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Couto RDS, Ramos EDSF, Abreu WU, Rodrigues LRR, Marinho LF, Morais VDS, Villanova F, Pandey RP, Deng X, Delwart E, da Costa AC, Leal E. Metagenomic of Liver Tissue Identified at Least Two Genera of Totivirus-like Viruses in Molossus molossus Bats. Microorganisms 2024; 12:206. [PMID: 38276191 PMCID: PMC10819564 DOI: 10.3390/microorganisms12010206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRpol). Most virions in this family are isometric in shape, approximately 40 nm in diameter, and lack an envelope. There are five genera within this family, including Totivirus, Victorivirus, Giardiavirus, Leishmaniavirus, and Trichomonasvirus. While Totivirus and Victorivirus primarily infect fungi, Giardiavirus, Leishmaniavirus, and Trichomonasvirus infect diverse hosts, including protists, insects, and vertebrates. Recently, new totivirus-like species have been discovered in fish and plant hosts, and through metagenomic analysis, a novel totivirus-like virus (named Tianjin totivirus) has been isolated from bat guano. Interestingly, Tianjin totivirus causes cytopathic effects in insect cells but cannot grow in mammalian cells, suggesting that it infects insects consumed by insectivorous bats. In this study, we used next-generation sequencing and identified totivirus-like viruses in liver tissue from Molossus molossus bats in the Amazon region of Brazil. Comparative phylogenetic analysis based on the RNA-dependent RNA polymerase region revealed that the viruses identified in Molossus bats belong to two distinct phylogenetic clades, possibly comprising different genera within the Totiviridae family. Notably, the mean similarity between the Tianjin totivirus and the totiviruses identified in Molossus bats is less than 18%. These findings suggest that the diversity of totiviruses in bats is more extensive than previously recognized and highlight the potential for bats to serve as reservoirs for novel toti-like viruses.
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Affiliation(s)
- Roseane da Silva Couto
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Endrya do Socorro Foro Ramos
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Wandercleyson Uchôa Abreu
- Programa de Pos-Graduação REDE Bionorte, Polo Pará, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | - Luis Reginaldo Ribeiro Rodrigues
- Laboratory of Genetics & Biodiversity, Institute of Educational Sciences, Universidade Federal do Oeste do Pará, Santarém 68040-255, PA, Brazil;
| | | | - Vanessa dos Santos Morais
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Fabiola Villanova
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
| | - Ramendra Pati Pandey
- School of Health Sciences and Technology (SoHST), UPES, Dehradun 248007, Uttarakhand, India;
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94143, USA;
| | - Eric Delwart
- Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA;
| | - Antonio Charlys da Costa
- Laboratory of Virology (LIM 52), Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, SP, Brazil; (V.d.S.M.); (A.C.d.C.)
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem 66075-000, PA, Brazil; (R.d.S.C.); (E.d.S.F.R.); (F.V.)
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2
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Trovato M, Valenti A. Medical Applications of Molecular Biotechnologies in the Context of Hashimoto's Thyroiditis. Diagnostics (Basel) 2023; 13:2114. [PMID: 37371008 DOI: 10.3390/diagnostics13122114] [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: 04/19/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Hashimoto's thyroiditis (HT) is a gender autoimmune disease that is manifested by chronic inflammation of the thyroid. Clinical trial studies (CTSs) use molecular biotechnologies (MB) to approach HT appearance. The aims of this study were to analyze the applications of MB in CTSs carried out in HT populations (HT-CTSs). Further, to evaluate the role of MB in the context of the hygiene hypothesis (HH). From 75 HT-CTSs found at clinicaltrials.gov web place, forty-five were considered for this investigation. Finally, six HT-CTSs were reported as molecular HT-CTSs (mHT-CTSs) because these were planning to utilize MB. Two of mHT-CTSs were programmed on the French population to isolate DNA viral sequences. Blood, urine, and thyroid tissue biospecimens were analyzed to pick out the parvo and polyoma viruses. Two mHT-CTSs carried out in China aimed to identify oral and fecal microbiotas by measuring PCR sequencing of the 16S rRNA gene. Two mHT-CTSs were programmed in the USA and Greece, respectively, for interception of DNA polymorphisms to associate with genetic susceptibility to HT. In conclusion, MB are mainly employed in HT-CTSs for infective pathogenesis and genetic fingerprinting of HT. Furthermore, MB do not provide evidence of HH; however, they are useful for providing direct evidence of the presence of viruses.
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Affiliation(s)
- Maria Trovato
- Department of Clinical and Experimental Medicine, University Hospital, 98125 Messina, Italy
| | - Andrea Valenti
- Department of Clinical and Experimental Medicine, University Hospital, 98125 Messina, Italy
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3
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Kosoltanapiwat N, van der Hoek L, Kinsella CM, Tongshoob J, Prasittichai L, Klein M, Jebbink MF, Deijs M, Reamtong O, Boonnak K, Khongsiri W, Phadungsombat J, Tongthainan D, Tulayakul P, Yindee M. A Novel Simian Adenovirus Associating with Human Adeno-virus Species G Isolated from Long-Tailed Macaque Feces. Viruses 2023; 15:1371. [PMID: 37376670 PMCID: PMC10303043 DOI: 10.3390/v15061371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Metagenomics has demonstrated its capability in outbreak investigations and pathogen surveillance and discovery. With high-throughput and effective bioinformatics, many disease-causing agents, as well as novel viruses of humans and animals, have been identified using metagenomic analysis. In this study, a VIDISCA metagenomics workflow was used to identify potential unknown viruses in 33 fecal samples from asymptomatic long-tailed macaques (Macaca fascicularis) in Ratchaburi Province, Thailand. Putatively novel astroviruses, enteroviruses, and adenoviruses were detected and confirmed by PCR analysis of long-tailed macaque fecal samples collected from areas in four provinces, Ratchaburi, Kanchanaburi, Lopburi, and Prachuap Khiri Khan, where humans and monkeys live in proximity (total n = 187). Astroviruses, enteroviruses, and adenoviruses were present in 3.2%, 7.5%, and 4.8% of macaque fecal samples, respectively. One adenovirus, named AdV-RBR-6-3, was successfully isolated in human cell culture. Whole-genome analysis suggested that it is a new member of the species Human adenovirus G, closely related to Rhesus adenovirus 53, with evidence of genetic recombination and variation in the hexon, fiber, and CR1 genes. Sero-surveillance showed neutralizing antibodies against AdV-RBR-6-3 in 2.9% and 11.2% of monkeys and humans, respectively, suggesting cross-species infection of monkeys and humans. Overall, we reported the use of metagenomics to screen for possible new viruses, as well as the isolation and molecular and serological characterization of the new adenovirus with cross-species transmission potential. The findings emphasize that zoonotic surveillance is important and should be continued, especially in areas where humans and animals interact, to predict and prevent the threat of emerging zoonotic pathogens.
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Affiliation(s)
- Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.T.); (W.K.)
| | - Lia van der Hoek
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Cormac M. Kinsella
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Jarinee Tongshoob
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.T.); (W.K.)
| | - Luxsana Prasittichai
- Wildlife Conservation Division, Protected Areas Regional Office 3 (Ban Pong), Department of National Parks, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Ratchaburi 70110, Thailand;
| | - Michelle Klein
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Maarten F. Jebbink
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Martin Deijs
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (L.v.d.H.); (C.M.K.); (M.K.); (M.F.J.); (M.D.)
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Kobporn Boonnak
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Wathusiri Khongsiri
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand; (J.T.); (W.K.)
| | - Juthamas Phadungsombat
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan;
| | - Daraka Tongthainan
- Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-ok, Chonburi 20110, Thailand;
| | - Phitsanu Tulayakul
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom 73140, Thailand;
| | - Marnoch Yindee
- Akkhraratchakumari Veterinary College, Walailak University, Nakhonsithammarat 80161, Thailand;
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4
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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: 4] [Impact Index Per Article: 4.0] [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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5
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Volpe E, Errani F, Mandrioli L, Ciulli S. Advances in Viral Aquatic Animal Disease Knowledge: The Molecular Methods' Contribution. BIOLOGY 2023; 12:biology12030466. [PMID: 36979158 PMCID: PMC10045235 DOI: 10.3390/biology12030466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Aquaculture is the fastest-growing food-producing sector, with a global production of 122.6 million tonnes in 2020. Nonetheless, aquatic animal production can be hampered by the occurrence of viral diseases. Furthermore, intensive farming conditions and an increasing number of reared fish species have boosted the number of aquatic animals' pathogens that researchers have to deal with, requiring the quick development of new detection and study methods for novel unknown pathogens. In this respect, the molecular tools have significantly contributed to investigating thoroughly the structural constituents of fish viruses and providing efficient detection methods. For instance, next-generation sequencing has been crucial in reassignment to the correct taxonomic family, the sturgeon nucleo-cytoplasmic large DNA viruses, a group of viruses historically known, but mistakenly considered as iridoviruses. Further methods such as in situ hybridisation allowed objectifying the role played by the pathogen in the determinism of disease, as the cyprinid herpesvirus 2, ostreid herpesvirus 1 and betanodaviruses. Often, a combination of molecular techniques is crucial to understanding the viral role, especially when the virus is detected in a new aquatic animal species. With this paper, the authors would critically revise the scientific literature, dealing with the molecular techniques employed hitherto to study the most relevant finfish and shellfish viral pathogens.
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Affiliation(s)
- Enrico Volpe
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, 47042 Cesenatico, FC, Italy
| | - Francesca Errani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, 47042 Cesenatico, FC, Italy
| | - Luciana Mandrioli
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, 47042 Cesenatico, FC, Italy
| | - Sara Ciulli
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, 47042 Cesenatico, FC, Italy
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6
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Kamani J, González-Miguel J, Msheliza EG, Goldberg TL. Straw-Colored Fruit Bats ( Eidolon helvum) and Their Bat Flies ( Cyclopodia greefi) in Nigeria Host Viruses with Multifarious Modes of Transmission. Vector Borne Zoonotic Dis 2022; 22:545-552. [DOI: 10.1089/vbz.2022.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Joshua Kamani
- Parasitology Division, National Veterinary Research Institute (NVRI), Vom, Nigeria
| | - Javier González-Miguel
- Laboratory of Parasitology, Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Salamanca, Spain
- Molecular Parasitology Laboratory, Centre of One Health (COH), Ryan Institute, National University of Ireland, Galway, Ireland
| | - Emmanuel G. Msheliza
- Parasitology Division, National Veterinary Research Institute (NVRI), Vom, Nigeria
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
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7
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Fleischer R, Schmid DW, Uddin W, Brändel SD, Rasche A, Corman VM, Drosten C, Tschapka M, Sommer S. Interaction between MHC diversity and constitution, gut microbiota and Astrovirus infections in a neotropical bat. Mol Ecol 2022; 31:3342-3359. [PMID: 35510794 DOI: 10.1111/mec.16491] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 11/28/2022]
Abstract
Astroviruses (AstVs) infect numerous mammalian species including reservoirs such as bats. Peptides encoded by the genes of the highly polymorphic Major Histocompatibility Complex (MHC) form the first line of host defence against pathogens. Aside from direct involvement in mounting adaptive immune responses, MHC class II genes are hypothesized to regulate gut commensal diversity and shape the production of immune-modulatory substances by microbes, indirectly affecting host susceptibility. Despite initial empirical evidence for the link between host MHC and the microbiota, associations among these factors remain largely unknown. To fill this gap, we examined MHC allelic diversity and constitution, the gut bacterial community and abundance pattern of a wild population of the neotropical bat (Artibeus jamaicensis) challenged by AstV infections. First, we show an age-dependent relationship between the host MHC class II diversity and constitution and the gut microbiota in AstV uninfected bats. Crucially, these associations changed in AstV infected bats. Additionally, we identify changes in abundance of specific bacterial taxa linked to the presence of certain MHC supertypes and AstV infection. We suggest changes in the microbiota to be either a result of AstV infection or the MHC-mediated modulation of microbial communities. The latter could subsequently affect microbe-mediated immunity and resistance against AstV infection. Our results underscore that the reciprocal nature of host immune genetics, gut microbial diversity and pathogen infection requires attention, which is particularly important given its repercussions for disease susceptibility and severity in wild animal populations with a history of zoonotic spillover and frequent human contact.
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Affiliation(s)
- Ramona Fleischer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Dominik Werner Schmid
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Wasim Uddin
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Stefan Dominik Brändel
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany.,Smithsonian Tropical Research Institute, Ancon, Panama
| | - Andrea Rasche
- Smithsonian Tropical Research Institute, Ancon, Panama.,Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Chariteplatz 1, 10117, Berlin, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Chariteplatz 1, 10117, Berlin, Germany.,German Centre for Infection Research (DZIF), associated partner Charité, Chariteplatz 1, 10117, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University, Humboldt-University and Berlin Institute of Health, Chariteplatz 1, 10117, Berlin, Germany.,German Centre for Infection Research (DZIF), associated partner Charité, Chariteplatz 1, 10117, Berlin, Germany
| | - Marco Tschapka
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany.,Smithsonian Tropical Research Institute, Ancon, Panama
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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8
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Bolatti EM, Viarengo G, Zorec TM, Cerri A, Montani ME, Hosnjak L, Casal PE, Bortolotto E, Di Domenica V, Chouhy D, Allasia MB, Barquez RM, Poljak M, Giri AA. Viral Metagenomic Data Analyses of Five New World Bat Species from Argentina: Identification of 35 Novel DNA Viruses. Microorganisms 2022; 10:microorganisms10020266. [PMID: 35208721 PMCID: PMC8880087 DOI: 10.3390/microorganisms10020266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/18/2022] Open
Abstract
Bats are natural reservoirs of a variety of zoonotic viruses, many of which cause severe human diseases. Characterizing viruses of bats inhabiting different geographical regions is important for understanding their viral diversity and for detecting viral spillovers between animal species. Herein, the diversity of DNA viruses of five arthropodophagous bat species from Argentina was investigated using metagenomics. Fecal samples of 29 individuals from five species (Tadarida brasiliensis, Molossus molossus, Eumops bonariensis, Eumops patagonicus, and Eptesicus diminutus) living at two different geographical locations, were investigated. Enriched viral DNA was sequenced using Illumina MiSeq, and the reads were trimmed and filtered using several bioinformatic approaches. The resulting nucleotide sequences were subjected to viral taxonomic classification. In total, 4,520,370 read pairs were sequestered by sequencing, and 21.1% of them mapped to viral taxa. Circoviridae and Genomoviridae were the most prevalent among vertebrate viral families in all bat species included in this study. Samples from the T. brasiliensis colony exhibited lower viral diversity than samples from other species of New World bats. We characterized 35 complete genome sequences of novel viruses. These findings provide new insights into the global diversity of bat viruses in poorly studied species, contributing to prevention of emerging zoonotic diseases and to conservation policies for endangered species.
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Affiliation(s)
- Elisa M. Bolatti
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Gastón Viarengo
- DETx MOL S.A., Centro Científico Tecnológico CONICET Rosario, Ocampo y Esmeralda, Rosario 2000, Argentina;
| | - Tomaz M. Zorec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
| | - Agustina Cerri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
| | - María E. Montani
- Museo Provincial de Ciencias Naturales “Dr. Ángel Gallardo”, San Lorenzo 1949, Rosario 2000, Argentina;
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina; (V.D.D.); (R.M.B.)
- Instituto PIDBA (Programa de Investigaciones de Biodiversidad Argentina), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán 4000, Argentina
| | - Lea Hosnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
| | - Pablo E. Casal
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
| | - Eugenia Bortolotto
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina; (E.B.); (M.B.A.)
| | - Violeta Di Domenica
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina; (V.D.D.); (R.M.B.)
| | - Diego Chouhy
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
- DETx MOL S.A., Centro Científico Tecnológico CONICET Rosario, Ocampo y Esmeralda, Rosario 2000, Argentina;
| | - María Belén Allasia
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina; (E.B.); (M.B.A.)
| | - Rubén M. Barquez
- Programa de Conservación de los Murciélagos de Argentina, Miguel Lillo 251, San Miguel de Tucumán 4000, Argentina; (V.D.D.); (R.M.B.)
- Instituto PIDBA (Programa de Investigaciones de Biodiversidad Argentina), Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, San Miguel de Tucumán 4000, Argentina
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, SI-1000 Ljubljana, Slovenia; (T.M.Z.); (L.H.)
- Correspondence: (M.P.); (A.A.G.); Tel.: +386-1-543-7454 (M.P.); +54-341-435-0661 (ext. 116) (A.A.G.); Fax: +54-341-439-0465 (A.A.G.)
| | - Adriana A. Giri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, Rosario 2000, Argentina; (E.M.B.); (A.C.); (D.C.)
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina;
- Correspondence: (M.P.); (A.A.G.); Tel.: +386-1-543-7454 (M.P.); +54-341-435-0661 (ext. 116) (A.A.G.); Fax: +54-341-439-0465 (A.A.G.)
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9
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Jager MC, Tomlinson JE, Lopez-Astacio RA, Parrish CR, Van de Walle GR. Small but mighty: old and new parvoviruses of veterinary significance. Virol J 2021; 18:210. [PMID: 34689822 PMCID: PMC8542416 DOI: 10.1186/s12985-021-01677-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
In line with the Latin expression "sed parva forti" meaning "small but mighty," the family Parvoviridae contains many of the smallest known viruses, some of which result in fatal or debilitating infections. In recent years, advances in metagenomic viral discovery techniques have dramatically increased the identification of novel parvoviruses in both diseased and healthy individuals. While some of these discoveries have solved etiologic mysteries of well-described diseases in animals, many of the newly discovered parvoviruses appear to cause mild or no disease, or disease associations remain to be established. With the increased use of animal parvoviruses as vectors for gene therapy and oncolytic treatments in humans, it becomes all the more important to understand the diversity, pathogenic potential, and evolution of this diverse family of viruses. In this review, we discuss parvoviruses infecting vertebrate animals, with a special focus on pathogens of veterinary significance and viruses discovered within the last four years.
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Affiliation(s)
- Mason C Jager
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Joy E Tomlinson
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Robert A Lopez-Astacio
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gerlinde R Van de Walle
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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10
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Hardmeier I, Aeberhard N, Qi W, Schoenbaechler K, Kraettli H, Hatt JM, Fraefel C, Kubacki J. Metagenomic analysis of fecal and tissue samples from 18 endemic bat species in Switzerland revealed a diverse virus composition including potentially zoonotic viruses. PLoS One 2021; 16:e0252534. [PMID: 34133435 PMCID: PMC8208571 DOI: 10.1371/journal.pone.0252534] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/17/2021] [Indexed: 01/02/2023] Open
Abstract
Many recent disease outbreaks in humans had a zoonotic virus etiology. Bats in particular have been recognized as reservoirs to a large variety of viruses with the potential to cross-species transmission. In order to assess the risk of bats in Switzerland for such transmissions, we determined the virome of tissue and fecal samples of 14 native and 4 migrating bat species. In total, sequences belonging to 39 different virus families, 16 of which are known to infect vertebrates, were detected. Contigs of coronaviruses, adenoviruses, hepeviruses, rotaviruses A and H, and parvoviruses with potential zoonotic risk were characterized in more detail. Most interestingly, in a ground stool sample of a Vespertilio murinus colony an almost complete genome of a Middle East respiratory syndrome-related coronavirus (MERS-CoV) was detected by Next generation sequencing and confirmed by PCR. In conclusion, bats in Switzerland naturally harbour many different viruses. Metagenomic analyses of non-invasive samples like ground stool may support effective surveillance and early detection of viral zoonoses.
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Affiliation(s)
| | - Nadja Aeberhard
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, Zurich, Switzerland
| | | | | | - Jean-Michel Hatt
- Clinic for Zoo Animals, Exotic Pets and Wildlife, University of Zurich, Zurich, Switzerland
| | - Cornel Fraefel
- Institute of Virology, University of Zurich, Zurich, Switzerland
| | - Jakub Kubacki
- Institute of Virology, University of Zurich, Zurich, Switzerland
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11
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Tan CW, Yang X, Anderson DE, Wang LF. Bat virome research: the past, the present and the future. Curr Opin Virol 2021; 49:68-80. [PMID: 34052731 DOI: 10.1016/j.coviro.2021.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023]
Abstract
Bats have been increasingly recognised as an exceptional reservoir for emerging zoonotic viruses for the past few decades. Recent studies indicate that the unique bat immune system may be partially responsible for their ability to co-exist with viruses with minimal or no clinical diseases. In this review, we discuss the history and importance of bat virome studies and contrast the vast difference between such studies before and after the introduction of next generation sequencing (NGS) in this area of research. We also discuss the role of discovery serology and high-throughput single cell RNA-seq in future bat virome research.
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Affiliation(s)
- Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Xinglou Yang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; SingHealth Duke-NUS Global Health Institute, 169857, Singapore.
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12
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Affiliation(s)
- Marcione B. De Oliveira
- Graduate Program in Zoology, National Museum, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista s/n, São Cristóvão, Rio de Janeiro, RJ, 20940-040, Brazil
| | - Cibele R. Bonvicino
- Graduate Program in Zoology, National Museum, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista s/n, São Cristóvão, Rio de Janeiro, RJ, 20940-040, Brazil
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13
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Syahbanu F, Giriwono PE, Tjandrawinata RR, Suhartono MT. Molecular analysis of a fibrin-degrading enzyme from Bacillus subtilis K2 isolated from the Indonesian soybean-based fermented food moromi. Mol Biol Rep 2020; 47:8553-8563. [PMID: 33111172 DOI: 10.1007/s11033-020-05898-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
Abstract
The screening of proteolytic and fibrinolytic bacteria from moromi (an Indonesian soybean-based fermented food) yielded a number of isolates. Based on morphological and biochemical analyses and sequencing of the 16S rRNA gene, the isolate that exhibited the highest proteolytic and fibrinolytic activity was identified as Bacillus subtilis K2. The study was performed to analyze molecular characteristic of a fibrin-degrading enzyme from B. subtilis K2. BLASTn analysis of the nucleotide sequence encoding this fibrinolytic protein demonstrated 73.6% homology with the gene encoding the fibrin-degrading enzyme nattokinase of the B. subtilis subsp. natto, which was isolated from fermented soybean in Japan. An analysis of the putative amino-acid sequence of this protein indicated that it is a serine protease enzyme with aspartate, histidine, and serine in the catalytic triad. This enzyme was determined to be a 26-kDa molecule, as confirmed with a zymogram assay. Further bioinformatic analysis using Protparam demonstrated that the enzyme has a pI of 6.02, low instability index, high aliphatic index, and low GRAVY value. Molecular docking analysis using HADDOCK indicated that there are favorable interactions between subtilisin K2 and the fibrin substrate, as demonstrated by a high binding affinity (ΔG: - 19.4 kcal/mol) and low Kd value (6.3E-15 M). Overall, the study concluded that subtilisin K2 belong to serine protease enzyme has strong interactions with its fibrin substrate and fibrin can be rapidly degraded by this enzyme, suggesting its application as a treatment for thrombus diseases.
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Affiliation(s)
- Fathma Syahbanu
- Department of Food Science and Technology, IPB University (Bogor Agricultural University), Dramaga, P.O. BOX 220, Bogor, Indonesia
| | - Puspo Edi Giriwono
- Department of Food Science and Technology, IPB University (Bogor Agricultural University), Dramaga, P.O. BOX 220, Bogor, Indonesia
| | | | - Maggy T Suhartono
- Department of Food Science and Technology, IPB University (Bogor Agricultural University), Dramaga, P.O. BOX 220, Bogor, Indonesia.
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14
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Pénzes JJ, Söderlund-Venermo M, Canuti M, Eis-Hübinger AM, Hughes J, Cotmore SF, Harrach B. Reorganizing the family Parvoviridae: a revised taxonomy independent of the canonical approach based on host association. Arch Virol 2020; 165:2133-2146. [PMID: 32533329 DOI: 10.1007/s00705-020-04632-4] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Parvoviridae, a diverse family of small single-stranded DNA viruses was established in 1975. It was divided into two subfamilies, Parvovirinae and Densovirinae, in 1993 to accommodate parvoviruses that infect vertebrate and invertebrate animals, respectively. This relatively straightforward segregation, using host association as the prime criterion for subfamily-level classification, has recently been challenged by the discovery of divergent, vertebrate-infecting parvoviruses, dubbed "chapparvoviruses", which have proven to be more closely related to viruses in certain Densovirinae genera than to members of the Parvovirinae. Viruses belonging to these genera, namely Brevi-, Hepan- and Penstyldensovirus, are responsible for the unmatched heterogeneity of the subfamily Densovirinae when compared to the Parvovirinae in matters of genome organization, protein sequence homology, and phylogeny. Another genus of Densovirinae, Ambidensovirus, has challenged traditional parvovirus classification, as it includes all newly discovered densoviruses with an ambisense genome organization, which introduces genus-level paraphyly. Lastly, current taxon definition and virus inclusion criteria have significantly limited the classification of certain long-discovered parvoviruses and impedes the classification of some potential family members discovered using high-throughput sequencing methods. Here, we present a new and updated system for parvovirus classification, which includes the introduction of a third subfamily, Hamaparvovirinae, resolves the paraphyly within genus Ambidensovirus, and introduces new genera and species into the subfamily Parvovirinae. These proposals were accepted by the ICTV in 2020 March.
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Affiliation(s)
- Judit J Pénzes
- Center for Structural Biology, Department of Biochemistry and Molecular Biology, The McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
| | | | - Marta Canuti
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | | | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Susan F Cotmore
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06520-8035, USA
| | - Balázs Harrach
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Budapest, Hungary
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15
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Nieto‐Rabiela F, Wiratsudakul A, Suzán G, Rico‐Chávez O. Viral networks and detection of potential zoonotic viruses in bats and rodents: A worldwide analysis. Zoonoses Public Health 2019; 66:655-666. [PMID: 31219223 PMCID: PMC7165641 DOI: 10.1111/zph.12618] [Citation(s) in RCA: 7] [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: 12/10/2018] [Revised: 04/11/2019] [Accepted: 05/28/2019] [Indexed: 12/13/2022]
Abstract
Bats and rodents are recognized to host a great diversity of viruses and several important viral zoonoses, but how this viral diversity is structured and how viruses are connected, shared and distributed among host networks is not well understood. To address this gap in knowledge, we compared the associative capacity of the host-virus networks in rodents and bats with the identification of those viruses with zoonotic potential. A virus database, detected by molecular methods, was constructed in the two taxonomic groups. We compiled 5,484 records: 825 in rodents and 4,659 in bats. We identified a total of 173 and 166 viruses, of which 53 and 40 are zoonotic viruses, in rodents and bats, respectively. Based on a network theory, a non-directed bipartite host-virus network was built for each group. Subsequently, the networks were collapsed to represent the connections among hosts and viruses. We identified both discrete and connected communities. We observed a greater degree of connectivity in bat viruses and more discrete communities in rodents. The Coronaviridae recorded in bats have the highest values of degree, betweenness and closeness centralities. In rodents, higher degree positions were distributed homogeneously between viruses and hosts. At least in our database, a higher proportion of rodent viruses were zoonotic. Rodents should thus not be underestimated as important reservoirs of zoonotic disease. We found that viruses were more frequently shared among bats than in rodents. Network theory can reveal some macroecological patterns and identify risks that were previously unrecognized. For example, we found that parvovirus in megabats and Gbagroube virus in rodents may represent a zoonotic risk due to the proximity to humans and other zoonotic viruses. We propose that epidemiological surveillance programmes should consider the connectivity of network actors as a measure of the risks of dispersion and transmission.
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Affiliation(s)
- Fabiola Nieto‐Rabiela
- Laboratorio de Ecología de Enfermedades y Una Salud, Facultad de Medicina Veterinaria y ZootecniaUniversidad Nacional Autónoma de MéxicoMéxico CityMéxico
| | - Anuwat Wiratsudakul
- Department of Clinical Sciences and Public Health, Faculty of Veterinary ScienceMahidol UniversityNakhon PathomThailand
| | - Gerardo Suzán
- Laboratorio de Ecología de Enfermedades y Una Salud, Facultad de Medicina Veterinaria y ZootecniaUniversidad Nacional Autónoma de MéxicoMéxico CityMéxico
| | - Oscar Rico‐Chávez
- Laboratorio de Ecología de Enfermedades y Una Salud, Facultad de Medicina Veterinaria y ZootecniaUniversidad Nacional Autónoma de MéxicoMéxico CityMéxico
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16
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Diversity and Evolution of Viral Pathogen Community in Cave Nectar Bats ( Eonycteris spelaea). Viruses 2019; 11:v11030250. [PMID: 30871070 PMCID: PMC6466414 DOI: 10.3390/v11030250] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 12/12/2022] Open
Abstract
Bats are unique mammals, exhibit distinctive life history traits and have unique immunological approaches to suppression of viral diseases upon infection. High-throughput next-generation sequencing has been used in characterizing the virome of different bat species. The cave nectar bat, Eonycteris spelaea, has a broad geographical range across Southeast Asia, India and southern China, however, little is known about their involvement in virus transmission. Here we investigate the diversity and abundance of viral communities from a colony of Eonycteris spelaea residing in Singapore. Our results detected 47 and 22 different virus families from bat fecal and urine samples, respectively. Among these, we identify a large number of virus families including Adenoviridae, Flaviviridae, Reoviridae, Papillomaviridae, Paramyxoviridae, Parvoviridae, Picornaviridae, and Polyomaviridae. In most cases, viral sequences from Eonycteris spelaea are genetically related to a group of bat viruses from other bat genera (e.g., Eidolon, Miniopterus, Rhinolophus and Rousettus). The results of this study improve our knowledge of the host range, spread and evolution of several important viral pathogens. More significantly, our findings provide a baseline to study the temporal patterns of virus shedding and how they correlate with bat phenological trends.
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17
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Detection of adenovirus, papillomavirus and parvovirus in Brazilian bats of the species Artibeus lituratus and Sturnira lilium. Arch Virol 2019; 164:1015-1025. [PMID: 30740637 PMCID: PMC7086806 DOI: 10.1007/s00705-018-04129-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 11/27/2018] [Indexed: 01/21/2023]
Abstract
Bats play a significant role in maintaining their ecosystems through pollination, dispersal of seeds, and control of insect populations, but they are also known to host many microorganisms and have been described as natural reservoirs for viruses with zoonotic potential. The diversity of viruses in these animals remains largely unknown, however, because studies are limited by species, location, virus target, or sample type. Therefore, the aim of this study was to detect fragments of viral genomes in bat samples. We performed high-throughput sequencing analysis and specific PCR and RT-PCR on pools of anal and oropharyngeal swabs from Artibeus lituratus and Sturnira lilium collected in southern Brazil. As a result, a member of the family Adenoviridae related to human adenovirus C was detected in anal swabs from S. lilium. In addition, we detected a papillomavirus in an anal swab from A. lituratus. Our analyses also allowed the detection of adenoviruses and parvoviruses in oropharyngeal swabs collected from A. lituratus. These results increase our knowledge about viral diversity and illustrate the importance of conducting virus surveillance in bats.
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18
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Yinda CK, Ghogomu SM, Conceição-Neto N, Beller L, Deboutte W, Vanhulle E, Maes P, Van Ranst M, Matthijnssens J. Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code. Virus Evol 2018; 4:vey008. [PMID: 29644096 PMCID: PMC5888411 DOI: 10.1093/ve/vey008] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most human emerging infectious diseases originate from wildlife and bats are a major reservoir of viruses, a few of which have been highly pathogenic to humans. In some regions of Cameroon, bats are hunted and eaten as a delicacy. This close proximity between human and bats provides ample opportunity for zoonotic events. To elucidate the viral diversity of Cameroonian fruit bats, we collected and metagenomically screened eighty-seven fecal samples of Eidolon helvum and Epomophorus gambianus fruit bats. The results showed a plethora of known and novel viruses. Phylogenetic analyses of the eleven gene segments of the first complete bat rotavirus H genome, showed clearly separated clusters of human, porcine, and bat rotavirus H strains, not indicating any recent interspecies transmission events. Additionally, we identified and analyzed a bat bastrovirus genome (a novel group of recently described viruses, related to astroviruses and hepatitis E viruses), confirming their recombinant nature, and provide further evidence of additional recombination events among bat bastroviruses. Interestingly, picobirnavirus-like RNA-dependent RNA polymerase gene segments were identified using an alternative mitochondrial genetic code, and further principal component analyses suggested that they may have a similar lifestyle to mitoviruses, a group of virus-like elements known to infect the mitochondria of fungi. Although identified bat coronavirus, parvovirus, and cyclovirus strains belong to established genera, most of the identified partitiviruses and densoviruses constitute putative novel genera in their respective families. Finally, the results of the phage community analyses of these bats indicate a very diverse geographically distinct bat phage population, probably reflecting different diets and gut bacterial ecosystems.
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Affiliation(s)
- Claude Kwe Yinda
- Laboratory of Viral Metagenomics
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
| | - Stephen Mbigha Ghogomu
- Molecular and Cell Biology Laboratory, Biotechnology Unit, Department of Biochemistry and Molecular Biology, University of Buea, Buea, 237, Cameroon
| | - Nádia Conceição-Neto
- Laboratory of Viral Metagenomics
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
| | | | | | | | - Piet Maes
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
| | - Marc Van Ranst
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
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19
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Lau SKP, Ahmed SS, Tsoi HW, Yeung HC, Li KSM, Fan RYY, Zhao PSH, Lau CCC, Lam CSF, Choi KKF, Chan BCH, Cai JP, Wong SSY, Chen H, Zhang HL, Zhang L, Wang M, Woo PCY, Yuen KY. Bats host diverse parvoviruses as possible origin of mammalian dependoparvoviruses and source for bat-swine interspecies transmission. J Gen Virol 2017; 98:3046-3059. [PMID: 29106348 DOI: 10.1099/jgv.0.000969] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Compared to the enormous species diversity of bats, relatively few parvoviruses have been reported. We detected diverse and potentially novel parvoviruses from bats in Hong Kong and mainland China. Parvoviruses belonging to Amdoparvovirus, Bocaparvovirus and Dependoparvovirus were detected in alimentary, liver and spleen samples from 16 different chiropteran species of five families by PCR. Phylogenetic analysis of partial helicase sequences showed that they potentially belonged to 25 bocaparvovirus, three dependoparvovirus and one amdoparvovirus species. Nearly complete genome sequencing confirmed the existence of at least four novel bat bocaparvovirus species (Rp-BtBoV1 and Rp-BtBoV2 from Rhinolophus pusillus, Rs-BtBoV2 from Rhinolophus sinicus and Rol-BtBoV1 from Rousettus leschenaultii) and two novel bat dependoparvovirus species (Rp-BtAAV1 from Rhinolophus pusillus and Rs-BtAAV1 from Rhinolophus sinicus). Rs-BtBoV2 was closely related to Ungulate bocaparvovirus 5 with 93, 72.1 and 78.7 % amino acid identities in the NS1, NP1 and VP1/VP2 genes, respectively. The detection of bat bocaparvoviruses, including Rs-BtBoV2, closely related to porcine bocaparvoviruses, suggests recent interspecies transmission of bocaparvoviruses between bats and swine. Moreover, Rp-BtAAV1 and Rs-BtAAV1 were most closely related to human AAV1 with 48.7 and 57.5 % amino acid identities in the rep gene. The phylogenetic relationship between BtAAVs and other mammalian AAVs suggests bats as the ancestral origin of mammalian AAVs. Furthermore, parvoviruses of the same species were detected from multiple bat species or families, supporting the ability of bat parvoviruses to cross species barriers. The results extend our knowledge on the diversity of bat parvoviruses and the role of bats in parvovirus evolution and emergence in humans and animals.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Syed Shakeel Ahmed
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Hoi-Wah Tsoi
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Hazel C Yeung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Kenneth S M Li
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Rachel Y Y Fan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Pyrear S H Zhao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Candy C C Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Carol S F Lam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Kelvin K F Choi
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Ben C H Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Jian-Piao Cai
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Samson S Y Wong
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Honglin Chen
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Hai-Lin Zhang
- Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, PR China.,Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan, PR China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangzhou, Guangdong Province, PR China.,Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangzhou, Guangdong Province, PR China.,Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong Province, PR China
| | - Ming Wang
- Guangzhou Centre for Disease Control, Guangzhou, Guangdong Province, PR China
| | - Patrick C Y Woo
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
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20
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Salmier A, Tirera S, de Thoisy B, Franc A, Darcissac E, Donato D, Bouchier C, Lacoste V, Lavergne A. Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana. PLoS One 2017; 12:e0186943. [PMID: 29117243 PMCID: PMC5695591 DOI: 10.1371/journal.pone.0186943] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/10/2017] [Indexed: 02/01/2023] Open
Abstract
Environmental disturbances in the Neotropics (e.g., deforestation, agriculture intensification, urbanization) contribute to an increasing risk of cross-species transmission of microorganisms and to disease outbreaks due to changing ecosystems of reservoir hosts. Although Amazonia encompasses the greatest diversity of reservoir species, the outsized viral population diversity (virome) has yet to be investigated. Here, through a metagenomic approach, we identified 10,991 viral sequences in the saliva and feces of two bat species, Desmodus rotundus (hematophagous), trapped in two different caves surrounded by primary lowland forest, and Molossus molossus (insectivorous), trapped in forest and urban habitats. These sequences are related to 51 viral families known to infect a wide range of hosts (i.e., bacteria, plants, insects and vertebrates). Most viruses detected reflected the diet of bat species, with a high proportion of plant and insect-related viral families for M. molossus and a high proportion of vertebrate-related viral families for D. rotundus, highlighting its influence in shaping the viral diversity of bats. Lastly, we reconstructed the phylogenetic relationships for five vertebrate-related viral families (Nairoviridae, Circoviridae, Retroviridae, Herpesviridae, Papillomaviridae). The results showed highly supported clustering with other viral sequences of the same viral family hosted by other bat species, highlighting the potential association of viral diversity with the host’s diet. These findings provide significant insight into viral bat diversity in French Guiana belonging to the Amazonian biome and emphasize that habitats and the host’s dietary ecology may drive the viral diversity in the bat communities investigated.
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Affiliation(s)
- Arielle Salmier
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Sourakhata Tirera
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Benoit de Thoisy
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Alain Franc
- UMR BIOGECO, Institut National de la Recherche Agronomique (INRA), Cestas, France
| | - Edith Darcissac
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Damien Donato
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | | | - Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Anne Lavergne
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
- * E-mail:
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21
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Manso CF, Bibby DF, Mbisa JL. Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples. Sci Rep 2017. [PMID: 28646219 PMCID: PMC5482852 DOI: 10.1038/s41598-017-02239-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses – HIV, HCV and HEV. We recovered complete genomes and up to 43% of the genome from samples with viral loads of 104 and 103 IU/ml respectively. Additionally, we demonstrated the utility of this method in detecting and characterising members of diverse RNA virus families within a human plasma background, some present at very low levels. By applying this method to a patient sample series, we have simultaneously determined the full genome of both a novel subtype of HCV genotype 6, and a co-infecting human pegivirus. This method builds upon earlier RNA metagenomic techniques and can play an important role in the surveillance and diagnostics of blood-borne viruses.
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Affiliation(s)
- Carmen F Manso
- Antiviral Unit, Virus Reference Department, National Infection Service, Public Health England, Colindale, London, NW9 5EQ, United Kingdom
| | - David F Bibby
- Antiviral Unit, Virus Reference Department, National Infection Service, Public Health England, Colindale, London, NW9 5EQ, United Kingdom.
| | - Jean L Mbisa
- Antiviral Unit, Virus Reference Department, National Infection Service, Public Health England, Colindale, London, NW9 5EQ, United Kingdom
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22
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Johnson RI, Smith IL. Virus discovery in bats. MICROBIOLOGY AUSTRALIA 2017. [DOI: 10.1071/ma17008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Comprising approximately 20% of known mammalian species, bats are abundant throughout the world1. In recent years, bats have been shown to be the reservoir host for many highly pathogenic viruses, leading to increased attempts to identify other zoonotic bat-borne viruses. These efforts have led to the discovery of over 200 viruses in bats and many more viral nucleic acid sequences from 27 different viral families2,3 (Table 1). Over half of the world’s recently emerged infectious diseases originated in wildlife15, with the genetic diversity of viruses greater in bats than in any other animal16. As humans continue to encroach on the habitat of bats, the risk of spillover of potentially zoonotic viruses is also continuing to increase. Therefore, the surveillance of bats and discovery of novel pathogens is necessary to prepare for these spillover events17.
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23
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Lau SKP, Ahmed SS, Yeung HC, Li KSM, Fan RYY, Cheng TYC, Cai JP, Wang M, Zheng BJ, Wong SSY, Woo PCY, Yuen KY. Identification and interspecies transmission of a novel bocaparvovirus among different bat species in China. J Gen Virol 2016; 97:3345-3358. [PMID: 27902362 DOI: 10.1099/jgv.0.000645] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We report the discovery of a novel bocaparvovirus, bat bocaparvovirus (BtBoV), in one spleen, four respiratory and 61 alimentary samples from bats of six different species belonging to three families, Hipposideridae, Rhinolophidae and Vespertilionidae. BtBoV showed a higher detection rate in alimentary samples of Rhinolophus sinicus (5.7 %) than those of other bat species (0.43-1.59 %), supporting R. sinicus as the primary reservoir and virus spillover to accidental bat species. BtBoV peaked during the lactating season of R. sinicus, and it was more frequently detected among female than male adult bats (P<0.05), and among lactating than non-lactating female bats (P<0.0001). Positive BtBoV detection was associated with lower body weight in lactating bats (P<0.05). Ten nearly complete BtBoV genomes from three bat species revealed a unique large ORF1 spanning NS1 and NP1 in eight genomes and conserved splicing signals leading to multiple proteins, as well as a unique substitution in the conserved replication initiator motif within NS1. BtBoV was phylogenetically distantly related to known bocaparvoviruses with ≤57.3 % genome identities, supporting BtBoV as a novel species. Ms-BtBoV from Miniopterus schreibersii and Hp-BtBoV from Hipposideros pomona demonstrated 97.2-99.9 % genome identities with Rs-BtBoVs from R. sinicus, supporting infection of different bat species by a single BtBoV species. Rs-BtBoV_str15 represents the first bat parvovirus genome with non-coding regions sequenced, which suggested the presence of head-to-tail genomic concatamers or episomal forms of the genome. This study represents the first to describe interspecies transmission in BoVs. The high detection rates in lactating female and juvenile bats suggest possible vertical transmission of BtBoV.
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Affiliation(s)
- Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Syed Shakeel Ahmed
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Hazel C Yeung
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Kenneth S M Li
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Rachel Y Y Fan
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Toni Y C Cheng
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Jian-Piao Cai
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Ming Wang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, PR China
| | - Bo-Jian Zheng
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Samson S Y Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China
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24
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Slavov SN, Otaguiri KK, Smid J, de Oliveira ACP, Casseb J, Martinez EZ, Covas DT, Eis-Hübinger AM, Kashima S. Human parvovirus 4 prevalence among HTLV-1/2 infected individuals in Brazil. J Med Virol 2016; 89:748-752. [PMID: 27589576 DOI: 10.1002/jmv.24673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 07/21/2016] [Accepted: 08/31/2016] [Indexed: 12/17/2022]
Abstract
Human parvovirus 4 (PARV4), a Tetraparvovirus, has been largely found in HIV, HBV, or HCV infected individuals. However, there is no data for the PARV4 occurrence in Human T-lymphotropic virus (HTLV-1/2) infected individuals, despite similar transmission routes. Here, PARV4 viremia was evaluated in 130 HTLV infected patients under care of a Brazilian HTLV outpatient clinic. PARV4 viremia was detected in 6.2% of the HTLV-1 infected patients. Most PARV4 positives showed no evidence for parenterally transmitted infections. It is suggested that in Brazil, transmission routes of PARV4 are more complex than in Europe and North America and resemble those in Africa. J. Med. Virol. 89:748-752, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Svetoslav Nanev Slavov
- Faculty of Medicine of Ribeirão Preto, Blood Center of Ribeirão Preto, University of São Paulo, São Paulo, Brazil.,Faculty of Medicine of Ribeirão Preto, Department of Clinical Medicine, University of São Paulo, São Paulo, Brazil
| | - Katia Kaori Otaguiri
- Faculty of Medicine of Ribeirão Preto, Blood Center of Ribeirão Preto, University of São Paulo, São Paulo, Brazil.,Faculty of Pharmaceutical Sciences, Department of Clinical, Toxicological and Bromatological Analyses, University of São Paulo, São Paulo, Brazil
| | - Jerusa Smid
- HTLV-Outpatient Clinic, Institute of Infectious Diseases "Emilio Ribas", São Paulo, Brazil
| | | | - Jorge Casseb
- HTLV-Outpatient Clinic, Institute of Infectious Diseases "Emilio Ribas", São Paulo, Brazil.,Laboratory of Medical Investigation 56, Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | - Edson Zangiacomi Martinez
- Faculty of Medicine of Ribeirão Preto, Department of Social Medicine, University of São Paulo, São Paulo, Brazil
| | - Dimas Tadeu Covas
- Faculty of Medicine of Ribeirão Preto, Blood Center of Ribeirão Preto, University of São Paulo, São Paulo, Brazil.,Faculty of Medicine of Ribeirão Preto, Department of Clinical Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Simone Kashima
- Faculty of Medicine of Ribeirão Preto, Blood Center of Ribeirão Preto, University of São Paulo, São Paulo, Brazil.,Faculty of Pharmaceutical Sciences, Department of Clinical, Toxicological and Bromatological Analyses, University of São Paulo, São Paulo, Brazil
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25
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Abstract
Bats are hosts of a range of viruses, including ebolaviruses, and many important human viral infections, such as measles and mumps, may have their ancestry traced back to bats. Here, I review viruses of all viral families detected in global bat populations. The viral diversity in bats is substantial, and viruses with all known types of genomic structures and replication strategies have been discovered in bats. However, the discovery of viruses is not geographically even, with some apparently undersampled regions, such as South America. Furthermore, some bat families, including those with global or wide distributions such as Emballonuridae and Miniopteridae, are underrepresented on viral databases. Future studies, including those that address these sampling gaps along with those that develop our understanding of viral-host relationships, are highlighted.
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Affiliation(s)
- David T S Hayman
- Molecular Epidemiology and Public Health Laboratory, Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North 4442, New Zealand;
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26
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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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27
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Abstract
The characterization of the human blood-associated viral community (also called blood virome) is essential for epidemiological surveillance and to anticipate new potential threats for blood transfusion safety. Currently, the risk of blood-borne agent transmission of well-known viruses (HBV, HCV, HIV and HTLV) can be considered as under control in high-resource countries. However, other viruses unknown or unsuspected may be transmitted to recipients by blood-derived products. This is particularly relevant considering that a significant proportion of transfused patients are immunocompromised and more frequently subjected to fatal outcomes. Several measures to prevent transfusion transmission of unknown viruses have been implemented including the exclusion of at-risk donors, leukocyte reduction of donor blood, and physicochemical treatment of the different blood components. However, up to now there is no universal method for pathogen inactivation, which would be applicable for all types of blood components and, equally effective for all viral families. In addition, among available inactivation procedures of viral genomes, some of them are recognized to be less effective on non-enveloped viruses, and inadequate to inactivate higher viral titers in plasma pools or derivatives. Given this, there is the need to implement new methodologies for the discovery of unknown viruses that may affect blood transfusion. Viral metagenomics combined with High Throughput Sequencing appears as a promising approach for the identification and global surveillance of new and/or unexpected viruses that could impair blood transfusion safety.
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Affiliation(s)
- V Sauvage
- Département d'études des agents transmissibles par le sang, Institut national de la transfusion sanguine (INTS), Centre national de référence des hépatites virales B et C et du VIH en transfusion, 75015 Paris, France.
| | - M Eloit
- PathoQuest, bâtiment François-Jacob, 25, rue du Dr-Roux, 75015 Paris, France; Inserm U1117, Biology of Infection Unit, Laboratory of Pathogen Discovery, Institut Pasteur, 28, rue du Docteur-Roux, 75724 Paris, France
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28
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Kilianski A, Carcel P, Yao S, Roth P, Schulte J, Donarum GB, Fochler ET, Hill JM, Liem AT, Wiley MR, Ladner JT, Pfeffer BP, Elliot O, Petrosov A, Jima DD, Vallard TG, Melendrez MC, Skowronski E, Quan PL, Lipkin WI, Gibbons HS, Hirschberg DL, Palacios GF, Rosenzweig CN. Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform. BMC Bioinformatics 2015; 16:416. [PMID: 26714571 PMCID: PMC4696252 DOI: 10.1186/s12859-015-0840-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/08/2015] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support. RESULTS The pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Insititute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify. CONCLUSIONS By accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available.
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Affiliation(s)
- Andy Kilianski
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA.
| | | | - Shijie Yao
- OptiMetrics, Inc, Abingdon, MD, USA. .,Joint Genome Institute, Department of Energy, LBNL, Berkley, CA, USA.
| | - Pierce Roth
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA. .,OptiMetrics, Inc, Abingdon, MD, USA.
| | | | | | | | - Jessica M Hill
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA. .,OptiMetrics, Inc, Abingdon, MD, USA.
| | - Alvin T Liem
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA. .,OptiMetrics, Inc, Abingdon, MD, USA.
| | - Michael R Wiley
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - Jason T Ladner
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - Bradley P Pfeffer
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - Oliver Elliot
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.
| | - Alexandra Petrosov
- The Center for Infection and Immunity, Columbia University, New York, NY, USA.
| | - Dereje D Jima
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, MD, USA.
| | - Tyghe G Vallard
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, MD, USA.
| | - Melanie C Melendrez
- Walter Reed Army Institute of Research, Viral Diseases Branch, Silver Spring, MD, USA.
| | | | - Phenix-Lan Quan
- The Center for Infection and Immunity, Columbia University, New York, NY, USA.
| | - W Ian Lipkin
- The Center for Infection and Immunity, Columbia University, New York, NY, USA.
| | - Henry S Gibbons
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA.
| | - David L Hirschberg
- The Center for Infection and Immunity, Columbia University, New York, NY, USA. .,Department of Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, WA, USA.
| | - Gustavo F Palacios
- Center for Genome Sciences, United States Medical Research Institute of Infectious Diseases, Ft. Detrick, Frederick, MD, USA.
| | - C Nicole Rosenzweig
- Biosciences Division, Edgewood Chemical and Biological Center, 5183 Blackhawk Rd, Aberdeen Proving Ground, Edgewood, MD, 21010, USA.
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29
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Affiliation(s)
- Shweta Kailasan
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610
| | - Colin R. Parrish
- Baker Institute for Animal Health and Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853;
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30
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Canuti M, van Beveren NJM, Jazaeri Farsani SM, de Vries M, Deijs M, Jebbink MF, Zaaijer HL, van Schaik BDC, van Kampen AHC, van der Kuyl AC, de Haan L, Storosum JG, van der Hoek L. Viral metagenomics in drug-naïve, first-onset schizophrenia patients with prominent negative symptoms. Psychiatry Res 2015; 229:678-84. [PMID: 26304023 DOI: 10.1016/j.psychres.2015.08.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 07/16/2015] [Accepted: 08/14/2015] [Indexed: 12/16/2022]
Abstract
Although several studies suggest a virus or (endogenous) retrovirus involvement at the time of onset of schizophrenia, the unequivocal identification of one or more infectious agents, by means of an undirected catch-all technique, has never been conducted. In this study VIDISCA, a virus discovery method, was used in combination with Roche-454 high-throughput sequencing as a tool to determine the possible presence of viruses (known or unknown) in blood of first-onset drugs-naïve schizophrenic patients with prominent negative symptoms. Two viruses (the Anellovirus Torque Teno virus and GB virus C) were detected. Both viruses are commonly found in healthy individuals and no clear link with disease was ever established. Viruses from the family Anelloviridae were also identified in the control population (4.8%). Besides, one patient sample was positive for human endogenous retroviruses type K (HML-2) RNA but no specific predominant strain was detected, instead 119 different variants were found. In conclusion, these findings indicate no evidence for viral or endogenous retroviral involvement in sera at the time of onset of schizophrenia.
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Affiliation(s)
- Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Nico J M van Beveren
- Antes, Institute for Mental Health Care, Rotterdam, The Netherlands; Erasmus University Medical Center, Department of Neuroscience, Rotterdam, The Netherlands; Department of Psychiatry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Seyed Mohammad Jazaeri Farsani
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands; Tehran University of Medical Sciences, Tehran, Iran
| | - Michel de Vries
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Hans L Zaaijer
- Department of Blood-Borne Infections, Sanquin Blood Supply Foundation, Amsterdam, The Netherlands; Laboratory of Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Amsterdam, The Netherlands
| | - Barbera D C van Schaik
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, The Netherlands
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, The Netherlands
| | - Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Lieuwe de Haan
- Department of Psychiatry, Academic Medical Center, Amsterdam, The Netherlands
| | - Jitschak G Storosum
- Department of Psychiatry, Academic Medical Center, Amsterdam, The Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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31
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A Novel Virus Causes Scale Drop Disease in Lates calcarifer. PLoS Pathog 2015; 11:e1005074. [PMID: 26252390 PMCID: PMC4529248 DOI: 10.1371/journal.ppat.1005074] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/07/2015] [Indexed: 11/19/2022] Open
Abstract
From 1992 onwards, outbreaks of a previously unknown illness have been reported in Asian seabass (Lates calcarifer) kept in maricultures in Southeast Asia. The most striking symptom of this emerging disease is the loss of scales. It was referred to as scale drop syndrome, but the etiology remained enigmatic. By using a next-generation virus discovery technique, VIDISCA-454, sequences of an unknown virus were detected in serum of diseased fish. The near complete genome sequence of the virus was determined, which shows a unique genome organization, and low levels of identity to known members of the Iridoviridae. Based on homology of a series of putatively encoded proteins, the virus is a novel member of the Megalocytivirus genus of the Iridoviridae family. The virus was isolated and propagated in cell culture, where it caused a cytopathogenic effect in infected Asian seabass kidney and brain cells. Electron microscopy revealed icosahedral virions of about 140 nm, characteristic for the Iridoviridae. In vitro cultured virus induced scale drop syndrome in Asian seabass in vivo and the virus could be reisolated from these infected fish. These findings show that the virus is the causative agent for the scale drop syndrome, as each of Koch's postulates is fulfilled. We have named the virus Scale Drop Disease Virus. Vaccines prepared from BEI- and formalin inactivated virus, as well as from E. coli produced major capsid protein provide efficacious protection against scale drop disease.
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32
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Canuti M, Buka S, Jazaeri Farsani SM, Oude Munnink BB, Jebbink MF, van Beveren NJM, de Haan L, Goldstein J, Seidman LJ, Tsuang MT, Storosum JG, van der Hoek L. Reduced maternal levels of common viruses during pregnancy predict offspring psychosis: potential role of enhanced maternal immune activity? Schizophr Res 2015; 166:248-54. [PMID: 26004694 DOI: 10.1016/j.schres.2015.04.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/22/2015] [Accepted: 04/27/2015] [Indexed: 01/09/2023]
Abstract
Viral infections during the prenatal or early childhood periods are one of the environmental factors which might play an etiological role in psychoses. Several studies report higher antibody levels against viruses during pregnancy in blood of mothers of offspring with psychotic disorders, but the presence of such viruses has never been demonstrated. The goal of this study was to investigate the potential association between viral infections during pregnancy and progeny with psychotic disorders and, for this purpose, we performed a nested case-control study involving pregnant mothers of offspring with schizophrenia or bipolar disorder with psychotic features (cases, N=43) and pregnant women with healthy offspring (controls, N=95). Since several potential viral candidates have been suggested in prior work, a broad-spectrum virus detection system was necessary. A metagenomic analysis performed with the virus discovery method VIDISCA-454 revealed only common blood-associated viruses in all cohorts. However, a significantly lower viral prevalence was detected in the group of cases and in the sub-population of pregnant mothers of offspring with schizophrenia (p<0.05). Consistent with the existing inverse correlation between the level of these viruses and the immunocompetence of an individual, we hypothesized the presence of a higher immune activity during pregnancy in mothers whose offspring later develop a psychotic disorder as compared to controls. Combining our results with previously available literature data on antibody levels during the gestation period suggests that a more prominent maternal immune activity can be considered a risk factor for developing psychosis.
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Affiliation(s)
- Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands.
| | - Stephen Buka
- Department of Epidemiology, Brown University, Providence, RI, USA.
| | - Seyed Mohammad Jazaeri Farsani
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Bas B Oude Munnink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Nico J M van Beveren
- Antes, Institute for Mental Health Care, Rotterdam, The Netherlands; Erasmus University Medical Center, Department of Neuroscience, Rotterdam, The Netherlands; Department of Psychiatry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lieuwe de Haan
- Department of Psychiatry, Academic Medical Center, Amsterdam, The Netherlands
| | - Jill Goldstein
- Connors Center for Women's Health and Gender Biology, Brigham and Women's Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Larry J Seidman
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA; Massachusetts Mental Health Center Public Psychiatry Division of the Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Ming T Tsuang
- Center for Behavioral Genomics, Department of Psychiatry, Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA; Harvard Institute of Psychiatric Epidemiology and Genetics, Boston, USA
| | - Jitschak G Storosum
- Department of Psychiatry, Academic Medical Center, Amsterdam, The Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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de Sales Lima FE, Cibulski SP, Witt AA, Franco AC, Roehe PM. Genomic characterization of two novel polyomaviruses in Brazilian insectivorous bats. Arch Virol 2015; 160:1831-6. [PMID: 25963124 PMCID: PMC7086640 DOI: 10.1007/s00705-015-2447-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 04/30/2015] [Indexed: 01/15/2023]
Abstract
Two novel genomes comprising ≈4.9 kb were identified by next-generation sequencing from pooled organs of Tadarida brasiliensis bats. The overall nucleotide sequence identities between the viral genomes characterized here were less than 80% in comparison to other polyomaviruses (PyVs), members of the family Polyomaviridae. The new genomes display the archetypal organization of PyVs, which includes open reading frames for the regulatory proteins small T antigen (STAg) and large T antigen (LTAg), as well as capsid proteins VP1, VP2 and VP3. In addition, an alternate ORF was identified in the early genome region that is conserved in a large monophyletic group of polyomaviruses. Phylogenetic analysis showed similar clustering with group of PyVs detected in Otomops and Chaerephon bats and some species of monkeys. In this study, the genomes of two novel PyVs were detected in bats of a single species, demonstrating that these mammals can harbor genetically diverse polyomaviruses.
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Affiliation(s)
- Francisco Esmaile de Sales Lima
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul (UFRGS), Rua Sarmento Leite 500, Porto Alegre, Rio Grande do Sul, CEP 90050-170, Brazil,
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A systematic approach to novel virus discovery in emerging infectious disease outbreaks. J Mol Diagn 2015; 17:230-41. [PMID: 25746799 PMCID: PMC7106266 DOI: 10.1016/j.jmoldx.2014.12.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/03/2014] [Accepted: 12/08/2014] [Indexed: 12/20/2022] Open
Abstract
The discovery of novel viruses is of great importance to human health-both in the setting of emerging infectious disease outbreaks and in disease syndromes of unknown etiology. Despite the recent proliferation of many efficient virus discovery methods, careful selection of a combination of methods is important to demonstrate a novel virus, its clinical associations, and its relevance in a timely manner. The identification of a patient or an outbreak with distinctive clinical features and negative routine microbiological workup is often the starting point for virus hunting. This review appraises the roles of culture, electron microscopy, and nucleic acid detection-based methods in optimizing virus discovery. Cell culture is generally slow but may yield viable virus. Although the choice of cell line often involves trial and error, it may be guided by the clinical syndrome. Electron microscopy is insensitive but fast, and may provide morphological clues to choice of cell line or consensus primers for nucleic acid detection. Consensus primer PCR can be used to detect viruses that are closely related to known virus families. Random primer amplification and high-throughput sequencing can catch any virus genome but cannot yield an infectious virion for testing Koch postulates. A systematic approach that incorporates carefully chosen combinations of virus detection techniques is required for successful virus discovery.
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Jazaeri Farsani SM, Oude Munnink BB, Canuti M, Deijs M, Cotten M, Jebbink MF, Verhoeven J, Kellam P, Loens K, Goossens H, Ieven M, van der Hoek L. Identification of a novel human rhinovirus C type by antibody capture VIDISCA-454. Viruses 2015; 7:239-51. [PMID: 25606972 PMCID: PMC4306836 DOI: 10.3390/v7010239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/08/2015] [Accepted: 01/13/2015] [Indexed: 12/31/2022] Open
Abstract
Causative agents for more than 30 percent of respiratory infections remain unidentified, suggesting that unknown respiratory pathogens might be involved. In this study, antibody capture VIDISCA-454 (virus discovery cDNA-AFLP combined with Roche 454 high-throughput sequencing) resulted in the discovery of a novel type of rhinovirus C (RV-C). The virus has an RNA genome of at least 7054 nt and carries the characteristics of rhinovirus C species. The gene encoding viral protein 1, which is used for typing, has only 81% nucleotide sequence identity with the closest known RV-C type, and, therefore, the virus represents the first member of a novel type, named RV-C54.
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Affiliation(s)
- Seyed Mohammad Jazaeri Farsani
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
| | - Bas B Oude Munnink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
| | - Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
| | - Matthew Cotten
- Department of Virus Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
| | - Joost Verhoeven
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
| | - Paul Kellam
- Department of Virus Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
| | - Katherine Loens
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, University Hospital, Antwerp B-2650, Belgium.
| | - Herman Goossens
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, University Hospital, Antwerp B-2650, Belgium.
| | - Margareta Ieven
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, University Hospital, Antwerp B-2650, Belgium.
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
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Farsani SMJ, Deijs M, Dijkman R, Molenkamp R, Jeeninga RE, Ieven M, Goossens H, van der Hoek L. Culturing of respiratory viruses in well-differentiated pseudostratified human airway epithelium as a tool to detect unknown viruses. Influenza Other Respir Viruses 2014; 9:51-7. [PMID: 25482367 PMCID: PMC4280819 DOI: 10.1111/irv.12297] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2014] [Indexed: 12/19/2022] Open
Abstract
Background Currently, virus discovery is mainly based on molecular techniques. Here, we propose a method that relies on virus culturing combined with state-of-the-art sequencing techniques. The most natural ex vivo culture system was used to enable replication of respiratory viruses. Method Three respiratory clinical samples were tested on well-differentiated pseudostratified tracheobronchial human airway epithelial (HAE) cultures grown at an air–liquid interface, which resemble the airway epithelium. Cells were stained with convalescent serum of the patients to identify infected cells and apical washes were analyzed by VIDISCA-454, a next-generation sequencing virus discovery technique. Results Infected cells were observed for all three samples. Sequencing subsequently indicated that the cells were infected by either human coronavirus OC43, influenzavirus B, or influenzavirus A. The sequence reads covered a large part of the genome (52%, 82%, and 57%, respectively). Conclusion We present here a new method for virus discovery that requires a virus culture on primary cells and an antibody detection. The virus in the harvest can be used to characterize the viral genome sequence and cell tropism, but also provides progeny virus to initiate experiments to fulfill the Koch's postulates.
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Affiliation(s)
- Seyed Mohammad Jazaeri Farsani
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; Tehran University of Medical Sciences, Tehran, Iran
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A nairovirus isolated from African bats causes haemorrhagic gastroenteritis and severe hepatic disease in mice. Nat Commun 2014; 5:5651. [PMID: 25451856 PMCID: PMC4268697 DOI: 10.1038/ncomms6651] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/23/2014] [Indexed: 01/30/2023] Open
Abstract
Bats can carry important zoonotic pathogens. Here we use a combination of next-generation sequencing and classical virus isolation methods to identify novel nairoviruses from bats captured from a cave in Zambia. This nairovirus infection is highly prevalent among giant leaf-nosed bats, Hipposideros gigas (detected in samples from 16 individuals out of 38). Whole-genome analysis of three viral isolates (11SB17, 11SB19 and 11SB23) reveals a typical bunyavirus tri-segmented genome. The strains form a single phylogenetic clade that is divergent from other known nairoviruses, and are hereafter designated as Leopards Hill virus (LPHV). When i.p. injected into mice, the 11SB17 strain causes only slight body weight loss, whereas 11SB23 produces acute and lethal disease closely resembling that observed with Crimean–Congo Haemorrhagic Fever virus in humans. We believe that our LPHV mouse model will be useful for research on the pathogenesis of nairoviral haemorrhagic disease. Bats carry viruses that can cause disease in other animals and in humans. Here, Ishii et al. identify new nairoviruses from African bats and show that some of them can produce a severe haemorrhagic disease in laboratory mice that is similar to Crimean–Congo haemorrhagic fever in humans.
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Canuti M, Williams CV, Gadi SR, Jebbink MF, Oude Munnink BB, Jazaeri Farsani SM, Cullen JM, van der Hoek L. Persistent viremia by a novel parvovirus in a slow loris (Nycticebus coucang) with diffuse histiocytic sarcoma. Front Microbiol 2014; 5:655. [PMID: 25520709 PMCID: PMC4249460 DOI: 10.3389/fmicb.2014.00655] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 11/13/2014] [Indexed: 12/13/2022] Open
Abstract
Cancer is one of the leading health concerns for human and animal health. Since the tumorigenesis process is not completely understood and it is known that some viruses can induce carcinogenesis, it is highly important to identify novel oncoviruses and extensively study underlying oncogenic mechanisms. Here, we investigated a case of diffuse histiocytic sarcoma in a 22 year old slow loris (Nycticebus coucang), using a broad spectrum virus discovery technique. A novel parvovirus was discovered and the phylogenetic analysis performed on its fully sequenced genome demonstrated that it represents the first member of a novel genus. The possible causative correlation between this virus and the malignancy was further investigated and 20 serum and 61 organ samples from 25 animals (N. coucang and N. pygmaeus) were screened for the novel virus but only samples collected from the originally infected animal were positive. The virus was present in all tested organs (intestine, liver, spleen, kidneys, and lungs) and in all banked serum samples collected up to 8 years before death. All attempts to identify a latent viral form (integrated or episomal) were unsuccessful and the increase of variation in the viral sequences during the years was consistent with absence of latency. Since it is well known that parvoviruses are dependent on cell division to successfully replicate, we hypothesized that the virus could have benefitted from the constantly dividing cancer cells and may not have been the cause of the histiocytic sarcoma. It is also possible to conjecture that the virus had a role in delaying the tumor progression and this report might bring new exciting opportunities in recognizing viruses to be used in cancer virotherapy.
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Affiliation(s)
- Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam Amsterdam, Netherlands
| | | | - Sashi R Gadi
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University Raleigh, NC, USA
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam Amsterdam, Netherlands
| | - Bas B Oude Munnink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam Amsterdam, Netherlands
| | - Seyed Mohammad Jazaeri Farsani
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam Amsterdam, Netherlands ; Department of Virology, Tehran University of Medical Sciences Tehran, Iran
| | - John M Cullen
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University Raleigh, NC, USA
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam Amsterdam, Netherlands
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Zhang W, Li L, Deng X, Kapusinszky B, Delwart E. What is for dinner? Viral metagenomics of US store bought beef, pork, and chicken. Virology 2014; 468-470:303-310. [PMID: 25217712 PMCID: PMC4252299 DOI: 10.1016/j.virol.2014.08.025] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 08/14/2014] [Accepted: 08/22/2014] [Indexed: 12/16/2022]
Abstract
We describe here the metagenomics-derived viral sequences detected in beef, pork, and chicken purchased from stores in San Francisco. In beef we detected four previously reported viruses (two parvoviruses belonging to different genera, an anellovirus, and one circovirus-like virus) and one novel bovine polyomavirus species (BPyV2-SF) whose closest relatives infect primates. Detection of porcine hokovirus in beef indicated that this parvovirus can infect both ungulate species. In pork we detected four known parvoviruses from three genera, an anellovirus, and pig circovirus 2. Chicken meat contained numerous gyrovirus sequences including those of chicken anemia virus and of a novel gyrovirus species (GyV7-SF). Our results provide an initial characterization of some of the viruses commonly found in US store-bought meats which included a diverse group of parvoviruses and viral families with small circular DNA genomes. Whether any of these viruses can infect humans will require testing human sera for specific antibodies. Eukaryotic viral genomes in store-bought beef, pork, and chicken are identified. A novel bovine polyomavirus genome, closest to a group of viruses from primates, is sequenced. Porcine hokovirus is detected in beef samples. A small circovirus-like circular DNA genome in beef is genetically characterized. Several species of gyrovirus including a novel species are detected in chicken meat.
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Affiliation(s)
- Wen Zhang
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Microbiology, School of Medicine, Jiangsu University, Jiangsu, Zhenjiang 212013, China; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Linlin Li
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Beatrix Kapusinszky
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA.
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Shaukat S, Angez M, Alam MM, Jebbink MF, Deijs M, Canuti M, Sharif S, de Vries M, Khurshid A, Mahmood T, van der Hoek L, Zaidi SSZ. Identification and characterization of unrecognized viruses in stool samples of non-polio acute flaccid paralysis children by simplified VIDISCA. Virol J 2014; 11:146. [PMID: 25112200 PMCID: PMC4254409 DOI: 10.1186/1743-422x-11-146] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/30/2014] [Indexed: 12/22/2022] Open
Abstract
Background The use of sequence independent methods combined with next generation sequencing for identification purposes in clinical samples appears promising and exciting results have been achieved to understand unexplained infections. One sequence independent method, Virus Discovery based on cDNA Amplified Fragment Length Polymorphism (VIDISCA) is capable of identifying viruses that would have remained unidentified in standard diagnostics or cell cultures. Methods VIDISCA is normally combined with next generation sequencing, however, we set up a simplified VIDISCA which can be used in case next generation sequencing is not possible. Stool samples of 10 patients with unexplained acute flaccid paralysis showing cytopathic effect in rhabdomyosarcoma cells and/or mouse cells were used to test the efficiency of this method. To further characterize the viruses, VIDISCA-positive samples were amplified and sequenced with gene specific primers. Results Simplified VIDISCA detected seven viruses (70%) and the proportion of eukaryotic viral sequences from each sample ranged from 8.3 to 45.8%. Human enterovirus EV-B97, EV-B100, echovirus-9 and echovirus-21, human parechovirus type-3, human astrovirus probably a type-3/5 recombinant, and tetnovirus-1 were identified. Phylogenetic analysis based on the VP1 region demonstrated that the human enteroviruses are more divergent isolates circulating in the community. Conclusion Our data support that a simplified VIDISCA protocol can efficiently identify unrecognized viruses grown in cell culture with low cost, limited time without need of advanced technical expertise. Also complex data interpretation is avoided thus the method can be used as a powerful diagnostic tool in limited resources. Redesigning the routine diagnostics might lead to additional detection of previously undiagnosed viruses in clinical samples of patients. Electronic supplementary material The online version of this article (doi:10.1186/1743-422X-11-146) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Syed Sohail Zahoor Zaidi
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad 45500, Pakistan.
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Maganga GD, Bourgarel M, Vallo P, Dallo TD, Ngoagouni C, Drexler JF, Drosten C, Nakouné ER, Leroy EM, Morand S. Bat distribution size or shape as determinant of viral richness in african bats. PLoS One 2014; 9:e100172. [PMID: 24959855 PMCID: PMC4069033 DOI: 10.1371/journal.pone.0100172] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 05/21/2014] [Indexed: 11/20/2022] Open
Abstract
The rising incidence of emerging infectious diseases (EID) is mostly linked to biodiversity loss, changes in habitat use and increasing habitat fragmentation. Bats are linked to a growing number of EID but few studies have explored the factors of viral richness in bats. These may have implications for role of bats as potential reservoirs. We investigated the determinants of viral richness in 15 species of African bats (8 Pteropodidae and 7 microchiroptera) in Central and West Africa for which we provide new information on virus infection and bat phylogeny. We performed the first comparative analysis testing the correlation of the fragmented geographical distribution (defined as the perimeter to area ratio) with viral richness in bats. Because of their potential effect, sampling effort, host body weight, ecological and behavioural traits such as roosting behaviour, migration and geographical range, were included into the analysis as variables. The results showed that the geographical distribution size, shape and host body weight have significant effects on viral richness in bats. Viral richness was higher in large-bodied bats which had larger and more fragmented distribution areas. Accumulation of viruses may be related to the historical expansion and contraction of bat species distribution range, with potentially strong effects of distribution edges on virus transmission. Two potential explanations may explain these results. A positive distribution edge effect on the abundance or distribution of some bat species could have facilitated host switches. Alternatively, parasitism could play a direct role in shaping the distribution range of hosts through host local extinction by virulent parasites. This study highlights the importance of considering the fragmentation of bat species geographical distribution in order to understand their role in the circulation of viruses in Africa.
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Affiliation(s)
- Gaël D. Maganga
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- Institut National Supérieur d'Agronomie et de Biotechnologies (INSAB), Franceville, Gabon
| | - Mathieu Bourgarel
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- CIRAD, UPR AGIRs, Montpellier, France
- CIRAD, UPR AGIRs, Harare, Zimbabwe
| | - Peter Vallo
- Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Institute of Experimental Ecology, Ulm University, Ulm, Germany
| | - Thierno D. Dallo
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | | | - Jan Felix Drexler
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | | | - Eric M. Leroy
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
- Institut de Recherche pour le Développement, UMR 224 (MIVEGEC), IRD/CNRS/UM1, Montpellier, France
| | - Serge Morand
- CIRAD, UPR AGIRs, Montpellier, France
- Institut des Sciences de l'Evolution, CNRS-UM2, CC065, Université de Montpellier 2, Montpellier, France
- Centre d'Infectiologie Christophe Mérieux du Laos, Vientiane, Lao PDR
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Cotten M, Oude Munnink B, Canuti M, Deijs M, Watson SJ, Kellam P, van der Hoek L. Full genome virus detection in fecal samples using sensitive nucleic acid preparation, deep sequencing, and a novel iterative sequence classification algorithm. PLoS One 2014; 9:e93269. [PMID: 24695106 PMCID: PMC3973683 DOI: 10.1371/journal.pone.0093269] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/02/2014] [Indexed: 12/18/2022] Open
Abstract
We have developed a full genome virus detection process that combines sensitive nucleic acid preparation optimised for virus identification in fecal material with Illumina MiSeq sequencing and a novel post-sequencing virus identification algorithm. Enriched viral nucleic acid was converted to double-stranded DNA and subjected to Illumina MiSeq sequencing. The resulting short reads were processed with a novel iterative Python algorithm SLIM for the identification of sequences with homology to known viruses. De novo assembly was then used to generate full viral genomes. The sensitivity of this process was demonstrated with a set of fecal samples from HIV-1 infected patients. A quantitative assessment of the mammalian, plant, and bacterial virus content of this compartment was generated and the deep sequencing data were sufficient to assembly 12 complete viral genomes from 6 virus families. The method detected high levels of enteropathic viruses that are normally controlled in healthy adults, but may be involved in the pathogenesis of HIV-1 infection and will provide a powerful tool for virus detection and for analyzing changes in the fecal virome associated with HIV-1 progression and pathogenesis.
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Affiliation(s)
- Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- * E-mail:
| | - Bas Oude Munnink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | | | - Paul Kellam
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Department of Infection, University College London, London, United Kingdom
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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Chen L, Liu B, Yang J, Jin Q. DBatVir: the database of bat-associated viruses. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau021. [PMID: 24647629 PMCID: PMC3958617 DOI: 10.1093/database/bau021] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Emerging infectious diseases remain a significant threat to public health. Most emerging infectious disease agents in humans are of zoonotic origin. Bats are important reservoir hosts of many highly lethal zoonotic viruses and have been implicated in numerous emerging infectious disease events in recent years. It is essential to enhance our knowledge and understanding of the genetic diversity of the bat-associated viruses to prevent future outbreaks. To facilitate further research, we constructed the database of bat-associated viruses (DBatVir). Known viral sequences detected in bat samples were manually collected and curated, along with the related metadata, such as the sampling time, location, bat species and specimen type. Additional information concerning the bats, including common names, diet type, geographic distribution and phylogeny were integrated into the database to bridge the gap between virologists and zoologists. The database currently covers >4100 bat-associated animal viruses of 23 viral families detected from 196 bat species in 69 countries worldwide. It provides an overview and snapshot of the current research regarding bat-associated viruses, which is essential now that the field is rapidly expanding. With a user-friendly interface and integrated online bioinformatics tools, DBatVir provides a convenient and powerful platform for virologists and zoologists to analyze the virome diversity of bats, as well as for epidemiologists and public health researchers to monitor and track current and future bat-related infectious diseases. Database URL:http://www.mgc.ac.cn/DBatVir/
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Affiliation(s)
- Lihong Chen
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Oude Munnink BB, Canuti M, Deijs M, de Vries M, Jebbink MF, Rebers S, Molenkamp R, van Hemert FJ, Chung K, Cotten M, Snijders F, Sol CJA, van der Hoek L. Unexplained diarrhoea in HIV-1 infected individuals. BMC Infect Dis 2014; 14:22. [PMID: 24410947 PMCID: PMC3925291 DOI: 10.1186/1471-2334-14-22] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 01/08/2014] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Gastrointestinal symptoms, in particular diarrhoea, are common in non-treated HIV-1 infected individuals. Although various enteric pathogens have been implicated, the aetiology of diarrhoea remains unexplained in a large proportion of HIV-1 infected patients. Our aim is to identify the cause of diarrhoea for patients that remain negative in routine diagnostics. METHODS In this study stool samples of 196 HIV-1 infected persons, including 29 persons with diarrhoea, were examined for enteropathogens and HIV-1. A search for unknown and unexpected viruses was performed using virus discovery cDNA-AFLP combined with Roche-454 sequencing (VIDISCA-454). RESULTS HIV-1 RNA was detected in stool of 19 patients with diarrhoea (66%) compared to 75 patients (45%) without diarrhoea. In 19 of the 29 diarrhoea cases a known enteropathogen could be identified (66%). Next to these known causative agents, a range of recently identified viruses was identified via VIDISCA-454: cosavirus, Aichi virus, human gyrovirus, and non-A non-B hepatitis virus. Moreover, a novel virus was detected which was named immunodeficiency-associated stool virus (IASvirus). However, PCR based screening for these viruses showed that none of these novel viruses was associated with diarrhoea. Notably, among the 34% enteropathogen-negative cases, HIV-1 RNA shedding in stool was more frequently observed (80%) compared to enteropathogen-positive cases (47%), indicating that HIV-1 itself is the most likely candidate to be involved in diarrhoea. CONCLUSION Unexplained diarrhoea in HIV-1 infected patients is probably not caused by recently described or previously unknown pathogens, but it is more likely that HIV-1 itself plays a role in intestinal mucosal abnormalities which leads to diarrhoea.
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Affiliation(s)
- Bas B Oude Munnink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Michel de Vries
- CBS-KNAW Fungal Biodiversity Center, Utrecht, The Netherlands
| | - Maarten F Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Sjoerd Rebers
- Laboratory of Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Richard Molenkamp
- Laboratory of Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Formijn J van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Kevin Chung
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | | | | | - Cees JA Sol
- Laboratory of Clinical Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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Eckerle I, Ehlen L, Kallies R, Wollny R, Corman VM, Cottontail VM, Tschapka M, Oppong S, Drosten C, Müller MA. Bat airway epithelial cells: a novel tool for the study of zoonotic viruses. PLoS One 2014; 9:e84679. [PMID: 24454736 PMCID: PMC3890267 DOI: 10.1371/journal.pone.0084679] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/25/2013] [Indexed: 01/01/2023] Open
Abstract
Bats have been increasingly recognized as reservoir of important zoonotic viruses. However, until now many attempts to isolate bat-borne viruses in cell culture have been unsuccessful. Further, experimental studies on reservoir host species have been limited by the difficulty of rearing these species. The epithelium of the respiratory tract plays a central role during airborne transmission, as it is the first tissue encountered by viral particles. Although several cell lines from bats were established recently, no well-characterized, selectively cultured airway epithelial cells were available so far. Here, primary cells and immortalized cell lines from bats of the two important suborders Yangochiroptera and Yinpterochiroptera, Carollia perspicillata (Seba's short-tailed bat) and Eidolon helvum (Straw-colored fruit bat), were successfully cultured under standardized conditions from both fresh and frozen organ specimens by cell outgrowth of organ explants and by the use of serum-free primary cell culture medium. Cells were immortalized to generate permanent cell lines. Cells were characterized for their epithelial properties such as expression of cytokeratin and tight junctions proteins and permissiveness for viral infection with Rift-Valley fever virus and vesicular stomatitis virus Indiana. These cells can serve as suitable models for the study of bat-borne viruses and complement cell culture models for virus infection in human airway epithelial cells.
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Affiliation(s)
- Isabella Eckerle
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Lukas Ehlen
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - René Kallies
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Robert Wollny
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Victor M. Corman
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | | | - Marco Tschapka
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
- Smithsonian Tropical Research Institute, Balboa, Panama
| | - Samuel Oppong
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Marcel A. Müller
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
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Väisänen E, Lahtinen A, Eis-Hübinger A, Lappalainen M, Hedman K, Söderlund-Venermo M. A two-step real-time PCR assay for quantitation and genotyping of human parvovirus 4. J Virol Methods 2014; 195:106-11. [DOI: 10.1016/j.jviromet.2013.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/26/2013] [Accepted: 10/01/2013] [Indexed: 01/11/2023]
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Oude Munnink BB, Jazaeri Farsani SM, Deijs M, Jonkers J, Verhoeven JTP, Ieven M, Goossens H, de Jong MD, Berkhout B, Loens K, Kellam P, Bakker M, Canuti M, Cotten M, van der Hoek L. Autologous antibody capture to enrich immunogenic viruses for viral discovery. PLoS One 2013; 8:e78454. [PMID: 24223808 PMCID: PMC3817278 DOI: 10.1371/journal.pone.0078454] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 09/11/2013] [Indexed: 11/19/2022] Open
Abstract
Discovery of new viruses has been boosted by novel deep sequencing technologies. Currently, many viruses can be identified by sequencing without knowledge of the pathogenicity of the virus. However, attributing the presence of a virus in patient material to a disease in the patient can be a challenge. One approach to meet this challenge is identification of viral sequences based on enrichment by autologous patient antibody capture. This method facilitates identification of viruses that have provoked an immune response within the patient and may increase the sensitivity of the current virus discovery techniques. To demonstrate the utility of this method, virus discovery deep sequencing (VIDISCA-454) was performed on clinical samples from 19 patients: 13 with a known respiratory viral infection and 6 with a known gastrointestinal viral infection. Patient sera was collected from one to several months after the acute infection phase. Input and antibody capture material was sequenced and enrichment was assessed. In 18 of the 19 patients, viral reads from immunogenic viruses were enriched by antibody capture (ranging between 1.5x to 343x in respiratory material, and 1.4x to 53x in stool). Enriched reads were also determined in an identity independent manner by using a novel algorithm Xcompare. In 16 of the 19 patients, 21% to 100% of the enriched reads were derived from infecting viruses. In conclusion, the technique provides a novel approach to specifically identify immunogenic viral sequences among the bulk of sequences which are usually encountered during virus discovery metagenomics.
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Affiliation(s)
- Bas B. Oude Munnink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Seyed Mohammad Jazaeri Farsani
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
- Tehran University of Medical Sciences, Tehran, Iran
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Jiri Jonkers
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Joost T. P. Verhoeven
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Margareta Ieven
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, University Hospital, Antwerp, Belgium
| | - Herman Goossens
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, University Hospital, Antwerp, Belgium
| | - Menno D. de Jong
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Katherine Loens
- Department of Medical Microbiology, Vaccine and Infectious Disease Institute, University Hospital, Antwerp, Belgium
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Marta Canuti
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
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Jazaeri Farsani SM, Jebbink MF, Deijs M, Canuti M, van Dort KA, Bakker M, Grady BPX, Prins M, van Hemert FJ, Kootstra NA, van der Hoek L. Identification of a new genotype of Torque Teno Mini virus. Virol J 2013; 10:323. [PMID: 24171716 PMCID: PMC3819664 DOI: 10.1186/1743-422x-10-323] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/25/2013] [Indexed: 11/27/2022] Open
Abstract
Background Although human torque teno viruses (TTVs) were first discovered in 1997, still many associated aspects are not clarified yet. The viruses reveal a remarkable heterogeneity and it is possible that some genotypes are more pathogenic than others. The identification of all genotypes is essential to confirm previous pathogenicity data, and an unbiased search for novel viruses is needed to identify TTVs that might be related to disease. Method The virus discovery technique VIDISCA-454 was used to screen serum of 55 HIV-1 positive injecting drug users, from the Amsterdam Cohort Studies, in search for novel blood-blood transmittable viruses which are undetectable via normal diagnostics or panvirus-primer PCRs. Results A novel torque teno mini virus (TTMV) was identified in two patients and the sequence of the full genomes were determined. The virus is significantly different from the known TTMVs (< 40% amino acid identity in ORF1), yet it contains conserved characteristics that are also present in other TTMVs. The virus is chronically present in both patients, and these patients both suffered from a pneumococcal pneumonia during follow up and had extremely low B-cells counts. Conclusion We describe a novel TTMV which we tentatively named TTMV-13. Further research is needed to address the epidemiology and pathogenicity of this novel virus.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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Phan TG, Vo NP, Boros Á, Pankovics P, Reuter G, Li OTW, Wang C, Deng X, Poon LLM, Delwart E. The viruses of wild pigeon droppings. PLoS One 2013; 8:e72787. [PMID: 24023772 PMCID: PMC3762862 DOI: 10.1371/journal.pone.0072787] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/12/2013] [Indexed: 01/14/2023] Open
Abstract
Birds are frequent sources of emerging human infectious diseases. Viral particles were enriched from the feces of 51 wild urban pigeons (Columba livia) from Hong Kong and Hungary, their nucleic acids randomly amplified and then sequenced. We identified sequences from known and novel species from the viral families Circoviridae, Parvoviridae, Picornaviridae, Reoviridae, Adenovirus, Astroviridae, and Caliciviridae (listed in decreasing number of reads), as well as plant and insect viruses likely originating from consumed food. The near full genome of a new species of a proposed parvovirus genus provisionally called Aviparvovirus contained an unusually long middle ORF showing weak similarity to an ORF of unknown function from a fowl adenovirus. Picornaviruses found in both Asia and Europe that are distantly related to the turkey megrivirus and contained a highly divergent 2A1 region were named mesiviruses. All eleven segments of a novel rotavirus subgroup related to a chicken rotavirus in group G were sequenced and phylogenetically analyzed. This study provides an initial assessment of the enteric virome in the droppings of pigeons, a feral urban species with frequent human contact.
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Affiliation(s)
- Tung Gia Phan
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Nguyen Phung Vo
- Blood Systems Research Institute, San Francisco, California, United States of America
- Pharmacology Department, School of Pharmacy, Ho Chi Minh City University of Medicine and Pharmacy, Ho Chi Minh, Vietnam
| | - Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Péter Pankovics
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Olive T. W. Li
- Centre of Influenza Research and School of Public Health, University of Hong Kong, Hong Kong SAR
| | - Chunling Wang
- Stanford Genome Technology Center, Stanford, California, United States of America
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Leo L. M. Poon
- Centre of Influenza Research and School of Public Health, University of Hong Kong, Hong Kong SAR
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Baylis SA, Tuke PW, Miyagawa E, Blümel J. Studies on the inactivation of human parvovirus 4. Transfusion 2013; 53:2585-92. [PMID: 24032592 DOI: 10.1111/trf.12372] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 07/03/2013] [Accepted: 07/03/2013] [Indexed: 12/15/2022]
Abstract
BACKGROUND Human parvovirus 4 (PARV4) is a novel parvovirus, which like parvovirus B19 (B19V) can be a contaminant of plasma pools used to prepare plasma-derived medicinal products. Inactivation studies of B19V have shown that it is more sensitive to virus inactivation strategies than animal parvoviruses. However, inactivation of PARV4 has not yet been specifically addressed. STUDY DESIGN AND METHODS Treatment of parvoviruses by heat or low-pH conditions causes externalization of the virus genome. Using nuclease treatment combined with real-time polymerase chain reaction, the extent of virus DNA externalization was used as an indirect measure of the inactivation of PARV4, B19V, and minute virus of mice (MVM) by pasteurization of albumin and by low-pH treatment. Infectivity studies were performed in parallel for B19V and MVM. RESULTS PARV4 showed greater resistance to pasteurization and low-pH treatment than B19V, although PARV4 was not as resistant as MVM. There was a 2- to 3-log reduction of encapsidated PARV4 DNA after pasteurization and low-pH treatment. In contrast, B19V was effectively inactivated while MVM was stable under these conditions. Divalent cations were found to have a stabilizing effect on PARV4 capsids. In the absence of divalent cations, even at neutral pH, there was a reduction of PARV4 titer, an effect not observed for B19V or MVM. CONCLUSION In the case of heat treatment and incubation at low pH, PARV4 shows intermediate resistance when compared to B19V and MVM. Divalent cations seem important for stabilizing PARV4 virus particles.
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