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Mogotsi MT, Ogunbayo AE, Bester PA, O'Neill HG, Nyaga MM. Longitudinal analysis of the enteric virome in paediatric subjects from the Free State Province, South Africa, reveals early gut colonisation and temporal dynamics. Virus Res 2024; 346:199403. [PMID: 38776984 PMCID: PMC11169482 DOI: 10.1016/j.virusres.2024.199403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/23/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
The gut of healthy neonates is devoid of viruses at birth, but rapidly becomes colonised by normal viral commensals that aid in important physiological functions like metabolism but can, in some instances, result in gastrointestinal illnesses. However, little is known about how this colonisation begins, its variability and factors shaping the gut virome composition. Thus, understanding the development, assembly, and progression of enteric viral communities over time is key. To explore early-life virome development, metagenomic sequencing was employed in faecal samples collected longitudinally from a cohort of 17 infants during their first six months of life. The gut virome analysis revealed a diverse and dynamic viral community, formed by a richness of different viruses infecting humans, non-human mammals, bacteria, and plants. Eukaryotic viruses were detected as early as one week of life, increasing in abundance and diversity over time. Most of the viruses detected are commonly associated with gastroenteritis and include members of the Caliciviridae, Picornaviridae, Astroviridae, Adenoviridae, and Sedoreoviridae families. The most common co-occurrences involved asymptomatic norovirus-parechovirus, norovirus-sapovirus, sapovirus-parechovirus, observed in at least 40 % of the samples. Majority of the plant-derived viruses detected in the infants' gut were from the Virgaviridae family. This study demonstrates the first longitudinal characterisation of the gastrointestinal virome in infants, from birth up to 6 months of age, in sub-Saharan Africa. Overall, the findings from this study delineate the composition and variability of the healthy infants' gut virome over time, which is a significant step towards understanding the dynamics and biogeography of viral communities in the infant gut.
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Affiliation(s)
- Milton Tshidiso Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Ayodeji Emmanuel Ogunbayo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Phillip Armand Bester
- Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Hester Gertruida O'Neill
- Department of Microbiology and Biochemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Martin Munene Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa.
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Li Y, Zhang L, Wang L, Li J, Zhao Y, Liu F, Wang Q. Structure and function of type IV IRES in picornaviruses: a systematic review. Front Microbiol 2024; 15:1415698. [PMID: 38855772 PMCID: PMC11157119 DOI: 10.3389/fmicb.2024.1415698] [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: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024] Open
Abstract
The Picornaviridae is a family of icosahedral viruses with single-stranded, highly diverse positive-sense RNA genomes. Virions consist of a capsid, without envelope, surrounding a core of RNA genome. A typical genome of picornavirus harbors a well-conserved and highly structured RNA element known as the internal ribosome entry site (IRES), functionally essential for viral replication and protein translation. Based on differences in their structures and mechanisms of action, picornaviral IRESs have been categorized into five types: type I, II, III, IV, and V. Compared with the type IV IRES, the others not only are structurally complicated, but also involve multiple initiation factors for triggering protein translation. The type IV IRES, often referred to as hepatitis C virus (HCV)-like IRES due to its structural resemblance to the HCV IRES, exhibits a simpler and more compact structure than those of the other four. The increasing identification of picornaviruses with the type IV IRES suggests that this IRES type seems to reveal strong retention and adaptation in terms of viral evolution. Here, we systematically reviewed structural features and biological functions of the type IV IRES in picornaviruses. A comprehensive understanding of the roles of type IV IRESs will contribute to elucidating the replication mechanism and pathogenesis of picornaviruses.
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Affiliation(s)
- Yan Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- Qingdao Center for Animal Disease Control and Prevention, Qingdao, China
| | - Lei Zhang
- Shandong New Hope Liuhe Group Co., Ltd., Qingdao, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao, China
| | - Jing Li
- Market Supervision Administration of Huangdao District, Qingdao, China
| | - Yanwei Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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de Moraes Pires WM, Cruz ACR, de Souza AJS, Silva SP, Souza Barbosa Coelho TF, Dias DD, Rosa Júnior JW, Mendes SB, da Costa Fraga E, Barros MC, Sampaio I. Genomic characterization of a novel Hepatovirus identified in Maranhão state, Brazil. Sci Rep 2024; 14:7981. [PMID: 38575654 PMCID: PMC10995186 DOI: 10.1038/s41598-024-58171-y] [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: 12/19/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Bats are efficient reservoirs of a number of viruses with zoonotic potential, and are involved directly in the transmission cycle of many zoonoses. In the present study, which is part of a larger project that is documenting the viromes of the bat species found in the Mid-North states of Maranhão and Piauí, we analyzed 16 pooled samples obtained from four species of bat of the genus Artibeus-Artibeus obscurus, Artibeus cinereus, Artibeus lituratus and Artibeus planirostris. We describe and identify a Hepatovirus, denominated Hepatovirus H isolate sotense, which was found in a pool of internal organs (liver and lungs) extracted from a specimen of A. planirostris, a frugivorous bat, collected in the Cerrado biome of Maranhão state. This material was analyzed using new generation sequencing, which produced a contig of 7390 nucleotides and presented a degree of identity with a number of existing Hepatovirus sequences available for bats (amino acid identity of 61.5% with Bat hepatovirus C of Miniopterus cf. manavi, 66.6% with Bat hepatovirus G of Coleura afra, 67.4% with Hepatovirus G2 of Rhinolophus landeri, and 75.3% with Hepatovirus H2 of Rhinolophus landeri). The analysis of the functional domains of this contig confirmed a pattern consistent with the characteristics of the genus Hepatovirus (Picornaviridae). In the phylogenetic tree with several other Hepatovirus species, this genome also grouped in a monophyletic clade with Hepatovirus H (HepV-H1; HepV-H2, and HepV-H3) albeit on an external branch, which suggests that it may be a distinct genotype within this species. This is the first isolate of Hepatovirus H identified in bats from South America, and represents an important discovery, given that most studies of viruses associated with bats in the state of Maranhão have focused on the family Rhabdoviridae.
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Affiliation(s)
| | - Ana Cecília Ribeiro Cruz
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | - Alex Junior Souza de Souza
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo, Brazil
| | - Sandro Patroca Silva
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | | | - Daniel Damous Dias
- Laboratory of Medical Entomology, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | - José Wilson Rosa Júnior
- Department of Arbovirology and Hemorrhagic Fevers, Instituto Evandro Chagas IEC/SVS/MS, Ananindeua, Pará, 67030-000, Brazil
| | - Samira Brito Mendes
- Graduate Program in Biodiversity and Biotechnology-Bionorte Network, Laboratory of Genetics and Molecular Biology, Universidade Estadual do Maranhão, São Luís, Maranhão, 65055-310, Brazil
| | - Elmary da Costa Fraga
- Laboratory of Genetics and Molecular Biology-GENBIMOL, Universidade Estadual Do Maranhão-Campus Caxias, Caxias, Maranhão, 65604-380, Brazil
| | - Maria Claudene Barros
- Laboratory of Genetics and Molecular Biology-GENBIMOL, Universidade Estadual Do Maranhão-Campus Caxias, Caxias, Maranhão, 65604-380, Brazil
| | - Iracilda Sampaio
- Laboratory of Evolution, Institute of Coastal Studies, Universidade Federal do Pará-UFPA-UFPA, Bragança, Pará, 68600-000, Brazil
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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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Stuehler DS, Hunter WB, Carrillo-Tarazona Y, Espitia H, Cicero JM, Bell T, Mann HR, Clarke SKV, Paris TM, Metz JL, D'Elia T, Qureshi JA, Cano LM. Wild lime psyllid Leuronota fagarae Burckhardt (Hemiptera: Psylloidea) picorna-like virus full genome annotation and classification. J Invertebr Pathol 2023; 201:107995. [PMID: 37748676 DOI: 10.1016/j.jip.2023.107995] [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: 06/04/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023]
Abstract
Picorna-like viruses of the order Picornavirales are a poorly defined group of positive-sense, single-stranded RNA viruses that include numerous pathogens known to infect plants, animals, and insects. A new picorna-like viral species was isolated from the wild lime psyllid (WLP), Leuronota fagarae, in the state of Florida, USA, and labelled: Leuronota fagarae picorna-like virus isolate FL (LfPLV-FL). The virus was found to have homology to a picorna-like virus identified in the Asian Citrus Psyllid (ACP), Diaphorina citri, collected in the state of Florida. Computational analysis of RNA extracts from WLP adult heads identified a 10,006-nucleotide sequence encoding a 2,942 amino acid polyprotein with similar functional domain structure to polyproteins of both Dicistroviridae and Iflaviridae. Sequence comparisons of nucleic acid and amino acid translations of the conserved RNA-dependent RNA polymerase, along with the entire N-terminal nonstructural coding region, provided insight into an evolutionary relationship of LfPLV-FL to insect-infecting iflaviruses. Viruses belonging to the family Iflaviridae encode a polyprotein of around 3000 amino acids in length that is processed post-translationally to produce components necessary for replication. The classification of a novel picorna-like virus in L. fagarae, with evolutionary characteristics similar to picorna-like viruses infecting Bactericera cockerelli and D. citri, provides an opportunity to examine virus host specificity, as well as identify critical components of the virus' genome required for successful transmission, infection, and replication. This bioinformatic classification allows for further insight into a novel virus species, and aids in the research of a closely related virus of the invasive psyllid, D. citri, a major pest of Floridian citriculture. The potential use of viral pathogens as expression vectors to manage the spread D. citri is an area that requires additional research; however, it may bring forth an effective control strategy to reduce the transmission of Candidatus Liberibacter asiaticus (CLas), the causative agent of Huanglongbing (HLB).
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Affiliation(s)
- Douglas S Stuehler
- ORISE Participant, DOE/USDA, ARS, Fort Pierce, FL 34945, USA; USDA, ARS, 2001 South Rock Road, Fort Pierce, FL 34945, USA.
| | - Wayne B Hunter
- USDA, ARS, 2001 South Rock Road, Fort Pierce, FL 34945, USA.
| | - Yisel Carrillo-Tarazona
- University of Florida, IFAS, Department of Plant Pathology, Indian River Research and Education Center, Fort Pierce, FL 34945, USA.
| | - Hector Espitia
- University of Florida, IFAS, Department of Plant Pathology, Indian River Research and Education Center, Fort Pierce, FL 34945, USA.
| | - Joseph M Cicero
- University of Florida, IFAS, Department of Plant Pathology, Indian River Research and Education Center, Fort Pierce, FL 34945, USA
| | - Tracey Bell
- Indian River State College, Fort Pierce, FL 34949, USA.
| | - Hannah R Mann
- Indian River State College, Fort Pierce, FL 34949, USA
| | | | - Thomson M Paris
- ORISE Participant, DOE/USDA, ARS, Fort Pierce, FL 34945, USA; USDA, ARS, 2001 South Rock Road, Fort Pierce, FL 34945, USA.
| | - Jackie L Metz
- University of Florida, IFAS, Department of Plant Pathology, Indian River Research and Education Center, Fort Pierce, FL 34945, USA.
| | - Tom D'Elia
- Department of Biology, Indian River State College, Fort Pierce, FL 34949, USA.
| | - Jawwad A Qureshi
- University of Florida, Southwest Florida Research and Education Center (SWFREC), 2685 SR 29 North Immokalee, FL 34142, USA.
| | - Liliana M Cano
- University of Florida, IFAS, Department of Plant Pathology, Indian River Research and Education Center, Fort Pierce, FL 34945, USA.
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Zhao Q, Zhao R, Sun Y, Ji L, Xi Y, Wang X, Shen Q, Ji L, Wang Y, You Z, Yang S, Zhang W. Identification of Multiple Novel Viruses in Fecal Samples of Black-Necked Cranes Using Viral Metagenomic Methods. Viruses 2023; 15:2068. [PMID: 37896845 PMCID: PMC10612090 DOI: 10.3390/v15102068] [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: 09/11/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
The black-necked crane is the only species of crane that lives in the high-altitude region of the Tibet Plateau. At present, there is little research on viral diseases of the black-necked crane (Grus nigricollis). In this study, a viral metagenomic approach was employed to investigate the fecal virome of black-necked cranes in Saga County, Shigatse City, Tibet, China. The identified virus families carried by black-necked cranes mainly include Genomoviridae, Parvoviridae, and Picornaviridae. The percentages of sequence reads belonging to these three virus families were 1.6%, 3.1%, and 93.7%, respectively. Among them, one genome was characterized as a novel species in the genus Grusopivirus of the family Picornaviridae, four new parvovirus genomes were obtained and classified into four different novel species within the genus Chaphamaparvovirus of the subfamily Hamaparvovirinae, and four novel genomovirus genomes were also acquired and identified as members of three different species, including Gemykroznavirus haeme1, Gemycircularvirus ptero6, and Gemycircularvirus ptero10. All of these viruses were firstly detected in fecal samples of black-necked cranes. This study provides valuable information for understanding the viral community composition in the digestive tract of black-necked cranes in Tibet, which can be used for monitoring, preventing, and treating potential viral diseases in black-necked cranes.
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Affiliation(s)
- Qifan Zhao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Ran Zhao
- Department of Prevention and Control, Xiamen Animal Disease Prevention and Control Center, Xiamen 361009, China;
| | - Yijie Sun
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Li Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Yuan Xi
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Yan Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Zhenqiang You
- School of Public Health, Hangzhou Medical College, Hangzhou 310013, China;
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
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7
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Cao X, Wang Z, Pang J, Sun L, Kondo H, Andika IB. Identification of a novel dicistro-like virus associated with the roots of tomato plants. Arch Virol 2023; 168:214. [PMID: 37523067 DOI: 10.1007/s00705-023-05843-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023]
Abstract
Viruses belonging to the family Dicistroviridae have a monopartite positive-sense single-stranded RNA genome and infect a variety of arthropods. Using high-throughput sequencing, we detected a novel dicistro-like virus, tentatively named "tomato root-associated dicistro-like virus" (TRaDLV), in the roots of tomato plants showing yellow mosaic symptoms on the leaves. The diseased tomato plants were coinfected with multiple plant viruses, and TRaDLV was present in the roots but not in the leaves. The genome of TRaDLV is 8726 nucleotides in length, excluding the poly(A) tail, and contains two open reading frames (ORFs) separated by an intergenic region (IGR). The TRaDLV genome showed characteristics similar to those of dicistroviruses, including the presence of a 3C-like protease domain, repeated amino acid sequences representing multiple copies of viral genome-linked protein (VPg)-like sequences in the ORF1 polyprotein, and a series of stem-loop structures resembling an internal ribosome entry site in the IGR. Phylogenetic analysis revealed that TRaDLV clustered with unclassified dicistro-like viruses from invertebrates or identified in samples of plant-derived material. These findings indicate the existence of a novel dicistro-like virus that may associate with plant roots or a root-inhabiting organism.
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Affiliation(s)
- Xinran Cao
- College of Plant Health and Medicine, Qingdao Agricultural University, 266109, Qingdao, China
- Shandong Agricultural University, 271018, Tai'an, China
- Shouguang International vegetable Sci-tech Fair Management Service Center, 262700, Shouguang, China
| | - Ziqi Wang
- College of Plant Health and Medicine, Qingdao Agricultural University, 266109, Qingdao, China
| | - Jianguo Pang
- University Library, Northwest A&F University, 712100, Xianyang, China
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, 712100, Xianyang, China
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, 710-0046, Kurashiki, Japan
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, 266109, Qingdao, China.
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Zhang Y, Ye ZX, Feng XX, Xu ZT, Chen JP, Zhang CX, Li JM. Prevalence of Reversed Genome Organizations for Viruses in the Family Iflaviridae, Order Picornavirales. Microbiol Spectr 2023; 11:e0473822. [PMID: 37125908 PMCID: PMC10269833 DOI: 10.1128/spectrum.04738-22] [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: 11/19/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Viruses in the order Picornavirales possess a positive-strand RNA genome that encodes structural proteins (SPs) and nonstructural proteins (NSPs). According to the recent report of the International Committee on Taxonomy of Viruses (ICTV), there are 8 families in Picornavirales, and monopartite picornaviruses in each family exhibit distinct types of genome organizations with rearranged genes coding for SPs and NSPs, namely, TypeI (5'-SPs-NSPs-3') and TypeII (5'-NSPs-SPs-3'). In the present study, 2 iflaviruses with the 2 genome types were unexpectedly identified in a damselfly host species, suggesting that these 2 genome types coexisted in the same host species, and the families of order Picornavirales might be more complex than previously thought. The consequent systematic homologous screening with all the publicly available picornaviruses successfully revealed a considerable number of candidates rearranged genome types of picornaviruses in various families of Picornavirales. Subsequently, phylogenetic trees were reconstructed based on RNA dependent RNA polymerase and coat protein, which evidently confirmed the prevalence of the 10 typeII iflaviruses in the Iflaviridae family. This suggests that genome types may not be relevant to viral taxonomy in this family. However, candidate picornaviruses with reversed genome types in the Secoviridae and Dicistroviridae families require further investigation. All in all, as the number of newly discovered viruses increases, more viruses with non-canonical genome arrangements will be uncovered, which can expand our current knowledge on the genome complexity and evolution of picornaviruses. IMPORTANCE Monopartite viruses in the order Picornavirales exhibit distinct genome arrangement of nonstructural proteins and structural proteins for each of the 8 families. Recent studies indicated that at least 4 ifla-like viruses possessed reversed genome organization in the family Iflaviridae, raising the possibility that this phenomenon may commonly present in different families of picornaviruses. Since we discovered 2 iflaviruses with exchanged structural and nonstructural proteins simultaneously in the damselfly, a systematic screening was subsequently performed for all of the current available picornaviruses (1,543 candidates). The results revealed 10 picornaviruses with reversed genome organization in the family Iflaviridae, implying that this phenomenon might prevalence in the order Picornavirales. These results will contribute to a better understanding for the future study on the genome complexity and taxonomy of picornaviruses.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
- College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Xiao-Xiao Feng
- Agricultural Experiment Station, Zhejiang University, Hangzhou, China
| | - Zhong-Tian Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
- College of Plant Protection, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
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9
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Chen B, Chen Y, Chen H, Liang Z, Chen J, Wu R, Zhang T, Zhou G, Yang X. Identification, characterization and prevalence in southern China of a new iflavirus in the leafhopper Recilia dorsalis (Hemiptera: Cicadellidae). Virus Res 2023; 323:199005. [PMID: 36410611 PMCID: PMC10194291 DOI: 10.1016/j.virusres.2022.199005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022]
Abstract
The leafhopper Recilia dorsalis (Hemiptera: Cicadellidae) is not only a significant pest in agriculture but also an important vector involved in transmitting numerous pathogens that are known to cause economic losses by affecting rice crops. Here, a new iflavirus was discovered in the leafhopper R. dorsalis by employing a transcriptomic approach. The complete viral genome was determined to be 10,711 nucleotides (nt) in length and contains a single open reading frame (ORF) encoding a putative polyprotein comprised of 3,161 amino acids (aa), which is flanked by 5' and 3' untranslated regions. The full viral genome nt and the deduced polyprotein aa sequence showed the highest similarity (71.6% and 77.8%, respectively) with Langfang leafhopper iflavirus. Phylogenetic analysis based on the RdRp domain indicated that the isolated virus, which we have tentatively named Recilia dorsalis iflavirus 2 (RdIV2), is clustered with the members of the family Iflaviridae. Moreover, the results of our surveys indicate that RdIV2 predominates in southwestern Guangdong and southeastern Guangxi, China, and was absent in the other three species of leafhoppers; Nephotettix cincticeps, N. virescens and N. nigropictus. Notably, R. dorsalis was found to be co-infected with RdIV2 and rice stripe mosaic virus (RSMV; a well-known rice-infecting virus vectored by R. dorsalis) in rice fields, although the co-infection rate is low.
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Affiliation(s)
- Biao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yulu Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Huazhou Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Zhenyi Liang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Jiahao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Ruifeng Wu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China.
| | - Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China.
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10
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Vieira AC, Lopes ÍS, Fonseca PLC, Olmo RP, Bittencourt F, de Vasconcelos LM, Pirovani CP, Gaiotto FA, Aguiar ERGR. Expanding the environmental virome: Infection profile in a native rainforest tree species. Front Microbiol 2022; 13:874319. [PMID: 35992690 PMCID: PMC9387356 DOI: 10.3389/fmicb.2022.874319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 06/29/2022] [Indexed: 11/21/2022] Open
Abstract
Agroforestry systems (AFS) for cocoa production combine traditional land-use practices with local biodiversity conservation, resulting in both ecological and agricultural benefits. The cacao-cabruca AFS model is widely implemented in regions of the Brazilian Atlantic Forest. Carpotroche brasiliensis (Raddi) A. Gray (Achariaceae) is a tree found in cabruca landscapes that is often used for reforestation and biotechnological applications. Despite its importance, we still lack information about viruses circulating in C. brasiliensis, particularly considering the possibility of spillover that could affect cocoa production. In our study, we analyzed the Carpotroche brasiliensis virome from Atlantic Forest and cacao-cabruca AFS regions using metatranscriptomics from several vegetative and reproductive organs. Our results revealed a diverse virome detecting near-complete or partial coding sequences of single- and double-stranded DNA and RNA viruses classified into at least six families (Botourmiaviridae, Bromoviridae, Caulimoviridae, Genomoviridae, Mitoviridae, and Rhabdoviridae) plus unclassified elements. We described with high confidence the near-complete and the partial genomes of two tentative novel viruses: Carpotroche-associated ilarvirus and Carpotroche-associated genomovirus, respectively. Interestingly, we also described sequences likely derived from a rhabdovirus, which could represent a novel member of the genus Gammanucleorhabdovirus. We observed higher viral diversity in cacao-cabruca AFS and reproductive organs of C. brasiliensis with preferential tropism to fruits, which could directly affect production. Altogether, our results provide data to better understand the virome in this unexplored agroecological interface, such as cacao-cabruca AFS and forest ecosystem, providing information on the aspects of virus–plant interactions.
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Affiliation(s)
- Anderson Carvalho Vieira
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Ícaro Santos Lopes
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paula Luize Camargos Fonseca
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
- Department of Genetics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Flora Bittencourt
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | | | - Carlos Priminho Pirovani
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Fernanda Amato Gaiotto
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
- *Correspondence: Fernanda Amato Gaiotto,
| | - Eric Roberto Guimarães Rocha Aguiar
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
- Eric Roberto Guimarães Rocha Aguiar,
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11
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Weinberg M, Yovel Y. Revising the paradigm: Are bats really pathogen reservoirs or do they possess an efficient immune system? iScience 2022; 25:104782. [PMID: 35982789 PMCID: PMC9379578 DOI: 10.1016/j.isci.2022.104782] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While bats are often referred to as reservoirs of viral pathogens, a meta-analysis of the literature reveals many cases in which there is not enough evidence to claim so. In many cases, bats are able to confront viruses, recover, and remain immune by developing a potent titer of antibodies, often without becoming a reservoir. In other cases, bats might have carried an ancestral virus that at some time point might have mutated into a human pathogen. Moreover, bats exhibit a balanced immune response against viruses that have evolved over millions of years. Using genomic tools, it is now possible to obtain a deeper understanding of that unique immune system and its variability across the order Chiroptera. We conclude, that with the exception of a few viruses, bats pose little zoonotic danger to humans and that they operate a highly efficient anti-inflammatory response that we should strive to understand.
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Affiliation(s)
- Maya Weinberg
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Corresponding author
| | - Yossi Yovel
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
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12
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Zell R, Groth M, Selinka L, Selinka HC. Picorna-Like Viruses of the Havel River, Germany. Front Microbiol 2022; 13:865287. [PMID: 35444619 PMCID: PMC9013969 DOI: 10.3389/fmicb.2022.865287] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
To improve the understanding of the virome diversity of riverine ecosystems in metropolitan areas, a metagenome analysis was performed with water collected in June 2018 from the river Havel in Berlin, Germany. After enrichment of virus particles and RNA extraction, paired-end Illumina sequencing was conducted and assignment to virus groups and families was performed. This paper focuses on picorna-like viruses, the most diverse and abundant group of viruses with impact on human, animal, and environmental health. Here, we describe altogether 166 viral sequences ranging in size from 1 to 11.5 kb. The 71 almost complete genomes are comprised of one candidate iflavirus, one picornavirus, two polycipiviruses, 27 marnaviruses, 27 dicistro-like viruses, and 13 untypeable viruses. Many partial picorna-like virus sequences up to 10.2 kb were also investigated. The sequences of the Havel picorna-like viruses represent genomes of seven of eight so far known Picornavirales families. Detection of numerous distantly related dicistroviruses suggests the existence of additional, yet unexplored virus groups with dicistronic genomes, including few viruses with unusual genome layout. Of special interest is a clade of dicistronic viruses with capsid protein-encoding sequences at the 5′-end of the genome. Also, monocistronic viruses with similarity of their polymerase and capsid proteins to those of dicistroviruses are interesting. A second protein with NTP-binding site present in the polyprotein of solinviviruses and related viruses needs further attention. The results underline the importance to study the viromes of fluvial ecosystems. So far acknowledged marnaviruses have been isolated from marine organisms. However, the present study and available sequence data suggest that rivers and limnic habitats are relevant ecosystems with circulation of marnaviruses as well as a plethora of unknown picorna-like viruses.
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Affiliation(s)
- Roland Zell
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Marco Groth
- CF DNA Sequencing, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Lukas Selinka
- Section of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Hans-Christoph Selinka
- Section II 1.4 Microbiological Risks, Department of Environmental Hygiene, German Environment Agency, Berlin, Germany
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13
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Enterovirus Sequence Data Obtained from Primate Samples in Central Africa Suggest a High Prevalence of Enteroviruses. Microbiol Resour Announc 2021; 10:e0088221. [PMID: 34881972 PMCID: PMC8656378 DOI: 10.1128/mra.00882-21] [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] [Indexed: 11/24/2022] Open
Abstract
Enteroviruses infect humans and animals and can cause disease, and some may be transmitted across species barriers. We tested Central African wildlife and found Enterovirus RNA in primates (17) and rodents (2). Some sequences were very similar, while others were dissimilar to known species, highlighting the underexplored enterovirus diversity in wildlife.
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14
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Zhang T, Li C, Cao M, Wang D, Wang Q, Xie Y, Gao S, Fu S, Zhou X, Wu J. A Novel Rice Curl Dwarf-Associated Picornavirus Encodes a 3C Serine Protease Recognizing Uncommon EPT/S Cleavage Sites. Front Microbiol 2021; 12:757451. [PMID: 34721366 PMCID: PMC8549817 DOI: 10.3389/fmicb.2021.757451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Picornaviruses cause diseases in a wide range of vertebrates, invertebrates and plants. Here, a novel picornavirus was identified by RNA-seq technology from rice plants showing dwarfing and curling symptoms, and the name rice curl dwarf-associated virus (RCDaV) is tentatively proposed. The RCDaV genome consists of an 8,987 nt positive-stranded RNA molecule, excluding a poly(A) tail, that encodes two large polyproteins. Using in vitro cleavage assays, we have identified that the RCDaV 3C protease (3Cpro) as a serine protease recognizes the conserved EPT/S cleavage site which differs from the classic Q(E)/G(S) sites cleaved by most picornaviral 3C chymotrypsin-like cysteine proteases. Therefore, we comprehensively deciphered the RCDaV genome organization and showed that the two polyproteins of RCDaV can be cleaved into 12 mature proteins. We found that seven unclassified picornaviruses also encode a 3Cpro similar to RCDaV, and use the highly conserved EPT/S as the cleavage site. The precise genome organizations of these viruses were illustrated. Moreover, RCDaV and the seven unclassified picornaviruses share high sequence identities and similar genome organizations, and cluster into a distinct clade in the order Picornavirales. Our study provides valuable information for the understanding of picornaviral 3Cpros, deciphers the genome organization of a few relatively obscure picornaviruses, and lays the foundation for further pathogenesis research on these viruses.
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Affiliation(s)
- Tianze Zhang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chenyang Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, China
| | - Dan Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Qi Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yi Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Shibo Gao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuai Fu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.,Hainan Research Institute of Zhejiang University, Hainan, China
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15
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Han Z, Song Y, Xiao J, Zhao X, Lu H, Zhang K, Jia S, Zhou J, Li J, Si F, Sun Q, Zhu S, Wang D, Yan D, Xu W, Fu X, Zhang Y. Monsavirus in monkey rectal swab and throat swab specimens in China: Proposal for Posaliviridae as a new family in Picornavirales. Virus Res 2021; 303:198501. [PMID: 34252491 DOI: 10.1016/j.virusres.2021.198501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/16/2022]
Abstract
Posa-like viruses have been detected in the fecal samples of several host species and are considered unclassified members of Picornavirales. Here, we identified genomic fragments of novel posa-like viruses (monsaviruses) in monkey specimens through next generation sequencing and obtained 11 full-length genomes. This monsavirus shared 88.5-89.2% nucleotide similarity with the Tottori-HG1 strain (GenBank accession LC123275). In total, 713 nucleotide polymorphism sites were identified, indicating their persistent evolution during circulation. The genomic organization and phylogenetic relationship of monsavirus were determined. Subsequent phylogenetic analysis of the conserved replication block of Hel-Pro-RdRp and core RNA-dependent RNA polymerase domain-based analysis of posa-like viruses showed significant separation compared with other known families. Further, posa-like virus genomes possessed the classical replication block of picornavirus in the 5' part of genome and picorna-like capsid domains at the structural coding region of 3' part of genome. Based on these results, we proposed the new family Posaliviridae, within Picornavirales. Four genera, which showed 68.6-75.5% amino acid distances but similar genomic organization including the conserved replication block of Hel-Pro-RdRp, the same order of the genomic coding region, and picorna-like capsid domains, were identified. The flexible genomic organization strategy and a large evolutionary scale of Posaliviridae was explicit. This study provides novel information on monsaviruses and important taxonomic data for the family Posaliviridae.
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Affiliation(s)
- Zhenzhi Han
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yang Song
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jinbo Xiao
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xiaonan Zhao
- Yunnan Center for Disease Control and Prevention, Kunming 650022, PR China
| | - Huanhuan Lu
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Keyi Zhang
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Senquan Jia
- Yunnan Center for Disease Control and Prevention, Kunming 650022, PR China
| | - Jienan Zhou
- Yunnan Center for Disease Control and Prevention, Kunming 650022, PR China
| | - Junhan Li
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Fenfen Si
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Qiang Sun
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shuangli Zhu
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dongyan Wang
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dongmei Yan
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Wenbo Xu
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China; Center for Biosafety Mega-Science, Chinese Academy of Sciences. Wuhan 430071, PR China
| | - Xiaoqing Fu
- Yunnan Center for Disease Control and Prevention, Kunming 650022, PR China.
| | - Yong Zhang
- National Laboratory for poliomyelitis, WHO WPRO Regional Polio Reference Laboratory, NHC Key Laboratory for Medical Virology, NHC Key Laboratory for Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China; Center for Biosafety Mega-Science, Chinese Academy of Sciences. Wuhan 430071, PR China.
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16
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Lazov CM, Belsham GJ, Bøtner A, Rasmussen TB. Full-Genome Sequences of Alphacoronaviruses and Astroviruses from Myotis and Pipistrelle Bats in Denmark. Viruses 2021; 13:1073. [PMID: 34199948 PMCID: PMC8229204 DOI: 10.3390/v13061073] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 12/16/2022] Open
Abstract
Bat species worldwide are receiving increased attention for the discovery of emerging viruses, cross-species transmission, and zoonoses, as well as for characterizing virus infections specific to bats. In a previous study, we investigated the presence of coronaviruses in faecal samples from bats at different locations in Denmark, and made phylogenies based on short, partial ORF1b sequences. In this study, selected samples containing bat coronaviruses from three different bat species were analysed, using a non-targeted approach of next-generation sequencing. From the resulting metagenomics data, we assembled full-genome sequences of seven distinct alphacoronaviruses, three astroviruses, and a polyomavirus, as well as partial genome sequences of rotavirus H and caliciviruses, from the different bat species. Comparisons to published sequences indicate that the bat alphacoronaviruses belong to three different subgenera-i.e., Pedacovirus, Nyctacovirus, and Myotacovirus-that the astroviruses may be new species in the genus Mamastrovirus, and that the polyomavirus could also be a new species, but unassigned to a genus. Furthermore, several viruses of invertebrates-including two Rhopalosiphum padi (aphid) viruses and a Kadipiro virus-present in the faecal material were assembled. Interestingly, this is the first detection in Europe of a Kadipiro virus.
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Affiliation(s)
- Christina M. Lazov
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark;
| | - Graham J. Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (G.J.B.); (A.B.)
| | - Anette Bøtner
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (G.J.B.); (A.B.)
| | - Thomas Bruun Rasmussen
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen, Denmark
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17
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Dastjerdi A, Everest DJ, Davies H, Denk D, Zell R. A novel dicistrovirus in a captive red squirrel ( Sciurus vulgaris). J Gen Virol 2021; 102. [PMID: 33565956 DOI: 10.1099/jgv.0.001555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Dicistroviruses are single-stranded RNA viruses in the family Dicistroviridae. The viruses have mainly been detected in arthropods and are the cause of several devastating diseases in many of these species such as honeybees. Increasingly, dicistroviruses have also been detected in both mammalian and avian species in faeces, blood and liver, but with unconfirmed pathology. Here, we report a novel dicistrovirus detected in the intestinal content of a captive red squirrel with enteritis along with the disease history, pathology and genomic characterisation of the virus. Virus particle morphology resembled those of picornaviruses with a diameter of 28-32 nm but failed to be detected using a mammalian/avian pan viral microarray. Next-generation sequencing confirmed a dicistrovirus having a typical dicistrovirus genome organization, but with the polyprotein 1 being shorter by about 100 amino acids, compared to that of other dicistroviruses. Phylogenetic analysis of ORF1 and ORF2 sequences clustered the virus with two yet unassigned dicistroviruses detected in Gorilla gorilla and a freshwater arthropod and likely to be designated to a new genus. Our data further highlights the ever-growing diversity of dicistroviruses, but the clinical significance of the virus in mammalian species and particularly red squirrels has yet to be established.
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Affiliation(s)
- Akbar Dastjerdi
- Animal and Plant Health Agency (APHA)-Weybridge, Addlestone, Surrey, KT15 3NB, UK
| | - David J Everest
- Animal and Plant Health Agency (APHA)-Weybridge, Addlestone, Surrey, KT15 3NB, UK
| | - Hannah Davies
- School of Veterinary Medicine, University of Surrey, Guildford, GU2 7XH, UK.,Animal and Plant Health Agency (APHA)-Weybridge, Addlestone, Surrey, KT15 3NB, UK
| | - Daniela Denk
- International Zoo Veterinary Group (IZVG), Station House, Parkwood Street, Keighley, West Yorkshire, BD21 4NQ, UK
| | - Roland Zell
- Section for Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich-Schiller-Universität Jena, Hans-Knöll-Str. 2, Germany
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18
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Jia W, Wang F, Li J, Chang X, Yang Y, Yao H, Bao Y, Song Q, Ye G. A Novel Iflavirus Was Discovered in Green Rice Leafhopper Nephotettix cincticeps and Its Proliferation Was Inhibited by Infection of Rice Dwarf Virus. Front Microbiol 2021; 11:621141. [PMID: 33488564 PMCID: PMC7820178 DOI: 10.3389/fmicb.2020.621141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022] Open
Abstract
The green rice leafhopper, Nephotettix cincticeps (Hemiptera: Cicadellidae), is a key insect vector transmitting rice dwarf virus (RDV) that causes rice dwarf disease. We discovered a novel iflavirus from the transcriptomes of N. cincticeps and named it as Nephotettix cincticeps positive-stranded RNA virus-1 (NcPSRV-1). The viral genome consists of 10,524 nucleotides excluding the poly(A) tail and contains one predicted open reading frame encoding a polyprotein of 3,192 amino acids, flanked by 5' and 3' untranslated regions. NcPSRV-1 has a typical iflavirus genome arrangement and is clustered with the members of the family Iflaviridae in the phylogenetic analysis. NcPSRV-1 was detected in all tested tissues and life stages of N. cincticeps and could be transmitted horizontally and vertically. Moreover, NcPSRV-1 had high prevalence in the laboratory populations and was widely spread in field populations of N. cincticeps. NcPSRV-1 could also infect the two-striped leafhopper, Nephotettix apicalis, at a 3.33% infection rate, but was absent in the zigzag leafhopper, Recilia dorsalis, and rice Oryza sativa variety TN1. The infection of RDV altered the viral load and infection rate of NcPSRV-1 in N. cincticeps, for which it seems that RDV has an antagonistic effect on NcPSRV-1 infection in the host.
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Affiliation(s)
- Wenxi Jia
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jingjing Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, United States
| | - Xuefei Chang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yi Yang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hongwei Yao
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yanyuan Bao
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, United States
| | - Gongyin Ye
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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19
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Kuhn JH, Sibley SD, Chapman CA, Knowles NJ, Lauck M, Johnson JC, Lawson CC, Lackemeyer MG, Valenta K, Omeja P, Jahrling PB, O’Connor DH, Goldberg TL. Discovery of Lanama Virus, a Distinct Member of Species Kunsagivirus C ( Picornavirales: Picornaviridae), in Wild Vervet Monkeys ( Chlorocebus pygerythrus). Viruses 2020; 12:v12121436. [PMID: 33327396 PMCID: PMC7764893 DOI: 10.3390/v12121436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 11/16/2022] Open
Abstract
We report the discovery and sequence-based molecular characterization of a novel virus, lanama virus (LNMV), in blood samples obtained from two wild vervet monkeys (Chlorocebus pygerythrus), sampled near Lake Nabugabo, Masaka District, Uganda. Sequencing of the complete viral genomes and subsequent phylogenetic analysis identified LNMV as a distinct member of species Kunsagivirus C, in the undercharacterized picornavirid genus Kunsagivirus.
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Affiliation(s)
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (J.C.J.); (C.C.L.); (M.G.L.); (P.B.J.)
- Correspondence: (J.H.K.); (T.L.G.); Tel.: +1-301-631-7245 (J.H.K.); +1-608-890-2618 (T.L.G.)
| | - Samuel D. Sibley
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Colin A. Chapman
- Department of Anthropology, Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA;
- School of Life Sciences, Pietermaritzburg Campus, University of KwaZulu-Natal, Scottsville 3209, South Africa
- Shaanxi Key Laboratory for Animal Conservation, School of Life Sciences, Northwest University, Xi’an 710069, China
- Makerere University Biological Field Station, P.O. Box 409, Fort Portal, Uganda;
| | - Nick J. Knowles
- The Pirbright Institute, Pirbright, Woking, Surrey GU24 0NF, UK;
| | - Michael Lauck
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (M.L.); (D.H.O.)
| | - Joshua C. Johnson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (J.C.J.); (C.C.L.); (M.G.L.); (P.B.J.)
| | - Cristine Campos Lawson
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (J.C.J.); (C.C.L.); (M.G.L.); (P.B.J.)
| | - Matthew G. Lackemeyer
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (J.C.J.); (C.C.L.); (M.G.L.); (P.B.J.)
| | - Kim Valenta
- Department of Anthropology, University of Florida, Gainesville, FL 32603, USA;
| | - Patrick Omeja
- Makerere University Biological Field Station, P.O. Box 409, Fort Portal, Uganda;
| | - Peter B. Jahrling
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (J.C.J.); (C.C.L.); (M.G.L.); (P.B.J.)
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; (M.L.); (D.H.O.)
- Wisconsin National Primate Research Center, Madison, WI 53715, USA
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA;
- Correspondence: (J.H.K.); (T.L.G.); Tel.: +1-301-631-7245 (J.H.K.); +1-608-890-2618 (T.L.G.)
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20
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Thekke-Veetil T, Lagos-Kutz D, McCoppin NK, Hartman GL, Ju HK, Lim HS, Domier LL. Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses. Viruses 2020; 12:E1376. [PMID: 33271916 PMCID: PMC7761488 DOI: 10.3390/v12121376] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/21/2020] [Accepted: 11/29/2020] [Indexed: 12/11/2022] Open
Abstract
Soybean thrips (Neohydatothrips variabilis) are one of the most efficient vectors of soybean vein necrosis virus, which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, the metatranscriptome of soybean thrips, collected by the Midwest Suction Trap Network during 2018, was analyzed. Contigs assembled from the data revealed a remarkable diversity of virus-like sequences. Of the 181 virus-like sequences identified, 155 were novel and associated primarily with taxa of arthropod-infecting viruses, but sequences similar to plant and fungus-infecting viruses were also identified. The novel viruses were predicted to have positive-sense RNA, negative-stranded RNA, double-stranded RNA, and single-stranded DNA genomes. The assembled sequences included 100 contigs that represented at least 95% coverage of a virus genome or genome segment. Sequences represented 12 previously described arthropod viruses including eight viruses reported from Hubei Province in China, and 12 plant virus sequences of which six have been previously described. The presence of diverse populations of plant viruses within soybean thrips suggests they feed on and acquire viruses from multiple host plant species that could be transmitted to soybean. Assessment of the virome of soybean thrips provides, for the first time, information on the diversity of viruses present in thrips.
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Affiliation(s)
| | - Doris Lagos-Kutz
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA; (D.L.-K.); (N.K.M.); (G.L.H.)
| | - Nancy K. McCoppin
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA; (D.L.-K.); (N.K.M.); (G.L.H.)
| | - Glen L. Hartman
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA; (D.L.-K.); (N.K.M.); (G.L.H.)
| | - Hye-Kyoung Ju
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 300-010, Korea; (H.-K.J.); (H.-S.L.)
| | - Hyoun-Sub Lim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 300-010, Korea; (H.-K.J.); (H.-S.L.)
| | - Leslie. L. Domier
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA; (D.L.-K.); (N.K.M.); (G.L.H.)
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21
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Genome sequence of a novel member of the order Picornavirales from the endoparasitoid wasp Diversinervus elegans. Arch Virol 2020; 166:295-297. [PMID: 33067649 DOI: 10.1007/s00705-020-04824-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/25/2020] [Indexed: 10/23/2022]
Abstract
Here, we report a novel RNA virus from an encyrtid endoparasitoid wasp (Diversinervus elegans). This virus has a genome of 8845 nucleotides in length with a poly(A) tail. It contains one open reading frame (ORF) encoding a single polyprotein that shares the most significant similarity to the polyproteins of dicistroviruses. Phylogenetic analysis suggested that this virus belongs to the family Dicistroviridae from the order Picornavirales, but its genomic organization is distinct from that of the other known dicistroviruses, which have two ORFs. Consequently, we propose that this virus is a member of a new species in the order Picornavirales, and have named it "Diversinervus elegans virus" (DEV).
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22
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Thi Kha Tu N, Thi Thu Hong N, Thi Han Ny N, My Phuc T, Thi Thanh Tam P, van Doorn HR, Dang Trung Nghia H, Thao Huong D, An Han D, Thi Thu Ha L, Deng X, Thwaites G, Delwart E, Virtala AMK, Vapalahti O, Baker S, Van Tan L. The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections. Viruses 2020; 12:E960. [PMID: 32872469 PMCID: PMC7552073 DOI: 10.3390/v12090960] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/11/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respiratory diseases. Fifteen virus RT-PCR-positive samples were included as controls, while the other 76 samples were RT-PCR negative for a wide panel of respiratory pathogens. Eukaryotic viruses detected by mNGS were then screened by PCR (using primers based on mNGS-derived contigs) in all samples to compare viral detection by mNGS versus PCR and assess the utility of mNGS in routine diagnostics. mNGS identified expected human rhinoviruses, enteroviruses, influenza A virus, coronavirus OC43, and respiratory syncytial virus (RSV) A in 13 of 15 (86.7%) positive control samples. Additionally, rotavirus, torque teno virus, human papillomavirus, human betaherpesvirus 7, cyclovirus, vientovirus, gemycircularvirus, and statovirus were identified through mNGS. Notably, complete genomes of novel cyclovirus, gemycircularvirus, and statovirus were genetically characterized. Using PCR screening, the novel cyclovirus was additionally detected in 5 and the novel gemycircularvirus in 12 of the remaining samples included for mNGS analysis. Our studies therefore provide pioneering data of the virome of acute-respiratory diseases from individuals at risk of zoonotic infections. The mNGS protocol/pipeline applied here is sensitive for the detection of a variety of viruses, including novel ones. More frequent detections of the novel viruses by PCR than by mNGS on the same samples suggests that PCR remains the most sensitive diagnostic test for viruses whose genomes are known. The detection of novel viruses expands our understanding of the respiratory virome of animal-exposed humans and warrant further studies.
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Affiliation(s)
- Nguyen Thi Kha Tu
- Doctoral School in Health Sciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
- Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam; (D.A.H.); (L.T.T.H.)
| | - Nguyen Thi Thu Hong
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Nguyen Thi Han Ny
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Tran My Phuc
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Pham Thi Thanh Tam
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Ha Noi 8000, Vietnam;
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Ho Dang Trung Nghia
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Dang Thao Huong
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
| | - Duong An Han
- Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam; (D.A.H.); (L.T.T.H.)
| | - Luu Thi Thu Ha
- Dong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, Vietnam; (D.A.H.); (L.T.T.H.)
| | - Xutao Deng
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LG, UK
| | - Eric Delwart
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA; (X.D.); (E.D.)
- Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Anna-Maija K. Virtala
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland;
| | - Olli Vapalahti
- Doctoral School in Health Sciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Virology and Immunology, HUSLAB, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK;
| | - Le Van Tan
- Oxford University Clinical Research Unit, Ho Chi Minh City 7000, Vietnam; (N.T.T.H.); (N.T.H.N.); (T.M.P.); (P.T.T.T.); (H.D.T.N.); (D.T.H.); (G.T.)
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23
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Yasmin T, Thekke-Veetil T, Hobbs HA, Nelson BD, McCoppin NK, Lagos-Kutz D, Hartman GL, Lambert KN, Walker DR, Domier LL. Aphis glycines virus 1, a new bicistronic virus with two functional internal ribosome entry sites, is related to a group of unclassified viruses in the Picornavirales. J Gen Virol 2020; 101:105-111. [PMID: 31769392 DOI: 10.1099/jgv.0.001355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A novel picorna-like virus, provisionally named Aphis glycines virus 1 (ApGlV1) was discovered by high-throughput sequencing of soybean total RNAs and detected in suction trap-collected Aphis glycines. The ApGlV1 genome contains two large ORFs organized similar to those of dicipiviruses in the Picornaviridae where ORFs 1 and 2 encode structural and nonstructural proteins, respectively. Both ORFs are preceded by internal ribosome entry site (IRES) elements. The 5' IRES was more active in dual luciferase activity assays than the IRES in the intergenic region. The ApGlV1 genome was predicted to encode a serine protease instead of a cysteine protease and showed very low aa sequence identities to recognized members of the Picornavirales. In phylogenetic analyses based on capsid protein and RNA-dependent RNA polymerase sequences, ApGlV1 consistently clustered with a group of unclassified bicistronic picorna-like viruses discovered from arthropods and plants that may represent a novel family in the order Picornavirales.
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Affiliation(s)
- Tuba Yasmin
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | | | - Houston A Hobbs
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Berlin D Nelson
- Deptartment of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Nancy K McCoppin
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL, USA.,Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Doris Lagos-Kutz
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL, USA.,Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Glen L Hartman
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL, USA.,Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Kris N Lambert
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - David R Walker
- Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL, USA.,Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA.,Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL, USA
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24
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Arhab Y, Bulakhov AG, Pestova TV, Hellen CU. Dissemination of Internal Ribosomal Entry Sites (IRES) Between Viruses by Horizontal Gene Transfer. Viruses 2020; 12:v12060612. [PMID: 32512856 PMCID: PMC7354566 DOI: 10.3390/v12060612] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/19/2022] Open
Abstract
Members of Picornaviridae and of the Hepacivirus, Pegivirus and Pestivirus genera of Flaviviridae all contain an internal ribosomal entry site (IRES) in the 5'-untranslated region (5'UTR) of their genomes. Each class of IRES has a conserved structure and promotes 5'-end-independent initiation of translation by a different mechanism. Picornavirus 5'UTRs, including the IRES, evolve independently of other parts of the genome and can move between genomes, most commonly by intratypic recombination. We review accumulating evidence that IRESs are genetic entities that can also move between members of different genera and even between families. Type IV IRESs, first identified in the Hepacivirus genus, have subsequently been identified in over 25 genera of Picornaviridae, juxtaposed against diverse coding sequences. In several genera, members have either type IV IRES or an IRES of type I, II or III. Similarly, in the genus Pegivirus, members contain either a type IV IRES or an unrelated type; both classes of IRES also occur in members of the genus Hepacivirus. IRESs utilize different mechanisms, have different factor requirements and contain determinants of viral growth, pathogenesis and cell type specificity. Their dissemination between viruses by horizontal gene transfer has unexpectedly emerged as an important facet of viral evolution.
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25
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Van Eynde B, Christiaens O, Delbare D, Shi C, Vanhulle E, Yinda CK, Matthijnssens J, Smagghe G. Exploration of the virome of the European brown shrimp (Crangon crangon). J Gen Virol 2020; 101:651-666. [DOI: 10.1099/jgv.0.001412] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Crangon crangon is economically a very important species. Recently, promising culture attempts have been made, but a major problem is the uncontrollable mortality during the grow-out phase. As of yet, the life cycle of C. crangon is not closed in captivity so wild-caught individuals are used for further rearing. Therefore, it is important to investigate the virome of C. crangon both in wild-caught animals as in cultured animals. In recent years, next-generation-sequencing (NGS) technologies have been very important in the unravelling of the virome of a wide range of environments and matrices, such as soil, sea, potable water, but also of a wide range of animal species. This will be the first report of a virome study in C. crangon using NGS in combination with the NetoVIR protocol. The near complete genomes of 16 novel viruses were described, most of which were rather distantly related to unclassified viruses or viruses belonging to the Picornavirales, Bunyavirales Nudiviridae, Parvoviridae, Flaviviridae, Hepeviridae, Tombusviridae, Narnaviridae, Nodaviridae, Sobemovirus. A difference in virome composition was observed between muscle and hepatopancreatic tissue, suggesting a distinct tissue tropism of several of these viruses. Some differences in the viral composition were noted between the cultured and wild shrimp, which could indicate that in sub-optimal aquaculture conditions some viruses become more abundant. This research showed that a plethora of unknown viruses is present in C. crangon and that more research is needed to determine which virus is potentially dangerous for the culture of C. crangon.
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Affiliation(s)
- Benigna Van Eynde
- Animal Sciences Unit-Fisheries, Flanders research institute for agriculture, fisheries and food (ILVO), 8400 Ostend, Belgium
- Department of Plant and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Olivier Christiaens
- Department of Plant and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Daan Delbare
- Animal Sciences Unit-Fisheries, Flanders research institute for agriculture, fisheries and food (ILVO), 8400 Ostend, Belgium
| | - Chenyan Shi
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Emiel Vanhulle
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Claude Kwe Yinda
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Guy Smagghe
- Department of Plant and Crops, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
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26
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Temmam S, Hul V, Bigot T, Bessaud M, Chrétien D, Hoem T, Gorman C, Duong V, Dussart P, Cappelle J, Eloit M. Whole genome sequencing and phylogenetic characterization of a novel bat-associated picornavirus-like virus with an unusual genome organization. INFECTION GENETICS AND EVOLUTION 2019; 78:104130. [PMID: 31785365 DOI: 10.1016/j.meegid.2019.104130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 11/19/2019] [Accepted: 11/26/2019] [Indexed: 11/30/2022]
Abstract
The order Picornavirales is one of the most important viral orders in terms of virus diversity and genome organizations, ranging from a mono- or bi-cistronic expression strategies to the recently described poly-cistronic Polycipiviridae viruses. We report here the description and characterization of a novel picorna-like virus identified in rectal swabs of frugivorous bats in Cambodia that presents an unusual genome organization. Kandabadicivirus presents a unique genome architecture and distant phylogenetic relationship to the proposed Badiciviridae family. These findings highlight a high mosaicism of genome organizations among the Picornavirales.
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Affiliation(s)
- Sarah Temmam
- Institut Pasteur, Biology of Infection Unit, Pathogen Discovery Laboratory, Inserm U1117, Paris, France
| | - Vibol Hul
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Thomas Bigot
- Institut Pasteur, Biology of Infection Unit, Pathogen Discovery Laboratory, Inserm U1117, Paris, France; Institut Pasteur, Bioinformatics and Biostatistics Hub, Computational Biology department, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Maël Bessaud
- Institut Pasteur, Viral Populations and Pathogenesis Unit, WHO Collaborating Center for Enteroviruses, Paris, France
| | - Delphine Chrétien
- Institut Pasteur, Biology of Infection Unit, Pathogen Discovery Laboratory, Inserm U1117, Paris, France
| | - Thavry Hoem
- Epidemiology and Public Health Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Christopher Gorman
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Julien Cappelle
- Epidemiology and Public Health Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia; UMR ASTRE, CIRAD, INRA, Université de Montpellier, Montpellier, France; UMR EpiA, VetAgro Sup, INRA, Marcy l'Etoile, France
| | - Marc Eloit
- Institut Pasteur, Biology of Infection Unit, Pathogen Discovery Laboratory, Inserm U1117, Paris, France; National Veterinary School of Alfort, Paris-Est University, Maisons-Alfort, 94704, Cedex, France.
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27
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Fumagalli MJ, de Souza WM, de Araujo J, Modha S, Queiroz LH, Durigon EL, Murcia PR, Figueiredo LTM. Krykféie dicistrovirus: A novel dicistrovirus in velvety free-tailed bats from Brazil. INFECTION GENETICS AND EVOLUTION 2019; 75:104036. [PMID: 31499226 DOI: 10.1016/j.meegid.2019.104036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 11/26/2022]
Abstract
The Dicistroviridae family comprises positive single-stranded RNA viruses that are classified into Picornavirales order. These viruses are identified in arthropod hosts, including some having devastating economic consequences. Here, we described and characterized a novel nearly complete dicistrovirus genome identified in liver samples of velvety free-tailed bats (Molossus molossus) collected in June 2010 in Araçatuba city, São Paulo State, Brazil. This novel virus presents a genome of 9262 nucleotides in length and a typical dicistrovirus genome organization. Based on our phylogenetic analysis and ICTV criteria, we propose this virus as a novel species into the Triatovirus genus. Attempts of viral propagation in Vero E6 and C6/36 cell lines were unsuccessful. The novel dicistrovirus was detected only in one out of nine liver bat samples, representing for the first time an internal organ detection from a representative of this virus family.
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Affiliation(s)
- Marcílio Jorge Fumagalli
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
| | - William Marciel de Souza
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Jansen de Araujo
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Sejal Modha
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | - Edison Luiz Durigon
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Pablo Ramiro Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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28
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Abstract
Polycipiviridae is a recently recognized viral family within the order Picornavirales with unusual genome organization and phylogenetic placement. Viruses belonging to this family were only reported from arthropod hosts. Polycipiviridae is a recently recognized viral family within the order Picornavirales with unusual genome organization and phylogenetic placement. Viruses belonging to this family were only reported from arthropod hosts. We describe here the first full genome of a distant polycipivirus-related virus identified in frugivorous bat stools in Cambodia.
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29
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Zhang C, Sheng J, Zhao Z, Yan C, Tu C, He B. Genomic Characterization of the First Parechovirus in Bats. Virol Sin 2019; 34:471-473. [PMID: 30953291 DOI: 10.1007/s12250-019-00108-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/05/2019] [Indexed: 11/29/2022] Open
Affiliation(s)
- Chang Zhang
- College of Animal Science, Fujian A&F University, Fuzhou, 350002, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, 130122, China
| | - Jinliang Sheng
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
| | - Zihan Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, 130122, China
| | - Chao Yan
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, 130122, China
| | - Changchun Tu
- College of Animal Science, Fujian A&F University, Fuzhou, 350002, China.,Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, 130122, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, China
| | - Biao He
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Institute, Academy of Military Medical Sciences, Changchun, 130122, China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou, 225009, China.
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30
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Gałan W, Bąk M, Jakubowska M. Host Taxon Predictor - A Tool for Predicting Taxon of the Host of a Newly Discovered Virus. Sci Rep 2019; 9:3436. [PMID: 30837511 PMCID: PMC6400966 DOI: 10.1038/s41598-019-39847-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 01/30/2019] [Indexed: 12/04/2022] Open
Abstract
Recent advances in metagenomics provided a valuable alternative to culture-based approaches for better sampling viral diversity. However, some of newly identified viruses lack sequence similarity to any of previously sequenced ones, and cannot be easily assigned to their hosts. Here we present a bioinformatic approach to this problem. We developed classifiers capable of distinguishing eukaryotic viruses from the phages achieving almost 95% prediction accuracy. The classifiers are wrapped in Host Taxon Predictor (HTP) software written in Python which is freely available at https://github.com/wojciech-galan/viruses_classifier. HTP’s performance was later demonstrated on a collection of newly identified viral genomes and genome fragments. In summary, HTP is a culture- and alignment-free approach for distinction between phages and eukaryotic viruses. We have also shown that it is possible to further extend our method to go up the evolutionary tree and predict whether a virus can infect narrower taxa.
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Affiliation(s)
- Wojciech Gałan
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, ul. Gronostajowa 7, 30-387, Kraków, Poland.
| | - Maciej Bąk
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Małgorzata Jakubowska
- AGH University of Science and Technology, Faculty of Materials Science and Ceramics, al. Mickiewicza 30, 30-059, Kraków, Poland
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31
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Yinda CK, Vanhulle E, Conceição-Neto N, Beller L, Deboutte W, Shi C, Ghogomu SM, Maes P, Van Ranst M, Matthijnssens J. Gut Virome Analysis of Cameroonians Reveals High Diversity of Enteric Viruses, Including Potential Interspecies Transmitted Viruses. mSphere 2019; 4:e00585-18. [PMID: 30674646 PMCID: PMC6344602 DOI: 10.1128/msphere.00585-18] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/17/2018] [Indexed: 12/11/2022] Open
Abstract
Diarrhea remains one of the most common causes of deaths in children. A limited number of studies have investigated the prevalence of enteric pathogens in Cameroon, and as in many other African countries, the cause of many diarrheal episodes remains unexplained. A proportion of these unknown cases of diarrhea are likely caused by yet-unidentified viral agents, some of which could be the result of (recent) interspecies transmission from animal reservoirs, like bats. Using viral metagenomics, we screened fecal samples of 221 humans (almost all with gastroenteritis symptoms) between 0 and 89 years of age with different degrees of bat contact. We identified viruses belonging to families that are known to cause gastroenteritis such as Adenoviridae, Astroviridae, Caliciviridae, Picornaviridae, and Reoviridae Interestingly, a mammalian orthoreovirus, picobirnaviruses, a smacovirus, and a pecovirus were also found. Although there was no evidence of interspecies transmission of the most common human gastroenteritis-related viruses (Astroviridae, Caliciviridae, and Reoviridae), the phylogenies of the identified orthoreovirus, picobirnavirus, and smacovirus indicate a genetic relatedness of these viruses identified in stools of humans and those of bats and/or other animals. These findings points out the possibility of interspecies transmission or simply a shared host of these viruses (bacterial, fungal, parasitic, …) present in both animals (bats) and humans. Further screening of bat viruses in humans or vice versa will elucidate the epidemiological potential threats of animal viruses to human health. Furthermore, this study showed a huge diversity of highly divergent novel phages, thereby expanding the existing phageome considerably.IMPORTANCE Despite the availability of diagnostic tools for different enteric viral pathogens, a large fraction of human cases of gastroenteritis remains unexplained. This could be due to pathogens not tested for or novel divergent viruses of potential animal origin. Fecal virome analyses of Cameroonians showed a very diverse group of viruses, some of which are genetically related to those identified in animals. This is the first attempt to describe the gut virome of humans from Cameroon. Therefore, the data represent a baseline for future studies on enteric viral pathogens in this area and contribute to our knowledge of the world's virome. The studies also highlight the fact that more viruses may be associated with diarrhea than the typical known ones. Hence, it provides meaningful epidemiological information on diarrhea-related viruses in this area.
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Affiliation(s)
- Claude Kwe Yinda
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Emiel Vanhulle
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Nádia Conceição-Neto
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Leen Beller
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Ward Deboutte
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Chenyan Shi
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Stephen Mbigha Ghogomu
- Department of Biochemistry and Molecular Biology, Biotechnology Unit, Molecular and Cell Biology Laboratory, University of Buea, Buea, Cameroon
| | - Piet Maes
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Jelle Matthijnssens
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium
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32
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de Barros BDCV, Chagas EN, Bezerra LW, Ribeiro LG, Duarte Júnior JWB, Pereira D, da Penha Junior ET, Silva JR, Bezerra DAM, Bandeira RS, Pinheiro HHC, Guerra SDFDS, Guimarães RJDPSE, Mascarenhas JDP. Rotavirus A in wild and domestic animals from areas with environmental degradation in the Brazilian Amazon. PLoS One 2018; 13:e0209005. [PMID: 30562373 PMCID: PMC6298726 DOI: 10.1371/journal.pone.0209005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 11/28/2018] [Indexed: 12/28/2022] Open
Abstract
Acute gastroenteritis is one of the main causes of mortality in humans and young animals. Domestic and mainly wild animals such as bats, small rodents and birds are highly diversified animals in relation to their habitats and ecological niches and are widely distributed geographically in environments of forest fragmentation in some areas of the Amazon, being considered important sources for viruses that affect humans and other animals. Due to the anthropical activities, these animals changed their natural habitat and adapted to urbanized environments, thus representing risks to human and animal health. Although the knowledge of the global diversity of enteric viruses is scarce, there are reports demonstrating the detection of rotavirus in domestic animals and animals of productive systems, such as bovines and pigs. The present study investigated the prevalence of Rotavirus A in 648 fecal samples of different animal species from the northeastern mesoregion of the state of Pará, Brazil, which is characterized as an urbanized area with forest fragments. The fecal specimens were collected from October 2014 to April 2016 and subjected to a Qualitative Real-Time Polymerase Chain Reaction (RT-qPCR), using the NSP3 gene as a target. It was observed that 27.5% (178/648) of the samples presented positive results for RVA, with 178 samples distributed in birds (23.6%), canines (21.35%), chiropterans (17.98%), bovines (14.6%), horses (8.43%), small rodents (6.74%), pigs (3.93%) and felines (3.37%), demonstrating the circulation of RVA in domestic animals and suggesting that such proximity could cause transmissions between different species and the occurrence of rearrangements in the genome of RVA as already described in the literature, associated to the traces of environmental degradation in the studied areas.
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Affiliation(s)
| | | | | | | | | | - Diego Pereira
- Amazon Metropolitan University Center, Belém, Pará, Brazil
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33
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Siqueira JD, Dominguez-Bello MG, Contreras M, Lander O, Caballero-Arias H, Xutao D, Noya-Alarcon O, Delwart E. Complex virome in feces from Amerindian children in isolated Amazonian villages. Nat Commun 2018; 9:4270. [PMID: 30323210 PMCID: PMC6189175 DOI: 10.1038/s41467-018-06502-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/06/2018] [Indexed: 01/22/2023] Open
Abstract
The number of viruses circulating in small isolated human populations may be reduced by viral extinctions and rare introductions. Here we used viral metagenomics to characterize the eukaryotic virome in feces from healthy children from a large urban center and from three Amerindian villages with minimal outside contact. Numerous human enteric viruses, mainly from the Picornaviridae and Caliciviridae families, were sequenced from each of the sites. Multiple children from the same villages shed closely related viruses reflecting frequent transmission clusters. Feces of isolated villagers also contained multiple viral genomes of unknown cellular origin from the Picornavirales order and CRESS-DNA group and higher levels of nematode and protozoan DNA. Despite cultural and geographic isolation, the diversity of enteric human viruses was therefore not reduced in these Amazonian villages. Frequent viral introductions and/or increased susceptibility to enteric infections may account for the complex fecal virome of Amerindian children in isolated villages.
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Affiliation(s)
- Juliana D Siqueira
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, 20.231-050, Brazil
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology and of Anthropology, Rutgers University, New Brunswick, NJ, 08901-8554, USA
| | - Monica Contreras
- Center for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Orlana Lander
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela
| | - Hortensia Caballero-Arias
- Department of Anthropology, Venezuelan Institute of Scientific Research (IVIC), Caracas, 01204, Venezuela
| | - Deng Xutao
- Blood Systems Research Institute, San Francisco, CA, 94118, USA.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA
| | - Oscar Noya-Alarcon
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, 1051, Venezuela.,Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho, 7101, Venezuela
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, 94118, USA. .,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA.
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34
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Cholleti H, Hayer J, Fafetine J, Berg M, Blomström AL. Genetic characterization of a novel picorna-like virus in Culex spp. mosquitoes from Mozambique. Virol J 2018; 15:71. [PMID: 29669586 PMCID: PMC5907373 DOI: 10.1186/s12985-018-0981-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/07/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Mosquitoes are the potential vectors for a variety of viruses that can cause diseases in the human and animal populations. Viruses in the order Picornavirales infect a broad range of hosts, including mosquitoes. In this study, we aimed to characterize a novel picorna-like virus from the Culex spp. of mosquitoes from the Zambezi Valley of Mozambique. METHODS The extracted RNA from mosquito pools was pre-amplified with the sequence independent single primer amplification (SISPA) method and subjected to high-throughput sequencing using the Ion Torrent platform. Reads that are classified as Iflaviridae, Picornaviridae and Dicistroviridae were assembled by CodonCode Aligner and SPAdes. Gaps between the viral contigs were sequenced by PCR. The genomic ends were analyzed by 5' and 3' RACE PCRs. The ORF was predicted with the NCBI ORF finder. The conserved domains were identified with ClustalW multiple sequence alignment, and a phylogenetic tree was built with MEGA. The presence of the virus in individual mosquito pools was detected by RT-PCR assay. RESULTS A near full-length viral genome (9740 nt) was obtained in Culex mosquitoes that encoded a complete ORF (3112 aa), named Culex picorna-like virus (CuPV-1). The predicted ORF had 38% similarity to the Hubei picorna-like virus 35. The sequence of the conserved domains, Helicase-Protease-RNA-dependent RNA polymerase, were identified by multiple sequence alignment and found to be at the 3' end, similar to iflaviruses. Phylogenetic analysis of the putative RdRP amino acid sequences indicated that the virus clustered with members of the Iflaviridae family. CuPV-1 was detected in both Culex and Mansonia individual pools with low infection rates. CONCLUSIONS The study reported a highly divergent, near full-length picorna-like virus genome from Culex spp. mosquitoes from Mozambique. The discovery and characterization of novel viruses in mosquitoes is an initial step, which will provide insights into mosquito-virus interaction mechanisms, genetic diversity and evolution.
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Affiliation(s)
- Harindranath Cholleti
- Section of Virology, Department of Biomedical and Veterinary Public Health, Box 7028, Swedish University of Agricultural Sciences (SLU), 75007, Uppsala, Sweden.
| | - Juliette Hayer
- SLU Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Box 7023, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jose Fafetine
- Division of Molecular Diagnostics and Epidemiology, Biotechnology Center, Eduardo Mondlane University, Maputo, Mozambique
| | - Mikael Berg
- Section of Virology, Department of Biomedical and Veterinary Public Health, Box 7028, Swedish University of Agricultural Sciences (SLU), 75007, Uppsala, Sweden
| | - Anne-Lie Blomström
- Section of Virology, Department of Biomedical and Veterinary Public Health, Box 7028, Swedish University of Agricultural Sciences (SLU), 75007, Uppsala, Sweden
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35
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Ruark CL, Gardner M, Mitchum MG, Davis EL, Sit TL. Novel RNA viruses within plant parasitic cyst nematodes. PLoS One 2018; 13:e0193881. [PMID: 29509804 PMCID: PMC5839581 DOI: 10.1371/journal.pone.0193881] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/20/2018] [Indexed: 02/06/2023] Open
Abstract
The study of invertebrate-and particularly nematode-viruses is emerging with the advancement of transcriptome sequencing. Five single-stranded RNA viruses have now been confirmed within the economically important soybean cyst nematode (SCN; Heterodera glycines). From previous research, we know these viruses to be widespread in greenhouse and field populations of SCN. Several of the SCN viruses were also confirmed within clover (H. trifolii) and beet (H. schachtii) cyst nematodes. In the presented study, we sequenced the transcriptomes of several inbred SCN populations and identified two previously undiscovered viral-like genomes. Both of these proposed viruses are negative-sense RNA viruses and have been named SCN nyami-like virus (NLV) and SCN bunya-like virus (BLV). Finally, we analyzed publicly available transcriptome data of two potato cyst nematode (PCN) species, Globodera pallida and G. rostochiensis. From these data, a third potential virus was discovered and called PCN picorna-like virus (PLV). PCN PLV is a positive-sense RNA virus, and to the best of our knowledge, is the first virus described within PCN. The presence of these novel viruses was confirmed via qRT-PCR, endpoint PCR, and Sanger sequencing with the exception of PCN PLV due to quarantine restrictions on the nematode host. While much work needs to be done to understand the biological and evolutionary significance of these viruses, they offer insight into nematode ecology and the possibility of novel nematode management strategies.
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Affiliation(s)
- Casey L. Ruark
- Department of Entomology and Plant Pathology, North Carolina State University, Thomas Hall, Raleigh, North Carolina, United States of America
| | - Michael Gardner
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, 371H Bond Life Sciences Center, Columbia, Missouri, United States of America
| | - Melissa G. Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, 371H Bond Life Sciences Center, Columbia, Missouri, United States of America
| | - Eric L. Davis
- Department of Entomology and Plant Pathology, North Carolina State University, Thomas Hall, Raleigh, North Carolina, United States of America
| | - Tim L. Sit
- Department of Entomology and Plant Pathology, North Carolina State University, Thomas Hall, Raleigh, North Carolina, United States of America
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36
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Van Borm S, Steensels M, Mathijs E, Yinda CK, Matthijnssens J, Lambrecht B. Complete coding sequence of a novel picorna-like virus in a blackbird infected with Usutu virus. Arch Virol 2018; 163:1701-1703. [PMID: 29442227 DOI: 10.1007/s00705-018-3761-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/22/2018] [Indexed: 11/25/2022]
Abstract
Using random high-throughput RNA sequencing, the complete coding sequence of a novel picorna-like virus (a 9,228-nt contig containing 212,202 reads) was determined from a blackbird (Turdus merula) infected with Usutu virus. This sequence shares only 36% amino acid sequence identity with its closest homolog, arivirus 1, (an unclassified member of the order Picornavirales), and shares its dicistronic genome arrangement. The new virus was therefore tentatively named "blackbird arilivirus" (ari-like virus). The nearly complete genome sequence consists of at least 9,228 nt and contains two open reading frames (ORFs) encoding the nonstructural polyprotein (2235 amino acids) and structural polyprotein (769 amino acids). Two TaqMan RT-qPCR assays specific for ORF1 confirmed the presence of high levels of this novel virus in the original sample. Nucleotide composition analysis suggests that blackbird arilivirus is of dietary (plant) origin.
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Affiliation(s)
- Steven Van Borm
- Directorate Viral Diseases, Veterinary and Agrochemical Research Center CODA-CERVA, Brussels, Belgium.
| | - Mieke Steensels
- Directorate Viral Diseases, Veterinary and Agrochemical Research Center CODA-CERVA, Brussels, Belgium
| | - Elisabeth Mathijs
- Directorate Viral Diseases, Veterinary and Agrochemical Research Center CODA-CERVA, Brussels, Belgium
| | - Claude Kwe Yinda
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Bénédicte Lambrecht
- Directorate Viral Diseases, Veterinary and Agrochemical Research Center CODA-CERVA, Brussels, Belgium
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37
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Greninger AL. A decade of RNA virus metagenomics is (not) enough. Virus Res 2018; 244:218-229. [PMID: 29055712 PMCID: PMC7114529 DOI: 10.1016/j.virusres.2017.10.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 10/14/2017] [Accepted: 10/17/2017] [Indexed: 12/16/2022]
Abstract
It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win. This review explores the history of RNA virus metagenomics, reasons for the successes so far in RNA virus metagenomics, and methodological concerns. In addition, the review briefly covers clinical metagenomics and environmental metagenomics and highlights some of the critical accomplishments that have defined the fast pace of RNA virus discoveries in recent years. Slightly more than a decade in, the field is exhausted from its discoveries but knows that there is yet even more out there to be found.
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Affiliation(s)
- Alexander L Greninger
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, WA, United States; Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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38
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Yinda CK, Ghogomu SM, Conceição-Neto N, Beller L, Deboutte W, Vanhulle E, Maes P, Van Ranst M, Matthijnssens J. Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code. Virus Evol 2018; 4:vey008. [PMID: 29644096 PMCID: PMC5888411 DOI: 10.1093/ve/vey008] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most human emerging infectious diseases originate from wildlife and bats are a major reservoir of viruses, a few of which have been highly pathogenic to humans. In some regions of Cameroon, bats are hunted and eaten as a delicacy. This close proximity between human and bats provides ample opportunity for zoonotic events. To elucidate the viral diversity of Cameroonian fruit bats, we collected and metagenomically screened eighty-seven fecal samples of Eidolon helvum and Epomophorus gambianus fruit bats. The results showed a plethora of known and novel viruses. Phylogenetic analyses of the eleven gene segments of the first complete bat rotavirus H genome, showed clearly separated clusters of human, porcine, and bat rotavirus H strains, not indicating any recent interspecies transmission events. Additionally, we identified and analyzed a bat bastrovirus genome (a novel group of recently described viruses, related to astroviruses and hepatitis E viruses), confirming their recombinant nature, and provide further evidence of additional recombination events among bat bastroviruses. Interestingly, picobirnavirus-like RNA-dependent RNA polymerase gene segments were identified using an alternative mitochondrial genetic code, and further principal component analyses suggested that they may have a similar lifestyle to mitoviruses, a group of virus-like elements known to infect the mitochondria of fungi. Although identified bat coronavirus, parvovirus, and cyclovirus strains belong to established genera, most of the identified partitiviruses and densoviruses constitute putative novel genera in their respective families. Finally, the results of the phage community analyses of these bats indicate a very diverse geographically distinct bat phage population, probably reflecting different diets and gut bacterial ecosystems.
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Affiliation(s)
- Claude Kwe Yinda
- Laboratory of Viral Metagenomics
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
| | - Stephen Mbigha Ghogomu
- Molecular and Cell Biology Laboratory, Biotechnology Unit, Department of Biochemistry and Molecular Biology, University of Buea, Buea, 237, Cameroon
| | - Nádia Conceição-Neto
- Laboratory of Viral Metagenomics
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
| | | | | | | | - Piet Maes
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
| | - Marc Van Ranst
- Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, B-3000 Leuven, Belgium
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39
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Zell R. Picornaviridae-the ever-growing virus family. Arch Virol 2017; 163:299-317. [PMID: 29058149 DOI: 10.1007/s00705-017-3614-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/30/2017] [Indexed: 12/30/2022]
Abstract
Picornaviruses are small, nonenveloped, icosahedral RNA viruses with positive-strand polarity. Although the vast majority of picornavirus infections remain asymptomatic, many picornaviruses are important human and animal pathogens and cause diseases that affect the central nervous system, the respiratory and gastrointestinal tracts, heart, liver, pancreas, skin and eye. A stunning increase in the number of newly identified picornaviruses in the past decade has shown that picornaviruses are globally distributed and infect vertebrates of all classes. Moreover, picornaviruses exhibit a surprising diversity of both genome sequences and genome layouts, sometimes challenging the definition of taxonomic relevant criteria. At present, 35 genera comprising 80 species and more than 500 types are acknowledged. Fifteen species within five new and three existing genera have been proposed in 2017, but more than 50 picornaviruses still remain unassigned.
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Affiliation(s)
- Roland Zell
- Division of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Hans-Knöll-Str. 2, 07745, Jena, Germany.
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Kobayashi D, Isawa H, Fujita R, Murota K, Itokawa K, Higa Y, Katayama Y, Sasaki T, Mizutani T, Iwanaga S, Ohta N, Garcia-Bertuso A, Sawabe K. Isolation and characterization of a new iflavirus from Armigeres spp. mosquitoes in the Philippines. J Gen Virol 2017; 98:2876-2881. [PMID: 29048274 DOI: 10.1099/jgv.0.000929] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
During an entomological surveillance for arthropod-borne viruses in the Philippines, we isolated a previously unrecognized virus from female Armigeres spp. mosquitoes. Whole-genome sequencing, genetic characterization and phylogenetic analysis revealed that the isolated virus, designated Armigeres iflavirus (ArIFV), is a novel member of the iflaviruses (genus Iflavirus, family Iflaviridae) and phylogenetically related to Moku virus, Hubei odonate virus 4, slow bee paralysis virus and Graminella nigrifrons virus 1. To our knowledge, this is the first successful isolation of iflavirus from a dipteran insect. Spherical ArIFV particles of approximately 30 nm in diameter contained at least three major structural proteins. ArIFV multiplied to high titres (~109 p.f.u. ml-1) and formed clear plaques in a mosquito cell line, C6/36. Our findings provide new insights into the infection mechanism, genetic diversity and evolution of the Iflaviridae family.
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Affiliation(s)
- Daisuke Kobayashi
- Department of Environmental Parasitology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.,Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Haruhiko Isawa
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Ryosuke Fujita
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.,Department of Research Promotion, Japan Agency for Medical Research and Development, 20F Yomiuri Shimbun Bldg. 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan.,Isotope Imaging Laboratory, Creative Research Institution, Hokkaido University, Kita 21 Nihi 10, Sapporo 001-0021, Japan
| | - Katsunori Murota
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.,Department of Research Promotion, Japan Agency for Medical Research and Development, 20F Yomiuri Shimbun Bldg. 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Kentaro Itokawa
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.,Department of Research Promotion, Japan Agency for Medical Research and Development, 20F Yomiuri Shimbun Bldg. 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Yukiko Higa
- Department of Vector Ecology and Environment, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-1-8 Harumi, Fuchu, Tokyo 183-8509, Japan
| | - Toshinori Sasaki
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-1-8 Harumi, Fuchu, Tokyo 183-8509, Japan
| | - Shiroh Iwanaga
- Department of Environmental Parasitology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Nobuo Ohta
- Department of Environmental Parasitology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Arlene Garcia-Bertuso
- Department of Parasitology, College of Public Health, University of the Philippines Manila, Ermita, 1000 Manila City, Philippines
| | - Kyoko Sawabe
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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41
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Genome Sequence of a Novel Picorna-Like RNA Virus from Feces of the Antarctic Fur Seal ( Arctocephalus gazella). GENOME ANNOUNCEMENTS 2017; 5:5/36/e01001-17. [PMID: 28883153 PMCID: PMC5589547 DOI: 10.1128/genomea.01001-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A novel RNA virus was detected in a fecal sample collected from the Antarctic fur seal (Arctocephalus gazella) in King George Island, Antarctica. The almost-complete genome sequence reveals two open reading frames and a dicistrovirus-like gene order.
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