka U, Fan Ng TF, Bucardo-Rivera F, Orlandi P, Ahmed K, Delwart E. Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage. Virology 2015; 482:98-104. [PMID: 25839169 DOI: 10.1016/j.virol.2015.03.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 02/16/2015] [Accepted: 03/03/2015] [Indexed: 01/02/2023]
Abstract
Viruses with small circular ssDNA genomes encoding a replication initiator protein can infect a wide range of eukaryotic organisms ranging from mammals to fungi. The genomes of two such viruses, a cyclovirus (CyCV-SL) and gemycircularvirus (GemyCV-SL) were detected by deep sequencing of the cerebrospinal fluids of Sri Lankan patients with unexplained encephalitis. One and three out of 201 CSF samples (1.5%) from unexplained encephalitis patients tested by PCR were CyCV-SL and GemyCV-SL DNA positive respectively. Nucleotide similarity searches of pre-existing metagenomics datasets revealed closely related genomes in feces from unexplained cases of diarrhea from Nicaragua and Brazil and in untreated sewage from Nepal. Whether the tropism of the cyclovirus and gemycircularvirus reported here include humans or other cellular sources in or on the human body remains to be determined.
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Affiliation(s)
- Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
| | - Daisuke Mori
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA 94118, USA
| | - Shaman Rajindrajith
- Department of Pediatrics, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Udaya Ranawaka
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Terry Fei Fan Ng
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
| | | | | | - Kamruddin Ahmed
- Department of Microbiology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan; Research Promotion Institute, Oita University, Yufu 879-5593, Oita, Japan; Department of Pathobiology and Medical Diagnostics, Faculty of Medicine, Universiti Malaysia Sabah, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA.
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Diverse small circular DNA viruses circulating amongst estuarine molluscs. INFECTION GENETICS AND EVOLUTION 2015; 31:284-95. [DOI: 10.1016/j.meegid.2015.02.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 02/06/2015] [Accepted: 02/11/2015] [Indexed: 01/22/2023]
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47
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Dayaram A, Potter KA, Pailes R, Marinov M, Rosenstein DD, Varsani A. Identification of diverse circular single-stranded DNA viruses in adult dragonflies and damselflies (Insecta: Odonata) of Arizona and Oklahoma, USA. INFECTION GENETICS AND EVOLUTION 2015; 30:278-287. [DOI: 10.1016/j.meegid.2014.12.037] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/17/2014] [Accepted: 12/31/2014] [Indexed: 12/16/2022]
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48
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Identification of novel Bromus- and Trifolium-associated circular DNA viruses. Arch Virol 2015; 160:1303-11. [PMID: 25701210 DOI: 10.1007/s00705-015-2358-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/29/2015] [Indexed: 12/17/2022]
Abstract
The genomes of a large number of highly diverse novel circular DNA viruses from a wide range of sources have been characterised in recent years, including circular single-stranded DNA (ssDNA) viruses that share similarities with plant-infecting ssDNA viruses of the family Geminiviridae. Here, we describe six novel circular DNA viral genomes that encode replication-associated (Rep) proteins that are most closely related to those of either geminiviruses or gemycircularviruses (a new group of ssDNA viruses that are closely related to geminiviruses). Four possible viral genomes were recovered from Bromus hordeaceus sampled in New Zealand, and two were recovered from B. hordeaceus and Trifolium resupinatum sampled in France. Two of the viral genomes from New Zealand (one from the North Island and one from the South Island each) share >99 % sequence identity, and two genomes recovered from B. hordeaceus and T. resupinatum sampled in France share 74 % identity. All of the viral genomes that were recovered were found to have a major open reading frame on both their complementary and virion-sense strands, one of which likely encodes a Rep and the other a capsid protein. Although future infectivity studies are needed to identify the host range of these viruses, this is the first report of circular DNA viruses associated with grasses in New Zealand.
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Virus characterization and discovery in formalin-fixed paraffin-embedded tissues. J Virol Methods 2015; 214:54-9. [PMID: 25681526 PMCID: PMC7119673 DOI: 10.1016/j.jviromet.2015.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/04/2014] [Accepted: 02/05/2015] [Indexed: 01/09/2023]
Abstract
Detection and characterization of novel viruses is often hampered by the lack of adequately stored materials. Formalin-fixed paraffin embedded (FFPE) tissues can be used to detect known viral sequences. The application of FFPE tissues for detection of novel viral sequences is currently unclear. Sequence-independent amplification and next-generation was performed on FFPE tissues. Sequences of known viruses and a novel rotavirus were detected, with relatively low sensitivity but standard accuracy.
Detection and characterization of novel viruses is hampered frequently by the lack of properly stored materials. Especially for the retrospective identification of viruses responsible for past disease outbreaks, often only formalin-fixed paraffin-embedded (FFPE) tissue samples are available. Although FFPE tissues can be used to detect known viral sequences, the application of FFPE tissues for detection of novel viruses is currently unclear. In the present study it was shown that sequence-independent amplification in combination with next-generation sequencing can be used to detect sequences of known and unknown viruses, although with relatively low sensitivity. These findings indicate that this technique could be useful for detecting novel viral sequences in FFPE tissues collected from humans and animals with disease of unknown origin, when other samples are not available. In addition, application of this method to FFPE tissues allows to correlate with the presence of histopathological changes in the corresponding tissue sections.
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Complete genome sequences of novel anelloviruses from laboratory rats. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01262-14. [PMID: 25657264 PMCID: PMC4319603 DOI: 10.1128/genomea.01262-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Anelloviruses are nonenveloped single-stranded DNA viruses infecting a wide range of mammals. We report three complete genomes of novel anelloviruses detected in laboratory rats. Phylogenetic analysis demonstrates that these viruses are related to but distinct from recently described rodent Torque teno viruses (RoTTVs) found in wild rodent species.
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