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Kobayashi D, Inoue Y, Suzuki R, Matsuda M, Shimoda H, Faizah AN, Kaku Y, Ishijima K, Kuroda Y, Tatemoto K, Virhuez-Mendoza M, Harada M, Nishino A, Inumaru M, Yonemitsu K, Kuwata R, Takano A, Watanabe M, Higa Y, Sawabe K, Maeda K, Isawa H. Identification and epidemiological study of an uncultured flavivirus from ticks using viral metagenomics and pseudoinfectious viral particles. Proc Natl Acad Sci U S A 2024; 121:e2319400121. [PMID: 38687787 PMCID: PMC11087778 DOI: 10.1073/pnas.2319400121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024] Open
Abstract
During their blood-feeding process, ticks are known to transmit various viruses to vertebrates, including humans. Recent viral metagenomic analyses using next-generation sequencing (NGS) have revealed that blood-feeding arthropods like ticks harbor a large diversity of viruses. However, many of these viruses have not been isolated or cultured, and their basic characteristics remain unknown. This study aimed to present the identification of a difficult-to-culture virus in ticks using NGS and to understand its epidemic dynamics using molecular biology techniques. During routine tick-borne virus surveillance in Japan, an unknown flaviviral sequence was detected via virome analysis of host-questing ticks. Similar viral sequences have been detected in the sera of sika deer and wild boars in Japan, and this virus was tentatively named the Saruyama virus (SAYAV). Because SAYAV did not propagate in any cultured cells tested, single-round infectious virus particles (SRIP) were generated based on its structural protein gene sequence utilizing a yellow fever virus-based replicon system to understand its nationwide endemic status. Seroepidemiological studies using SRIP as antigens have demonstrated the presence of neutralizing antibodies against SAYAV in sika deer and wild boar captured at several locations in Japan, suggesting that SAYAV is endemic throughout Japan. Phylogenetic analyses have revealed that SAYAV forms a sister clade with the Orthoflavivirus genus, which includes important mosquito- and tick-borne pathogenic viruses. This shows that SAYAV evolved into a lineage independent of the known orthoflaviviruses. This study demonstrates a unique approach for understanding the epidemiology of uncultured viruses by combining viral metagenomics and pseudoinfectious viral particles.
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Affiliation(s)
- Daisuke Kobayashi
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Yusuke Inoue
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama City, Tokyo208-0011, Japan
| | - Mami Matsuda
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama City, Tokyo208-0011, Japan
| | - Hiroshi Shimoda
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Astri Nur Faizah
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Yoshihiro Kaku
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Keita Ishijima
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Yudai Kuroda
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Kango Tatemoto
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Milagros Virhuez-Mendoza
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Michiko Harada
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Ayano Nishino
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Mizue Inumaru
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Kenzo Yonemitsu
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Ryusei Kuwata
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari City, Ehime794-8555, Japan
| | - Ai Takano
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Mamoru Watanabe
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Yukiko Higa
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Kyoko Sawabe
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
| | - Ken Maeda
- Department of Veterinary Science, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
- Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi City, Yamaguchi753-8515, Japan
| | - Haruhiko Isawa
- Department of Medical Entomology, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo162-8640, Japan
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Adhikari BN, Paskey AC, Frey KG, Bennett AJ, Long KA, Kuhn JH, Hamilton T, Glang L, Cer RZ, Goldberg TL, Bishop-Lilly KA. Virome profiling of fig wasps (Ceratosolen spp.) reveals virus diversity spanning four realms. Virology 2024; 591:109992. [PMID: 38246037 PMCID: PMC10849055 DOI: 10.1016/j.virol.2024.109992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
We investigated the virome of agaonid fig wasps (Ceratosolen spp.) inside syconia ("fruits") of various Ficus trees fed upon by frugivores such as pteropodid bats in Sub-Saharan Africa. This virome includes representatives of viral families spanning four realms and includes near-complete genome sequences of three novel viruses and fragments of five additional potentially novel viruses evolutionarily associated with insects, fungi, plants, and vertebrates. Our study provides evidence that frugivorous animals are exposed to a plethora of viruses by coincidental consumption of fig wasps, which are obligate pollinators of figs worldwide.
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Affiliation(s)
- Bishwo N Adhikari
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Adrian C Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Leidos, Inc., Reston, VA 20190, USA
| | - Kenneth G Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA
| | - Andrew J Bennett
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; Leidos, Inc., Reston, VA 20190, USA
| | - Kyle A Long
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Leidos, Inc., Reston, VA 20190, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA
| | - Lindsay Glang
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA; Leidos, Inc., Reston, VA 20190, USA
| | - Regina Z Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; Global Health Institute, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Zoology, Makerere University, Kampala, Uganda
| | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, Fort Detrick, MD 21702, USA.
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3
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Waller SJ, Tortosa P, Thurley T, O’Donnell CFJ, Jackson R, Dennis G, Grimwood RM, Holmes EC, McInnes K, Geoghegan JL. Virome analysis of New Zealand's bats reveals cross-species viral transmission among the Coronaviridae. Virus Evol 2024; 10:veae008. [PMID: 38379777 PMCID: PMC10878368 DOI: 10.1093/ve/veae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/02/2023] [Accepted: 01/21/2024] [Indexed: 02/22/2024] Open
Abstract
The lesser short-tailed bat (Mystacina tuberculata) and the long-tailed bat (Chalinolobus tuberculatus) are Aotearoa New Zealand's only native extant terrestrial mammals and are believed to have migrated from Australia. Long-tailed bats arrived in New Zealand an estimated two million years ago and are closely related to other Australian bat species. Lesser short-tailed bats, in contrast, are the only extant species within the Mystacinidae and are estimated to have been living in isolation in New Zealand for the past 16-18 million years. Throughout this period of isolation, lesser short-tailed bats have become one of the most terrestrial bats in the world. Through a metatranscriptomic analysis of guano samples from eight locations across New Zealand, we aimed to characterise the viromes of New Zealand's bats and determine whether viruses have jumped between these species over the past two million years. High viral richness was observed among long-tailed bats with viruses spanning seven different viral families. In contrast, no bat-specific viruses were identified in lesser short-tailed bats. Both bat species harboured an abundance of likely dietary- and environment-associated viruses. We also identified alphacoronaviruses in long-tailed bat guano that had previously been identified in lesser short-tailed bats, suggesting that these viruses had jumped the species barrier after long-tailed bats migrated to New Zealand. Of note, an alphacoronavirus species discovered here possessed a complete genome of only 22,416 nucleotides with entire deletions or truncations of several non-structural proteins, thereby representing what may be the shortest genome within the Coronaviridae identified to date. Overall, this study has revealed a diverse range of novel viruses harboured by New Zealand's only native terrestrial mammals, in turn expanding our understanding of bat viral dynamics and evolution globally.
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Affiliation(s)
- Stephanie J Waller
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9016, New Zealand
| | - Pablo Tortosa
- UMR PIMIT Processus Infectieux en Milieu Insulaire Tropical, Université de La Réunion, CNRS 9192, INSERM 1187, IRD 249, Plateforme de recherche CYROI, 2 rue Maxime Rivière, Ste Clotilde 97490, France
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Tertia Thurley
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Colin F J O’Donnell
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Rebecca Jackson
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Gillian Dennis
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9016, New Zealand
| | | | - Kate McInnes
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9016, New Zealand
- Institute of Environmental Science and Research, 34 Kenepuru Drive, Kenepuru, Porirua, Wellington 5022, New Zealand
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Westmead Hospital, Level 5, Block K, Westmead, Sydney, NSW 2006, Australia
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Zhang S, Yang C, Qiu Y, Liao R, Xuan Z, Ren F, Dong Y, Xie X, Han Y, Wu D, Ramos-González PL, Freitas-Astúa J, Yang H, Zhou C, Cao M. Conserved untranslated regions of multipartite viruses: Natural markers of novel viral genomic components and tags of viral evolution. Virus Evol 2024; 10:veae004. [PMID: 38361819 PMCID: PMC10868557 DOI: 10.1093/ve/veae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024] Open
Abstract
Viruses with split genomes are classified as being either segmented or multipartite based on whether their genomic segments occur within a single virion or across different virions. Despite variations in number and sequence during evolution, the genomic segments of many viruses are conserved within the untranslated regions (UTRs). In this study, we present a methodology that combines RNA sequencing with iterative BLASTn of UTRs (https://github.com/qq371260/Iterative-blast-v.1.0) to identify new viral genomic segments. Some novel multipartite-like viruses related to the phylum Kitrinoviricota were annotated using sequencing data from field plant samples and public databases. We identified potentially plant-infecting jingmen-related viruses (order Amarillovirales) and jivi-related viruses (order Martellivirales) with at least six genomic components. The number of RNA molecules associated with a genome of the novel viruses in the families Closteroviridae, Kitaviridae, and Virgaviridae within the order Martellivirales reached five. Several of these viruses seem to represent new taxa at the subgenus, genus, and family levels. The diversity of novel genomic components and the multiple duplication of proteins or protein domains within single or multiple genomic components emphasize the evolutionary roles of genetic recombination (horizontal gene transfer), reassortment, and deletion. The relatively conserved UTRs at the genome level might explain the relationships between monopartite and multipartite viruses, as well as how subviral agents such as defective RNAs and satellite viruses can coexist with their helper viruses.
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Affiliation(s)
| | - Caixia Yang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, 21 Huanan Street, Shenyang, Liaoning 110044, China
| | - Yuanjian Qiu
- National Citrus Engineering and Technology Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400712, China
| | - Ruiling Liao
- National Citrus Engineering and Technology Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400712, China
| | - Zhiyou Xuan
- National Citrus Engineering and Technology Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400712, China
| | - Fang Ren
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, 98 Xinghainan Street, Xingcheng, Liaoning 125100, China
| | - Yafeng Dong
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, 98 Xinghainan Street, Xingcheng, Liaoning 125100, China
| | - Xiaoying Xie
- Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, Fujian 350002, China
| | - Yanhong Han
- Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, Fujian 350002, China
| | - Di Wu
- College of Horticulture and Landscape Architecture, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400712, China
| | - Pedro Luis Ramos-González
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, Av. Cons. Rodrigues Alves 1252, São Paulo SP, 04014-002, Brazil
| | - Juliana Freitas-Astúa
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, Av. Cons. Rodrigues Alves 1252, São Paulo SP, 04014-002, Brazil
- Embrapa Mandioca e Fruticultura, Rua da Embrapa, Caixa Postal 007, CEP, Cruz das Almas BA, 44380-000, Brazil
| | - Huadong Yang
- Hunan Agricultural University, 1 Nongda Road, Changsha, Hunan 410125, China
| | - Changyong Zhou
- National Citrus Engineering and Technology Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400712, China
- Guangxi Citrus Breeding and Cultivation Technology Innovation Center, Guangxi Academy of Specialty Crops, 40 Putuo Road, Guilin, Guangxi 541010, China
- Guangxi Key Laboratory of Germplasm Innovation and Utilization of Specialty Commercial Crops in North Guangxi, Guangxi Academy of Specialty Crops, 40 Putuo Road, Guilin, Guangxi 541010, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, 2 Tiansheng Road, Beibei, Chongqing 400712, China
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5
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Karlin DG. WIV, a protein domain found in a wide number of arthropod viruses, which probably facilitates infection. J Gen Virol 2024; 105. [PMID: 38193819 DOI: 10.1099/jgv.0.001948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
The most powerful approach to detect distant homologues of a protein is based on structure prediction and comparison. Yet this approach is still inapplicable to many viral proteins. Therefore, we applied a powerful sequence-based procedure to identify distant homologues of viral proteins. It relies on three principles: (1) traces of sequence similarity can persist beyond the significance cutoff of homology detection programmes; (2) candidate homologues can be identified among proteins with weak sequence similarity to the query by using 'contextual' information, e.g. taxonomy or type of host infected; (3) these candidate homologues can be validated using highly sensitive profile-profile comparison. As a test case, this approach was applied to a protein without known homologues, encoded by ORF4 of Lake Sinai viruses (which infect bees). We discovered that the ORF4 protein contains a domain that has homologues in proteins from >20 taxa of viruses infecting arthropods. We called this domain 'widespread, intriguing, versatile' (WIV), because it is found in proteins with a wide variety of functions and within varied domain contexts. For example, WIV is found in the NSs protein of tospoviruses, a global threat to food security, which infect plants as well as their arthropod vectors; in the RNA2 ORF1-encoded protein of chronic bee paralysis virus, a widespread virus of bees; and in various proteins of cypoviruses, which infect the silkworm Bombyx mori. Structural modelling with AlphaFold indicated that the WIV domain has a previously unknown fold, and bibliographical evidence suggests that it facilitates infection of arthropods.
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Affiliation(s)
- David G Karlin
- Division Phytomedicine, Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55/57, D-14195 Berlin, Germany
- Independent Researcher, Marseille, France
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Parry RH, Slonchak A, Campbell LJ, Newton ND, Debat HJ, Gifford RJ, Khromykh AA. A novel tamanavirus ( Flaviviridae) of the European common frog ( Rana temporaria) from the UK. J Gen Virol 2023; 104:001927. [PMID: 38059479 PMCID: PMC10770923 DOI: 10.1099/jgv.0.001927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023] Open
Abstract
Flavivirids are small, enveloped, positive-sense RNA viruses from the family Flaviviridae with genomes of ~9-13 kb. Metatranscriptomic analyses of metazoan organisms have revealed a diversity of flavivirus-like or flavivirid viral sequences in fish and marine invertebrate groups. However, no flavivirus-like virus has been identified in amphibians. To remedy this, we investigated the virome of the European common frog (Rana temporaria) in the UK, utilizing high-throughput sequencing at six catch locations. De novo assembly revealed a coding-complete virus contig of a novel flavivirid ~11.2 kb in length. The virus encodes a single ORF of 3456 aa and 5' and 3' untranslated regions (UTRs) of 227 and 666 nt, respectively. We named this virus Rana tamanavirus (RaTV), as BLASTp analysis of the polyprotein showed the closest relationships to Tamana bat virus (TABV) and Cyclopterus lumpus virus from Pteronotus parnellii and Cyclopterus lumpus, respectively. Phylogenetic analysis of the RaTV polyprotein compared to Flavivirus and Flavivirus-like members indicated that RaTV was sufficiently divergent and basal to the vertebrate Tamanavirus clade. In addition to the Mitcham strain, partial but divergent RaTV, sharing 95.64-97.39 % pairwise nucleotide identity, were also obtained from the Poole and Deal samples, indicating that RaTV is widespread in UK frog samples. Bioinformatic analyses of predicted secondary structures in the 3'UTR of RaTV showed the presence of an exoribonuclease-resistant RNA (xrRNA) structure standard in flaviviruses and TABV. To examine this biochemically, we conducted an in vitro Xrn1 digestion assay showing that RaTV probably forms a functional Xrn1-resistant xrRNA.
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Affiliation(s)
- Rhys H. Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Andrii Slonchak
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
| | - Lewis J. Campbell
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Institute of Zoology, Zoological Society of London, London, UK
- Environment and Sustainability Institute, University of Exeter, Penryn, UK
| | - Natalee D. Newton
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
| | - Humberto J. Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola (UFYMA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba X5020ICA, Argentina
| | | | - Alexander A. Khromykh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre (AIDRC), Brisbane, QLD, Australia
- AIDRC Global Virus Network Centre of Excellence, Brisbane, QLD, Australia
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7
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Butina TV, Zemskaya TI, Bondaryuk AN, Petrushin IS, Khanaev IV, Nebesnykh IA, Bukin YS. Viral Diversity in Samples of Freshwater Gastropods Benedictia baicalensis (Caenogastropoda: Benedictiidae) Revealed by Total RNA-Sequencing. Int J Mol Sci 2023; 24:17022. [PMID: 38069344 PMCID: PMC10707223 DOI: 10.3390/ijms242317022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Previously, the main studies were focused on viruses that cause disease in commercial and farmed shellfish and cause damage to food enterprises (for example, Ostreavirusostreidmalaco1, Aurivirus haliotidmalaco1 and Aquabirnavirus tellinae). Advances in high-throughput sequencing technologies have extended the studies to natural populations of mollusks (and other invertebrates) as unexplored niches of viral diversity and possible sources of emerging diseases. These studies have revealed a huge diversity of mostly previously unknown viruses and filled gaps in the evolutionary history of viruses. In the present study, we estimated the viral diversity in samples of the Baikal endemic gastropod Benedictia baicalensis using metatranscriptomic analysis (total RNA-sequencing); we were able to identify a wide variety of RNA-containing viruses in four samples (pools) of mollusks collected at three stations of Lake Baikal. Most of the identified viral genomes (scaffolds) had only distant similarities to known viruses or (in most cases) to metagenome-assembled viral genomes from various natural samples (mollusks, crustaceans, insects and others) mainly from freshwater ecosystems. We were able to identify viruses similar to those previously identified in mollusks (in particular to the picornaviruses Biomphalaria virus 1 and Biomphalaria virus 3 from the freshwater gastropods); it is possible that picorna-like viruses (as well as a number of other identified viruses) are pathogenic for Baikal gastropods. Our results also suggested that Baikal mollusks, like other species, may bioaccumulate or serve as a reservoir for numerous viruses that infect a variety of organisms (including vertebrates).
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Affiliation(s)
| | - Tamara I. Zemskaya
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia; (T.V.B.); (A.N.B.); (I.S.P.); (I.V.K.); (I.A.N.); (Y.S.B.)
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8
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Ternovoi VA, Shvalov AN, Kartashov MY, Ponomareva EP, Tupota NL, Khoroshavin YA, Bayandin RB, Gladysheva AV, Mikryukova TP, Tregubchak TV, Loktev VB. The Viromes of Mosquitoes from the Natural Landscapes of Western Siberia. Viruses 2023; 15:1896. [PMID: 37766302 PMCID: PMC10537626 DOI: 10.3390/v15091896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
The metagenomic analysis of mosquitoes allows for the genetic characterization of mosquito-associated viruses in different regions of the world. This study applied a metagenomic approach to identify novel viral sequences in seven species of mosquitoes collected from the Novosibirsk region of western Siberia. Using NGS sequencing, we identified 15 coding-complete viral polyproteins (genomes) and 15 viral-like partial sequences in mosquitoes. The complete sequences for novel viruses or the partial sequences of capsid proteins, hypothetical viral proteins, and RdRps were used to identify their taxonomy. The novel viral sequences were classified within the orders Tymovirales and Picornavirales and the families Partitiviridae, Totiviridae, Tombusviridae, Iflaviridae, Nodaviridae, Permutotetraviridae, and Solemoviridae, with several attributed to four unclassified RNA viruses. Interestingly, the novel putative viruses and viral sequences were mainly associated with the mosquito Coquillettidia richardii. This study aimed to increase our understanding of the viral diversity in mosquitoes found in the natural habitats of Siberia, which is characterized by very long, snowy, and cold winters.
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Affiliation(s)
- Vladimir A. Ternovoi
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Alexander N. Shvalov
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Mikhail Yu. Kartashov
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Eugenia P. Ponomareva
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Natalia L. Tupota
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Yuri A. Khoroshavin
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Roman B. Bayandin
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Anastasia V. Gladysheva
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Tamara P. Mikryukova
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Tatyana V. Tregubchak
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Valery B. Loktev
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
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9
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Olendraite I, Brown K, Firth AE. Identification of RNA Virus-Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets. Mol Biol Evol 2023; 40:msad060. [PMID: 37014783 PMCID: PMC10101049 DOI: 10.1093/molbev/msad060] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/15/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023] Open
Abstract
RNA viruses are abundant and highly diverse and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost-effectively expand the diversity of known RNA virus sequences, we mined publicly available transcriptomic data sets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA-dependent RNA polymerase (RdRp)-the only universal "hallmark" gene of RNA viruses. By using these to search the National Center for Biotechnology Information Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analyzed their diversity, taxonomic classification, phylogeny, and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp Profile Hidden Markov Models provide a useful resource for the virus discovery community.
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Affiliation(s)
- Ingrida Olendraite
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Brown
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Andrew E Firth
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
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10
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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] [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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11
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Postler TS, Rubino L, Adriaenssens EM, Dutilh BE, Harrach B, Junglen S, Kropinski AM, Krupovic M, Wada J, Crane A, Kuhn JH, Mushegian A, Rūmnieks J, Sabanadzovic S, Simmonds P, Varsani A, Zerbini FM, Callanan J, Draper LA, Hill C, Stockdale SR. Guidance for creating individual and batch latinized binomial virus species names. J Gen Virol 2022; 103. [PMID: 36748479 DOI: 10.1099/jgv.0.001800] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains optional, a standardized nomenclature based on Latinized binomials has the advantage of comparability with all other biological taxonomies. As a language without living native speakers, Latin is more culturally neutral than many contemporary languages, and words built from Latin roots are already widely used in the language of science across the world. Conversion of established species names to Latinized binomials or creation of Latinized binomials de novo may seem daunting, but the rules for name creation are straightforward and can be implemented in a formulaic manner. Here, we describe approaches, strategies and steps for creating Latinized binomials for virus species without prior knowledge of Latin. We also discuss a novel approach to the automated generation of large batches of novel genus and species names. Importantly, conversion to a binomial format does not affect virus names, many of which are created from local languages.
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Affiliation(s)
- Thomas S Postler
- Department of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, 70126 Bari, Italy
| | | | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany.,Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, 3584 CH Utrecht, Netherlands
| | - Balázs Harrach
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary
| | - Sandra Junglen
- Institute of Virology, Charité - Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Andrew M Kropinski
- Departments of Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015 Paris, France
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Anya Crane
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Arcady Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, VA 22314, USA
| | - Jānis Rūmnieks
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Peter Simmonds
- Nuffield Department of Experimental Medicine, University of Oxford, Peter Medawar Building, Oxford, OX1 3SY, UK
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287-4701, USA.,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - F Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Julie Callanan
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
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12
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Colmant AMG, Charrel RN, Coutard B. Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses. Front Microbiol 2022; 13:997058. [PMID: 36299728 PMCID: PMC9589506 DOI: 10.3389/fmicb.2022.997058] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/22/2022] [Indexed: 11/21/2022] Open
Abstract
Jingmenviruses are a group of viruses identified recently, in 2014, and currently classified by the International Committee on Taxonomy of Viruses as unclassified Flaviviridae. These viruses closely related to flaviviruses are unique due to the segmented nature of their genome. The prototype jingmenvirus, Jingmen tick virus (JMTV), was discovered in Rhipicephalus microplus ticks collected from China in 2010. Jingmenviruses genomes are composed of four to five segments, encoding for up to seven structural proteins and two non-structural proteins, both of which display strong similarities with flaviviral non-structural proteins (NS2B/NS3 and NS5). Jingmenviruses are currently separated into two phylogenetic clades. One clade includes tick- and vertebrate-associated jingmenviruses, which have been detected in ticks and mosquitoes, as well as in humans, cattle, monkeys, bats, rodents, sheep, and tortoises. In addition to these molecular and serological detections, over a hundred human patients tested positive for jingmenviruses after developing febrile illness and flu-like symptoms in China and Serbia. The second phylogenetic clade includes insect-associated jingmenvirus sequences, which have been detected in a wide range of insect species, as well as in crustaceans, plants, and fungi. In addition to being found in various types of hosts, jingmenviruses are endemic, as they have been detected in a wide range of environments, all over the world. Taken together, all of these elements show that jingmenviruses correspond exactly to the definition of emerging viruses at risk of causing a pandemic, since they are already endemic, have a close association with arthropods, are found in animals in close contact with humans, and have caused sporadic cases of febrile illness in multiple patients. Despite these arguments, the vast majority of published data is from metagenomics studies and many aspects of jingmenvirus replication remain to be elucidated, such as their tropism, cycle of transmission, structure, and mechanisms of replication and restriction or epidemiology. It is therefore crucial to prioritize jingmenvirus research in the years to come, to be prepared for their emergence as human or veterinary pathogens.
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13
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Abstract
Flaviviruses are positive-sense single-stranded RNA viruses, including some well-known human pathogens such as Zika, dengue, and yellow fever viruses, which are primarily associated with mosquito and tick vectors. The vast majority of flavivirus research has focused on terrestrial environments; however, recent findings indicate that a range of flaviviruses are also present in aquatic environments, both marine and freshwater. These flaviviruses are found in various hosts, including fish, crustaceans, molluscs, and echinoderms. Although the effects of aquatic flaviviruses on the hosts they infect are not all known, some have been detected in farmed species and may have detrimental effects on the aquaculture industry. Exploration of the evolutionary history through the discovery of the Wenzhou shark flavivirus in both a shark and crab host is of particular interest since the potential dual-host nature of this virus may indicate that the invertebrate-vertebrate relationship seen in other flaviviruses may have a more profound evolutionary root than previously expected. Potential endogenous viral elements and the range of novel aquatic flaviviruses discovered thus shed light on virus origins and evolutionary history and may indicate that, like terrestrial life, the origins of flaviviruses may lie in aquatic environments.
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14
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Bamford CGG, de Souza WM, Parry R, Gifford RJ. Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae). Virus Evol 2022; 8:veac085. [PMID: 36533146 PMCID: PMC9752770 DOI: 10.1093/ve/veac085] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/06/2022] [Accepted: 09/05/2022] [Indexed: 01/24/2023] Open
Abstract
Flavivirids (family Flaviviridae) are a group of positive-strand ribonucleic acid (RNA) viruses that pose serious risks to human and animal health on a global scale. Here, we use flavivirid-derived deoxyribonucleic acid (DNA) sequences, identified in animal genomes, to reconstruct the long-term evolutionary history of family Flaviviridae. We demonstrate that flavivirids are >100 million years old and show that this timing can be combined with dates inferred from co-phyletic analysis to produce a cohesive overview of their evolution, distribution, and diversity wherein the main flavivirid subgroups originate in early animals and broadly co-diverge with major animal phyla. In addition, we reveal evidence that the 'classical flaviviruses' of vertebrates, most of which are transmitted via blood-feeding arthropod vectors, originally evolved in haematophagous arachnids and later acquired the capacity to be transmitted by insects. Our findings imply that the biological properties of flavivirids have been acquired gradually over the course of animal evolution. Thus, broad-scale comparative analysis will likely reveal fundamental insights into their biology. We therefore published our results via an open, extensible, database (Flavivirid-GLUE), which we constructed to facilitate the wider utilisation of genomic data and evolution-related domain knowledge in flavivirid research.
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15
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Schönegger D, Marais A, Faure C, Candresse T. A new flavi-like virus identified in populations of wild carrots. Arch Virol 2022; 167:2407-2409. [PMID: 35962825 DOI: 10.1007/s00705-022-05544-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/13/2022] [Indexed: 11/24/2022]
Abstract
We report the discovery of a new flavi-like virus identified in wild carrots (Daucus carota subsp. carota), using a double-stranded (ds)RNA high-throughput sequencing (HTS) approach. The new virus, tentatively named "carrot flavi-like virus 1" (CtFLV-1), has a large genome of 21.8 kb that harbours a single open reading frame encoding a 7,078-aa polyprotein with conserved RNA helicase (Hel) and RNA-dependent RNA polymerase (RdRp) domains. The new virus is phylogenetically related to recently described flavi-like viruses from arthropods, but its closest relative is a plant-associated virus, gentian Kobu-sho-associated virus (GKSaV). A pairwise comparison showed that these two viruses share 38.4% amino acid (aa) sequence identity in their polyproteins and 73% and 47.8% aa sequence identity in their conserved RdRp and Hel domains, respectively. Based on their similar genome organization and phylogenetic relationship, GKSaV and CtFLV-1 could form the basis for a new genus of plant-associated viruses, possibly within the family Flaviviridae, for which the name "Koshovirus" is proposed.
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Affiliation(s)
- Deborah Schönegger
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Chantal Faure
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France.
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16
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Pang Z, Jin Y, Pan M, Zhang Y, Wu Z, Liu L, Niu G. Geographical distribution and phylogenetic analysis of Jingmen tick virus in China. iScience 2022; 25:105007. [PMID: 36097615 PMCID: PMC9463580 DOI: 10.1016/j.isci.2022.105007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/08/2022] [Accepted: 08/19/2022] [Indexed: 11/26/2022] Open
Abstract
Jingmen tick virus (JMTV) is a novel tick-borne segmented RNA virus that is closely related to un-segmental RNA virus in evolution. It has been confirmed that JMTV could be a causative agent of human disease. In this study, a total of 3658 ticks were sampled from 7 provinces of China and then divided into 545 pools according to the location and species. QRT-PCR and nested PCR were performed to confirm the presence of JMTV. The results showed JMTV was identified in 5 out of 7 provinces with an average infection rate of 1.4% (51/3658). Phylogenetic analysis indicated that all JMTV strains identified in this study were closely related to each other and formed a well-supported sub-lineage. Our results provide molecular evidence of JMTV in different species of ticks from endemic and non-endemic regions and demonstrate that JMTV, as a natural foci pathogen, may be widely distributed all over China. JMTV was first identified in unrecognized endemic regions of China Two complete genomes and 13 partial S1 segments of JMTV were sequenced and analyzed JMTV was relatively conservative in evolution JMTV was widely distributed in China as a potential health threat to humans and animals
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17
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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; 14:1522. [PMID: 35891501 PMCID: PMC9319252 DOI: 10.3390/v14071522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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
| | - 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
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Xu Y, Jiang J, Lin X, Shi W, Cao C. Identification of Diverse Viruses Associated with Grasshoppers Unveils Parallel Relationship Between Host Phylogeny and Virome Composition. Virus Evol 2022; 8:veac057. [PMID: 35821717 PMCID: PMC9271882 DOI: 10.1093/ve/veac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/02/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
Grasshoppers (Orthoptera: Acridoidea) are one of the most dangerous agricultural pests. Environmentally benign microbial pesticides are increasingly desirable for controlling grasshopper outbreaks in fragile ecosystems. However, little is known about natural pathogens infecting this pest. Here we profile the rich viral communities in forty-five grasshopper species and report 302 viruses, including 231 novel species. Most of the identified viruses are related to other insect viruses, and small RNA sequencing indicates that some are targeted by host antiviral RNA interference (RNAi) pathway. Our analysis of relationships between host phylogeny and virus diversity suggests that the composition of viromes is closely allied with host evolution. Overall, this study is a first extensive exploration of viruses in grasshoppers and provides a valuable comparative dataset of both academic and applied interest.
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Affiliation(s)
- Yao Xu
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Jingyi Jiang
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Xiaoju Lin
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Wangpeng Shi
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
| | - Chuan Cao
- Department of Entomology, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China
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Abstract
Echinoderms are a phylum of marine invertebrates that include model organisms, keystone species, and animals commercially harvested for seafood. Despite their scientific, ecological, and economic importance, there is little known about the diversity of RNA viruses that infect echinoderms compared to other invertebrates. We screened over 900 transcriptomes and viral metagenomes to characterize the RNA virome of 38 echinoderm species from all five classes (Crinoidea, Holothuroidea, Asteroidea, Ophiuroidea and Echinoidea). We identified 347 viral genome fragments that were classified to genera and families within nine viral orders - Picornavirales, Durnavirales, Martellivirales, Nodamuvirales, Reovirales, Amarillovirales, Ghabrivirales, Mononegavirales, and Hepelivirales. We compared the relative viral representation across three life stages (embryo, larvae, adult) and characterized the gene content of contigs which encoded complete or near-complete genomes. The proportion of viral reads in a given transcriptome was not found to significantly differ between life stages though the majority of viral contigs were discovered from transcriptomes of adult tissue. This study illuminates the biodiversity of RNA viruses from echinoderms, revealing the occurrence of viral groups in natural populations.
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Affiliation(s)
- Elliot W Jackson
- Department of Microbiology, Cornell University, Ithaca, NY, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla CA, USA
| | - Roland C Wilhelm
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, NY, USA
| | - Daniel H Buckley
- Department of Microbiology, Cornell University, Ithaca, NY, USA.,School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, NY, USA
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY, USA
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Colmant AMG, Furlong MJ, Etebari K. Discovery of a Novel Jingmenvirus in Australian Sugarcane Soldier Fly ( Inopus flavus) Larvae. Viruses 2022; 14:v14061140. [PMID: 35746612 PMCID: PMC9229714 DOI: 10.3390/v14061140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/03/2022] [Accepted: 05/19/2022] [Indexed: 02/07/2023] Open
Abstract
In Australia, soldier flies are major pests of sugarcane, and they can cause significant yield losses in some areas, possibly due to the virus’ transmission to the plants. We sequenced fly larvae salivary glands and identified a novel jingmenvirus, putatively named Inopus flavus jingmenvirus 1 (IFJV1). Phylogenetic trees confirmed that IFJV1 groups with insect-associated jingmenviruses, newly identified flavivirus-like viruses with a segmented genome. After the design and the validation of molecular detection systems for IFJV1, larval homogenates were passaged on insect and vertebrate cells, but IFJV1 could only be detected in the first two passages in insect cells and not at all in vertebrate cells. Despite this lack of consistent replication in laboratory models, this virus does replicate in its host Inopus flavus, as sequenced, small RNA from the larvae matched the IFJV1 sequences. Moreover, they were found to be predominantly 21 nucleotides long and map to the whole sequences on both strands, which is typical of an actively replicating virus. This discovery confirms the worldwide presence of jingmenviruses which, until now, had only been detected on four continents. However, the study of IFJV1 tropism and the possible pathogenicity to its host or the sugarcane it parasitizes requires the development of a stable replication model.
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Affiliation(s)
- Agathe M. G. Colmant
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), 13005 Marseille, France;
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael J. Furlong
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence: (M.J.F.); (K.E.)
| | - Kayvan Etebari
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence: (M.J.F.); (K.E.)
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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] [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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Martinez-Mercado MA, de Jesús JLD, Galindo-Sánchez CE, Saavedra-Flores A, Carrillo-Tripp J. Novel viral RNA genomes of the vine mealybug Planococcus ficus. J Gen Virol 2022; 103. [PMID: 35259086 DOI: 10.1099/jgv.0.001717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The vine mealybug, Planococcus ficus (Signoret, 1875), is the most important insect pest in growing areas of the grapevine Vitis vinifera L. in several countries, including Mexico. In Mexico, Baja California (B.C.) is the region with the highest production of V. vinifera L. grapes for industrial purposes. Recently, the diversity of viruses infecting insects only (insect-specific viruses) has been broadly explored to elucidate further ecological viral-host interactions in many insect species, which in some cases has resulted in the application of virus-based biological control agents for insect pests. However, a survey of the Pl. ficus virome has not been done yet. In the present study, we pooled Pl. ficus individuals collected through different vineyards of Ensenada, B.C., Mexico and analysed them by meta-transcriptomics. Novel nearly complete genomes of five RNA viruses were retrieved. These viruses were related to the Iflaviridae and Reoviridae families, and to the Picornavirales and Tolivirales orders. A new isolate belonging to the Dicistroviridae family was also found. Phylogenetic analyses showed that these putative viral genomes group with viruses having hemipteran (including a mealybug species) or other insect hosts, or with viruses associated with insects. Our results suggest that the identified novel RNA viruses could be insect-specific viruses of Pl. ficus. This work is the first insight into the Pl. ficus virome; it guarantees further studies aimed to characterize those viruses with potential for application in biological control of this economically important insect.
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Affiliation(s)
- Miguel A Martinez-Mercado
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
| | - José Luis Duarte de Jesús
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
| | - Clara E Galindo-Sánchez
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
| | - Anaid Saavedra-Flores
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
| | - Jimena Carrillo-Tripp
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Baja California 22860, Mexico
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Abstract
The COVID-19 pandemic has given the study of virus evolution and ecology new relevance. Although viruses were first identified more than a century ago, we likely know less about their diversity than that of any other biological entity. Most documented animal viruses have been sampled from just two phyla - the Chordata and the Arthropoda - with a strong bias towards viruses that infect humans or animals of economic and social importance, often in association with strong disease phenotypes. Fortunately, the recent development of unbiased metagenomic next-generation sequencing is providing a richer view of the animal virome and shedding new light on virus evolution. In this Review, we explore our changing understanding of the diversity, composition and evolution of the animal virome. We outline the factors that determine the phylogenetic diversity and genomic structure of animal viruses on evolutionary timescales and show how this impacts assessment of the risk of disease emergence in the short term. We also describe the ongoing challenges in metagenomic analysis and outline key themes for future research. A central question is how major events in the evolutionary history of animals, such as the origin of the vertebrates and periodic mass extinction events, have shaped the diversity and evolution of the viruses they carry.
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Possible Arbovirus Found in Virome of Melophagus ovinus. Viruses 2021; 13:v13122375. [PMID: 34960644 PMCID: PMC8707155 DOI: 10.3390/v13122375] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 11/22/2022] Open
Abstract
Members of the Lipopteninae subfamily are blood-sucking ectoparasites of mammals. The sheep ked (Melophagus ovinus) is a widely distributed ectoparasite of sheep. It can be found in most sheep-rearing areas and can cause skin irritation, restlessness, anemia, weight loss and skin injuries. Various bacteria and some viruses have been detected in M. ovinus; however, the virome of this ked has never been studied using modern approaches. Here, we study the virome of M. ovinus collected in the Republic of Tuva, Russia. In our research, we were able to assemble full genomes for five novel viruses, related to the Rhabdoviridae (Sigmavirus), Iflaviridae, Reoviridae and Solemoviridae families. Four viruses were found in all five of the studied pools, while one virus was found in two pools. Phylogenetically, all of the novel viruses clustered together with various recently described arthropod viruses. All the discovered viruses were tested on their ability to replicate in the mammalian porcine embryo kidney (PEK) cell line. Aksy-Durug Melophagus sigmavirus RNA was detected in the PEK cell line cultural supernate after the first, second and third passages. Such data imply that this virus might be able to replicate in mammalian cells, and thus, can be considered as a possible arbovirus.
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