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Eckstrand CD, Torrevillas BK, Wolking RM, Bradway DS, Reno JL, McMenamin-Snekvik KM, Snekvik KR. Detection, sequencing, and tissue distribution of piscine orthoreovirus 2-like virus in diseased coho salmon in Alaska. J Vet Diagn Invest 2024:10406387241250119. [PMID: 38693675 DOI: 10.1177/10406387241250119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024] Open
Abstract
We performed a diagnostic disease investigation on a cohort of coho salmon (Oncorhynchus kisutch) fingerlings in Alaska exhibiting anorexia, gaping mouths, anemia, and increased mortality. Histologic examination revealed mild-to-severe myocardial degeneration and lymphohistiocytic and neutrophilic myocarditis, moderate splenic histiocytosis, and mild renal histiocytosis. Piscine orthoreoviruses 1 and 3 were not detected by molecular methods, and no other viruses could be cultured on 3 common diagnostic fish cell lines. De novo assembly produced a viral genome of 10 linear segments with >80% homology to piscine orthoreovirus 2 (PRV2) encoding all 11 PRV2 proteins. An in situ hybridization probe using RNAscope was developed against 697 viral nucleotides identified by sequencing, which revealed viral genome in heart, spleen, gill, kidney, liver, blood, and the lamina propria of the intestines. Our findings are supportive of a novel piscine orthoreovirus most closely related to PRV2 associated with morbidity and mortality of coho salmon in the northeastern Pacific.
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Affiliation(s)
- Chrissy D Eckstrand
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Brandi K Torrevillas
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Rebecca M Wolking
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Daniel S Bradway
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Joetta Lynn Reno
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Kathleen M McMenamin-Snekvik
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Kevin R Snekvik
- Washington Animal Disease Diagnostic Laboratory, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
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2
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Kadlečková D, Saláková M, Erban T, Tachezy R. Discovery and characterization of novel DNA viruses in Apis mellifera: expanding the honey bee virome through metagenomic analysis. mSystems 2024; 9:e0008824. [PMID: 38441971 PMCID: PMC11019937 DOI: 10.1128/msystems.00088-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
To date, many viruses have been discovered to infect honey bees. In this study, we used high-throughput sequencing to expand the known virome of the honey bee, Apis mellifera, by identifying several novel DNA viruses. While the majority of previously identified bee viruses are RNA, our study reveals nine new genomes from the Parvoviridae family, tentatively named Bee densoviruses 1 to 9. In addition, we characterized a large DNA virus, Apis mellifera filamentous-like virus (AmFLV), which shares limited protein identities with the known Apis mellifera filamentous virus. The complete sequence of AmFLV, obtained by a combination of laboratory techniques and bioinformatics, spans 152,678 bp. Linear dsDNA genome encodes for 112 proteins, of which 49 are annotated. Another large virus we discovered is Apis mellifera nudivirus, which belongs to a group of Alphanudivirus. The virus has a length of 129,467 bp and a circular dsDNA genome, and has 106 protein encoding genes. The virus contains most of the core genes of the family Nudiviridae. This research demonstrates the effectiveness of viral binning in identifying viruses in honey bee virology, showcasing its initial application in this field.IMPORTANCEHoney bees contribute significantly to food security by providing pollination services. Understanding the virome of honey bees is crucial for the health and conservation of bee populations and also for the stability of the ecosystems and economies for which they are indispensable. This study unveils previously unknown DNA viruses in the honey bee virome, expanding our knowledge of potential threats to bee health. The use of the viral binning approach we employed in this study offers a promising method to uncovering and understanding the vast viral diversity in these essential pollinators.
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Affiliation(s)
- Dominika Kadlečková
- Department of Genetics and Microbiology, Faculty of Science BIOCEV, Charles University, Vestec, Průmyslová, Czechia
| | - Martina Saláková
- Department of Genetics and Microbiology, Faculty of Science BIOCEV, Charles University, Vestec, Průmyslová, Czechia
| | - Tomáš Erban
- Crop Research Institute, Drnovská, Prague, Czechia
| | - Ruth Tachezy
- Department of Genetics and Microbiology, Faculty of Science BIOCEV, Charles University, Vestec, Průmyslová, Czechia
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3
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François S, Hill SC, Perrins CM, Pybus OG. Characterization of the genomic sequence of a circo-like virus and of three chaphamaparvoviruses detected in mute swan ( Cygnus olor). Microbiol Resour Announc 2024; 13:e0118623. [PMID: 38376411 DOI: 10.1128/mra.01186-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
We report the complete genomes of four ssDNA viruses: a circular replication-associated protein-encoding single-stranded DNA virus belonging to a clade previously detected only in mammals, and three chaphamaparvoviruses, which were detected by viromic surveillance of mute swan (Cygnus olor) fecal samples from the United Kingdom.
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Affiliation(s)
- Sarah François
- Department of Biology, University of Oxford, Oxford, United Kingdom
- DGIMI, Univ Montpellier, INRAE, Montpellier, France
| | - Sarah C Hill
- Department of Pathobiology and Population Science, Royal Veterinary College, Hatfield, United Kingdom
| | | | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Science, Royal Veterinary College, Hatfield, United Kingdom
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4
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Roy A, Grinstead S, Leon Martínez G, Pinzón JCC, Nunziata SO, Padmanabhan C, Hammond J. Meta-Transcriptomic Analysis Uncovers the Presence of Four Novel Viruses and Multiple Known Virus Genera in a Single Hibiscus rosa-sinensis Plant in Colombia. Viruses 2024; 16:267. [PMID: 38400042 PMCID: PMC10891833 DOI: 10.3390/v16020267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Hibiscus is not native to Colombia but well suited to its arid soil and dry climates. A single hibiscus plant from Risaralda, showing black spots on upper and lower sides of its leaves, was collected for virome analysis using meta-transcriptomic high-throughput sequencing technology. Bioinformatic analysis identified 12.5% of the total reads in the Ribo-Zero cDNA library which mapped to viral genomes. BLAST searches revealed the presence of carlavirus, potexvirus, and of known members of the genera Betacarmovirus, Cilevirus, Nepovirus, and Tobamovirus in the sample; confirmed by RT-PCR with virus-specific primers followed by amplicon sequencing. Furthermore, in silico analysis suggested the possibility of a novel soymovirus, and a new hibiscus strain of citrus leprosis virus C2 in the mixed infection. Both RNA dependent RNA polymerase and coat protein gene sequences of the potex and carla viruses shared less than 72% nucleotide and 80% amino acid identities with any alphaflexi- and betaflexi-virus sequences available in GenBank, identifying three novel carlavirus and one potexvirus species in the Hibiscus rosa-sinensis plant. The detection of physalis vein necrosis nepovirus and passion fruit green spot cilevirus in hibiscus are also new reports from Colombia. Overall, the meta-transcriptome analysis identified the complex virome associated with the black spot symptoms on hibiscus leaves and demonstrated the diversity of virus genera tolerated in the mixed infection of a single H. rosa-sinensis plant.
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Affiliation(s)
- Avijit Roy
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture (USDA), Beltsville, MD 20705, USA;
| | - Sam Grinstead
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture (USDA), Beltsville, MD 20705, USA;
| | - Guillermo Leon Martínez
- AGROSAVIA, Centro de Investigación La Libertad, Km.17 vía Pto. Lopez, Villavicencio, Meta, Colombia; (G.L.M.); (J.C.C.P.)
| | - Juan Carlos Campos Pinzón
- AGROSAVIA, Centro de Investigación La Libertad, Km.17 vía Pto. Lopez, Villavicencio, Meta, Colombia; (G.L.M.); (J.C.C.P.)
| | - Schyler O. Nunziata
- Plant Pathogen Confirmatory Diagnostics Laboratory, Science and Technology, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, USDA, Laurel, MD 20708, USA; (S.O.N.); (C.P.)
| | - Chellappan Padmanabhan
- Plant Pathogen Confirmatory Diagnostics Laboratory, Science and Technology, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, USDA, Laurel, MD 20708, USA; (S.O.N.); (C.P.)
| | - John Hammond
- Floral and Nursery Plants Research Unit, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA;
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5
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Lin Y, Pascall DJ. Characterisation of putative novel tick viruses and zoonotic risk prediction. Ecol Evol 2024; 14:e10814. [PMID: 38259958 PMCID: PMC10800298 DOI: 10.1002/ece3.10814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/02/2023] [Accepted: 11/24/2023] [Indexed: 01/24/2024] Open
Abstract
Tick-associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta-genomic and -transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta-genomic and -transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick-associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick-associated viruses using a genome composition-based machine learning model. We found five high-risk tick-associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick-associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick-associated diseases.
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Affiliation(s)
- Yuting Lin
- MRC Biostatistics UnitUniversity of CambridgeCambridgeUK
- Royal Veterinary CollegeUniversity of LondonLondonUK
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6
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Brait N, Hackl T, Morel C, Exbrayat A, Gutierrez S, Lequime S. A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data. Virus Evol 2023; 10:vead088. [PMID: 38516656 PMCID: PMC10956553 DOI: 10.1093/ve/vead088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/24/2023] [Accepted: 12/22/2023] [Indexed: 03/23/2024] Open
Abstract
Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs and exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs. Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key in enhancing our ability to capture the full spectrum of viral diversity.
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Affiliation(s)
- Nadja Brait
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen 9747 AG, The Netherlands
| | | | - Côme Morel
- ASTRE research unit, Cirad, INRAe, Université de Montpellier, Montpellier 34398, France
| | - Antoni Exbrayat
- ASTRE research unit, Cirad, INRAe, Université de Montpellier, Montpellier 34398, France
| | - Serafin Gutierrez
- ASTRE research unit, Cirad, INRAe, Université de Montpellier, Montpellier 34398, France
| | - Sebastian Lequime
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen 9747 AG, The Netherlands
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7
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Zhao R, Su X, Yu F, Liu Z, Huang X. Identification and characterization of two closely related virga-like viruses latently infecting rubber trees ( Hevea brasiliensis). Front Microbiol 2023; 14:1286369. [PMID: 38156006 PMCID: PMC10752949 DOI: 10.3389/fmicb.2023.1286369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
A novel virga-like virus, provisionally named Rubber tree latent virus 2 (RTLV2), was identified from rubber tree (Hevea brasiliensis). It is a close relative of the previously reported Rubber tree latent virus 1 (RTLV1). The complete genomes of RTLV1 and RTLV2 were sequenced and comparatively analyzed in terms of genome organization, putative gene products and phylogenetic relationship. Both RTLV1 and RTLV2 have positive-sense single-stranded RNA genomes that encode seven open reading frames (ORFs), forming a similar genomic layout. In phylogenetic analyses based on replicase and coat protein amino acid sequences, RTLV1 and RTLV2 were clustered with unclassified virga-like viruses. They are distinct from currently recognized plant virus families. RTLV1 and RTLV2 can be distinguished from members of Virgaviridae by the presence of a putative coat protein duplex and a poly(A) tail at the 3'-terminus. The authenticity of RTLV1 and RTLV2 as infectious viruses was confirmed through field investigations and transmissibility assays. In conclusion, RTLV1 and RTLV2 represent a novel plant virus group that does not readily fit into current virus families.
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Affiliation(s)
- Ruibai Zhao
- College of Tropical Crops, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- School of Life Sciences, Hainan University, Haikou, China
| | - Xiaoqi Su
- College of Tropical Crops, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Fengjuan Yu
- College of Tropical Crops, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Zhu Liu
- School of Life Sciences, Hainan University, Haikou, China
| | - Xi Huang
- College of Tropical Crops, Sanya Nanfan Research Institute of Hainan University, Sanya, China
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8
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Bejerman N, Dietzgen R, Debat H. Novel Tri-Segmented Rhabdoviruses: A Data Mining Expedition Unveils the Cryptic Diversity of Cytorhabdoviruses. Viruses 2023; 15:2402. [PMID: 38140643 PMCID: PMC10747219 DOI: 10.3390/v15122402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Cytorhabdoviruses (genus Cytorhabdovirus, family Rhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genus Cytorhabdovirus have unsegmented single-stranded negative-sense RNA genomes (ca. 10-16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 93 novel viruses with genetic and evolutionary cues of cytorhabdoviruses. Strikingly, five unprecedented viruses with tri-segmented genomes were also identified. This finding represents the first tri-segmented viruses in the family Rhabdoviridae, and they should be classified in a novel genus within this family for which we suggest the name "Trirhavirus". Interestingly, the nucleocapsid and polymerase were the only typical rhabdoviral proteins encoded by those tri-segmented viruses, whereas in three of them, a protein similar to the emaravirus (family Fimoviridae) silencing suppressor was found, while the other predicted proteins had no matches in any sequence databases. Genetic distance and evolutionary insights suggest that all these novel viruses may represent members of novel species. Phylogenetic analyses, of both novel and previously classified plant rhabdoviruses, provide compelling support for the division of the genus Cytorhabdovirus into three distinct genera. This proposed reclassification not only enhances our understanding of the evolutionary dynamics within this group of plant rhabdoviruses but also illuminates the remarkable genomic diversity they encompass. This study not only represents a significant expansion of the genomics of cytorhabdoviruses that will enable future research on the evolutionary peculiarity of this genus but also shows the plasticity in the rhabdovirus genome organization with the discovery of tri-segmented members with a unique evolutionary trajectory.
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Affiliation(s)
- Nicolas Bejerman
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
| | - Ralf Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Humberto Debat
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
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9
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Horemans M, Van Bets J, Joly Maes T, Maes P, Vanmechelen B. Discovery and genome characterization of six new orthoparamyxoviruses in small Belgian mammals. Virus Evol 2023; 9:vead065. [PMID: 38034864 PMCID: PMC10684267 DOI: 10.1093/ve/vead065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/24/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023] Open
Abstract
In the future, zoonotic spillover events are expected to occur more frequently. Consequences of such events have clearly been demonstrated by recent outbreaks of monkeypox, Ebola virus, and the well-known severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Virus discovery has proven to be an important tool in the preparation against viral outbreaks, generating data concerning the diversity, quantity, and ecology of the vertebrate virome. Orthoparamyxoviruses, a subfamily within the Paramyxoviridae, are important biosurveillance targets, since they include several known animal, human, and zoonotic pathogens such as Nipah virus, measles virus, and Hendra virus. During this study, 127 bat samples, thirty-four rodent samples, and seventeen shrew samples originating from Belgium were screened for orthoparamyxovirus presence using nested reverse transcription-polymerase chain reaction assays and nanopore sequencing. We present here the complete genomes of six putative new viral species, belonging to the genera Jeilongvirus and Henipavirus. Characterization of these genomes revealed significant differences in gene composition and organization, both within viruses of the same genus and between viruses of different genera. Remarkably, a previously undetected gene coding for a protein of unknown function was identified in the genome of a putative new Henipavirus. Additionally, phylogenetic analysis of jeilongviruses and henipaviruses reveals a division of both genera into two clades, one consisting of bat-borne viruses and the other consisting of rodent- and shrew-borne viruses, elucidating the need for proper reclassification.
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Affiliation(s)
| | - Jessica Van Bets
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, Leuven BE3000, Belgium
| | - Tibe Joly Maes
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, Leuven BE3000, Belgium
| | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, Leuven BE3000, Belgium
| | - Bert Vanmechelen
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Herestraat 49/Box 1040, Leuven BE3000, Belgium
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10
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Yang J, Lan PX, Wang Y, Li JM, Li R, Wylie S, Chen XJ, Yang GH, Cai H, Li F. Virome Analysis of Aconitum carmichaelii Reveals Infection by Eleven Viruses, including Two Potentially New Species. Int J Mol Sci 2023; 24:15558. [PMID: 37958540 PMCID: PMC10650655 DOI: 10.3390/ijms242115558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
Aconitum carmichaelii is a herbaceous herb indigenous to China that has been cultivated for traditional medicine for centuries. Virus-like symptoms of A. carmichaelii plants were observed on leaves in some A. carmichaelii plantations in Zhanyi and Wuding Counties, Yunnan Province, southwest China. High-throughput sequencing (HTS) was performed on 28 symptomatic plants, and the results revealed infection with 11 viruses, including 2 novel viruses and 9 previously described viruses: Aconitum amalgavirus 1 (AcoAV-1), aconite virus A (AcVA), cucumber mosaic virus (CMV), currant latent virus (CuLV), apple stem grooving virus (ASGV), chilli veinal mottle virus (ChiVMV), tomato spotted wilt orthotospovirus (TSWV), tobacco vein distorting virus (TVDV), and potato leafroll virus (PLRV). Two novel viruses tentatively named Aconitum potyvirus 1 and Aconitum betapartitivirus 1, were supported by sequence and phylogenetic analysis results of their genomes. We proposed the names Potyvirus aconiti and Betapartitivirus aconiti. RT-PCR assays of 142 plants revealed the predominance and widespread distribution of CMV, AcVA, and AcoPV-1 in plantations. The detection of isolates of CuLV, ASGV, ChiVMV, TSWV, TVDV, and PLRV infections for the first time in A. carmichaelii expands their known host ranges.
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Affiliation(s)
- Jie Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Ping-Xiu Lan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Yun Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Jin-Ming Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Ruhui Li
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD 20705, USA
| | - Steve Wylie
- Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150, Australia
| | - Xiao-Jiao Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Gen-Hua Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Hong Cai
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Fan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
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Harvey E, Mifsud JCO, Holmes EC, Mahar JE. Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids). Virus Evol 2023; 9:vead061. [PMID: 37941997 PMCID: PMC10630069 DOI: 10.1093/ve/vead061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under threat of extinction due to habitat loss, hunting, disease, and competition and predation by introduced species such as feral cats. We utilised publicly available RNA-seq data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to document the viral diversity within four Dasyuromorph species. Accordingly, we identified fifteen novel virus sequences from five DNA virus families (Adenoviridae, Anelloviridae, Gammaherpesvirinae, Papillomaviridae, and Polyomaviridae) and three RNA virus taxa: the order Jingchuvirales, the genus Hepacivirus, and the delta-like virus group. Of particular note was the identification of a marsupial-specific clade of delta-like viruses that may indicate an association of deltaviruses with marsupial species. In addition, we identified a highly divergent hepacivirus in a numbat liver transcriptome that falls outside of the larger mammalian clade. We also detect what may be the first Jingchuvirales virus in a mammalian host-a chu-like virus in Tasmanian devils-thereby expanding the host range beyond invertebrates and ectothermic vertebrates. As many of these Dasyuromorphia species are currently being used in translocation efforts to reseed populations across Australia, understanding their virome is of key importance to prevent the spread of viruses to naive populations.
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Affiliation(s)
- Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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12
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Hufsky F, Abecasis AB, Babaian A, Beck S, Brierley L, Dellicour S, Eggeling C, Elena SF, Gieraths U, Ha AD, Harvey W, Jones TC, Lamkiewicz K, Lovate GL, Lücking D, Machyna M, Nishimura L, Nocke MK, Renard BY, Sakaguchi S, Sakellaridi L, Spangenberg J, Tarradas-Alemany M, Triebel S, Vakulenko Y, Wijesekara RY, González-Candelas F, Krautwurst S, Pérez-Cataluña A, Randazzo W, Sánchez G, Marz M. The International Virus Bioinformatics Meeting 2023. Viruses 2023; 15:2031. [PMID: 37896809 PMCID: PMC10612056 DOI: 10.3390/v15102031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 10/29/2023] Open
Abstract
The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24-26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting.
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Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Ana B. Abecasis
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisboa, Portugal
| | - Artem Babaian
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
- Donnelly Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Sebastian Beck
- Leibniz Institute of Virology, Department Viral Zoonoses—One Health, 20251 Hamburg, Germany;
| | - Liam Brierley
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Health Data Science, University of Liverpool, Liverpool L69 3GF, UK
| | - Simon Dellicour
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, 1050 Bruxelles, Belgium
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, University of Leuven, 3000 Leuven, Belgium
| | - Christian Eggeling
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Max-Wien-Platz 1, 07743 Jena, Germany
| | - Santiago F. Elena
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Valencia, Catedratico Agustin Escardino 9, 46980 Valencia, Spain
| | - Udo Gieraths
- Institute of Virology, Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Anh D. Ha
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Will Harvey
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Terry C. Jones
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute of Virology, Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Kevin Lamkiewicz
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Gabriel L. Lovate
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Dominik Lücking
- Max-Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Martin Machyna
- Paul-Ehrlich-Institut, Host-Pathogen-Interactions, 63225 Langen, Germany
| | - Luca Nishimura
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Maximilian K. Nocke
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department for Molecular & Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Bernard Y. Renard
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Digital Engineering Faculty, Hasso Plattner Institute, University of Potsdam, 14482 Potsdam, Germany
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka 569-8686, Japan;
| | - Lygeri Sakellaridi
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078 Würzburg, Germany
| | - Jannes Spangenberg
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Maria Tarradas-Alemany
- Computational Genomics Lab., Department of Genetics, Microbiology and Statistics, Institut de Biomedicina UB (IBUB), Universitat de Barcelona (UB), 08028 Barcelona, Spain
| | - Sandra Triebel
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Yulia Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Rajitha Yasas Wijesekara
- Institute for Bioinformatics, University of Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Fernando González-Candelas
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Valencia, Catedratico Agustin Escardino 9, 46980 Valencia, Spain
- Joint Research Unit “Infection and Public Health” FISABIO, University of Valencia, 46010 Valencia, Spain
| | - Sarah Krautwurst
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Alba Pérez-Cataluña
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Walter Randazzo
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Gloria Sánchez
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany (A.B.A.); (L.B.); (S.D.); (C.E.); (S.F.E.); (T.C.J.); (K.L.); (G.L.L.); (M.K.N.); (B.Y.R.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Michael Stifel Center Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07745 Jena, Germany
- Leibniz Institute for Age Research—Fritz Lippman Institute, 07745 Jena, Germany
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Alvarez-Quinto R, Amao M, Muller G, Fuentes S, Grinstead S, Fuentes-Bueno I, Roenhorst A, Westenberg M, Botermans M, Kreuze J, Mollov D. Evidence that an Unnamed Isometric Virus Associated with Potato Rugose Disease in Peru Is a New Species of Genus Torradovirus. Phytopathology 2023; 113:1716-1728. [PMID: 37486151 DOI: 10.1094/phyto-11-22-0449-v] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
A previously uncharacterized torradovirus species infecting potatoes was detected by high-throughput sequencing from field samples from Peru and in customs intercepts in potato tubers that originated from South America in the United States of America and the Netherlands. This new potato torradovirus showed high nucleotide sequence identity to an unidentified isometric virus (SB26/29), which was associated with a disease named potato rugose stunting in southern Peru characterized over two decades ago. Thus, this virus is tentatively named potato rugose stunting virus (PotRSV). The genome of PotRSV isolates sequenced in this study were composed of two polyadenylated RNA segments. RNA1 ranges from 7,086 to 7,089 nt and RNA2 from 5,228 to 5,230 nt. RNA1 encodes a polyprotein containing the replication block (helicase-protease-polymerase), whereas RNA2 encodes a polyprotein cleaved into a movement protein and the three capsid proteins (CPs). Pairwise comparison among PotRSV isolates revealed amino acid identity values greater than 86% in the protease-polymerase (Pro-Pol) region and greater than 82% for the combined CPs. The closest torradovirus species, squash chlorotic leaf spot virus, shares amino acid identities of ∼58 and ∼41% in the Pro-Pol and the combined CPs, respectively. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Robert Alvarez-Quinto
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, U.S.A
| | - Melody Amao
- Crop and System Sciences Division, International Potato Center, La Molina, Lima 15023, Peru
| | - Giovanna Muller
- Crop and System Sciences Division, International Potato Center, La Molina, Lima 15023, Peru
| | - Segundo Fuentes
- Crop and System Sciences Division, International Potato Center, La Molina, Lima 15023, Peru
| | - Samuel Grinstead
- U.S. Department of Agriculture-Agricultural Research Service, National Germplasm Resources Laboratory, Beltsville, MD 20705, U.S.A
| | - Irazema Fuentes-Bueno
- U.S. Department of Agriculture-Agricultural Research Service, National Germplasm Resources Laboratory, Beltsville, MD 20705, U.S.A
| | - Annelien Roenhorst
- Netherlands Institute for Vectors, Invasive Plants and Plant Health (NIVIP), National Plant Protection Organization, Geertjesweg 15, 6706EA Wageningen, The Netherlands
| | - Marcel Westenberg
- Netherlands Institute for Vectors, Invasive Plants and Plant Health (NIVIP), National Plant Protection Organization, Geertjesweg 15, 6706EA Wageningen, The Netherlands
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive Plants and Plant Health (NIVIP), National Plant Protection Organization, Geertjesweg 15, 6706EA Wageningen, The Netherlands
| | - Jan Kreuze
- Crop and System Sciences Division, International Potato Center, La Molina, Lima 15023, Peru
| | - Dimitre Mollov
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330, U.S.A
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Mohamed Ali S, Rakotonirina A, Heng K, Jacquemet E, Volant S, Temmam S, Boyer S, Eloit M. Longitudinal Study of Viral Diversity Associated with Mosquito Species Circulating in Cambodia. Viruses 2023; 15:1831. [PMID: 37766237 PMCID: PMC10535147 DOI: 10.3390/v15091831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Arthropod-borne viruses (arboviruses) pose a significant global health threat and are primarily transmitted by mosquitoes. In Cambodia, there are currently 290 recorded mosquito species, with at least 17 of them considered potential vectors of arboviruses to humans. Effective surveillance of virome profiles in mosquitoes from Cambodia is vital, as it could help prevent and control arbovirus diseases in a country where epidemics occur frequently. The objective of this study was to identify and characterize the viral diversity in mosquitoes collected during a one-year longitudinal study conducted in various habitats across Cambodia. For this purpose, we used a metatranscriptomics approach and detected the presence of chikungunya virus in the collected mosquitoes. Additionally, we identified viruses categorized into 26 taxa, including those known to harbor arboviruses such as Flaviviridae and Orthomyxoviridae, along with a group of viruses not yet taxonomically identified and provisionally named "unclassified viruses". Interestingly, the taxa detected varied in abundance and composition depending on the mosquito genus, with no significant influence of the collection season. Furthermore, most of the identified viruses were either closely related to viruses found exclusively in insects or represented new viruses belonging to the Rhabdoviridae and Birnaviridae families. The transmission capabilities of these novel viruses to vertebrates remain unknown.
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Affiliation(s)
- Souand Mohamed Ali
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (S.M.A.); (S.T.)
| | - Antsa Rakotonirina
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh 12201, Cambodia; (A.R.); (S.B.)
| | - Kimly Heng
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh 12201, Cambodia; (A.R.); (S.B.)
| | - Elise Jacquemet
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, 75015 Paris, France (S.V.)
| | - Stevenn Volant
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, 75015 Paris, France (S.V.)
| | - Sarah Temmam
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (S.M.A.); (S.T.)
| | - Sebastien Boyer
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh 12201, Cambodia; (A.R.); (S.B.)
- Ecology and Emergence of Arthropod-Borne Diseases, Institut Pasteur, 75015 Paris, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (S.M.A.); (S.T.)
- Ecole Nationale Vétérinaire d’Alfort, University of Paris-Est, 94704 Maisons-Alfort, France
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Zhang P, Zhang Y, Cao L, Li J, Wu C, Tian M, Zhang Z, Zhang C, Zhang W, Li Y. A Diverse Virome Is Identified in Parasitic Flatworms of Domestic Animals in Xinjiang, China. Microbiol Spectr 2023; 11:e0070223. [PMID: 37042768 PMCID: PMC10269781 DOI: 10.1128/spectrum.00702-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/17/2023] [Indexed: 04/13/2023] Open
Abstract
Parasitic flatworms infect diverse vertebrates and are major threats to animal and even human health; however, little is known about the virome of these lower life forms. Using viral metagenomic sequencing, we characterized the virome of the parasitic flatworms collected from major domestic animals, including Dicrocoelium lanceatum and Taenia hydatigena, Echinococcus granulosus sensu stricto and Echinococcus multilocularis. Seven and three different viruses were discovered from D. lanceatum and T. hydatigena, respectively, and no viral sequences were found in adult tapeworms and protoscoleces of E. granulosus sensu stricto and E. multilocularis. Two out of the five parasitic flatworm species carry viruses, showing a host specificity of these viruses. These viruses belong to the Parvoviridae, Circoviridae, unclassified circular, Rep-encoding single-stranded (CRESS) DNA virus, Rhabdoviridae, Endornaviridae, and unclassified RNA viruses. The presence of multiple highly divergent RNA viruses, especially those that cluster with viruses found in marine animals, implies a deep evolutionary history of parasite-associated viruses. In addition, we found viruses with high identity to common pathogens in dogs, including canine circovirus and canine parvovirus 2. The presence of these viruses in the parasites implies that they may infect parasitic flatworms but does not completely exclude the possibility of contamination from host intestinal contents. Furthermore, we demonstrated that certain viruses, such as CRESS DNA virus may integrate into the genome of their host. Our results expand the knowledge of viral diversity in parasites of important domestic animals, highlighting the need for further investigations of their prevalence among other parasites of key animals. IMPORTANCE Characterizing the virome of parasites is important for unveiling the viral diversity, evolution, and ecology and will help to understand the "Russian doll" pattern among viruses, parasites, and host animals. Our data indicate that diverse viruses are present in specific parasitic flatworms, including viruses that may have an ancient evolutionary history and viruses currently circulating in parasite-infected host animals. These data also raise the question of whether parasitic flatworms acquire and/or carry some viruses that may have transmission potential to animals. In addition, through the study of virus-parasite-host interactions, including the influence of viral infection on the life cycle of the parasite, as well as its fitness and pathogenicity to the host, we could find new strategies to prevent and control parasitic diseases.
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Affiliation(s)
- Peng Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Le Cao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun Li
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Chuanchuan Wu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Mengxiao Tian
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Zhuangzhi Zhang
- Veterinary Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Wenbao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
- Veterinary Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Yanpeng Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Eckstrand CD, Torrevillas BK, Wolking RM, Bradway DS, Warg JV, Clayton RD, Williams LB, Pessier AP, Reno JL, McMenamin-Snekvik KM, Thompson J, Baszler T, Snekvik KR. Investigation of laboratory methods for characterization of aquatic viruses in fish infected experimentally with infectious salmon anemia virus. J Vet Diagn Invest 2023:10406387231173332. [PMID: 37203453 DOI: 10.1177/10406387231173332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
Rapid growth in aquaculture has resulted in high-density production systems in ecologically and geographically novel conditions in which the emergence of diseases is inevitable. Well-characterized methods for detection and surveillance of infectious diseases are vital for rapid identification, response, and recovery to protect economic and food security. We implemented a proof-of-concept approach for virus detection using a known high-consequence fish pathogen, infectious salmon anemia virus (ISAV), as the archetypal pathogen. In fish infected with ISAV, we integrated histopathology, virus isolation, whole-genome sequencing (WGS), electron microscopy (EM), in situ hybridization (ISH), and reverse transcription real-time PCR (RT-rtPCR). Fresh-frozen and formalin-fixed tissues were collected from virus-infected, control, and sham-infected Atlantic salmon (Salmo salar). Microscopic differences were not evident between uninfected and infected fish. Viral cytopathic effect was observed in cell cultures inoculated with fresh-frozen tissue homogenates from 3 of 3 ISAV-infected and 0 of 4 uninfected or sham-infected fish. The ISAV genome was detected by shotgun metagenomics in RNA extracted from the medium from 3 of 3 inoculated cell cultures, 3 of 3 infected fish, and 0 of 4 uninfected or sham-infected fish, yielding sufficient coverage for de novo assembly. An ISH probe against ISAV revealed ISAV genome in multiple organs, with abundance in renal hematopoietic tissue. Virus was detected by RT-rtPCR in gill, heart, kidney, liver, and spleen. EM and metagenomic WGS from tissues were challenging and unsuccessful. Our proof-of-concept methodology has promise for detection and characterization of unknown aquatic pathogens and also highlights some associated methodology challenges that require additional investigation.
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Affiliation(s)
- Chrissy D Eckstrand
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA
| | - Brandi K Torrevillas
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA
| | - Rebecca M Wolking
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA
| | - Daniel S Bradway
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA
| | - Janet V Warg
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Ames, IA, USA
| | - Richard D Clayton
- National Veterinary Services Laboratories, U.S. Department of Agriculture, Ames, IA, USA
| | - Laura B Williams
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA
| | - Allan P Pessier
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA
| | - Joetta Lynn Reno
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA
| | | | - Jim Thompson
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA
| | - Timothy Baszler
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA
| | - Kevin R Snekvik
- Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA, USA
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18
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Chong LC, Lauber C. Viroid-like RNA-dependent RNA polymerase-encoding ambiviruses are abundant in complex fungi. Front Microbiol 2023; 14:1144003. [PMID: 37275138 PMCID: PMC10237039 DOI: 10.3389/fmicb.2023.1144003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/24/2023] [Indexed: 06/07/2023] Open
Abstract
Ambiviruses are hybrid infectious elements encoding the hallmark gene of RNA viruses, the RNA-dependent RNA polymerase, and self-cleaving RNA ribozymes found in many viroids. Ambiviruses are thought to be pathogens of fungi, although the majority of reported genomes have been identified in metatranscriptomes. Here, we present a comprehensive screen for ambiviruses in more than 46,500 fungal transcriptomes from the Sequence Read Archive (SRA). Our data-driven virus discovery approach identified more than 2,500 ambiviral sequences across the kingdom Fungi with a striking expansion in members of the phylum Basidiomycota representing the most complex fungal organisms. Our study unveils a large diversity of unknown ambiviruses with as little as 27% protein sequence identity to known members and sheds new light on the evolution of this distinct class of infectious agents with RNA genomes. No evidence for the presence of ambiviruses in human microbiomes was obtained from a comprehensive screen of respective metatranscriptomes available in the SRA.
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19
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Roberts AJ, Suttle CA. Pathogens and Passengers: Roles for Crustacean Zooplankton Viruses in the Global Ocean. Microorganisms 2023; 11:microorganisms11041054. [PMID: 37110477 PMCID: PMC10142142 DOI: 10.3390/microorganisms11041054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Viruses infect all living organisms, but the viruses of most marine animals are largely unknown. Crustacean zooplankton are a functional lynchpin in marine food webs, but very few have been interrogated for their associated viruses despite the profound potential effects of viral infection. Nonetheless, it is clear that the diversity of viruses in crustacean zooplankton is enormous, including members of all realms of RNA viruses, as well as single- and double-stranded DNA viruses, in many cases representing deep branches of viral evolution. As there is clear evidence that many of these viruses infect and replicate in zooplankton species, we posit that viral infection is likely responsible for a significant portion of unexplained non-consumptive mortality in this group. In turn, this infection affects food webs and alters biogeochemical cycling. In addition to the direct impacts of infection, zooplankton can vector economically devastating viruses of finfish and other crustaceans. The dissemination of these viruses is facilitated by the movement of zooplankton vertically between epi- and mesopelagic communities through seasonal and diel vertical migration (DVM) and across long distances in ship ballast water. The large potential impact of viruses on crustacean zooplankton emphasises the need to clearly establish the relationships between specific viruses and the zooplankton they infect and investigate disease and mortality for these host-virus pairs. Such data will enable investigations into a link between viral infection and seasonal dynamics of host populations. We are only beginning to uncover the diversity and function of viruses associated with crustacean zooplankton.
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Affiliation(s)
- Alastair J Roberts
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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20
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Laiton-Donato K, Guzmán C, Perdomo-Balaguera E, Sarmiento L, Torres-Fernandez O, Ruiz HA, Rosales-Munar A, Peláez-Carvajal D, Navas MC, Wong MC, Junglen S, Ajami NJ, Parra-Henao G, Usme-Ciro JA. Novel Putative Tymoviridae-like Virus Isolated from Culex Mosquitoes in Colombia. Viruses 2023; 15:v15040953. [PMID: 37112933 PMCID: PMC10143313 DOI: 10.3390/v15040953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
The family Tymoviridae comprises positive-sense RNA viruses, which mainly infect plants. Recently, a few Tymoviridae-like viruses have been found in mosquitoes, which feed on vertebrate sources. We describe a novel Tymoviridae-like virus, putatively named, Guachaca virus (GUAV), isolated from Culex pipiens and Culex quinquefasciatus species of mosquitoes and collected in the rural area of Santa Marta, Colombia. After a cytopathic effect was observed in C6/36 cells, RNA was extracted and processed through the NetoVIR next-generation sequencing protocol, and data were analyzed through the VirMAP pipeline. Molecular and phenotypic characterization of the GUAV was achieved using a 5'/3' RACE, transmission electron microscopy, amplification in vertebrate cells, and phylogenetic analysis. A cytopathic effect was observed in C6/36 cells three days post-infection. The GUAV genome was successfully assembled, and its polyadenylated 3' end was corroborated. GUAV shared only 54.9% amino acid identity with its closest relative, Ek Balam virus, and was grouped with the latter and other unclassified insect-associated tymoviruses in a phylogenetic analysis. GUAV is a new member of a family previously described as comprising plant-infecting viruses, which seem to infect and replicate in mosquitoes. The sugar- and blood-feeding behavior of the Culex spp., implies a sustained contact with plants and vertebrates and justifies further studies to unravel the ecological scenario for transmission.
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Affiliation(s)
- Katherine Laiton-Donato
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
- Grupo Genómica de Microorganismos Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Camila Guzmán
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Erik Perdomo-Balaguera
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia
- Secretaría de Salud Distrital, Programa de Enfermedades Transmitidas por Vectores, Santa Marta 470004, Colombia
| | - Ladys Sarmiento
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Orlando Torres-Fernandez
- Grupo de Morfología Celular, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Héctor Alejandro Ruiz
- Grupo Genómica de Microorganismos Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Alicia Rosales-Munar
- Grupo Genómica de Microorganismos Emergentes, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Dioselina Peláez-Carvajal
- Grupo de Virología, Dirección de Redes en Salud Pública, Instituto Nacional de Salud, Bogota 111321, Colombia
| | - Maria-Cristina Navas
- Grupo de Gastrohepatología, Facultad de Medicina, Universidad de Antioquia, Medellin 050010, Colombia
| | - Matthew C Wong
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Viroworks, Houston, TX 77030, USA
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Nadim J Ajami
- Platform for Innovative Microbiome and Translational Research (PRIME-TR), Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Viroworks, Houston, TX 77030, USA
| | - Gabriel Parra-Henao
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia
| | - José A Usme-Ciro
- CIST-Centro de Investigación en Salud para el Trópico, Facultad de Medicina, Universidad Cooperativa de Colombia, Santa Marta 470003, Colombia
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21
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Orf GS, Perez LJ, Meyer TV, Luk KC, Forberg K, Rodgers MA, Hadji A, James L, Mampunza S, Achari A, Yu G, Federman S, Chiu CY, McArthur CA, Cloherty GA, Berg MG. Purifying selection decreases the potential for Bangui orthobunyavirus outbreaks in humans. Virus Evol 2023; 9:vead018. [PMID: 37025159 PMCID: PMC10072187 DOI: 10.1093/ve/vead018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/28/2023] [Accepted: 03/07/2023] [Indexed: 04/07/2023] Open
Abstract
Pathogens carried by insects, such as bunyaviruses, are frequently transmitted into human populations and cause diseases. Knowing which spillover events represent a public health threat remains a challenge. Metagenomic next-generation sequencing (mNGS) can support infectious disease diagnostics by enabling the detection of any pathogen from clinical specimens. mNGS was performed on blood samples to identify potential viral coinfections in human immunodeficiency virus (HIV)-positive individuals from Kinshasa, the Democratic Republic of the Congo (DRC), participating in an HIV diversity cohort study. Time-resolved phylogenetics and molecular assay development assisted in viral characterization. The nearly complete genome of a novel orthobunyavirus related to Nyangole virus, a virus previously identified in neighboring Uganda, was assembled from a hepatitis B virus–positive patient. A quantitative polymerase chain reaction assay was designed and used to screen >2,500 plasma samples from Cameroon, the DRC, and Uganda, failing to identify any additional cases. The recent sequencing of a US Center for Disease Control Arbovirus Reference Collection revealed that this same virus, now named Bangui virus, was first isolated in 1970 from an individual in the Central African Republic. Time-scaled phylogenetic analyses of Bangui with the related Anopheles and Tanga serogroup complexes indicate that this virus emerged nearly 10,000 years ago. Pervasive and episodic models further suggest that this virus is under purifying selection and that only distant common ancestors were subject to positive selection events. This study represents only the second identification of a Bangui virus infection in over 50 years. The presumed rarity of Bangui virus infections in humans can be explained by its constraint to an avian host and insect vector, precluding efficient transmission into the human population. Our results demonstrate that molecular phylogenetic analyses can provide insights into the threat posed by novel or re-emergent viruses identified by mNGS.
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Affiliation(s)
| | | | - Todd V Meyer
- Abbott Laboratories and Abbott Pandemic Defense Coalition, Abbott Park, IL 60064, USA
| | - Ka-Cheung Luk
- Abbott Laboratories and Abbott Pandemic Defense Coalition, Abbott Park, IL 60064, USA
| | - Kenn Forberg
- Abbott Laboratories and Abbott Pandemic Defense Coalition, Abbott Park, IL 60064, USA
| | - Mary A Rodgers
- Abbott Laboratories and Abbott Pandemic Defense Coalition, Abbott Park, IL 60064, USA
| | - Abbas Hadji
- Abbott Laboratories and Abbott Pandemic Defense Coalition, Abbott Park, IL 60064, USA
| | - Linda James
- Université Protestante au Congo, Kinshasa, Democratic Republic of the Congo
| | - Samuel Mampunza
- Université Protestante au Congo, Kinshasa, Democratic Republic of the Congo
| | - Asmeeta Achari
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Guixia Yu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Gavin A Cloherty
- Abbott Laboratories and Abbott Pandemic Defense Coalition, Abbott Park, IL 60064, USA
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22
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Perinet LC, Mutebi JP, Powers AM, Lutwama JJ, Mossel EC. Yata Virus (Family Rhabdoviridae, Genus Ephemerovirus) Isolation from Mosquitoes from Uganda, the First Reported Isolation since 1969. Diseases 2023; 11:diseases11010021. [PMID: 36810535 PMCID: PMC9944095 DOI: 10.3390/diseases11010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
As a part of a systematic study of mosquitoes and associated viruses in Uganda, a virus was isolated from a pool of Mansonia uniformis collected in July 2017, in the Kitgum District of northern Uganda. Sequence analysis determined that the virus is Yata virus (YATAV; Ephemerovirus yata; family Rhabdoviridae). The only previous reported isolation of YATAV was in 1969 in Birao, Central African Republic, also from Ma. uniformis mosquitoes. The current sequence is over 99% identical at the nucleotide level to the original isolate, indicating a high level of YATAV genomic stability.
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Affiliation(s)
- Lara C. Perinet
- Division of Vector-Borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - John-Paul Mutebi
- Division of Vector-Borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Ann M. Powers
- Division of Vector-Borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging, and Re-emerging Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Eric C. Mossel
- Division of Vector-Borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
- Correspondence:
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23
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Costa VA, Bellwood DR, Mifsud JCO, Van Brussel K, Geoghegan JL, Holmes EC, Harvey E. Limited cross-species virus transmission in a spatially restricted coral reef fish community. Virus Evol 2023; 9:vead011. [PMID: 36910859 PMCID: PMC9994595 DOI: 10.1093/ve/vead011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/18/2023] [Accepted: 02/01/2023] [Indexed: 02/04/2023] Open
Abstract
The Great Barrier Reef (GBR)-the largest coral reef ecosystem in the world-supports over 1,200 fish species with some of the highest population densities and diversities observed in vertebrates, offering a high potential for virus transmission among species. As such, the GBR represents an exceptional natural ecosystem to determine the impact of host community diversity on virus evolution and emergence. In recent decades, the GBR has also experienced significant threats of extinction, making it one of the most vulnerable ecosystems on the planet. Despite the global importance of the GBR, our understanding of virus diversity and connectivity in tropical reef fishes remains poor. Here, we employed metatranscriptomic sequencing to reveal the viromes of sixty-one reef fish species. This identified transcripts representing 132 putative viral sequences, 38 of which exhibited strong phylogenetic relationships with known vertebrate-associated viral genera, including a novel Santee-Cooper ranavirus (Iridoviridae). We found little evidence for virus transmission between fish species living within a very restricted geographical space-a 100-m2 coral reef ecosystem-suggesting that there might be important host barriers to successful cross-species transmission despite regular exposure. We also identified differences in virome composition among reef fish families, such that cryptobenthic reef fishes-characterized by small body sizes and short life spans-exhibited greater virome richness compared to large reef fishes. This study suggests that there are important barriers to cross-species virus transmission and that successful emergence in a reef fish community likely requires active host adaptation, even among closely related host species.
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Affiliation(s)
- Vincenzo A Costa
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - David R Bellwood
- Research Hub for Coral Reef Ecosystem Functions, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Kate Van Brussel
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand.,Institute of Environmental Science and Research, Wellington 5022, New Zealand
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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24
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Edridge AWD, van den Brekel N, Mukungu P, Nakayima R, Bbosa S, Isagara P, van Boele Hensbroek M, van der Hoek L, Kayiwa J, Lutwama JJ, Idro R. No Evidence of Ntwetwe Virus Infections in Children Presenting to Kiboga Hospital, Uganda. Trop Med Infect Dis 2022; 8:21. [PMID: 36668928 DOI: 10.3390/tropicalmed8010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/27/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
We investigated whether Ntwetwe virus-a novel orthobunyavirus discovered in a Ugandan girl with a fatal encephalopathy-was a common reason for hospital admission for children to Kiboga hospital, Uganda. A case-control was conducted between September 2019 and September 2020, including cases with severe neurological disease and mild febrile illness, matched to a healthy control without fever. Among 143 subjects, no cases with an acute infection were identified. This result suggests that Ntwetwe virus does not cause a major burden of disease amongst children presenting to Kiboga hospital during the study period.
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Mifsud JCO, Costa VA, Petrone ME, Marzinelli EM, Holmes EC, Harvey E. Transcriptome mining extends the host range of the Flaviviridae to non-bilaterians. Virus Evol 2022; 9:veac124. [PMID: 36694816 PMCID: PMC9854234 DOI: 10.1093/ve/veac124] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 12/27/2022] Open
Abstract
The flavivirids (family Flaviviridae) are a group of positive-sense RNA viruses that include well-documented agents of human disease. Despite their importance and ubiquity, the timescale of flavivirid evolution is uncertain. An ancient origin, spanning millions of years, is supported by their presence in both vertebrates and invertebrates and by the identification of a flavivirus-derived endogenous viral element in the peach blossom jellyfish genome (Craspedacusta sowerbii, phylum Cnidaria), implying that the flaviviruses arose early in the evolution of the Metazoa. To date, however, no exogenous flavivirid sequences have been identified in these hosts. To help resolve the antiquity of the Flaviviridae, we mined publicly available transcriptome data across the Metazoa. From this, we expanded the diversity within the family through the identification of 32 novel viral sequences and extended the host range of the pestiviruses to include amphibians, reptiles, and ray-finned fish. Through co-phylogenetic analysis we found cross-species transmission to be the predominate macroevolutionary event across the non-vectored flavivirid genera (median, 68 per cent), including a cross-species transmission event between bats and rodents, although long-term virus-host co-divergence was still a regular occurrence (median, 23 per cent). Notably, we discovered flavivirus-like sequences in basal metazoan species, including the first associated with Cnidaria. This sequence formed a basal lineage to the genus Flavivirus and was closer to arthropod and crustacean flaviviruses than those in the tamanavirus group, which includes a variety of invertebrate and vertebrate viruses. Combined, these data attest to an ancient origin of the flaviviruses, likely close to the emergence of the metazoans 750-800 million years ago.
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Affiliation(s)
| | - Vincenzo A Costa
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney NSW 2006, Australia
| | - Mary E Petrone
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney NSW 2006, Australia
| | - Ezequiel M Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney NSW 2006, Australia,Sydney Institute of Marine Science, 19 Chowder Bay Rd, Mosman, NSW 2088, Australia,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551 Singapore
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Canuti M, Rodrigues B, Lang AS, Dufour SC, Verhoeven JTP. Novel Divergent Members of the Kitrinoviricota Discovered through Metagenomics in the Intestinal Contents of Red-Backed Voles (Clethrionomys gapperi). Int J Mol Sci 2022; 24. [PMID: 36613573 DOI: 10.3390/ijms24010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/10/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Metagenomic methods are powerful tools to investigate viral diversity in biological or environmental samples and to identify previously unknown viruses. We used RNA metagenomics to identify, in the gut of red-backed voles, the nearly complete genomes of two novel members of the Kitrinoviricota, a phylum including viruses with positive-sense ssRNA genomes encoding an RNA-directed RNA polymerase. The genome of a novel member of the Tombusviridae presented four open reading frames (ORFs); a -1 frameshift is potentially involved in generating the viral replicase. This sequence was part of a phylogenetic clade that did not include any officially classified species. The second genome presented a large ORF coding for a viral polyprotein containing the typical protein domains common to flexiviruses. The sequence clustered with currently known members of the Deltaflexiviridae. Both viruses appear to represent the first members of novel species in yet undefined genera. The identified viruses likely originated from the vole diet as members of the two viral families are known to infect plants and fungi, respectively. Investigating public databases demonstrated that a much higher richness than currently recognized exists for these two viral families, highlighting the need to update taxonomy systems and possibly also include genomes identified through metagenomics.
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Mifsud JCO, Gallagher RV, Holmes EC, Geoghegan JL. Transcriptome Mining Expands Knowledge of RNA Viruses across the Plant Kingdom. J Virol 2022; 96:e0026022. [PMID: 35638822 DOI: 10.1128/jvi.00260-22] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Our current understanding of plant viruses stems largely from those affecting economically important plants. Yet plant species in cultivation represent a small and biased subset of the plant kingdom. Here, we describe virus diversity and abundance in 1,079 transcriptomes from species across the breadth of the plant kingdom (Archaeplastida) by analyzing open-source data from the 1000 Plant Transcriptomes Initiative (1KP). We identified 104 potentially novel viruses, of which 40% were single-stranded positive-sense RNA viruses across eight orders, including members of the Hepelivirales, Tymovirales, Cryppavirales, Martellivirales, and Picornavirales. One-third of the newly described viruses were double-stranded RNA viruses from the orders Durnavirales and Ghabrivirales. The remaining were negative-sense RNA viruses from the Rhabdoviridae, Aspiviridae, Yueviridae, and Phenuiviridae and the newly proposed Viridisbunyaviridae. Our analysis considerably expands the known host range of 13 virus families to include lower plants (e.g., Benyviridae and Secoviridae) and 4 virus families to include alga hosts (e.g., Tymoviridae and Chrysoviridae). More broadly, however, a cophylogeny analysis revealed that the evolutionary history of these families is largely driven by cross-species transmission events. The discovery of the first 30-kDa movement protein in a nonvascular plant suggests that the acquisition of plant virus movement proteins occurred prior to the emergence of the plant vascular system. Together, these data highlight that numerous RNA virus families are associated with older evolutionary plant lineages than previously thought and that the apparent scarcity of RNA viruses found in lower plants likely reflects a lack of investigation rather than their absence. IMPORTANCE Our knowledge of plant viruses is mainly limited to those infecting economically important host species. In particular, we know little about those viruses infecting basal plant lineages such as the ferns, lycophytes, bryophytes, and charophytes. To expand this understanding, we conducted a broad-scale viral survey of species across the breadth of the plant kingdom. We found that basal plants harbor a wide diversity of RNA viruses, including some that are sufficiently divergent to likely compose a new virus family. The basal plant virome revealed offers key insights into the evolutionary history of core plant virus gene modules and genome segments. More broadly, this work emphasizes that the scarcity of viruses found in these species to date most likely reflects the limited research in this area.
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Abstract
The transmission of viruses between different host species is a major source of emerging diseases and is of particular concern in the case of zoonotic transmission from mammals to humans. Several zoonosis risk factors have been identified, but it is currently unclear which viral traits primarily determine this process as previous work has focused on a few hundred viruses that are not representative of actual viral diversity. Here, we investigate fundamental virological traits that influence cross-species transmissibility and zoonotic propensity by interrogating a database of over 12,000 mammalian virus-host associations. Our analysis reveals that enveloped viruses tend to infect more host species and are more likely to be zoonotic than nonenveloped viruses, while other viral traits such as genome composition, structure, size, or the viral replication compartment play a less obvious role. This contrasts with the previous notion that viral envelopes did not significantly impact or even reduce zoonotic risk and should help better prioritize outbreak prevention efforts. We suggest several mechanisms by which viral envelopes could promote cross-species transmissibility, including structural flexibility of receptor-binding proteins and evasion of viral entry barriers.
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Debat HJ. A South American Mouse Morbillivirus Provides Insight into a Clade of Rodent-Borne Morbilliviruses. Viruses 2022; 14:v14112403. [PMID: 36366501 PMCID: PMC9697977 DOI: 10.3390/v14112403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 01/31/2023] Open
Abstract
Morbilliviruses are negative-sense single-stranded monosegmented RNA viruses in the family Paramyxoviridae (order Mononegavirales). Morbilliviruses infect diverse mammals including humans, dogs, cats, small ruminants, seals, and cetaceans, which serve as natural hosts. Here, I report the identification and characterization of novel viruses detected in public RNAseq datasets of South American long-haired and olive field mice. The divergent viruses dubbed Ratón oliváceo morbillivirus (RoMV) detected in renal samples from mice collected from Chile and Argentina are characterized by an unusually large genome including long intergenic regions and the presence of an accessory protein between the F and H genes redounding in a genome architecture consisting in 3'-N-P/V/C-M-F-hp-H-L-5'. Structural and functional annotation, genetic distance, and evolutionary insights suggest that RoMV is a member of a novel species within genus Morbillivirus tentatively named as South American mouse morbillivirus. Phylogenetic analysis suggests that this mouse morbillivirus is closely related to and clusters into a monophyletic group of novel rodent-borne morbilliviruses. This subclade of divergent viruses expands the host range, redefines the genomic organization and provides insights on the evolutionary history of genus Morbillivirus.
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Affiliation(s)
- Humberto J. Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba X5020ICA, Argentina; ; Tel./Fax: +54-9-351-4973636
- Unidad de Fitopatología y Modelización Agrícola (UFYMA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5020ICA, Argentina
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Kinsella CM, Deijs M, Gittelbauer HM, van der Hoek L, van Dijk K. Human Clinical Isolates of Pathogenic Fungi Are Host to Diverse Mycoviruses. Microbiol Spectr 2022; 10:e0161022. [PMID: 35993766 PMCID: PMC9603141 DOI: 10.1128/spectrum.01610-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/08/2022] [Indexed: 12/31/2022] Open
Abstract
Fungi host viruses from many families, and next-generation sequencing can be used to discover previously unknown genomes. Some fungus-infecting viruses (mycoviruses) confer hypovirulence on their pathogenic hosts, raising the possibility of therapeutic application in the treatment of fungal diseases. Though all fungi probably host mycoviruses, many human pathogens have none documented, implying the mycoviral catalogue remains at an early stage. Here, we carried out virus discovery on 61 cultures of pathogenic fungi covering 27 genera and at least 56 species. Using next-generation sequencing of total nucleic acids, we found no DNA viruses but did find a surprising RNA virus diversity of 11 genomes from six classified families and two unclassified lineages, including eight genomes likely representing new species. Among these was the first jivivirus detected in a fungal host (Aspergillus lentulus). We separately utilized rolling circle amplification and next-generation sequencing to identify ssDNA viruses specifically. We identified 13 new cressdnaviruses across all libraries, but unlike the RNA viruses, they could not be confirmed by PCR in either the original unamplified samples or freshly amplified nucleic acids. Their distributions among sequencing libraries and inconsistent detection suggest low-level contamination of reagents. This highlights both the importance of validation assays and the risks of viral host prediction on the basis of highly amplified sequencing libraries. Meanwhile, the detected RNA viruses provide a basis for experimentation to characterize possible hypovirulent effects, and hint at a wealth of uncharted viral diversity currently frozen in biobanks. IMPORTANCE Fungal pathogens of humans are a growing global health burden. Viruses of fungi may represent future therapeutic tools, but for many fungal pathogens there are no known viruses. Our study examined the viral content of diverse human-pathogenic fungi in a clinical biobank, identifying numerous viral genomes, including one lineage previously not known to infect fungi.
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Affiliation(s)
- Cormac M. Kinsella
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Martin Deijs
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - H. M. Gittelbauer
- Amsterdam UMC, Laboratory of Mycology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
| | - Lia van der Hoek
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Karin van Dijk
- Amsterdam UMC, Laboratory of Mycology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
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Costa VA, Geoghegan JL, Holmes EC, Harvey E. Genetic Reassortment between Endemic and Introduced Macrobrachium rosenbergii Nodaviruses in the Murray-Darling Basin, Australia. Viruses 2022; 14:2186. [PMID: 36298741 DOI: 10.3390/v14102186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 11/05/2022] Open
Abstract
Macrobrachium rosenbergii nodavirus (MrNV)—the aetiological agent of white tail disease—is a major limiting factor of crustacean aquaculture as it causes up to 100% mortality in M. rosenbergii larvae and juveniles. Despite the importance of MrNV, there have been few studies on the phylogenetic diversity and geographic range of this virus in Australian waterways. Here, we detected MrNV genomes in common carp (Cyprinus carpio) metatranscriptomes sampled at five freshwater sites across the Murray-Darling Basin (MDB), Australia. We identified genetic divergence of the RNA-dependent RNA polymerase gene between MrNV sequences identified in the northern and southern rivers of the MDB. Northern viruses exhibited strong phylogenetic clustering with MrNV from China, whereas the southern viruses were more closely related to MrNV from Australia. However, all five viruses were closely related in the capsid protein, indicative of genetic reassortment of the RNA1 and RNA2 segments between Australian and introduced MrNV. In addition, we identified Macrobrachium australiense in two of the five MrNV-positive libraries, suggesting that these species may be important reservoir hosts in the MDB. Overall, this study reports the first occurrence of MrNV outside of the Queensland region in Australia and provides evidence for genetic reassortment between endemic and introduced MrNV.
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Abstract
Viruses are part of the microbiome and have essential roles in immunology, evolution, biogeochemical cycles, health, and disease progression. Viruses influence a wide variety of systems and processes, and the continued discovery of novel viruses is anticipated to reveal new mechanisms influencing the biology of diverse environments. While the identity and roles of viruses continue to be discovered and understood through viral metagenomics, most of the sequences in virome datasets cannot be attributed to known viruses or may be only distantly related to species already described in public sequence databases, at best. Such viruses are known as the viral dark matter. Ongoing discoveries from the viral dark matter have provided insights into novel viruses from a variety of environments, as well as their potential in immunological processes, virus evolution, health, disease, therapeutics, and surveillance. Increased understanding of the viral dark matter will continue with a combination of cultivation, microscopy, sequencing, and bioinformatic efforts, which are discussed in the present review.
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Canuti M, Large G, Verhoeven JTP, Dufour SC. A Novel Iridovirus Discovered in Deep-Sea Carnivorous Sponges. Viruses 2022; 14:v14081595. [PMID: 35893660 PMCID: PMC9330688 DOI: 10.3390/v14081595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
Carnivorous sponges (family Cladorhizidae) use small invertebrates as their main source of nutrients. We discovered a novel iridovirus (carnivorous sponge-associated iridovirus, CaSpA-IV) in Chondrocladia grandis and Cladorhiza oxeata specimens collected in the Arctic and Atlantic oceans at depths of 537–852 m. The sequenced viral genome (~190,000 bp) comprised 185 predicted ORFs, including those encoding 26 iridoviral core proteins, and phylogenetic analyses showed that CaSpA-IV is a close relative to members of the genus Decapodiridovirus and highly identical to a partially sequenced virus pathogenic to decapod shrimps. CaSpA-IV was found in various anatomical regions of six C. grandis (sphere, stem, root) from the Gulf of Maine and Baffin Bay and of two C. oxeata (sphere, secondary axis) from Baffin Bay. Partial MCP sequencing revealed a divergent virus (CaSpA-IV-2) in one C. oxeata. The analysis of a 10 nt long tandem repeat showed a number of repeats consistent across sub-sections of the same sponges but different between animals, suggesting the presence of different strains. As the genetic material of crustaceans, particularly from the zooplanktonic copepod order Calanoida, was identified in the investigated samples, further studies are required to elucidate whether CaSpA-IV infects the carnivorous sponges, their crustacean prey, or both.
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Hufsky F, Abecasis A, Agudelo-Romero P, Bletsa M, Brown K, Claus C, Deinhardt-Emmer S, Deng L, Friedel CC, Gismondi MI, Kostaki EG, Kühnert D, Kulkarni-Kale U, Metzner KJ, Meyer IM, Miozzi L, Nishimura L, Paraskevopoulou S, Pérez-Cataluña A, Rahlff J, Thomson E, Tumescheit C, van der Hoek L, Van Espen L, Vandamme AM, Zaheri M, Zuckerman N, Marz M. Women in the European Virus Bioinformatics Center. Viruses 2022; 14:v14071522. [PMID: 35891501 PMCID: PMC9319252 DOI: 10.3390/v14071522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.
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Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
- Correspondence: (F.H.); (M.M.)
| | - Ana Abecasis
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, New University of Lisbon, 1349-008 Lisbon, Portugal
| | - Patricia Agudelo-Romero
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, WA 6009, Australia
| | - Magda Bletsa
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Katherine Brown
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Claudia Claus
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Microbiology and Virology, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Stefanie Deinhardt-Emmer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany
| | - Li Deng
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Virology, Helmholtz Centre Munich-German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Caroline C. Friedel
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Informatics, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - María Inés Gismondi
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Agrobiotechnology and Molecular Biology (IABIMO), National Institute for Agriculture Technology (INTA), National Research Council (CONICET), Hurlingham B1686IGC, Argentina
- Department of Basic Sciences, National University of Luján, Luján B6702MZP, Argentina
| | - Evangelia Georgia Kostaki
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Denise Kühnert
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Urmila Kulkarni-Kale
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Karin J. Metzner
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Irmtraud M. Meyer
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
- Faculty of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Laura Miozzi
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute for Sustainable Plant Protection, National Research Council of Italy, 10135 Torino, Italy
| | - Luca Nishimura
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Sofia Paraskevopoulou
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Methods Development and Research Infrastructure, Bioinformatics and Systems Biology, Robert Koch Institute, 13353 Berlin, Germany
| | - Alba Pérez-Cataluña
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Janina Rahlff
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linneaus University, 391 82 Kalmar, Sweden
| | - Emma Thomson
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow G51 4TF, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Charlotte Tumescheit
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Lia van der Hoek
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1012 WX Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, 1100 DD Amsterdam, The Netherlands
| | - Lore Van Espen
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Anne-Mieke Vandamme
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
- Institute for the Future, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium
| | - Maryam Zaheri
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
| | - Neta Zuckerman
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center, Ramat Gan 52621, Israel
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (A.A.); (P.A.-R.); (M.B.); (K.B.); (C.C.); (S.D.-E.); (L.D.); (C.C.F.); (M.I.G.); (E.G.K.); (D.K.); (U.K.-K.); (K.J.M.); (I.M.M.); (L.M.); (L.N.); (S.P.); (A.P.-C.); (J.R.); (E.T.); (C.T.); (L.v.d.H.); (L.V.E.); (A.-M.V.); (M.Z.); (N.Z.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany
- Correspondence: (F.H.); (M.M.)
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Abstract
Currently, both pathogenic and commensal viruses are continuously being discovered and acknowledged as ubiquitous components of microbial communities. The advancements of systems microbiological approaches have changed the face of virome research. Here, we focus on viral metagenomic approach to study virus community and their interactions with other microbial members as well as their hosts. This review also summarizes challenges, limitations, and benefits of the current virome approaches. Potentially, the studies of virome can be further applied in various biological and clinical fields.
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Affiliation(s)
- Suwalak Chitcharoen
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand,Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pavaret Sivapornnukul
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Sunchai Payungporn.
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Pienaar RD, Gilbert C, Belliardo C, Herrero S, Herniou EA. First Evidence of Past and Present Interactions between Viruses and the Black Soldier Fly, Hermetia illucens. Viruses 2022; 14:1274. [PMID: 35746744 DOI: 10.3390/v14061274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 12/10/2022] Open
Abstract
Black soldier flies (BSFs, Hermetia illucens) are becoming a prominent research model encouraged by the insect as food and feed and waste bioconversion industries. Insect mass-rearing facilities are at risk from the spread of viruses, but so far, none have been described in BSFs. To fill this knowledge gap, a bioinformatic approach was undertaken to discover viruses specifically associated with BSFs. First, BSF genomes were screened for the presence of endogenous viral elements (EVEs). This led to the discovery and mapping of seven orthologous EVEs integrated into three BSF genomes originating from five viral families. Secondly, a virus discovery pipeline was used to screen BSF transcriptomes. This led to detecting a new exogenous totivirus that we named hermetia illucens totivirus 1 (HiTV1). Phylogenetic analyses showed this virus belongs to a clade of insect-specific totiviruses and is closely related to the largest EVE located on chromosome 1 of the BSF genome. Lastly, this EVE was found to express a small transcript in some BSFs infected by HiTV1. Altogether, this data mining study showed that far from being unscathed from viruses, BSFs bear traces of past interactions with several viral families and of present interactions with the exogenous HiTV1.
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Ma Y, Che H, Gao S, Lin Y, Li S. Diverse Novel Viruses Coinfecting the Tropical Ornamental Plant Polyscias balfouriana in China. Viruses 2022; 14:v14061120. [PMID: 35746592 PMCID: PMC9228080 DOI: 10.3390/v14061120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/10/2022] Open
Abstract
The viromic profile of Polyscias balfouriana cv. Marginata, a perennial woody and ornamental plant, was determined using ribosomal RNA-depleted total RNA (rRNA-depleted totRNA) sequencing. Five viruses (i.e., polyscias mosaic virus, PoMV; one potential novel rhabdovirus; and three novel viruses of Betaflexiviridae and Closteroviridae) were detected and prevalence-surveyed in Hainan province, China. The genomes of polyscias capillovirus 1 (PCaV-1) and polyscias citrivirus 1 (PCiV-1) of family Betaflexiviridae were completed, and the genomes of polyscias crinivirus 1 (PCrV-1) of Closteroviridae were nearly completed lacking the 5′ and 3′ termini. PCaV-1 shares 68% genome nucleotide (nt) identity and 66% replicase (Rep) amino acid (aa) identity with homologues in apple stem grooving virus (ASGV). PCiV-1 shares 65% genome nt identity and 64% Rep aa identity with homologs in citrus leaf blotch virus (CLBV). Meeting the species demarcation criteria, PCaV-1 and PCiV-1 were considered to be new species in genera Capillovirus and Citrivirus, respectively. PCrV-1 shares high genome nt identity (62%), heat shock protein 70-like protein (HSP70h) and RNA-dependent RNA polymerase (RdRp) aa identity (78−80%) with homologues in tomato chlorosis virus (ToCV). We tentatively consider PCrV-1 to be an unclassified member of the Crinivirus genus. PoMV, PCaV-1, PCiV-1, and PCrV-1 are the prevalent viruses with >73% occurrence in the Xinglong Tropical Botanical Garden, Hainan, China.
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Affiliation(s)
- Yuxin Ma
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.M.); (H.C.); (Y.L.)
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering/Key Laboratory of Ministry of Education, Guizhou University, Guiyang 550025, China
| | - Haiyan Che
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.M.); (H.C.); (Y.L.)
| | - Shengfeng Gao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China;
| | - Yating Lin
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.M.); (H.C.); (Y.L.)
| | - Shifang Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.M.); (H.C.); (Y.L.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence:
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Vieira P, Subbotin SA, Alkharouf N, Eisenback J, Nemchinov LG. Expanding the RNA virome of nematodes and other soil-inhabiting organisms. Virus Evol 2022; 8:veac019. [PMID: 35371560 PMCID: PMC8967085 DOI: 10.1093/ve/veac019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/02/2022] [Accepted: 03/10/2022] [Indexed: 07/25/2023] Open
Abstract
In recent years, several newly discovered viruses infecting free-living nematodes, sedentary plant-parasitic nematodes, and migratory root lesion nematodes have been described. However, to the best of our knowledge, no comprehensive research focusing exclusively on metagenomic analysis of the soil nematode community virome has thus far been carried out. In this work, we have attempted to bridge this gap by investigating viral communities that are associated with soil-inhabiting organisms, particularly nematodes. This study demonstrates a remarkable diversity of RNA viruses in the natural soil environment. Over 150 viruses were identified in different soil-inhabiting hosts, of which more than 139 are potentially new virus species. Many of these viruses belong to the nematode virome, thereby enriching our understanding of the diversity and evolution of this complex part of the natural ecosystem.
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Affiliation(s)
- Paulo Vieira
- USDA-ARS Mycology & Nematology Genetic Diversity & Biology Laboratory, Beltsville, MD 20705, USA
| | - Sergei A Subbotin
- Plant Pest Diagnostics Branch, California Department of Food & Agriculture, Sacramento, CA 95832, USA
- Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow 117071, Russia
| | - Nadim Alkharouf
- Department of Computer & Information Sciences Faculty, Towson University, Towson, MD 21204, USA
| | - Jonathan Eisenback
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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Manny AR, Hetzel CA, Mizani A, Nibert ML. Discovery of a Novel Species of Trichomonasvirus in the Human Parasite Trichomonas vaginalis Using Transcriptome Mining. Viruses 2022; 14:548. [PMID: 35336955 PMCID: PMC8953718 DOI: 10.3390/v14030548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 11/16/2022] Open
Abstract
Trichomonas vaginalis is the most common non-viral cause of sexually transmitted infections globally. Infection by this protozoan parasite results in the clinical syndrome trichomoniasis, which manifests as an inflammatory disease with acute and chronic consequences. Half or more isolates of this parasite are themselves infected with one or more dsRNA viruses that can exacerbate the inflammatory syndrome. At least four distinct viruses have been identified in T. vaginalis to date, constituting species Trichomonas vaginalis virus 1 through Trichomonas vaginalis virus 4 in genus Trichomonasvirus. Despite the global prevalence of these viruses, few complete coding sequences have been reported. We conducted viral sequence mining in publicly available transcriptomes across 60 RNA-Seq accessions representing at least 13 distinct T. vaginalis isolates. The results led to sequence assemblies for 27 novel trichomonasvirus strains across all four recognized species. Using a strategy of de novo sequence assembly followed by taxonomic classification, we additionally discovered six strains of a newly identified fifth species, for which we propose the name Trichomonas vaginalis virus 5, also in genus Trichomonasvirus. These additional strains exhibit high sequence identity to each other, but low sequence identity to strains of the other four species. Phylogenetic analyses corroborate the species-level designations. These results substantially increase the number of trichomonasvirus genome sequences and demonstrate the utility of mining publicly available transcriptomes for virus discovery in a critical human pathogen.
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Affiliation(s)
- Austin R. Manny
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; (A.R.M.); (C.A.H.); (A.M.)
- Program in Virology, Division of Medical Sciences, Graduate School of Arts & Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Carrie A. Hetzel
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; (A.R.M.); (C.A.H.); (A.M.)
- Program in Virology, Division of Medical Sciences, Graduate School of Arts & Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Arshan Mizani
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; (A.R.M.); (C.A.H.); (A.M.)
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Max L. Nibert
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; (A.R.M.); (C.A.H.); (A.M.)
- Program in Virology, Division of Medical Sciences, Graduate School of Arts & Sciences, Harvard University, Cambridge, MA 02138, USA
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40
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Berg MG, Forberg K, Perez LJ, Luk KC, Meyer TV, Cloherty GA. Emergence of a Distinct Picobirnavirus Genotype Circulating in Patients Hospitalized with Acute Respiratory Illness. Viruses 2021; 13:2534. [PMID: 34960803 DOI: 10.3390/v13122534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/07/2021] [Indexed: 01/01/2023] Open
Abstract
Picobirnaviruses (PBV) are found in a wide range of hosts and typically associated with gastrointestinal infections in immunocompromised individuals. Here, a divergent PBV genome was assembled from a patient hospitalized for acute respiratory illness (ARI) in Colombia. The RdRp protein branched with sequences previously reported in patients with ARI from Cambodia and China. Sputa from hospitalized individuals (n = 130) were screened by RT-qPCR which enabled detection and subsequent metagenomic characterization of 25 additional PBV infections circulating in Colombia and the US. Phylogenetic analysis of RdRp highlighted the emergence of two dominant lineages linked to the index case and Asian strains, which together clustered as a distinct genotype. Bayesian inference further established capsid and RdRp sequences as both significantly associated with ARI. Various respiratory-tropic pathogens were detected in PBV+ patients, yet no specific bacteria was common among them and four individuals lacked co-infections, suggesting PBV may not be a prokaryotic virus nor exclusively opportunistic, respectively. Competing models for the origin and transmission of this PBV genotype are presented that attempt to reconcile vectoring by a bacterial host with human pathogenicity. A high prevalence in patients with ARI, an ability to reassort, and demonstrated global spread indicate PBV warrant greater public health concern.
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41
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Cebriá-Mendoza M, Bracho MA, Arbona C, Larrea L, Díaz W, Sanjuán R, Cuevas JM. Exploring the Diversity of the Human Blood Virome. Viruses 2021; 13:v13112322. [PMID: 34835128 PMCID: PMC8621239 DOI: 10.3390/v13112322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 01/01/2023] Open
Abstract
Metagenomics is greatly improving our ability to discover new viruses, as well as their possible associations with disease. However, metagenomics has also changed our understanding of viruses in general. The vast expansion of currently known viral diversity has revealed a large fraction of non-pathogenic viruses, and offers a new perspective in which viruses function as important components of many ecosystems. In this vein, studies of the human blood virome are often motivated by the search for new viral diseases, especially those associated with blood transfusions. However, these studies have revealed the common presence of apparently non-pathogenic viruses in blood, particularly human anelloviruses and, to a lower extent, human pegiviruses (HPgV). To shed light on the diversity of the human blood virome, we subjected pooled plasma samples from 587 healthy donors in Spain to a viral enrichment protocol, followed by massive parallel sequencing. This showed that anelloviruses were clearly the major component of the blood virome and showed remarkable diversity. In total, we assembled 332 complete or near-complete anellovirus genomes, 50 of which could be considered new species. HPgV was much less frequent, but we, nevertheless, recovered 17 different isolates that we subsequently used for characterizing the diversity of this virus. In-depth investigation of the human blood virome should help to elucidate the ecology of these viruses, and to unveil potentially associated diseases.
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Affiliation(s)
- María Cebriá-Mendoza
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 València, Spain; (M.C.-M.); (W.D.); (R.S.)
| | - María A. Bracho
- Joint Research Unit “Infection and Public Health”, FISABIO-Universitat de València I2SysBio, 46020 València, Spain;
- CIBER in Epidemiology and Public Health (CIBERESP), 46020 València, Spain
| | - Cristina Arbona
- Centro de Transfusión de la Comunidad Valenciana, 46020 València, Spain; (C.A.); (L.L.)
| | - Luís Larrea
- Centro de Transfusión de la Comunidad Valenciana, 46020 València, Spain; (C.A.); (L.L.)
| | - Wladimiro Díaz
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 València, Spain; (M.C.-M.); (W.D.); (R.S.)
- Department of Informatics, Universitat de València, 46020 València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 València, Spain; (M.C.-M.); (W.D.); (R.S.)
- Department of Genetics, Universitat de València, 46020 València, Spain
| | - José M. Cuevas
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 València, Spain; (M.C.-M.); (W.D.); (R.S.)
- Department of Genetics, Universitat de València, 46020 València, Spain
- Correspondence:
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42
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Canuti M, Bouchard É, Rodrigues B, Whitney HG, Hopson M, Gilroy C, Stenson G, Dufour SC, Lang AS, Verhoeven JTP. Newlavirus, a Novel, Highly Prevalent, and Highly Diverse Protoparvovirus of Foxes ( Vulpes spp.). Viruses 2021; 13:1969. [PMID: 34696399 PMCID: PMC8537079 DOI: 10.3390/v13101969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/15/2022] Open
Abstract
The genus Protoparvovirus (family Parvoviridae) includes several viruses of carnivores. We describe a novel fox protoparvovirus, which we named Newlavirus as it was discovered in samples from Newfoundland and Labrador, Canada. Analysis of the full non-structural protein (NS1) sequence indicates that this virus is a previously uncharacterized species. Newlavirus showed high prevalence in foxes from both the mainland (Labrador, 54/137, 39.4%) and the island of Newfoundland (22/50, 44%) but was not detected in samples from other carnivores, including coyotes (n = 92), lynx (n = 58), martens (n = 146), mink (n = 47), ermines (n = 17), dogs (n = 48), and ringed (n = 4), harp (n = 6), bearded (n = 6), and harbor (n = 2) seals. Newlavirus was found at similar rates in stool and spleen (24/80, 30% vs. 59/152, 38.8%, p = 0.2) but at lower rates in lymph nodes (2/37, 5.4%, p < 0.01). Sequencing a fragment of approximately 750 nt of the capsid protein gene from 53 samples showed a high frequency of co-infection by more than one strain (33.9%), high genetic diversity with 13 genotypes with low sequence identities (70.5-87.8%), and no geographic segregation of strains. Given the high prevalence, high diversity, and the lack of identification in other species, foxes are likely the natural reservoir of Newlavirus, and further studies should investigate its distribution.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
| | - Émilie Bouchard
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada;
- Research Group on Epidemiology of Zoonoses and Public Health (GREZOSP), Faculty of Veterinary Medicine, Université de Montréal, 3200 rue Sicotte, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Bruce Rodrigues
- Wildlife Division, Newfoundland and Labrador Department of Fisheries, Forestry, and Agriculture, PO Box 2007, Corner Brook, NL A2H 7S1, Canada;
| | - Hugh G. Whitney
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
| | - Marti Hopson
- Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PE C1A 4P3, Canada;
| | - Cornelia Gilroy
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PE C1A 4P3, Canada;
| | - Garry Stenson
- Fisheries and Oceans Canada, Government of Canada, P.O. Box 5667, St. John’s, NL A1C 5X1, Canada;
| | - Suzanne C. Dufour
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
| | - Andrew S. Lang
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
| | - Joost T. P. Verhoeven
- Department of Biology, Memorial, University of Newfoundland, 232 Elizabeth Ave., St. John’s, NL A1B 3X9, Canada; (H.G.W.); (S.C.D.); (J.T.P.V.)
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43
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Remnant EJ, Baty JW, Bulgarella M, Dobelmann J, Quinn O, Gruber MAM, Lester PJ. A Diverse Viral Community from Predatory Wasps in Their Native and Invaded Range, with a New Virus Infectious to Honey Bees. Viruses 2021; 13:1431. [PMID: 34452301 PMCID: PMC8402789 DOI: 10.3390/v13081431] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 12/15/2022] Open
Abstract
Wasps of the genus Vespula are social insects that have become major pests and predators in their introduced range. Viruses present in these wasps have been studied in the context of spillover from honey bees, yet we lack an understanding of the endogenous virome of wasps as potential reservoirs of novel emerging infectious diseases. We describe the characterization of 68 novel and nine previously identified virus sequences found in transcriptomes of Vespula vulgaris in colonies sampled from their native range (Belgium) and an invasive range (New Zealand). Many viruses present in the samples were from the Picorna-like virus family (38%). We identified one Luteo-like virus, Vespula vulgaris Luteo-like virus 1, present in the three life stages examined in all colonies from both locations, suggesting this virus is a highly prevalent and persistent infection in wasp colonies. Additionally, we identified a novel Iflavirus with similarity to a recently identified Moku virus, a known wasp and honey bee pathogen. Experimental infection of honey bees with this novel Vespula vulgaris Moku-like virus resulted in an active infection. The high viral diversity present in these invasive wasps is a likely indication that their polyphagous diet is a rich source of viral infections.
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Affiliation(s)
- Emily J. Remnant
- Behaviour, Ecology and Evolution Laboratory, School of Life and Environmental Sciences, Science Road, University of Sydney, Sydney, NSW 2006, Australia
| | - James W. Baty
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand; (J.W.B.); (M.B.); (J.D.); (O.Q.); (M.A.M.G.); (P.J.L.)
| | - Mariana Bulgarella
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand; (J.W.B.); (M.B.); (J.D.); (O.Q.); (M.A.M.G.); (P.J.L.)
| | - Jana Dobelmann
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand; (J.W.B.); (M.B.); (J.D.); (O.Q.); (M.A.M.G.); (P.J.L.)
- Institute of Evolutionary Ecology and Conservation Genomics, Department of Biology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Oliver Quinn
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand; (J.W.B.); (M.B.); (J.D.); (O.Q.); (M.A.M.G.); (P.J.L.)
- Bacteriology and Aquatic Animal Diseases, Ministry for Primary Industries, P.O. Box 2526, Wellington 6140, New Zealand
| | - Monica A. M. Gruber
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand; (J.W.B.); (M.B.); (J.D.); (O.Q.); (M.A.M.G.); (P.J.L.)
| | - Philip J. Lester
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington 6140, New Zealand; (J.W.B.); (M.B.); (J.D.); (O.Q.); (M.A.M.G.); (P.J.L.)
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Vanmechelen B, Merino M, Vergote V, Laenen L, Thijssen M, Martí-Carreras J, Claerebout E, Maes P. Exploration of the Ixodes ricinus virosphere unveils an extensive virus diversity including novel coltiviruses and other reoviruses. Virus Evol 2021; 7:veab066. [PMID: 34532065 PMCID: PMC8438917 DOI: 10.1093/ve/veab066] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/25/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022] Open
Abstract
Recent metagenomics studies have revealed several tick species to host a variety of previously undiscovered RNA viruses. Ixodes ricinus, which is known to be a vector for many viral, bacterial, and protozoan pathogens, is the most prevalent tick species in Europe. For this study, we decided to investigate the virosphere of Belgian I. ricinus ticks. High-throughput sequencing of tick pools collected from six different sampling sites revealed the presence of viruses belonging to many different viral orders and families, including Mononegavirales, Bunyavirales, Partitiviridae, and Reoviridae. Of particular interest was the detection of several new reoviruses, two of which cluster together with members of the genus Coltivirus. This includes a new strain of Eyach virus, a known causative agent of tick-borne encephalitis. All genome segments of this new strain are highly similar to those of previously published Eyach virus genomes, except for the fourth segment, encoding VP4, which is markedly more dissimilar, potentially indicating the occurrence of a genetic reassortment. Further polymerase chain reaction-based screening of over 230 tick pools for 14 selected viruses showed that most viruses could be found in all six sampling sites, indicating the wide spread of these viruses throughout the Belgian tick population. Taken together, these results illustrate the role of ticks as important virus reservoirs, highlighting the need for adequate tick control measures.
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Affiliation(s)
| | - Michelle Merino
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven—University of Leuven, Herestraat 49, Box 1040, Leuven BE3000, Belgium
| | - Valentijn Vergote
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven—University of Leuven, Herestraat 49, Box 1040, Leuven BE3000, Belgium
| | - Lies Laenen
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven—University of Leuven, Herestraat 49, Box 1040, Leuven BE3000, Belgium
| | - Marijn Thijssen
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven—University of Leuven, Herestraat 49, Box 1040, Leuven BE3000, Belgium
| | - Joan Martí-Carreras
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven—University of Leuven, Herestraat 49, Box 1040, Leuven BE3000, Belgium
| | - Edwin Claerebout
- Faculty of Veterinary Medicine, Laboratory of Parasitology, Ghent University, Salisburylaan 133-D13, Merelbeke BE9820, Belgium
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Navas-Suárez PE, Sacristán C, Kluyber D, Yogui DR, Alves AC, Dalazen GT, Díaz-Delgado J, Guerra JM, de Azevedo Fernandes NCC, Réssio RA, da Silva TC, Cogliati B, Desbiez ALJ, Catão-Dias JL. Novel gammaherpesvirus associated with primary gastric T-cell lymphoma in a free-ranging giant armadillo in Brazil. Transbound Emerg Dis 2021; 69:2045-2051. [PMID: 34132049 DOI: 10.1111/tbed.14189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/12/2021] [Accepted: 06/12/2021] [Indexed: 11/29/2022]
Abstract
The number of viral-associated neoplasms reported in wildlife has increased over the last decades, likely because of growing research efforts and a potentially greater burden of carcinogenic pathogens. Herein, we describe a primary gastric T-cell lymphoma in one free-ranging giant armadillo (Priodontes maximus) from Brazilian Pantanal infected by a novel gammaherpesvirus, proposed as Cingulatid gammaherpesvirus 1 (CiHV-1). By chromogenic in situ hybridisation against Epstein-Barr virus some neoplastic cells were labeled. Subsequently, a molecular screening was carried out to detect the occurrence of this pathogen in other giant armadillos in the same region. Overall, this novel virus was detected in 14.3% (3/21) of the tested giant armadillos. We suggest this herpesvirus, the first in Xenarthra, as a plausible aetiology of the neoplasm. The implications of CiHV-1 for this species are uncertain; while no outbreaks of disease have been recorded, the present study raises concerns. Further research is warranted to assess the real significance of CiHV-1 and its potential oncogenic role in this species.
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Affiliation(s)
- Pedro Enrique Navas-Suárez
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo State, Brazil
| | - Carlos Sacristán
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo State, Brazil
| | - Danilo Kluyber
- Giant Armadillo Conservation Project, Instituto de Conservação de Animais Silvestres (ICAS), Campo, Grande, Brazil.,Naples Zoo at Caribbeans Gardens, Naples, Florida, USA
| | - Débora Regina Yogui
- Giant Armadillo Conservation Project, Instituto de Conservação de Animais Silvestres (ICAS), Campo, Grande, Brazil.,The Royal Zoological Society of Scotland (RZSS), Edinburgh Zoo, Edinburgh, Scotland
| | - Amanda Carolina Alves
- Giant Armadillo Conservation Project, Instituto de Conservação de Animais Silvestres (ICAS), Campo, Grande, Brazil
| | - Gislaine Taimara Dalazen
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo State, Brazil
| | - Josué Díaz-Delgado
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, Texas, USA
| | | | | | | | - Tereza Cristina da Silva
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo State, Brazil
| | - Bruno Cogliati
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo State, Brazil
| | - Arnaud Leonard Jean Desbiez
- Giant Armadillo Conservation Project, Instituto de Conservação de Animais Silvestres (ICAS), Campo, Grande, Brazil., , Nashville Zoo, Nashville, USA
| | - José Luiz Catão-Dias
- Laboratory of Wildlife Comparative Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo State, Brazil
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46
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Miller AK, Mifsud JCO, Costa VA, Grimwood RM, Kitson J, Baker C, Brosnahan CL, Pande A, Holmes EC, Gemmell NJ, Geoghegan JL. Slippery when wet: cross-species transmission of divergent coronaviruses in bony and jawless fish and the evolutionary history of the Coronaviridae. Virus Evol 2021; 7:veab050. [PMID: 34527280 PMCID: PMC8244743 DOI: 10.1093/ve/veab050] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/19/2021] [Accepted: 05/28/2021] [Indexed: 01/31/2023] Open
Abstract
The Nidovirales comprise a genetically diverse group of positive-sense single-stranded RNA virus families that infect a range of invertebrate and vertebrate hosts. Recent metagenomic studies have identified nido-like virus sequences, particularly those related to the Coronaviridae, in a range of aquatic hosts including fish, amphibians, and reptiles. We sought to identify additional members of the Coronaviridae in both bony and jawless fish through a combination of total RNA sequencing (meta-transcriptomics) and data mining of published RNA sequencing data and from this reveal more of the long-term patterns and processes of coronavirus evolution. Accordingly, we identified a number of divergent viruses that fell within the Letovirinae subfamily of the Coronaviridae, including those in a jawless fish-the pouched lamprey. By mining fish transcriptome data, we identified additional virus transcripts matching these viruses in bony fish from both marine and freshwater environments. These new viruses retained sequence conservation in the RNA-dependant RNA polymerase across the Coronaviridae but formed a distinct and diverse phylogenetic group. Although there are broad-scale topological similarities between the phylogenies of the major groups of coronaviruses and their vertebrate hosts, the evolutionary relationship of viruses within the Letovirinae does not mirror that of their hosts. For example, the coronavirus found in the pouched lamprey fell within the phylogenetic diversity of bony fish letoviruses, indicative of past host switching events. Hence, despite possessing a phylogenetic history that likely spans the entire history of the vertebrates, coronavirus evolution has been characterised by relatively frequent cross-species transmission, particularly in hosts that reside in aquatic habitats.
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Affiliation(s)
| | | | | | - Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Jane Kitson
- Kitson Consulting Ltd 9 Black Road, Invercargill 9879, Invercargill/Waihopai, New Zealand
| | - Cindy Baker
- National Institute of Water and Atmospheric Research, Hamilton 3216, New Zealand
| | - Cara L Brosnahan
- Animal Health Laboratory and Diagnostic and Surveillance Directorate, Ministry for Primary Industries, Upper Hutt 5018, New Zealand
| | - Anjali Pande
- National Institute of Water and Atmospheric Research, Hamilton 3216, New Zealand,Animal Health Laboratory and Diagnostic and Surveillance Directorate, Ministry for Primary Industries, Upper Hutt 5018, New Zealand
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, Johns Hopkins Drive, The University of Sydney, Sydney, NSW 2006, Australia
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
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Rivarez MPS, Vučurović A, Mehle N, Ravnikar M, Kutnjak D. Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing. Front Microbiol 2021; 12:671925. [PMID: 34093492 PMCID: PMC8175903 DOI: 10.3389/fmicb.2021.671925] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/12/2021] [Indexed: 11/30/2022] Open
Abstract
Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato.
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Affiliation(s)
- Mark Paul Selda Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Faculty of Agriculture, University of Belgrade, Belgrade, Serbia
| | - Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,School for Viticulture and Enology, University of Nova Gorica, Nova Gorica, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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Jandrig B, Krause H, Zimmermann W, Vasiliunaite E, Gedvilaite A, Ulrich RG. Hamster Polyomavirus Research: Past, Present, and Future. Viruses 2021; 13:v13050907. [PMID: 34068409 PMCID: PMC8153644 DOI: 10.3390/v13050907] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/29/2021] [Accepted: 05/09/2021] [Indexed: 12/11/2022] Open
Abstract
Hamster polyomavirus (Mesocricetus auratus polyomavirus 1, HaPyV) was discovered as one of the first rodent polyomaviruses at the end of the 1960s in a colony of Syrian hamsters (Mesocricetus auratus) affected by skin tumors. Natural HaPyV infections have been recorded in Syrian hamster colonies due to the occurrence of skin tumors and lymphomas. HaPyV infections of Syrian hamsters represent an important and pioneering tumor model. Experimental infections of Syrian hamsters of different colonies are still serving as model systems (e.g., mesothelioma). The observed phylogenetic relationship of HaPyV to murine polyomaviruses within the genus Alphapolyomavirus, and the exclusive detection of other cricetid polyomaviruses, i.e., common vole (Microtus arvalis polyomavirus 1) and bank vole (Myodes glareolus polyomavirus 1) polyomaviruses, in the genus Betapolyomavirus, must be considered with caution, as knowledge of rodent-associated polyomaviruses is still limited. The genome of HaPyV shows the typical organization of polyomaviruses with an early and a late transcriptional region. The early region encodes three tumor (T) antigens including a middle T antigen; the late region encodes three capsid proteins. The major capsid protein VP1 of HaPyV was established as a carrier for the generation of autologous, chimeric, and mosaic virus-like particles (VLPs) with a broad range of applications, e.g., for the production of epitope-specific antibodies. Autologous VLPs have been applied for entry and maturation studies of dendritic cells. The generation of chimeric and mosaic VLPs indicated the high flexibility of the VP1 carrier protein for the insertion of foreign sequences. The generation of pseudotype VLPs of original VP1 and VP2–foreign protein fusion can further enhance the applicability of this system. Future investigations should evaluate the evolutionary origin of HaPyV, monitor its occurrence in wildlife and Syrian hamster breeding, and prove its value for the generation of potential vaccine candidates and as a gene therapy vehicle.
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Affiliation(s)
- Burkhard Jandrig
- Department of Urology, University Medical Center Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
- Correspondence:
| | - Hans Krause
- Charité—Universitätsmedizin Berlin, Urologische Klinik, Charitéplatz 1, 10117 Berlin, Germany;
| | | | - Emilija Vasiliunaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (E.V.); (A.G.)
| | - Alma Gedvilaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania; (E.V.); (A.G.)
| | - Rainer G. Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany;
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Insel Riems, Germany
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49
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Folgueiras-González A, van den Braak R, Deijs M, van der Hoek L, de Groof A. A Versatile Processing Workflow to Enable Pathogen Detection in Clinical Samples from Organs Using VIDISCA. Diagnostics (Basel) 2021; 11:diagnostics11050791. [PMID: 33925752 PMCID: PMC8145099 DOI: 10.3390/diagnostics11050791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/16/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
In recent years, refined molecular methods coupled with powerful high throughput sequencing technologies have increased the potential of virus discovery in clinical samples. However, host genetic material remains a complicating factor that interferes with discovery of novel viruses in solid tissue samples as the relative abundance of the virus material is low. Physical enrichment processing methods, although usually complicated, labor-intensive, and costly, have proven to be successful for improving sensitivity of virus detection in complex samples. In order to further increase detectability, we studied the application of fast and simple high-throughput virus enrichment methods on tissue homogenates. Probe sonication in high EDTA concentrations, organic extraction with Vertrel™ XF, or a combination of both, were applied prior to chromatography-like enrichment using Capto™ Core 700 resin, after which effects on virus detection sensitivity by the VIDISCA method were determined. Sonication in the presence of high concentrations of EDTA showed the best performance with an increased proportion of viral reads, up to 9.4 times, yet minimal effect on the host background signal. When this sonication procedure in high EDTA concentrations was followed by organic extraction with Vertrel™ XF and two rounds of core bead chromatography enrichment, an increase up to 10.5 times in the proportion of viral reads in the processed samples was achieved, with reduction of host background sequencing. We present a simple and semi-high-throughput method that can be used to enrich homogenized tissue samples for viral reads.
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Affiliation(s)
- Alba Folgueiras-González
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Robin van den Braak
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (M.D.); (L.v.d.H.)
| | - Ad de Groof
- Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830 AA Boxmeer, The Netherlands; (A.F.-G.); (R.v.d.B.)
- Correspondence:
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Jenckel M, Hall RN, Strive T. First description of hepatitis E virus in Australian rabbits. Aust Vet J 2021; 99:356-358. [PMID: 33904188 DOI: 10.1111/avj.13073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/21/2021] [Accepted: 04/02/2021] [Indexed: 12/27/2022]
Abstract
We report the first detection of hepatitis E virus in rabbits in Australia. While conducting metatranscriptomic sequencing of liver samples collected from domestic rabbits that had died, we detected hepatitis E virus in three samples. Two viral genome sequences were obtained, which shared 96% nucleotide identity and clustered with hepatitis E strains isolated from rabbits and humans in Europe. This raises a potential public health risk in Australia, as the abundance of wild rabbits and the increasing popularity of domestic rabbits as pets represent a substantial human/rabbit interface to allow for potential zoonotic infections to occur.
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Affiliation(s)
- M Jenckel
- Health and Biosecurity, CSIRO, Canberra, Australian Capital Territory, 2601, Australia
| | - R N Hall
- Health and Biosecurity, CSIRO, Canberra, Australian Capital Territory, 2601, Australia.,Centre for Invasive Species Solutions, University of Canberra, Bruce, Australian Capital Territory, 2601, Australia
| | - T Strive
- Health and Biosecurity, CSIRO, Canberra, Australian Capital Territory, 2601, Australia.,Centre for Invasive Species Solutions, University of Canberra, Bruce, Australian Capital Territory, 2601, Australia
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