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Michael P, Panchavarnam S, Bagthasingh C, Palaniappan S, Velu R, Mohaideenpitchai MM, Palraj M, Muthumariyapan S, David EP. Innate immune response of snakehead fish to Indian strain of snakehead rhabdovirus (SHRV-In) infection and the infectivity potential of the virus to other freshwater fishes. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109577. [PMID: 38643957 DOI: 10.1016/j.fsi.2024.109577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/08/2024] [Accepted: 04/18/2024] [Indexed: 04/23/2024]
Abstract
A new virus known as snakehead rhabdovirus (SHRV-In) was discovered in South India in striped snakehead (Channa striata) that had hemorrhagic patches and cutaneous ulcerations. The virus is the most potentially harmful pathogen of snakehead because it could cause 100% mortality within 5 days. The goal of the current investigation was to evaluate the infectivity of rhabdovirus in freshwater fishes and to analyze the immune response in snakehead fish after challenge with SHRV-In. The infectivity study of SHRV-In against three freshwater fish such as tilapia, grass carp and loach showed that the virus could not induce mortality in any of them. Snakehead fish challenged with SHRV-In showed significant (p < 0.05) changes in haematological parameters such as red blood cell (RBC), haemoglobin (HGB), haematocrit (HCT), mean corpuscular haemoglobin concentration (MCHC), mean corpuscular volume (MCV), mean corpuscular haemoglobin (MCH), white blood cell (WBC), total platelet (PLT) counts, mean platelet volume (MPV) and immunological markers such as respiratory burst, superoxide dismutase, catalase activity and myeloperoxidase activity at 6, 12, 24 and 48 hpi. Real time PCR was executed to examine the expression profile of innate immune genes such as IRF-7, IL-8 and IL-12 in Snakehead fish at 6, 12, 24 and 48 h post SHRV-In infection. Immune gene expression of IRF-7, IL-8 and IL-12 were up-regulated in the spleen when compared to kidney at 6 and 12 hpi. However, the expression level of all the genes was down-regulated at 24 and 48 hpi. The down regulation of innate immune genes after 24 hpi in these tissues may be the result of increased multiplication of SHRV-In by interfering with the immune signaling pathway.
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Affiliation(s)
- Priyadharshini Michael
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Thoothukudi, 628 008, Tamil Nadu Dr.J.Jayalalithaa Fisheries University, Tamil Nadu, India
| | - Sivasankar Panchavarnam
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Thoothukudi, 628 008, Tamil Nadu Dr.J.Jayalalithaa Fisheries University, Tamil Nadu, India.
| | - Chrisolite Bagthasingh
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Thoothukudi, 628 008, Tamil Nadu Dr.J.Jayalalithaa Fisheries University, Tamil Nadu, India
| | - Subash Palaniappan
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Thoothukudi, 628 008, Tamil Nadu Dr.J.Jayalalithaa Fisheries University, Tamil Nadu, India
| | - Rani Velu
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Thoothukudi, 628 008, Tamil Nadu Dr.J.Jayalalithaa Fisheries University, Tamil Nadu, India
| | - Mohamed Mansoor Mohaideenpitchai
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Thoothukudi, 628 008, Tamil Nadu Dr.J.Jayalalithaa Fisheries University, Tamil Nadu, India
| | - Mageshkumar Palraj
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Thoothukudi, 628 008, Tamil Nadu Dr.J.Jayalalithaa Fisheries University, Tamil Nadu, India
| | - Selvamagheswaran Muthumariyapan
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Thoothukudi, 628 008, Tamil Nadu Dr.J.Jayalalithaa Fisheries University, Tamil Nadu, India
| | - Evangelin Paripoorana David
- Department of Fish Pathology and Health Management, Fisheries College and Research Institute, Thoothukudi, 628 008, Tamil Nadu Dr.J.Jayalalithaa Fisheries University, Tamil Nadu, India
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Ramos-González PL, Alexandre MAV, Potsclam-Barro M, Duarte LML, Michea Gonzalez GL, Chabi-Jesus C, Ramos AF, Harakava R, Lorenzi H, Freitas-Astúa J, Kitajima EW. Two Novel Betarhabdovirins Infecting Ornamental Plants and the Peculiar Intracellular Behavior of the Cytorhabdovirus in the Liana Aristolochia gibertii. Viruses 2024; 16:322. [PMID: 38543688 PMCID: PMC10976027 DOI: 10.3390/v16030322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 05/23/2024] Open
Abstract
Two novel members of the subfamily Betarhabdovirinae, family Rhabdoviridae, were identified in Brazil. Overall, their genomes have the typical organization 3'-N-P-P3-M-G-L-5' observed in mono-segmented plant-infecting rhabdoviruses. In aristolochia-associated cytorhabdovirus (AaCV), found in the liana aristolochia (Aristolochia gibertii Hook), an additional short orphan ORF encoding a transmembrane helix was detected between P3 and M. The AaCV genome and inferred encoded proteins share the highest identity values, consistently < 60%, with their counterparts of the yerba mate chlorosis-associated virus (Cytorhabdovirus flaviyerbamate). The second virus, false jalap virus (FaJV), was detected in the herbaceous plant false jalap (Mirabilis jalapa L.) and represents together with tomato betanucleorhabdovirus 2, originally found in tomato plants in Slovenia, a tentative new species of the genus Betanucleorhabdovirus. FaJV particles accumulate in the perinuclear space, and electron-lucent viroplasms were observed in the nuclei of the infected cells. Notably, distinct from typical rhabdoviruses, most virions of AaCV were observed to be non-enclosed within membrane-bounded cavities. Instead, they were frequently seen in close association with surfaces of mitochondria or peroxisomes. Unlike FaJV, AaCV was successfully graft-transmitted to healthy plants of three species of the genus Aristolochia, while mechanical and seed transmission proved unsuccessful for both viruses. Data suggest that these viruses belong to two new tentative species within the subfamily Betarhabdovirinae.
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Affiliation(s)
- Pedro Luis Ramos-González
- Laboratório de Biologia Molecular Aplicada, Centro de Pesquisa e Sanidade Vegetal, Instituto Biológico de São Paulo, Av. Cons. Rodrigues Alves, 1252, São Paulo 04014-002, SP, Brazil; (M.P.-B.); (G.L.M.G.); (C.C.-J.); (R.H.)
| | - Maria Amelia Vaz Alexandre
- Laboratório de Fitovirologia Fisiopatológica, Centro de Pesquisa e Sanidade Vegetal, Instituto Biológico de São Paulo, Av. Cons. Rodrigues Alves, 1252, São Paulo 04014-002, SP, Brazil; (M.A.V.A.); (L.M.L.D.); (A.F.R.)
| | - Matheus Potsclam-Barro
- Laboratório de Biologia Molecular Aplicada, Centro de Pesquisa e Sanidade Vegetal, Instituto Biológico de São Paulo, Av. Cons. Rodrigues Alves, 1252, São Paulo 04014-002, SP, Brazil; (M.P.-B.); (G.L.M.G.); (C.C.-J.); (R.H.)
| | - Lígia Maria Lembo Duarte
- Laboratório de Fitovirologia Fisiopatológica, Centro de Pesquisa e Sanidade Vegetal, Instituto Biológico de São Paulo, Av. Cons. Rodrigues Alves, 1252, São Paulo 04014-002, SP, Brazil; (M.A.V.A.); (L.M.L.D.); (A.F.R.)
| | - Gianluca L. Michea Gonzalez
- Laboratório de Biologia Molecular Aplicada, Centro de Pesquisa e Sanidade Vegetal, Instituto Biológico de São Paulo, Av. Cons. Rodrigues Alves, 1252, São Paulo 04014-002, SP, Brazil; (M.P.-B.); (G.L.M.G.); (C.C.-J.); (R.H.)
| | - Camila Chabi-Jesus
- Laboratório de Biologia Molecular Aplicada, Centro de Pesquisa e Sanidade Vegetal, Instituto Biológico de São Paulo, Av. Cons. Rodrigues Alves, 1252, São Paulo 04014-002, SP, Brazil; (M.P.-B.); (G.L.M.G.); (C.C.-J.); (R.H.)
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba 13418-900, SP, Brazil;
| | - Alyne F. Ramos
- Laboratório de Fitovirologia Fisiopatológica, Centro de Pesquisa e Sanidade Vegetal, Instituto Biológico de São Paulo, Av. Cons. Rodrigues Alves, 1252, São Paulo 04014-002, SP, Brazil; (M.A.V.A.); (L.M.L.D.); (A.F.R.)
| | - Ricardo Harakava
- Laboratório de Biologia Molecular Aplicada, Centro de Pesquisa e Sanidade Vegetal, Instituto Biológico de São Paulo, Av. Cons. Rodrigues Alves, 1252, São Paulo 04014-002, SP, Brazil; (M.P.-B.); (G.L.M.G.); (C.C.-J.); (R.H.)
| | - Harri Lorenzi
- Instituto Plantarum, Nova Odessa 13380-410, SP, Brazil;
| | | | - Elliot Watanabe Kitajima
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba 13418-900, SP, Brazil;
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Ghorani S, Massumi H, Farhangi SH, Mansouri M, Heydarnejad J, Hosseinipour A. Metatranscriptome analysis of symptomatic bitter apple plants revealed mixed viral infections with a putative novel polerovirus. BMC Genomics 2024; 25:181. [PMID: 38360528 PMCID: PMC10868029 DOI: 10.1186/s12864-024-10057-z] [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: 11/14/2023] [Accepted: 01/27/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Next-generation Sequencing (NGS) combined with bioinformatic analyses constitutes a powerful approach for identifying and characterizing previously unknown viral genomes. In this study, leaf samples from bitter apple plants (Citrullus colocynthis (L.) Schrad) exhibiting symptoms such as dwarfing, leaf crinkling, and chlorosis were collected from the southern part of Kerman province, Iran. RESULTS Putative infecting viruses were identified through de novo assembly of sequencing reads using various tools, followed by BLAST analysis. Complete genomes for Squash vein yellowing virus (SqVYV), Citrus-associated rhabdovirus (CiaRV), and a novel polerovirus-related strain termed Bitter apple aphid-borne yellows virus (BaABYV) were assembled and characterized. Additionally, a partial genome for Watermelon mosaic virus (WMV) was assembled. The genomic organization of the BaABYV was determined to be 5'-ORF0-ORF1-ORF1,2-ORF3a-ORF3-ORF3,5-ORF4-3'. Amino acid sequence identities for inferred proteins (P0 and P1, P1,2) with known poleroviruses were found to be the 90% species delineation limit, implying that BaABYV should be considered a new member of the genus Polerovirus. Recombination events were observed in the BaABYV and WMV strains; such events were not found in the CiaRV strain. CONCLUSIONS Molecular evidence from this study suggests that C. colocynthis is a reservoir host of several plant viruses. Among them, BaABYV is proposed as a new member of the genus Polerovirus. Furthermore, the CiaRV strain has been reported for the first time from Iran.
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Affiliation(s)
- Shahrbanou Ghorani
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111, Iran
| | - Hossein Massumi
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111, Iran.
- Research and Technology Institute of Plant Production (RTIPP), Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Samin H Farhangi
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mehdi Mansouri
- Department of Agricultural Biotechnology, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Jahangir Heydarnejad
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111, Iran
| | - Akbar Hosseinipour
- Department of Plant Protection, College of Agriculture, Shahid Bahonar University of Kerman, Kerman, 7616914111, Iran
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Waller SJ, Tortosa P, Thurley T, O’Donnell CFJ, Jackson R, Dennis G, Grimwood RM, Holmes EC, McInnes K, Geoghegan JL. Virome analysis of New Zealand's bats reveals cross-species viral transmission among the Coronaviridae. Virus Evol 2024; 10:veae008. [PMID: 38379777 PMCID: PMC10878368 DOI: 10.1093/ve/veae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/02/2023] [Accepted: 01/21/2024] [Indexed: 02/22/2024] Open
Abstract
The lesser short-tailed bat (Mystacina tuberculata) and the long-tailed bat (Chalinolobus tuberculatus) are Aotearoa New Zealand's only native extant terrestrial mammals and are believed to have migrated from Australia. Long-tailed bats arrived in New Zealand an estimated two million years ago and are closely related to other Australian bat species. Lesser short-tailed bats, in contrast, are the only extant species within the Mystacinidae and are estimated to have been living in isolation in New Zealand for the past 16-18 million years. Throughout this period of isolation, lesser short-tailed bats have become one of the most terrestrial bats in the world. Through a metatranscriptomic analysis of guano samples from eight locations across New Zealand, we aimed to characterise the viromes of New Zealand's bats and determine whether viruses have jumped between these species over the past two million years. High viral richness was observed among long-tailed bats with viruses spanning seven different viral families. In contrast, no bat-specific viruses were identified in lesser short-tailed bats. Both bat species harboured an abundance of likely dietary- and environment-associated viruses. We also identified alphacoronaviruses in long-tailed bat guano that had previously been identified in lesser short-tailed bats, suggesting that these viruses had jumped the species barrier after long-tailed bats migrated to New Zealand. Of note, an alphacoronavirus species discovered here possessed a complete genome of only 22,416 nucleotides with entire deletions or truncations of several non-structural proteins, thereby representing what may be the shortest genome within the Coronaviridae identified to date. Overall, this study has revealed a diverse range of novel viruses harboured by New Zealand's only native terrestrial mammals, in turn expanding our understanding of bat viral dynamics and evolution globally.
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Affiliation(s)
- Stephanie J Waller
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9016, New Zealand
| | - Pablo Tortosa
- UMR PIMIT Processus Infectieux en Milieu Insulaire Tropical, Université de La Réunion, CNRS 9192, INSERM 1187, IRD 249, Plateforme de recherche CYROI, 2 rue Maxime Rivière, Ste Clotilde 97490, France
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Tertia Thurley
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Colin F J O’Donnell
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Rebecca Jackson
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Gillian Dennis
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9016, New Zealand
| | | | - Kate McInnes
- Department of Conservation, New Zealand Government, P.O. Box 10420, Wellington 6143, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, 720 Cumberland Street, Dunedin 9016, New Zealand
- Institute of Environmental Science and Research, 34 Kenepuru Drive, Kenepuru, Porirua, Wellington 5022, New Zealand
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Westmead Hospital, Level 5, Block K, Westmead, Sydney, NSW 2006, Australia
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Potter-Birriel JM, Pollio AR, Knott BD, Chunashvili T, Fung CK, Conte MA, Reinbold-Wasson DD, Hang J. Metagenomics analysis reveals presence of the Merida-like virus in Georgia. Front Microbiol 2023; 14:1258810. [PMID: 37901812 PMCID: PMC10602647 DOI: 10.3389/fmicb.2023.1258810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/27/2023] [Indexed: 10/31/2023] Open
Abstract
Arbovirus surveillance is fundamental for the discovery of novel viruses and prevention of febrile vector-borne illnesses. Vector-borne pathogens can rapidly expand and adapt in new geographic and environmental conditions. In this study, metagenomic surveillance was conducted to identify novel viruses in the Country of Georgia. A total of 521 mosquitoes were captured near a military training facility and pooled from species Culex pipiens (Linnaeus) (87%) and Aedes albopictus (Skuse) (13%). We decided to further analyze the Culex pipiens mosquitoes, due to the more extensive number of samples collected. Our approach was to utilize an unbiased total RNA-seq for pathogen discovery in order to explore the mosquito virome. The viral reads from this analysis were mostly aligned to Insect-specific viruses from two main families, the Iflaviridae; a positive-stranded RNA virus and the Rhabdoviridae; a negative- and single-stranded RNA virus. Our pathogen discovery analysis revealed viral reads aligning to the Merida-like virus Turkey (MERDLVT) strain among the Rhabdoviridae. To further validate this result, we conducted a BLAST sequence comparison analysis of our samples with the MERDLVT strain. Our positive samples aligned to the MERDLVT strain with 96-100% sequence identity and 99.7-100% sequence coverage. A bootstrapped maximum-likelihood phylogenetic tree was used to evaluate the evolutionary relationships among these positive pooled specimens with the (MERDLVT) strain. The Georgia samples clustered most closely with two strains from Turkey, the Merida-like virus KE-2017a isolate 139-1-21 and the Merida-like virus Turkey isolate P431. Collectively, these results show the presence of the MERDLVT strain in Georgia.
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Affiliation(s)
| | - Adam R. Pollio
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Brian D. Knott
- U.S. Army Medical Research Directorate – Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Tamar Chunashvili
- U.S. Army Medical Research Directorate – Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Christian K. Fung
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Matthew A. Conte
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Drew D. Reinbold-Wasson
- U.S. Army Medical Research Directorate – Georgia (USAMRD-G), Walter Reed Army Institute of Research, Tbilisi, Georgia
| | - Jun Hang
- Walter Reed Army Institute of Research, Silver Spring, MD, United States
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Ma H, Bosma TJ, Khan AS. Long-Read High-Throughput Sequencing (HTS) Revealed That the Sf-Rhabdovirus X + Genome Contains a 3.7 kb Internal Duplication. Viruses 2023; 15:1998. [PMID: 37896775 PMCID: PMC10612052 DOI: 10.3390/v15101998] [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: 06/29/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
We previously reported a novel rhabdovirus produced from the Spodoptera frugiperda Sf9 cell line, designated as Sf-rhabdovirus X+ since it contained a unique accessory gene X. The Sf-rhabdovirus X+ genome sequence was generated using Sanger sequencing and short-read high-throughput sequencing (HTS). In this study, we have used long-read HTS technologies, PacBio's single-molecule real-time sequencing and Oxford's Nanopore RNA direct sequencing, to analyze the parent Sf9 cell line transcriptome and the virus RNA produced from an X+ cell clone, respectively. A unique 3.7 kb duplication was identified in the L gene between nucleotide position 8523 and 8524, preceded by a GA dinucleotide insertion. This duplication contained a partial G gene, the complete X gene, and a partial L gene, which extended from nucleotide positions 4767-8523 in the X+ virus. Thus, the X+ genome length is 17,361 nucleotides, and we have re-designated the virus as Sf-rhabdovirus X+3.7. The 3.7 kb duplication was found in all Sf9 cell clones producing the X+ variant virus. Furthermore, the Sf-rhabdovirus X+3.7 genome was stable at passage 30, which was the highest passage tested. These results highlight the importance of combining short-read and long-read technologies for accurately sequencing virus genomes using HTS.
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Affiliation(s)
| | | | - Arifa S. Khan
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (T.J.B.)
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Ternovoi VA, Shvalov AN, Kartashov MY, Ponomareva EP, Tupota NL, Khoroshavin YA, Bayandin RB, Gladysheva AV, Mikryukova TP, Tregubchak TV, Loktev VB. The Viromes of Mosquitoes from the Natural Landscapes of Western Siberia. Viruses 2023; 15:1896. [PMID: 37766302 PMCID: PMC10537626 DOI: 10.3390/v15091896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
The metagenomic analysis of mosquitoes allows for the genetic characterization of mosquito-associated viruses in different regions of the world. This study applied a metagenomic approach to identify novel viral sequences in seven species of mosquitoes collected from the Novosibirsk region of western Siberia. Using NGS sequencing, we identified 15 coding-complete viral polyproteins (genomes) and 15 viral-like partial sequences in mosquitoes. The complete sequences for novel viruses or the partial sequences of capsid proteins, hypothetical viral proteins, and RdRps were used to identify their taxonomy. The novel viral sequences were classified within the orders Tymovirales and Picornavirales and the families Partitiviridae, Totiviridae, Tombusviridae, Iflaviridae, Nodaviridae, Permutotetraviridae, and Solemoviridae, with several attributed to four unclassified RNA viruses. Interestingly, the novel putative viruses and viral sequences were mainly associated with the mosquito Coquillettidia richardii. This study aimed to increase our understanding of the viral diversity in mosquitoes found in the natural habitats of Siberia, which is characterized by very long, snowy, and cold winters.
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Affiliation(s)
- Vladimir A. Ternovoi
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Alexander N. Shvalov
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Mikhail Yu. Kartashov
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Eugenia P. Ponomareva
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Natalia L. Tupota
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Yuri A. Khoroshavin
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Roman B. Bayandin
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Anastasia V. Gladysheva
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Tamara P. Mikryukova
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Tatyana V. Tregubchak
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
| | - Valery B. Loktev
- State Research Center Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing of Russia, World-Class Genomic Research Center for Biological Safety and Technological Independence, 630559 Koltsovo, Russia (M.Y.K.); (E.P.P.); (N.L.T.); (Y.A.K.); (R.B.B.); (A.V.G.); (T.P.M.); (T.V.T.)
- Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia
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Dundarova H, Ivanova-Aleksandrova N, Bednarikova S, Georgieva I, Kirov K, Miteva K, Neov B, Ostoich P, Pikula J, Zukal J, Hristov P. Phylogeographic Aspects of Bat Lyssaviruses in Europe: A Review. Pathogens 2023; 12:1089. [PMID: 37764897 PMCID: PMC10534866 DOI: 10.3390/pathogens12091089] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/08/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
During the last few decades, bat lyssaviruses have become the topic of intensive molecular and epidemiological investigations. Since ancient times, rhabdoviruses have caused fatal encephalitis in humans which has led to research into effective strategies for their eradication. Modelling of potential future cross-species virus transmissions forms a substantial component of the recent infection biology of rabies. In this article, we summarise the available data on the phylogeography of both bats and lyssaviruses in Europe and the adjacent reg ions, especially in the contact zone between the Palearctic and Ethiopian realms. Within these zones, three bat families are present with high potential for cross-species transmission and the spread of lyssaviruses in Phylogroup II to Europe (part of the western Palearctic). The lack of effective therapies for rabies viruses in Phylogroup II and the most divergent lyssaviruses generates impetus for additional phylogenetic and virological research within this geographical region.
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Affiliation(s)
- Heliana Dundarova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | | | - Sarka Bednarikova
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| | - Irina Georgieva
- National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Krasimir Kirov
- Faculty of Biology, University of Plovdiv “Paisii Hilendarski”, 24 Tzar Assen Str., 4000 Plovdiv, Bulgaria
| | - Kalina Miteva
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - Boyko Neov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - Peter Ostoich
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - Jiri Pikula
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| | - Jan Zukal
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | - Peter Hristov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
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9
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Shepherd JG, Davis C, Streicker DG, Thomson EC. Emerging Rhabdoviruses and Human Infection. BIOLOGY 2023; 12:878. [PMID: 37372162 PMCID: PMC10294888 DOI: 10.3390/biology12060878] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Rhabdoviridae is a large viral family, with members infecting a diverse range of hosts including, vertebrate species, arthropods, and plants. The predominant human pathogen within the family is Rabies lyssavirus, the main cause of human rabies. While rabies is itself a neglected disease, there are other, less well studied, rhabdoviruses known to cause human infection. The increasing application of next-generation sequencing technology to clinical samples has led to the detection of several novel or rarely detected rhabdoviruses associated with febrile illness. Many of these viruses have been detected in low- and middle-income countries where the extent of human infection and the burden of disease remain largely unquantified. This review describes the rhabdoviruses other than Rabies lyssavirus that have been associated with human infection. The discovery of the Bas Congo virus and Ekpoma virus is discussed, as is the re-emergence of species such as Le Dantec virus, which has recently been detected in Africa 40 years after its initial isolation. Chandipura virus and the lyssaviruses that are known to cause human rabies are also described. Given their association with human disease, the viruses described in this review should be prioritised for further study.
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Affiliation(s)
- James G. Shepherd
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK; (C.D.); (D.G.S.)
| | - Chris Davis
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK; (C.D.); (D.G.S.)
| | - Daniel G. Streicker
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK; (C.D.); (D.G.S.)
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Emma C. Thomson
- Centre for Virus Research, MRC-University of Glasgow, Glasgow G61 1QH, UK; (C.D.); (D.G.S.)
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10
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Zhang P, Zhang Y, Cao L, Li J, Wu C, Tian M, Zhang Z, Zhang C, Zhang W, Li Y. A Diverse Virome Is Identified in Parasitic Flatworms of Domestic Animals in Xinjiang, China. Microbiol Spectr 2023; 11:e0070223. [PMID: 37042768 PMCID: PMC10269781 DOI: 10.1128/spectrum.00702-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/17/2023] [Indexed: 04/13/2023] Open
Abstract
Parasitic flatworms infect diverse vertebrates and are major threats to animal and even human health; however, little is known about the virome of these lower life forms. Using viral metagenomic sequencing, we characterized the virome of the parasitic flatworms collected from major domestic animals, including Dicrocoelium lanceatum and Taenia hydatigena, Echinococcus granulosus sensu stricto and Echinococcus multilocularis. Seven and three different viruses were discovered from D. lanceatum and T. hydatigena, respectively, and no viral sequences were found in adult tapeworms and protoscoleces of E. granulosus sensu stricto and E. multilocularis. Two out of the five parasitic flatworm species carry viruses, showing a host specificity of these viruses. These viruses belong to the Parvoviridae, Circoviridae, unclassified circular, Rep-encoding single-stranded (CRESS) DNA virus, Rhabdoviridae, Endornaviridae, and unclassified RNA viruses. The presence of multiple highly divergent RNA viruses, especially those that cluster with viruses found in marine animals, implies a deep evolutionary history of parasite-associated viruses. In addition, we found viruses with high identity to common pathogens in dogs, including canine circovirus and canine parvovirus 2. The presence of these viruses in the parasites implies that they may infect parasitic flatworms but does not completely exclude the possibility of contamination from host intestinal contents. Furthermore, we demonstrated that certain viruses, such as CRESS DNA virus may integrate into the genome of their host. Our results expand the knowledge of viral diversity in parasites of important domestic animals, highlighting the need for further investigations of their prevalence among other parasites of key animals. IMPORTANCE Characterizing the virome of parasites is important for unveiling the viral diversity, evolution, and ecology and will help to understand the "Russian doll" pattern among viruses, parasites, and host animals. Our data indicate that diverse viruses are present in specific parasitic flatworms, including viruses that may have an ancient evolutionary history and viruses currently circulating in parasite-infected host animals. These data also raise the question of whether parasitic flatworms acquire and/or carry some viruses that may have transmission potential to animals. In addition, through the study of virus-parasite-host interactions, including the influence of viral infection on the life cycle of the parasite, as well as its fitness and pathogenicity to the host, we could find new strategies to prevent and control parasitic diseases.
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Affiliation(s)
- Peng Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Le Cao
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun Li
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Chuanchuan Wu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Mengxiao Tian
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Zhuangzhi Zhang
- Veterinary Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Wenbao Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, WHO-Collaborating Centre for Prevention and Care Management of Echinococcosis, Xinjiang Medical University, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
- Veterinary Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Yanpeng Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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11
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Černe D, Hostnik P, Toplak I, Presetnik P, Maurer-Wernig J, Kuhar U. Discovery of a novel bat lyssavirus in a Long-fingered bat (Myotis capaccinii) from Slovenia. PLoS Negl Trop Dis 2023; 17:e0011420. [PMID: 37384601 DOI: 10.1371/journal.pntd.0011420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/25/2023] [Indexed: 07/01/2023] Open
Abstract
Lyssaviruses are the causative agents of rabies, a zoonotic, fatal disease that is thought to be ancestral to bats. In the last decade, the detection of bat associated lyssaviruses is increasing also in Europe. Within a retrospective bat associated lyssavirus surveillance study a total of 225 dead bats of 21 bat species were collected in Slovenia between 2012 and 2019 and tested by specific real-time RT-PCR method. The first lyssavirus positive sample in bats in Slovenia was detected using the real-time RT-PCR, the fluorescent antibody test, and next generation sequencing, while the rabies tissue culture inoculation test was unsuccessful due to sample degradation and storage conditions. The nearly complete genome of Divača bat lyssavirus from Slovenia consists of 11,871 nucleotides and reflects the characteristic gene organization known for lyssaviruses, encoding the five viral proteins. Phylogenetic analysis of Divača bat lyssavirus revealed that it belongs to phylogroup I lyssaviruses and is most closely related to Kotalahti bat lyssavirus (KBLV) with 87.20% nucleotide and 99.22% amino acid identity. Together with KBLV, Khujand virus, European bat lyssavirus 2, Bakeloh bat lyssavirus, and Aravan virus, Divača bat lyssavirus was detected in the genus Myotis suggesting its key role in the transmission and maintenance of certain lyssaviruses.
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Affiliation(s)
- Danijela Černe
- Institute of Microbiology and Parasitology, Virology Unit, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Peter Hostnik
- Institute of Microbiology and Parasitology, Virology Unit, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Ivan Toplak
- Institute of Microbiology and Parasitology, Virology Unit, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Primož Presetnik
- Centre for Cartography of Fauna and Flora, Ljubljana office, Ljubljana, Slovenia
| | - Jedrt Maurer-Wernig
- Administration of the Republic of Slovenia for food safety, veterinary sector, and plant protection, Ljubljana, Slovenia
| | - Urška Kuhar
- Institute of Microbiology and Parasitology, Virology Unit, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
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12
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Nagalo BM, Zhou Y, Loeuillard EJ, Dumbauld C, Barro O, Elliott NM, Baker AT, Arora M, Bogenberger JM, Meurice N, Petit J, Uson PLS, Aslam F, Raupach E, Gabere M, Basnakian A, Simoes CC, Cannon MJ, Post SR, Buetow K, Chamcheu JC, Barrett MT, Duda DG, Jacobs B, Vile R, Barry MA, Roberts LR, Ilyas S, Borad MJ. Characterization of Morreton virus as an oncolytic virotherapy platform for liver cancers. Hepatology 2023; 77:1943-1957. [PMID: 36052732 DOI: 10.1002/hep.32769] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Morreton virus (MORV) is an oncolytic Vesiculovirus , genetically distinct from vesicular stomatitis virus (VSV). AIM To report that MORV induced potent cytopathic effects (CPEs) in cholangiocarcinoma (CCA) and hepatocellular carcinoma (HCC) in vitro models. APPROACH AND RESULTS In preliminary safety analyses, high intranasal doses (up to 10 10 50% tissue culture infectious dose [TCID 50 ]) of MORV were not associated with significant adverse effects in immune competent, non-tumor-bearing mice. MORV was shown to be efficacious in a Hep3B hepatocellular cancer xenograft model but not in a CCA xenograft HuCCT1 model. In an immune competent, syngeneic murine CCA model, single intratumoral treatments with MORV (1 × 10 7 TCID 50 ) triggered a robust antitumor immune response leading to substantial tumor regression and disease control at a dose 10-fold lower than VSV (1 × 10 8 TCID 50 ). MORV led to increased CD8 + cytotoxic T cells without compensatory increases in tumor-associated macrophages and granulocytic or monocytic myeloid-derived suppressor cells. CONCLUSIONS Our findings indicate that wild-type MORV is safe and can induce potent tumor regression via immune-mediated and immune-independent mechanisms in HCC and CCA animal models without dose limiting adverse events. These data warrant further development and clinical translation of MORV as an oncolytic virotherapy platform.
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Affiliation(s)
- Bolni Marius Nagalo
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Department of Pathology , University of Arkansas for Medical Sciences , Little Rock , Arkansas , USA
- The Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences , Little Rock , Arkansas , USA
| | - Yumei Zhou
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
| | - Emilien J Loeuillard
- Division of Gastroenterology and Hepatology , Mayo Clinic , Rochester , Minnesota , USA
| | - Chelsae Dumbauld
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
| | - Oumar Barro
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
| | - Natalie M Elliott
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
| | - Alexander T Baker
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
| | - Mansi Arora
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
| | - James M Bogenberger
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
| | - Nathalie Meurice
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
| | - Joachim Petit
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
| | - Pedro Luiz Serrano Uson
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
- Center for Personalized Medicine , Hospital Israelita Albert Einstein , São Paulo , Brazil
| | - Faaiq Aslam
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
| | - Elizabeth Raupach
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
| | - Musa Gabere
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
| | - Alexei Basnakian
- Department of Pathology , University of Arkansas for Medical Sciences , Little Rock , Arkansas , USA
- Department of Pharmacology and Toxicology , University of Arkansas for Medical Sciences , Little Rock , Arkansas , USA
| | - Camila C Simoes
- Department of Pathology , University of Arkansas for Medical Sciences , Little Rock , Arkansas , USA
- The Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences , Little Rock , Arkansas , USA
| | - Martin J Cannon
- The Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences , Little Rock , Arkansas , USA
- Department of Microbiology and Immunology , University of Arkansas for Medical Sciences , Little Rock , Arkansas , USA
| | - Steven R Post
- Department of Pathology , University of Arkansas for Medical Sciences , Little Rock , Arkansas , USA
- The Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences , Little Rock , Arkansas , USA
| | - Kenneth Buetow
- Computational Sciences and Informatics Program for Complex Adaptive System Arizona State University , Tempe , Arizona , USA
| | - Jean Christopher Chamcheu
- School of Basic Pharmaceutical and Toxicological Sciences , College of Pharmacy, University of Louisiana , Monroe , Louisiana , USA
| | - Michael T Barrett
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
| | - Dan G Duda
- Steele Laboratories for Tumor Biology, Department of Radiation Oncology , Massachusetts General Hospital and Harvard Medical School , Boston , Massachusetts , USA
| | - Bertram Jacobs
- Center for Infectious Diseases and Vaccinology , the Biodesign Institute, Arizona State University , Tempe , Arizona , USA
| | - Richard Vile
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Mayo Clinic Comprehensive Cancer Center , Phoenix , Minnesota , USA
| | - Michael A Barry
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Mayo Clinic Comprehensive Cancer Center , Phoenix , Minnesota , USA
- Division of Infectious Diseases, Department of Internal Medicine , Mayo Clinic Rochester , Rochester , Minnesota , USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology , Mayo Clinic , Rochester , Minnesota , USA
| | - Sumera Ilyas
- Division of Gastroenterology and Hepatology , Mayo Clinic , Rochester , Minnesota , USA
| | - Mitesh J Borad
- Department of Molecular Medicine , Mayo Clinic , Rochester , Minnesota , USA
- Division of Hematology and Medical Oncology , Mayo Clinic , Phoenix , Arizona , USA
- Mayo Clinic Comprehensive Cancer Center , Phoenix , Minnesota , USA
- Mayo Clinic Center for Individualized Medicine , Rochester , Minnesota , USA
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13
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Goldberg TL, Blevins E, Leis EM, Standish IF, Richard JC, Lueder MR, Cer RZ, Bishop-Lilly KA. Plasticity, Paralogy, and Pseudogenization: Rhabdoviruses of Freshwater Mussels Elucidate Mechanisms of Viral Genome Diversification and the Evolution of the Finfish-Infecting Rhabdoviral Genera. J Virol 2023; 97:e0019623. [PMID: 37154732 PMCID: PMC10231222 DOI: 10.1128/jvi.00196-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/07/2023] [Indexed: 05/10/2023] Open
Abstract
Viruses in the family Rhabdoviridae display remarkable genomic variation and ecological diversity. This plasticity occurs despite the fact that, as negative sense RNA viruses, rhabdoviruses rarely if ever recombine. Here, we describe nonrecombinatorial evolutionary processes leading to genomic diversification in the Rhabdoviridae inferred from two novel rhabdoviruses of freshwater mussels (Mollusca: Bivalvia: Unionida). Killamcar virus 1 (KILLV-1) from a plain pocketbook (Lampsilis cardium) is closely related phylogenetically and transcriptionally to finfish-infecting viruses in the subfamily Alpharhabdovirinae. KILLV-1 offers a novel example of glycoprotein gene duplication, differing from previous examples in that the paralogs overlap. Evolutionary analyses reveal a clear pattern of relaxed selection due to subfunctionalization in rhabdoviral glycoprotein paralogs, which has not previously been described in RNA viruses. Chemarfal virus 1 (CHMFV-1) from a western pearlshell (Margaritifera falcata) is closely related phylogenetically and transcriptionally to viruses in the genus Novirhabdovirus, the sole recognized genus in the subfamily Gammarhabdovirinae, representing the first known gammarhabdovirus of a host other than finfish. The CHMFV-1 G-L noncoding region contains a nontranscribed remnant gene of precisely the same length as the NV gene of most novirhabdoviruses, offering a compelling example of pseudogenization. The unique reproductive strategy of freshwater mussels involves an obligate parasitic stage in which larvae encyst in the tissues of finfish, offering a plausible ecological mechanism for viral host-switching. IMPORTANCE Viruses in the family Rhabdoviridae infect a variety of hosts, including vertebrates, invertebrates, plants and fungi, with important consequences for health and agriculture. This study describes two newly discovered viruses of freshwater mussels from the United States. One virus from a plain pocketbook (Lampsilis cardium) is closely related to fish-infecting viruses in the subfamily Alpharhabdovirinae. The other virus from a western pearlshell (Margaritifera falcata) is closely related to viruses in the subfamily Gammarhabdovirinae, which until now were only known to infect finfish. Genome features of both viruses provide new evidence of how rhabdoviruses evolved their extraordinary variability. Freshwater mussel larvae attach to fish and feed on tissues and blood, which may explain how rhabdoviruses originally jumped between mussels and fish. The significance of this research is that it improves our understanding of rhabdovirus ecology and evolution, shedding new light on these important viruses and the diseases they cause.
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Affiliation(s)
- Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Emilie Blevins
- Xerces Society for Invertebrate Conservation, Portland, Oregon, USA
| | - Eric M. Leis
- U.S. Fish and Wildlife Service, La Crosse Fish Health Center, Midwest Fisheries Center, Onalaska, Wisconsin, USA
| | - Isaac F. Standish
- U.S. Fish and Wildlife Service, La Crosse Fish Health Center, Midwest Fisheries Center, Onalaska, Wisconsin, USA
| | - Jordan C. Richard
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
- U.S. Fish and Wildlife Service, Southwestern Virginia Field Office, Abingdon, Virginia, USA
| | - Matthew R. Lueder
- Leidos, Reston, Virginia, USA
- Biological Defense Research Directorate, Naval Medical Research Command–Frederick, Fort Detrick, Maryland, USA
| | - Regina Z. Cer
- Biological Defense Research Directorate, Naval Medical Research Command–Frederick, Fort Detrick, Maryland, USA
| | - Kimberly A. Bishop-Lilly
- Biological Defense Research Directorate, Naval Medical Research Command–Frederick, Fort Detrick, Maryland, USA
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14
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Wu Y, Yang M, Yang H, Qiu Y, Xuan Z, Xing F, Cao M. Identification and molecular characterization of a novel cytorhabdovirus from rose plants (Rosa chinensis Jacq.). Arch Virol 2023; 168:118. [PMID: 36952055 DOI: 10.1007/s00705-023-05742-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/06/2023] [Indexed: 03/24/2023]
Abstract
A novel negative-sense single-stranded RNA virus, tentatively named "rose-associated cytorhabdovirus" (RaCV), was identified by high-throughput sequencing. RaCV is 16,067 nucleotides in length and contains eight open reading frames (ORFs 1-8) encoding a nucleocapsid protein (N), a putative phosphoprotein (P), a putative P3 protein (P3), a putative P4 protein (P4), a putative matrix protein (M), a glycoprotein (G), a putative P7 protein (P7), and an RNA-dependent RNA polymerase (L), respectively. The coding genes are flanked by a 3' leader sequence (228 nt) and a 5' trailer sequence (251 nt) and are separated by conserved intergenic junctions (3'-AUUCUUUUUG(N)nCUN-5'). Phylogenetic analysis showed that RaCV clustered with yerba mate virus A (YmVA) within the cytorhabdovirus clade, and it exhibited low a degree of nt sequence similarity (<40% identity) to other rhabdoviruses. Amino acid sequence comparisons between the putative proteins of RaCV and the corresponding proteins of other cytorhabdoviruses showed that the sequence identity levels were far below the species demarcation cutoff of 80% for cytorhabdoviruses. These results suggest that RaCV should be classified as a new member of the genus Cytorhabdovirus.
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Affiliation(s)
- Yujiao Wu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Mengxue Yang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Han Yang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yuanjian Qiu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Zhiyou Xuan
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Fei Xing
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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15
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First Discovery of Phenuiviruses within Diverse RNA Viromes of Asiatic Toad (Bufo gargarizans) by Metagenomics Sequencing. Viruses 2023; 15:v15030750. [PMID: 36992458 PMCID: PMC10056474 DOI: 10.3390/v15030750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
Most zoonotic pathogens originate from mammals and avians, but viral diversity and related biosafety risk assessment in lower vertebrates also need to be explored. Amphibians are an important group of lower vertebrates that played a momentous role in animal evolution. To elucidate the diversity of RNA viruses in one important species of amphibians, the Asiatic toad (Bufo gargarizans), we obtained 44 samples including lung, gut, liver, and kidney tissues from Asiatic toads in Sichuan and Jilin provinces, China, for viral metagenomics sequencing. More than 20 novel RNA viruses derived from the order Bunyavirales and 7 families of Astroviridae, Dicistroviridae, Leviviridae, Partitiviridae, Picornaviridae, Rhabdoviridae, and Virgaviridae were discovered, which were distinct from previously described viruses and formed new clusters, as revealed by phylogenetic analyses. Notably, a novel bastrovirus, AtBastV/GCCDC11/2022, of the family Astroviridae was identified from the gut library, the genome of which contains three open reading frames, with the RNA-dependent RNA polymerase (RdRp) coded by ORF1 closely related to that of hepeviruses, and ORF2 encoding an astrovirus-related capsid protein. Notably, phenuiviruses were discovered for the first time in amphibians. AtPhenV1/GCCDC12/2022 and AtPhenV2/GCCDC13/2022 clustered together and formed a clade with the group of phenuiviruses identified from rodents. Picornaviruses and several invertebrate RNA viruses were also detected. These findings improve our understanding of the high RNA viral diversity in the Asiatic toad and provide new insights in the evolution of RNA viruses in amphibians.
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16
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Zhao Z, Wang B, Wu S, Zhang Z, Chen Y, Zhang J, Wang Y, Zhu D, Li Y, Xu J, Hou L, Chen W. Regulated control of virus replication by 4-hydroxytamoxifen-induced splicing. Front Microbiol 2023; 14:1112580. [PMID: 36992923 PMCID: PMC10040539 DOI: 10.3389/fmicb.2023.1112580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/14/2023] [Indexed: 03/14/2023] Open
Abstract
Designing a modified virus that can be controlled to replicate will facilitate the study of pathogenic mechanisms of virus and virus–host interactions. Here, we report a universal switch element that enables precise control of virus replication after exposure to a small molecule. Inteins mediate a traceless protein splicing–ligation process, and we generate a series of modified vesicular stomatitis virus (VSV) with intein insertion into the nucleocapsid, phosphoprotein, or large RNA-dependent RNA polymerase of VSV. Two recombinant VSV, LC599 and LY1744, were screened for intein insertion in the large RNA-dependent RNA polymerase of VSV, and their replication was regulated in a dose-dependent manner with the small molecule 4-hydroxytamoxifen, which induces intein splicing to restore the VSV replication. Furthermore, in the presence of 4-hydroxytamoxifen, the intein-modified VSV LC599 replicated efficiently in an animal model like a prototype of VSV. Thus, we present a simple and highly adaptable tool for regulating virus replication.
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Affiliation(s)
| | - Busen Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Shipo Wu
- Beijing Institute of Biotechnology, Beijing, China
| | - Zhe Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Yi Chen
- Beijing Institute of Biotechnology, Beijing, China
| | | | - Yudong Wang
- Beijing Institute of Biotechnology, Beijing, China
| | - Danni Zhu
- Beijing Institute of Biotechnology, Beijing, China
- Qingdao Special Servicemen Recuperation Center of PLA Navy, Qingdao, Shandong, China
| | - Yao Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Jinghan Xu
- Beijing Institute of Biotechnology, Beijing, China
| | - Lihua Hou
- Beijing Institute of Biotechnology, Beijing, China
- *Correspondence: Lihua Hou, ; Wei Chen,
| | - Wei Chen
- Beijing Institute of Biotechnology, Beijing, China
- *Correspondence: Lihua Hou, ; Wei Chen,
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17
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Ribeiro JMC, Bayona-Vásquez NJ, Budachetri K, Kumar D, Frederick JC, Tahir F, Faircloth BC, Glenn TC, Karim S. A draft of the genome of the Gulf Coast tick, Amblyomma maculatum. Ticks Tick Borne Dis 2023; 14:102090. [PMID: 36446165 PMCID: PMC9898150 DOI: 10.1016/j.ttbdis.2022.102090] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 10/17/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022]
Abstract
The Gulf Coast tick, Amblyomma maculatum, inhabits the Southeastern states of the USA bordering the Gulf of Mexico, Mexico, and other Central and South American countries. More recently, its U.S. range has extended West to Arizona and Northeast to New York state and Connecticut. It is a vector of Rickettsia parkeri and Hepatozoon americanum. This tick species has become a model to study tick/Rickettsia interactions. To increase our knowledge of the basic biology of A. maculatum we report here a draft genome of this tick and an extensive functional classification of its proteome. The DNA from a single male tick was used as a genomic source, and a 10X genomics protocol determined 28,460 scaffolds having equal or more than 10 Kb, totaling 1.98 Gb. The N50 scaffold size was 19,849 Kb. The BRAKER pipeline was used to find the protein-coding gene boundaries on the assembled A. maculatum genome, discovering 237,921 CDS. After trimming and classifying the transposable elements, bacterial contaminants, and truncated genes, a set of 25,702 were annotated and classified as the core gene products. A BUSCO analysis revealed 83.4% complete BUSCOs. A hyperlinked spreadsheet is provided, allowing browsing of the individual gene products and their matches to several databases.
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Affiliation(s)
- Jose M C Ribeiro
- NIAID NIH Laboratory of Malaria and Vector Research, Bethesda, MD 20892-8132, USA.
| | - Natalia J Bayona-Vásquez
- Department of Environmental Health Science and Georgia Genomics Facility, Environmental Health Science Building, University of Georgia, Athens, GA 30602, USA
| | - Khemraj Budachetri
- Center for Molecular and Cellular Biology, School of Biological, Environmental, and Earth Sciences, 118 College Drive, 5018, University of Southern Mississippi, Hattiesburg, MS 39406, USA; The Ohio State University, Columbus, OH 43210, USA
| | - Deepak Kumar
- Department of Environmental Health Science and Georgia Genomics Facility, Environmental Health Science Building, University of Georgia, Athens, GA 30602, USA
| | - Julia Catherine Frederick
- Department of Environmental Health Science and Georgia Genomics Facility, Environmental Health Science Building, University of Georgia, Athens, GA 30602, USA
| | - Faizan Tahir
- Center for Molecular and Cellular Biology, School of Biological, Environmental, and Earth Sciences, 118 College Drive, 5018, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Brant C Faircloth
- Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Travis C Glenn
- Department of Environmental Health Science and Georgia Genomics Facility, Environmental Health Science Building, University of Georgia, Athens, GA 30602, USA
| | - Shahid Karim
- Center for Molecular and Cellular Biology, School of Biological, Environmental, and Earth Sciences, 118 College Drive, 5018, University of Southern Mississippi, Hattiesburg, MS 39406, USA
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18
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Yang Z, Wang H, Yang S, Wang X, Shen Q, Ji L, Zeng J, Zhang W, Gong H, Shan T. Virome diversity of ticks feeding on domestic mammals in China. Virol Sin 2023; 38:208-221. [PMID: 36781125 PMCID: PMC10176445 DOI: 10.1016/j.virs.2023.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 02/08/2023] [Indexed: 02/13/2023] Open
Abstract
Ticks are considered the second most common pathogen vectors transmitting a broad range of vital human and veterinary viruses. From 2017 to 2018, 640 ticks were collected in eight different provinces in central and western China. Six species were detected, including H.longicornis, De.everestianus, Rh.microplus, Rh.turanicus, Rh.sanguineous, and Hy.asiaticum. Sixty-four viral metagenomic libraries were constructed on the MiSeq Illumina platform, resulting in 13.44 G (5.88 × 107) of 250-bp-end reads, in which 2,437,941 are viral reads. We found 27 nearly complete genome sequences, including 16 genome sequences encoding entire protein-coding regions (lack of 3' or 5' end non-coding regions) and complete viral genomes, distributed in the arboviral family (Chuviridae, Rhabdoviridae, Nairoviridae, Phenuiviridae, Flaviviridae, Iflaviridae) as well as Parvoviridae and Polyomaviridae that cause disease in mammals and even humans. In addition, 13 virus sequences found in Chuviridae, Nairoviridae, Flaviviridae, Iflaviridae, Hepeviridae, Parvoviridae, and Polyomaviridae were identified as belonging to a new virus species in the identified viral genera. Besides, an epidemiological survey shows a high prevalence (9.38% and 15.63%) of two viruses (Ovine Copiparvovirus and Bovine parvovirus 2) in the tick cohort.
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Affiliation(s)
- Zijun Yang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China; Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an, 223002, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Likai Ji
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Jian Zeng
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, China.
| | - Haiyan Gong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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19
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Perinet LC, Mutebi JP, Powers AM, Lutwama JJ, Mossel EC. Yata Virus (Family Rhabdoviridae, Genus Ephemerovirus) Isolation from Mosquitoes from Uganda, the First Reported Isolation since 1969. Diseases 2023; 11:diseases11010021. [PMID: 36810535 PMCID: PMC9944095 DOI: 10.3390/diseases11010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
As a part of a systematic study of mosquitoes and associated viruses in Uganda, a virus was isolated from a pool of Mansonia uniformis collected in July 2017, in the Kitgum District of northern Uganda. Sequence analysis determined that the virus is Yata virus (YATAV; Ephemerovirus yata; family Rhabdoviridae). The only previous reported isolation of YATAV was in 1969 in Birao, Central African Republic, also from Ma. uniformis mosquitoes. The current sequence is over 99% identical at the nucleotide level to the original isolate, indicating a high level of YATAV genomic stability.
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Affiliation(s)
- Lara C. Perinet
- Division of Vector-Borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - John-Paul Mutebi
- Division of Vector-Borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Ann M. Powers
- Division of Vector-Borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging, and Re-emerging Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Eric C. Mossel
- Division of Vector-Borne Diseases, US Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
- Correspondence:
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20
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Tangudu CS, Hargett AM, Laredo-Tiscareño SV, Smith RC, Blitvich BJ. Isolation of a novel rhabdovirus and detection of multiple novel viral sequences in Culex species mosquitoes in the United States. Arch Virol 2022; 167:2577-2590. [PMID: 36056958 DOI: 10.1007/s00705-022-05586-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/21/2022] [Indexed: 12/14/2022]
Abstract
To increase our understanding of the diversity of the mosquito virome, 6956 mosquitoes of five species (Culex erraticus, Culex pipiens, Culex restuans, Culex tarsalis, and Culex territans) collected in Iowa in the United States in 2017 and 2020 were assayed for novel viruses by performing polyethylene glycol precipitation, virus isolation in cell culture, and unbiased high-throughput sequencing. A novel virus, provisionally named "Walnut Creek virus", was isolated from Cx. tarsalis, and its genomic sequence and organization are characteristic of viruses in the genus Hapavirus (family Rhabdoviridae). Replication of Walnut Creek virus occurred in avian, mammalian, and mosquito, but not tick, cell lines. A novel virus was also isolated from Cx. restuans, and partial genome sequencing revealed that it is distantly related to an unclassified virus of the genus Phytoreovirus (family Sedoreoviridae). Two recognized viruses were also isolated: Culex Y virus (family Birnaviridae) and Houston virus (family Mesoniviridae). We also identified sequences of eight novel viruses from six families (Amalgaviridae, Birnaviridae, Partitiviridae, Sedoreoviridae, Tombusviridae, and Totiviridae), two viruses that do not belong to any established families, and many previously recognized viruses. In summary, we provide evidence of multiple novel and recognized viruses in Culex spp. mosquitoes in the United States.
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Affiliation(s)
- Chandra S Tangudu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Alissa M Hargett
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - S Viridiana Laredo-Tiscareño
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Ryan C Smith
- Department of Entomology, College of Agriculture and Life Sciences, Iowa State University, Ames, IA, USA
| | - Bradley J Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA.
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21
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Kamani J, González-Miguel J, Msheliza EG, Goldberg TL. Straw-Colored Fruit Bats ( Eidolon helvum) and Their Bat Flies ( Cyclopodia greefi) in Nigeria Host Viruses with Multifarious Modes of Transmission. Vector Borne Zoonotic Dis 2022; 22:545-552. [DOI: 10.1089/vbz.2022.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Joshua Kamani
- Parasitology Division, National Veterinary Research Institute (NVRI), Vom, Nigeria
| | - Javier González-Miguel
- Laboratory of Parasitology, Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Salamanca, Spain
- Molecular Parasitology Laboratory, Centre of One Health (COH), Ryan Institute, National University of Ireland, Galway, Ireland
| | - Emmanuel G. Msheliza
- Parasitology Division, National Veterinary Research Institute (NVRI), Vom, Nigeria
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
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22
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Alisoltani A, Jaroszewski L, Iyer M, Iranzadeh A, Godzik A. Increased Frequency of Indels in Hypervariable Regions of SARS-CoV-2 Proteins—A Possible Signature of Adaptive Selection. Front Genet 2022; 13:875406. [PMID: 35719386 PMCID: PMC9201826 DOI: 10.3389/fgene.2022.875406] [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: 02/14/2022] [Accepted: 04/08/2022] [Indexed: 11/29/2022] Open
Abstract
Most attention in the surveillance of evolving SARS-CoV-2 genome has been centered on nucleotide substitutions in the spike glycoprotein. We show that, as the pandemic extends into its second year, the numbers and ratio of genomes with in-frame insertions and deletions (indels) increases significantly, especially among the variants of concern (VOCs). Monitoring of the SARS-CoV-2 genome evolution shows that co-occurrence (i.e., highly correlated presence) of indels, especially deletions on spike N-terminal domain and non-structural protein 6 (NSP6) is a shared feature in several VOCs such as Alpha, Beta, Delta, and Omicron. Indels distribution is correlated with spike mutations associated with immune escape and growth in the number of genomes with indels coincides with the increasing population resistance due to vaccination and previous infections. Indels occur most frequently in the spike, but also in other proteins, especially those involved in interactions with the host immune system. We also showed that indels concentrate in regions of individual SARS-CoV-2 proteins known as hypervariable regions (HVRs) that are mostly located in specific loop regions. Structural analysis suggests that indels remodel viral proteins’ surfaces at common epitopes and interaction interfaces, affecting the virus’ interactions with host proteins. We hypothesize that the increased frequency of indels, the non-random distribution of them and their independent co-occurrence in several VOCs is another mechanism of response to elevated global population immunity.
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Affiliation(s)
- Arghavan Alisoltani
- Biosciences Division, School of Medicine, University of California, Riverside, Riverside, CA, United States
| | - Lukasz Jaroszewski
- Biosciences Division, School of Medicine, University of California, Riverside, Riverside, CA, United States
| | - Mallika Iyer
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Arash Iranzadeh
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Adam Godzik
- Biosciences Division, School of Medicine, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Adam Godzik,
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23
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Walker PJ, Freitas-Astúa J, Bejerman N, Blasdell KR, Breyta R, Dietzgen RG, Fooks AR, Kondo H, Kurath G, Kuzmin IV, Ramos-González PL, Shi M, Stone DM, Tesh RB, Tordo N, Vasilakis N, Whitfield AE, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Rhabdoviridae 2022. J Gen Virol 2022; 103. [PMID: 35723908 DOI: 10.1099/jgv.0.001689] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The family Rhabdoviridae comprises viruses with negative-sense (-) RNA genomes of 10-16 kb. Virions are typically enveloped with bullet-shaped or bacilliform morphology but can also be non-enveloped filaments. Rhabdoviruses infect plants or animals, including mammals, birds, reptiles, amphibians or fish, as well as arthropods, which serve as single hosts or act as biological vectors for transmission to animals or plants. Rhabdoviruses include important pathogens of humans, livestock, fish or agricultural crops. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Rhabdoviridae, which is available at ictv.global/report/rhabdoviridae.
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Affiliation(s)
- Peter J Walker
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | | | - Nicolas Bejerman
- Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET) and Instituto Nacional de Tecnología Agropecuaria (INTA), Argentina
| | - Kim R Blasdell
- CSIRO Health and Biosecurity, Geelong, VIC 3220, Australia
| | | | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD 4072, Australia
| | - Anthony R Fooks
- Animal and Plant Health Agency Addlestone, Surrey KT15 3NB, UK
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Gael Kurath
- Western Fisheries Research Center, Seattle, WA 98115, USA
| | - Ivan V Kuzmin
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Mang Shi
- Sun Yat Sen University, Guangzhou, Guangdong, PR China
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, DT4 8UB, UK
| | - Robert B Tesh
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Noël Tordo
- Institut Pasteur de Guinée, Gamal Abdel Nasser University, Conakry, Guinea
| | - Nikos Vasilakis
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh NC 27606, USA
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24
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Walker PJ, Bigarré L, Kurath G, Dacheux L, Pallandre L. Revised Taxonomy of Rhabdoviruses Infecting Fish and Marine Mammals. Animals (Basel) 2022; 12:ani12111363. [PMID: 35681827 PMCID: PMC9179924 DOI: 10.3390/ani12111363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The Rhabdoviridae is a family of viruses that includes some important pathogens of fish and marine mammals. Aspects of the taxonomic classification of fish viruses assigned to this family have recently been reviewed by the International Committee on Taxonomy of Viruses (ICTV). This paper describes the newly approved taxonomy, including the assignment of new subfamilies and new virus species. The paper also considers a taxonomic conundrum presented by viruses assigned to one group of fish rhabdoviruses (genus Novirhabdovirus) for which assignment to the family Rhabdoviridae may not be appropriate. Abstract The Rhabdoviridae is a large family of negative-sense (-) RNA viruses that includes important pathogens of ray-finned fish and marine mammals. As for all viruses, the taxonomic assignment of rhabdoviruses occurs through a process implemented by the International Committee on Taxonomy of Viruses (ICTV). A recent revision of taxonomy conducted in conjunction with the ICTV Rhabdoviridae Study Group has resulted in the establishment of three new subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae) within the Rhabdoviridae, as well as three new genera (Cetarhavirus, Siniperhavirus, and Scophrhavirus) and seven new species for viruses infecting fish or marine mammals. All rhabdovirus species have also now been named or renamed to comply with the binomial format adopted by the ICTV in 2021, comprising the genus name followed by a species epithet. Phylogenetic analyses of L protein (RNA-dependent RNA polymerase) sequences of (-) RNA viruses indicate that members of the genus Novirhabdovirus (subfamily Gammarhabdovirinae) do not cluster within the Rhabdoviridae, suggesting the need for a review of their current classification.
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Affiliation(s)
- Peter J. Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4067, Australia
- Correspondence:
| | - Laurent Bigarré
- Laboratory of Ploufragan-Plouzané-Niort, Technopole Brest Iroise, ANSES, 29280 Plouzané, France; (L.B.); (L.P.)
| | - Gael Kurath
- Western Fisheries Research Center, US Geological Survey, 6505 NE 65th Street, Seattle, WA 98115, USA;
| | - Laurent Dacheux
- Unit Lyssavirus Epidemiology and Neuropathology, Université Paris Cité, Institut Pasteur, 28 Rue du Docteur Roux, CEDEX 15, 75724 Paris, France;
| | - Laurane Pallandre
- Laboratory of Ploufragan-Plouzané-Niort, Technopole Brest Iroise, ANSES, 29280 Plouzané, France; (L.B.); (L.P.)
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25
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Steenwyk JL, Buida Iii TJ, Gonçalves C, Goltz DC, Morales G, Mead ME, LaBella AL, Chavez CM, Schmitz JE, Hadjifrangiskou M, Li Y, Rokas A. BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. Genetics 2022; 221:6583183. [PMID: 35536198 PMCID: PMC9252278 DOI: 10.1093/genetics/iyac079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/03/2022] [Indexed: 11/14/2022] Open
Abstract
Bioinformatic analysis-such as genome assembly quality assessment, alignment summary statistics, relative synonymous codon usage, file format conversion, and processing and analysis-is integrated into diverse disciplines in the biological sciences. Several command-line pieces of software have been developed to conduct some of these individual analyses, but unified toolkits that conduct all these analyses are lacking. To address this gap, we introduce BioKIT, a versatile command line toolkit that has, upon publication, 42 functions, several of which were community-sourced, that conduct routine and novel processing and analysis of genome assemblies, multiple sequence alignments, coding sequences, sequencing data, and more. To demonstrate the utility of BioKIT, we conducted a comprehensive examination of relative synonymous codon usage across 171 fungal genomes that use alternative genetic codes, showed that the novel metric of gene-wise relative synonymous codon usage can accurately estimate gene-wise codon optimization, evaluated the quality and characteristics of 901 eukaryotic genome assemblies, and calculated alignment summary statistics for 10 phylogenomic data matrices. BioKIT will be helpful in facilitating and streamlining sequence analysis workflows. BioKIT is freely available under the MIT license from GitHub (https://github.com/JLSteenwyk/BioKIT), PyPi (https://pypi.org/project/jlsteenwyk-biokit/), and the Anaconda Cloud (https://anaconda.org/jlsteenwyk/jlsteenwyk-biokit). Documentation, user tutorials, and instructions for requesting new features are available online (https://jlsteenwyk.com/BioKIT).
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Affiliation(s)
- Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA.,Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | | | - Carla Gonçalves
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA.,Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.,Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal.,UCIBIO-Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | | | - Grace Morales
- Department of Pathology, Microbiology & Immunology, Center for Personalized Microbiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Matthew E Mead
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA.,Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA.,Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Christina M Chavez
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA.,Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Jonathan E Schmitz
- Department of Pathology, Microbiology & Immunology, Center for Personalized Microbiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Maria Hadjifrangiskou
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.,Department of Pathology, Microbiology & Immunology, Center for Personalized Microbiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yuanning Li
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN 37235, USA.,Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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A World of Viruses Nested within Parasites: Unraveling Viral Diversity within Parasitic Flatworms (Platyhelminthes). Microbiol Spectr 2022; 10:e0013822. [PMID: 35536058 PMCID: PMC9241645 DOI: 10.1128/spectrum.00138-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Because parasites have an inextricable relationship with their host, they have the potential to serve as viral reservoirs or facilitate virus host shifts. And yet, little is known about viruses infecting parasitic hosts except for blood-feeding arthropods that are well-known vectors of zoonotic viruses. Herein, we uncovered viruses of flatworms (phylum Platyhelminthes, group Neodermata) that specialize in parasitizing vertebrates and their ancestral free-living relatives. We discovered 115 novel viral sequences, including 1 in Macrostomorpha, 5 in Polycladida, 44 in Tricladida, 1 in Monogenea, 15 in Cestoda, and 49 in Trematoda, through data mining. The majority of newly identified viruses constitute novel families or genera. Phylogenetic analyses show that the virome of flatworms changed dramatically during the transition of neodermatans to a parasitic lifestyle. Most Neodermata viruses seem to codiversify with their host, with the exception of rhabdoviruses, which may switch hosts more often, based on phylogenetic relationships. Neodermata rhabdoviruses also have a position ancestral to vertebrate-associated rhabdo viruses, including lyssaviruses, suggesting that vertebrate-associated rhabdoviruses emerged from a flatworm rhabdovirus in a parasitized host. This study reveals an extensive diversity of viruses in Platyhelminthes and highlights the need to evaluate the role of viral infection in flatworm-associated diseases. IMPORTANCE Little is known about the diversity of parasite-associated viruses and how these viruses may impact parasite fitness, parasite-host interactions, and virus evolution. The discovery of over a hundred viruses associated with a range of free-living and parasitic flatworms, including parasites of economic and clinical relevance, allowed us to compare the viromes of flatworms with contrasting lifestyles. The results suggest that flatworms acquired novel viruses after their transition to a parasitic lifestyle and highlight the possibility that they acquired viruses from their hosts and vice versa. An interesting example is the discovery of flatworm rhabdoviruses that have a position ancestral to rabies viruses and other vertebrate-associated rhabdoviruses, demonstrating that flatworm-associated viruses have emerged in a vertebrate host at least once in history. Therefore, parasitic flatworms may play a role in virus diversity and emergence. The roles that parasite-infecting viruses play in parasite-associated diseases remain to be investigated.
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Abstract
Rhabdoviruses are ubiquitous and diverse viruses that propagate owing to bidirectional interactions with their vertebrate, arthropod, and plant hosts, and some of them could pose global health or agricultural threats. However, rhabdoviruses have rarely been reported in fungi. Here, two newly identified fungal rhabdoviruses, Rhizoctonia solani rhabdovirus 1 (RsRhV1) and RsRhV2, were discovered and molecularly characterized from the phytopathogenic fungus Rhizoctonia solani. The genomic organizations of RsRhV1 and RsRhV2 are 11,716 and 11,496 nucleotides (nt) in length, respectively, and consist of five open reading frames (ORFs) (ORFs I to V). ORF I, ORF IV, and ORF V encode the viral nucleocapsid (N), glycoprotein (G), and RNA polymerase (L), respectively. The putative protein encoded by ORF III has a lower level of identity with the matrix protein of rhabdoviruses. ORF II encodes a hypothetical protein with unknown function. Phylogenetic trees based on multiple alignments of N, L, and G proteins revealed that RsRhV1 and RsRhV2 are new members of the family Rhabdoviridae, but they form an independent evolutionary branch significantly distinct from other known nonfungal rhabdoviruses, suggesting that they represent a novel viral evolutionary lineage within Rhabdoviridae. Compared to strains lacking rhabdoviruses, strains harboring RsRhV2 and RsRhV1 showed hypervirulence, suggesting that RsRhV1 and RsRhV2 might be associated with the virulence of R. solani. Taken together, this study enriches our understanding of the diversity and host range of rhabdoviruses. IMPORTANCE Mycoviruses have been attracting an increasing amount of attention due to their impact on important medical, agricultural, and industrial fungi. Rhabdoviruses are prevalent across a wide spectrum of hosts, from plants to invertebrates and vertebrates. This study molecularly characterized two novel rhabdoviruses from four Rhizoctonia solani strains, based on their genomic structures, transcription strategy, phylogenetic relationships, and biological impact on their host. Our study makes a significant contribution to the literature because it not only enriches the mycovirus database but also expands the known host range of rhabdoviruses. It also offers insight into the evolutionary linkage between animal viruses and mycoviruses and the transmission of viruses from one host to another. Our study will also help expand the contemporary knowledge of the classification of rhabdoviruses, as well as providing a new model to study rhabdovirus-host interactions, which will benefit the agriculture and medical areas of human welfare.
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Muñoz-Baena L, Poon AFY. Using networks to analyze and visualize the distribution of overlapping genes in virus genomes. PLoS Pathog 2022; 18:e1010331. [PMID: 35202429 PMCID: PMC8903798 DOI: 10.1371/journal.ppat.1010331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 03/08/2022] [Accepted: 02/02/2022] [Indexed: 11/19/2022] Open
Abstract
Gene overlap occurs when two or more genes are encoded by the same nucleotides. This phenomenon is found in all taxonomic domains, but is particularly common in viruses, where it may increase the information content of compact genomes or influence the creation of new genes. Here we report a global comparative study of overlapping open reading frames (OvRFs) of 12,609 virus reference genomes in the NCBI database. We retrieved metadata associated with all annotated open reading frames (ORFs) in each genome record to calculate the number, length, and frameshift of OvRFs. Our results show that while the number of OvRFs increases with genome length, they tend to be shorter in longer genomes. The majority of overlaps involve +2 frameshifts, predominantly found in dsDNA viruses. Antisense overlaps in which one of the ORFs was encoded in the same frame on the opposite strand (−0) tend to be longer. Next, we develop a new graph-based representation of the distribution of overlaps among the ORFs of genomes in a given virus family. In the absence of an unambiguous partition of ORFs by homology at this taxonomic level, we used an alignment-free k-mer based approach to cluster protein coding sequences by similarity. We connect these clusters with two types of directed edges to indicate (1) that constituent ORFs are adjacent in one or more genomes, and (2) that these ORFs overlap. These adjacency graphs not only provide a natural visualization scheme, but also a novel statistical framework for analyzing the effects of gene- and genome-level attributes on the frequencies of overlaps.
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Affiliation(s)
- Laura Muñoz-Baena
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Art F. Y. Poon
- Department of Microbiology and Immunology, Western University, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- * E-mail:
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29
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Edridge AWD, Abd-Elfarag G, Deijs M, Jebbink MF, Boele van Hensbroek M, van der Hoek L. Divergent Rhabdovirus Discovered in a Patient with New-Onset Nodding Syndrome. Viruses 2022; 14:v14020210. [PMID: 35215803 PMCID: PMC8880091 DOI: 10.3390/v14020210] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/15/2022] Open
Abstract
A divergent rhabdovirus was discovered in the bloodstream of a 15-year-old girl with Nodding syndrome from Mundri West County in South Sudan. Nodding syndrome is a progressive degenerative neuropathy of unknown cause affecting thousands of individuals in Sub-Saharan Africa. The index case was previously healthy until she developed head-nodding seizures four months prior to presentation. Virus discovery by VIDISCA-NGS on the patient’s plasma detected multiple sequence reads belonging to a divergent rhabdovirus. The viral load was 3.85 × 103 copies/mL in the patient’s plasma and undetectable in her cerebrospinal fluid. Further genome walking allowed for the characterization of full coding sequences of all the viral proteins (N, P, M, U1, U2, G, U3, and L). We tentatively named the virus “Mundri virus” (MUNV) and classified it as a novel virus species based on the high divergence from other known viruses (all proteins had less than 43% amino acid identity). Phylogenetic analysis revealed that MUNV forms a monophyletic clade with several human-infecting tibroviruses prevalent in Central Africa. A bioinformatic machine-learning algorithm predicted MUNV to be an arbovirus (bagged prediction strength (BPS) of 0.9) transmitted by midges (BPS 0.4) with an artiodactyl host reservoir (BPS 0.9). An association between MUNV infection and Nodding syndrome was evaluated in a case–control study of 72 patients with Nodding syndrome (including the index case) matched to 65 healthy households and 48 community controls. No subject, besides the index case, was positive for MUNV RNA in their plasma. A serological assay detecting MUNV anti-nucleocapsid found, respectively, in 28%, 22%, and 16% of cases, household controls and community controls to be seropositive with no significant differences between cases and either control group. This suggests that MUNV commonly infects children in South Sudan yet may not be causally associated with Nodding syndrome.
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Affiliation(s)
- Arthur W. D. Edridge
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.D.); (M.F.J.)
- Center for Global Child Health, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (G.A.-E.); (M.B.v.H.)
- Correspondence: (A.W.D.E.); (L.v.d.H.)
| | - Gasim Abd-Elfarag
- Center for Global Child Health, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (G.A.-E.); (M.B.v.H.)
| | - Martin Deijs
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.D.); (M.F.J.)
| | - Maarten F. Jebbink
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.D.); (M.F.J.)
| | - Michael Boele van Hensbroek
- Center for Global Child Health, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (G.A.-E.); (M.B.v.H.)
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; (M.D.); (M.F.J.)
- Correspondence: (A.W.D.E.); (L.v.d.H.)
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30
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Gong Z, Cheng M, Botella JR. Non-GM Genome Editing Approaches in Crops. Front Genome Ed 2022; 3:817279. [PMID: 34977860 PMCID: PMC8715957 DOI: 10.3389/fgeed.2021.817279] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
CRISPR/Cas-based genome editing technologies have the potential to fast-track large-scale crop breeding programs. However, the rigid cell wall limits the delivery of CRISPR/Cas components into plant cells, decreasing genome editing efficiency. Established methods, such as Agrobacterium tumefaciens-mediated or biolistic transformation have been used to integrate genetic cassettes containing CRISPR components into the plant genome. Although efficient, these methods pose several problems, including 1) The transformation process requires laborious and time-consuming tissue culture and regeneration steps; 2) many crop species and elite varieties are recalcitrant to transformation; 3) The segregation of transgenes in vegetatively propagated or highly heterozygous crops, such as pineapple, is either difficult or impossible; and 4) The production of a genetically modified first generation can lead to public controversy and onerous government regulations. The development of transgene-free genome editing technologies can address many problems associated with transgenic-based approaches. Transgene-free genome editing have been achieved through the delivery of preassembled CRISPR/Cas ribonucleoproteins, although its application is limited. The use of viral vectors for delivery of CRISPR/Cas components has recently emerged as a powerful alternative but it requires further exploration. In this review, we discuss the different strategies, principles, applications, and future directions of transgene-free genome editing methods.
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Affiliation(s)
- Zheng Gong
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Ming Cheng
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
| | - Jose R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Science, The University of Queensland, Brisbane, QLD, Australia
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31
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Luo DS, Zhou ZJ, Ge XY, Bourhy H, Shi ZL, Grandadam M, Dacheux L. Genome Characterization of Bird-Related Rhabdoviruses Circulating in Africa. Viruses 2021; 13:v13112168. [PMID: 34834974 PMCID: PMC8622386 DOI: 10.3390/v13112168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Rhabdoviridae is the most diverse family of the negative, single-stranded RNA viruses, which includes 40 ecologically different genera that infect plants, insects, reptiles, fishes, and mammals, including humans, and birds. To date, only a few bird-related rhabdoviruses among the genera Sunrhavirus, Hapavirus, and Tupavirus have been described and analyzed at the molecular level. In this study, we characterized seven additional and previously unclassified rhabdoviruses, which were isolated from various bird species collected in Africa during the 1960s and 1970s. Based on the analysis of their genome sequences obtained by next generation sequencing, we observed a classical genomic structure, with the presence of the five canonical rhabdovirus genes, i.e., nucleoprotein (N), phosphoprotein (P), matrix protein (M), glycoprotein (G), and polymerase (L). In addition, different additional open reading frames which code putative proteins of unknown function were identified, with the common presence of the C and the SH proteins, within the P gene and between the M and G genes, respectively. Genetic comparisons and phylogenetic analysis demonstrated that these seven bird-related rhabdoviruses could be considered as putative new species within the genus Sunrhavirus, where they clustered into a single group (named Clade III), a companion to two other groups that encompass mainly insect-related viruses. The results of this study shed light on the high diversity of the rhabdoviruses circulating in birds, mainly in Africa. Their close relationship with other insect-related sunrhaviruses raise questions about their potential role and impact as arboviruses that affect bird communities.
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Affiliation(s)
- Dong-Sheng Luo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (D.-S.L.); (Z.-L.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université de Paris, 75015 Paris, France;
| | - Zhi-Jian Zhou
- Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410082, China; (Z.-J.Z.); (X.-Y.G.)
| | - Xing-Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410082, China; (Z.-J.Z.); (X.-Y.G.)
| | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université de Paris, 75015 Paris, France;
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (D.-S.L.); (Z.-L.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Marc Grandadam
- Institut de Recherche Biomédicale des Armées, 91220 Bretigny-sur-Orge, France;
- National Reference Center for Arboviruses, Institut Pasteur, Université de Paris, 75015 Paris, France
| | - Laurent Dacheux
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université de Paris, 75015 Paris, France;
- Correspondence: ; Tel.: +33-140613303
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Wang Y, Wang G, Bai J, Zhang Y, Wang Y, Wen S, Li L, Yang Z, Hong N. A novel Actinidia cytorhabdovirus characterized using genomic and viral protein interaction features. MOLECULAR PLANT PATHOLOGY 2021; 22:1271-1287. [PMID: 34288324 PMCID: PMC8435229 DOI: 10.1111/mpp.13110] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
A novel cytorhabdovirus, tentatively named Actinidia virus D (AcVD), was identified from kiwifruit (Actinidia chinensis) in China using high-throughput sequencing technology. The genome of AcVD consists of 13,589 nucleotides and is organized into seven open reading frames (ORFs) in its antisense strand, coding for proteins in the order N-P-P3-M-G-P6-L. The ORFs were flanked by a 3' leader sequence and a 5' trailer sequence and are separated by conserved intergenic junctions. The genome sequence of AcVD was 44.6%-51.5% identical to those of reported cytorhabdoviruses. The proteins encoded by AcVD shared the highest sequence identities, ranging from 27.3% (P6) to 44.5% (L), with the respective proteins encoded by reported cytorhabdoviruses. Phylogenetic analysis revealed that AcVD clustered together with the cytorhabdovirus Wuhan insect virus 4. The subcellular locations of the viral proteins N, P, P3, M, G, and P6 in epidermal cells of Nicotiana benthamiana leaves were determined. The M protein of AcVD uniquely formed filament structures and was associated with microtubules. Bimolecular fluorescence complementation assays showed that three proteins, N, P, and M, self-interact, protein N plays a role in the formation of cytoplasm viroplasm, and protein M recruits N, P, P3, and G to microtubules. In addition, numerous paired proteins interact in the nucleus. This study presents the first evidence of a cytorhabdovirus infecting kiwifruit plants and full location and interaction maps to gain insight into viral protein functions.
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Affiliation(s)
- Yanxiang Wang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Guoping Wang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Jianyu Bai
- Laboratory of Fruit Trees DiseaseInstitute of Economic ForestryXinjiang Academy of Forestry SciencesUrumqiChina
| | - Yongle Zhang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ying Wang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Shaohua Wen
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Liu Li
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Zuokun Yang
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Ni Hong
- Key Laboratory of Plant Pathology of Hubei ProvinceCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
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Liu G, Cao W, Salawudeen A, Zhu W, Emeterio K, Safronetz D, Banadyga L. Vesicular Stomatitis Virus: From Agricultural Pathogen to Vaccine Vector. Pathogens 2021; 10:1092. [PMID: 34578125 PMCID: PMC8470541 DOI: 10.3390/pathogens10091092] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 11/16/2022] Open
Abstract
Vesicular stomatitis virus (VSV), which belongs to the Vesiculovirus genus of the family Rhabdoviridae, is a well studied livestock pathogen and prototypic non-segmented, negative-sense RNA virus. Although VSV is responsible for causing economically significant outbreaks of vesicular stomatitis in cattle, horses, and swine, the virus also represents a valuable research tool for molecular biologists and virologists. Indeed, the establishment of a reverse genetics system for the recovery of infectious VSV from cDNA transformed the utility of this virus and paved the way for its use as a vaccine vector. A highly effective VSV-based vaccine against Ebola virus recently received clinical approval, and many other VSV-based vaccines have been developed, particularly for high-consequence viruses. This review seeks to provide a holistic but concise overview of VSV, covering the virus's ascension from perennial agricultural scourge to promising medical countermeasure, with a particular focus on vaccines.
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Affiliation(s)
- Guodong Liu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Wenguang Cao
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Abdjeleel Salawudeen
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Wenjun Zhu
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3M4, Canada
| | - Karla Emeterio
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - David Safronetz
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Logan Banadyga
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
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Mu F, Li B, Cheng S, Jia J, Jiang D, Fu Y, Cheng J, Lin Y, Chen T, Xie J. Nine viruses from eight lineages exhibiting new evolutionary modes that co-infect a hypovirulent phytopathogenic fungus. PLoS Pathog 2021; 17:e1009823. [PMID: 34428260 PMCID: PMC8415603 DOI: 10.1371/journal.ppat.1009823] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 09/03/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
Mycoviruses are an important component of the virosphere, but our current knowledge of their genome organization diversity and evolution remains rudimentary. In this study, the mycovirus composition in a hypovirulent strain of Sclerotinia sclerotiorum was molecularly characterized. Nine mycoviruses were identified and assigned into eight potential families. Of them, six were close relatives of known mycoviruses, while the other three had unique genome organizations and evolutionary positions. A deltaflexivirus with a tripartite genome has evolved via arrangement and horizontal gene transfer events, which could be an evolutionary connection from unsegmented to segmented RNA viruses. Two mycoviruses had acquired a second helicase gene by two different evolutionary mechanisms. A rhabdovirus representing an independent viral evolutionary branch was the first to be confirmed to occur naturally in fungi. The major hypovirulence-associated factor, an endornavirus, was finally corroborated. Our study expands the diversity of mycoviruses and potential virocontrol agents, and also provides new insights into virus evolutionary modes including virus genome segmentation. Identification of mycoviruses in phytopathogenic fungi is necessary for understanding the origin of viruses and developing virocontrol strategies to protect plants. Nine mycoviruses with RNA genomes were identified in a hypovirulent strain of Sclerotinia sclerotiorum and were classified into eight potential viral families, suggesting that the composition of mycoviral communities was complex in this single fungal strain. They included four previously characterized mycoviruses and three distant relatives of known mycoviruses, as well as the first reports of a deltaflexivirus with a tripartite genome, and a fungal rhabdovirus. In addition, we found an endornavirus associated with hypovirulence in a phytopathogenic fungus. Our study makes a significant contribution because it not only expands the diversity-related knowledge of mycoviruses and potential virocontrol agents, but also provides new insights into mycovirus evolution.
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Affiliation(s)
- Fan Mu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shufen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jichun Jia
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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35
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Tokarz R, Lipkin WI. Discovery and Surveillance of Tick-Borne Pathogens. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:1525-1535. [PMID: 33313662 PMCID: PMC8285023 DOI: 10.1093/jme/tjaa269] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Indexed: 05/06/2023]
Abstract
Within the past 30 yr molecular assays have largely supplanted classical methods for detection of tick-borne agents. Enhancements provided by molecular assays, including speed, throughput, sensitivity, and specificity, have resulted in a rapid increase in the number of newly characterized tick-borne agents. The use of unbiased high throughput sequencing has enabled the prompt identification of new pathogens and the examination of tick microbiomes. These efforts have led to the identification of hundreds of new tick-borne agents in the last decade alone. However, little is currently known about the majority of these agents beyond their phylogenetic classification. Our article outlines the primary methods involved in tick-borne agent discovery and the current status of our understanding of tick-borne agent diversity.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY
- Corresponding author, e-mail:
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY
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Isolation of a Novel Bat Rhabdovirus with Evidence of Human Exposure in China. mBio 2021; 13:e0287521. [PMID: 35164557 PMCID: PMC8844929 DOI: 10.1128/mbio.02875-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bats are well-recognized reservoirs of zoonotic viruses. Several spillover events from bats to humans have been reported, causing severe epidemic or endemic diseases including severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), SARS-CoV, Middle East respiratory syndrome-CoV (MERS-CoV), henipaviruses, and filoviruses. In this study, a novel rhabdovirus species, provisionally named Rhinolophus rhabdovirus DPuer (DPRV), was identified from the horseshoe bat (Rhinolophus affinis) in Yunnan province, China, using next-generation sequencing. DPRV shedding in the spleen, liver, lung, and intestinal contents of wild bats with high viral loads was detected by real-time quantitative PCR, indicating that DPRV has tropism for multiple host tissues. Furthermore, DPRV can replicate in vitro in multiple mammalian cell lines, including BHK-21, A549, and MA104 cells, with the highest efficiency in hamster kidney cell line BHK-21, suggesting infectivity of DPRV in these cell line-derived hosts. Ultrastructure analysis revealed a characteristic bullet-shaped morphology and tightly clustered distribution of DPRV particles in the intracellular space. DPRV replicated efficiently in suckling mouse brains and caused death of suckling mice; death rates increased with passaging of DPRV in suckling mice. Moreover, 421 serum samples were collected from individuals who lived near the bat collection site and had fever symptoms within 1 year. DPRV-specific antibodies were detected in 20 (4.75%) human serum samples by indirect immunofluorescence assay. Furthermore, 10 (2.38%) serum samples were DPRV positive according to plaque reduction neutralization assay, which revealed potential transmission of DPRV from bats to humans and highlighted the potential public health risk. Potential vector association with DPRV was not found with negative viral RNA in bloodsucking arthropods. IMPORTANCE We identified a novel rhabdovirus from the horseshoe bat (Rhinolophus thomasi) in China with probable infectivity in humans. DPRV was isolated in vitro from several mammalian cell lines, indicating wide host tropism, excluding bats, of DPRV. DPRV replicated in the brains of suckling mice, and the death rate of suckling mice increased with passaging of DPRV in vivo. Serological tests indicated the possible infectivity of DPRV in humans and the potential transmission to humans. The present findings provide preliminary evidence for the potential risk of DPRV to public health. Additional studies with active surveillance are needed to address interspecies transmission and determine the pathogenicity of DPRV in humans.
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Liu Q, Jin J, Yang L, Zhang S, Cao M. Molecular characterization of a novel cytorhabdovirus associated with chrysanthemum yellow dwarf disease. Arch Virol 2021; 166:1253-1257. [PMID: 33575895 DOI: 10.1007/s00705-021-04987-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/20/2020] [Indexed: 01/22/2023]
Abstract
Deep-sequencing analysis of a chrysanthemum plant with yellow dwarf symptoms led to the discovery of a novel putative cytorhabdovirus, here tentatively named "chrysanthemum yellow dwarf associated virus" (CYDaV). Its negative-sense single-stranded RNA genome comprises 14,086 nucleotides and contains eight open reading frames in the order 3' leader-N-P'-P-P3-M-G-P6-L-5' trailer. CYDaV shares moderate sequence similarity (< 54.2% nucleotide and 51% amino acid sequence identity) with its cytorhabdovirus counterparts in cognate genes. Phylogenetic analysis showed that CYDaV clustered with strong support with alfalfa dwarf virus, raspberry vein chlorosis virus, and strawberry crinkle virus. These findings suggest that CYDaV should be considered a novel member of the genus Cytorhabdovirus, family Rhabdoviridae.
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Affiliation(s)
- Qiyan Liu
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Jingjing Jin
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Liu Yang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Song Zhang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China.
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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Jia W, Wang F, Xiao S, Yang Y, Chen L, Li J, Bao Y, Song Q, Ye G. Identification and characterization of a novel rhabdovirus in green rice leafhopper, Nephotettix cincticeps. Virus Res 2021; 296:198281. [PMID: 33548414 DOI: 10.1016/j.virusres.2020.198281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 12/26/2020] [Indexed: 10/22/2022]
Abstract
The family Rhabdoviridae is one of the most ecological diverse groups of RNA viruses, with remarkable genome complexity and wide host range. Rhabdoviruses are discovered in many insect species, and insects, such as midges, mosquitoes, aphids and leafhoppers, act as crucial vectors for rhabdovirus transmission. Here, a novel rhabdovirus was identified in green rice leafhopper, Nephotettix cincticeps (Hemiptera: Cicadellidae), a common virus vector on rice. This virus was named as Nephotettix cincticeps negative-stranded RNA virus-1 (NcNSRV-1). The genome of NcNSRV-1 is 12,361 nucleotides in length, flanked by untranslated 3' leader and 5' trailer. The anti-sense viral genome consists of five major structural protein genes (N, P, M, G and L), which shares a typical architecture with the family Rhabdoviridae. An additional gene, P6, is interposed between G and L genes. NcNSRV-1 is phylogenetically clustered with the unclassified rhabdoviruses isolated from insects and exhibits low sequence identities with other viruses. The transcription regulatory sequences in NcNSRV-1 gene junctions were determined, revealing a unique transcription initiation sequence. In view of the phylogeny, sequence identity and genome organization, NcNSRV-1 is likely to be an insect rhabdovirus. Field surveys showed NcNSRV-1 was prevalent in the rice field populations of N. cincticeps in China.
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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, 310058, 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, 310058, China
| | - Shan Xiao
- 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, 310058, 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, 310058, China
| | - Longfei Chen
- 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, 310058, 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, 310058, China; Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, 65211, USA
| | - 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, 310058, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, 65211, USA
| | - 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, 310058, China.
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Complete Genome Sequence of a Rhabdovirus Strain from Culex Mosquitos Collected in Southern Switzerland. Microbiol Resour Announc 2021; 10:10/1/e01234-20. [PMID: 33414339 PMCID: PMC8407715 DOI: 10.1128/mra.01234-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We report here the full-length genome sequence of a rhabdovirus strain detected in a pool of 21 Culex pipiens and Culex torrentium mosquitos collected in southern Switzerland. The genome has a length of 11,914 nucleotides and encodes five major putative open reading frames. We report here the full-length genome sequence of a rhabdovirus strain detected in a pool of 21 Culex pipiens and Culex torrentium mosquitos collected in southern Switzerland. The genome has a length of 11,914 nucleotides and encodes five major putative open reading frames.
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Luo DS, Li B, Shen XR, Jiang RD, Zhu Y, Wu J, Fan Y, Bourhy H, Hu B, Ge XY, Shi ZL, Dacheux L. Characterization of Novel Rhabdoviruses in Chinese Bats. Viruses 2021; 13:v13010064. [PMID: 33466539 PMCID: PMC7824899 DOI: 10.3390/v13010064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/24/2020] [Accepted: 12/30/2020] [Indexed: 12/25/2022] Open
Abstract
Bats, the second largest order of mammals worldwide, harbor specific characteristics such as sustaining flight, a special immune system, unique habits, and ecological niches. In addition, they are the natural reservoirs of a variety of emerging or re-emerging zoonotic pathogens. Rhabdoviridae is one of the most diverse families of RNA viruses, which consists of 20 ecologically diverse genera, infecting plants, mammals, birds, reptiles, and fish. To date, three bat-related genera are described, named Lyssavirus, Vesiculovirus, and Ledantevirus. However, the prevalence and the distribution of these bat-related rhabdoviruses remain largely unknown, especially in China. To fill this gap, we performed a large molecular retrospective study based on the real-time reverse transcription polymerase chain reaction (RT-qPCR) detection of lyssavirus in bat samples (1044 brain and 3532 saliva samples, from 63 different bat species) originating from 21 provinces of China during 2006–2018. None of them were positive for lyssavirus, but six bat brains (0.6%) of Rhinolophus bat species, originating from Hubei and Hainan provinces, were positive for vesiculoviruses or ledanteviruses. Based on complete genomes, these viruses were phylogenetically classified into three putative new species, tentatively named Yinshui bat virus (YSBV), Taiyi bat virus (TYBV), and Qiongzhong bat virus (QZBV). These results indicate the novel rhabdoviruses circulated in different Chinese bat populations.
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Affiliation(s)
- Dong-Sheng Luo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (D.-S.L.); (B.L.); (X.-R.S.); (R.-D.J.); (Y.Z.); (J.W.); (Y.F.); (B.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institut Pasteur, Lyssavirus Epidemiology and Neuropathology Unit, 75724 Paris, France;
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (D.-S.L.); (B.L.); (X.-R.S.); (R.-D.J.); (Y.Z.); (J.W.); (Y.F.); (B.H.)
| | - Xu-Rui Shen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (D.-S.L.); (B.L.); (X.-R.S.); (R.-D.J.); (Y.Z.); (J.W.); (Y.F.); (B.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ren-Di Jiang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (D.-S.L.); (B.L.); (X.-R.S.); (R.-D.J.); (Y.Z.); (J.W.); (Y.F.); (B.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Zhu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (D.-S.L.); (B.L.); (X.-R.S.); (R.-D.J.); (Y.Z.); (J.W.); (Y.F.); (B.H.)
| | - Jia Wu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (D.-S.L.); (B.L.); (X.-R.S.); (R.-D.J.); (Y.Z.); (J.W.); (Y.F.); (B.H.)
| | - Yi Fan
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (D.-S.L.); (B.L.); (X.-R.S.); (R.-D.J.); (Y.Z.); (J.W.); (Y.F.); (B.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hervé Bourhy
- Institut Pasteur, Lyssavirus Epidemiology and Neuropathology Unit, 75724 Paris, France;
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (D.-S.L.); (B.L.); (X.-R.S.); (R.-D.J.); (Y.Z.); (J.W.); (Y.F.); (B.H.)
| | - Xing-Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410082, China;
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (D.-S.L.); (B.L.); (X.-R.S.); (R.-D.J.); (Y.Z.); (J.W.); (Y.F.); (B.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Z.-L.S.); (L.D.); Tel.: +86-02787197311 (Z.-L.S.); +33-140613303 (L.D.)
| | - Laurent Dacheux
- Institut Pasteur, Lyssavirus Epidemiology and Neuropathology Unit, 75724 Paris, France;
- Correspondence: (Z.-L.S.); (L.D.); Tel.: +86-02787197311 (Z.-L.S.); +33-140613303 (L.D.)
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Rose virus R, a cytorhabdovirus infecting rose. Arch Virol 2021; 166:655-658. [PMID: 33394170 DOI: 10.1007/s00705-020-04927-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/05/2020] [Indexed: 12/30/2022]
Abstract
RNA was extracted from 'Hugh Dickson' rose leaves displaying virus-like symptoms in Maryland, USA. Using high-throughput sequencing, we identified a new virus, tentatively named "rose virus R". This virus has a negative-sense, single-stranded RNA genome and exhibits genomic features of a rhabdovirus, including a genome organization of 3'-N-P-P3-M-G-P6-L-5' and a gene junction region consensus sequence 3'-AUUUAUUUUGACUCUA-5'. Rose virus R is phylogenetically related to cytorhabdoviruses, and the nucleotide and amino acid sequences of rose virus R and related cytorhabdoviruses have diverged considerably, suggesting that rose virus R should be classified as a member of a novel species in the genus Cytorhabdovirus.
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Zhang S, Huang A, Zhou X, Li Z, Dietzgen RG, Zhou C, Cao M. Natural Defect of a Plant Rhabdovirus Glycoprotein Gene: A Case Study of Virus-Plant Coevolution. PHYTOPATHOLOGY 2021; 111:227-236. [PMID: 32648524 DOI: 10.1094/phyto-05-20-0191-fi] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Seven isolates of a putative cytorhabdovirus (family Rhabdoviridae, order Mononegavirales) designated as citrus-associated rhabdovirus (CiaRV) were identified in citrus, passion fruit, and paper bush from the same geographical area in China. CiaRV, bean-associated cytorhabdovirus (Brazil), and papaya virus E (Ecuador) should be taxonomically classified in the species Papaya cytorhabdovirus. Due to natural mutations, the glycoprotein (G) and P4 genes were impaired in citrus-infecting isolates of CiaRV, resulting in an atypical rhabdovirus genome organization of 3' leader-N-P-P3-M-L-5' trailer. The P3 protein of CiaRV shared a common origin with begomoviral movement proteins (family Geminiviridae). Secondary structure analysis and trans-complementation of movement-deficient tomato mosaic virus and potato virus X mutants by CiaRV P3 supported its function in viral cell-to-cell trafficking. The wide geographical dispersal of CiaRV and related viruses suggests an efficient transmission mechanism, as well as an underlying risk to global agriculture. Both the natural phenomenon and experimental analyses demonstrated presence of the "degraded" type of CiaRV in citrus, in parallel to "undegraded" types in other host plant species. This case study shows a plant virus losing the function of an important but nonessential gene, likely due to host shift and adaption, which deepened our understanding of course of natural viral diversification.
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Affiliation(s)
- Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Aijun Huang
- National Navel Orange Research Center, College of Life Science, Gannan Normal University, Ganzhou, China
| | - Xin Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Changyong Zhou
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
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43
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Novel and Diverse Non-Rabies Rhabdoviruses Identified in Bats with Human Exposure, South Dakota, USA. Viruses 2020; 12:v12121408. [PMID: 33302422 PMCID: PMC7762532 DOI: 10.3390/v12121408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 11/22/2022] Open
Abstract
Bats are a host and reservoir for a large number of viruses, many of which are zoonotic. In North America, the big brown bat (Eptesicus fuscus) is widely distributed and common. Big brown bats are a known reservoir for rabies virus, which, combined with their propensity to roost in human structures, necessitates testing for rabies virus following human exposure. The current pandemic caused by severe acute respiratory syndrome coronavirus 2, likely of bat origin, illustrates the need for continued surveillance of wildlife and bats for potentially emerging zoonotic viruses. Viral metagenomic sequencing was performed on 39 big brown bats and one hoary bat submitted for rabies testing due to human exposure in South Dakota. A new genotype of American bat vesiculovirus was identified in seven of 17 (41%) heart and lung homogenates at high levels in addition to two of 23 viscera pools. A second rhabdovirus, Sodak rhabdovirus 1 (SDRV1), was identified in four of 23 (17%) viscera pools. Phylogenetic analysis placed SDRV1 in the genus Alphanemrhavirus, which includes two recognized species that were identified in nematodes. Finally, a highly divergent rhabdovirus, Sodak rhabdovirus 2 (SDRV2), was identified in two of 23 (8.7%) big brown bats. Phylogenetic analysis placed SDRV2 as ancestral to the dimarhabdovirus supergroup and Lyssavirus. Intracranial inoculation of mouse pups with rhabdovirus-positive tissue homogenates failed to elicit clinical disease. Further research is needed to determine the zoonotic potential of these non-rabies rhabdoviruses.
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Kuhn JH, Adkins S, Alioto D, Alkhovsky SV, Amarasinghe GK, Anthony SJ, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bartonička T, Basler C, Bavari S, Beer M, Bente DA, Bergeron É, Bird BH, Blair C, Blasdell KR, Bradfute SB, Breyta R, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Buzkan N, Calisher CH, Cao M, Casas I, Chamberlain J, Chandran K, Charrel RN, Chen B, Chiumenti M, Choi IR, Clegg JCS, Crozier I, da Graça JV, Dal Bó E, Dávila AMR, de la Torre JC, de Lamballerie X, de Swart RL, Di Bello PL, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolja VV, Dolnik O, Drebot MA, Drexler JF, Dürrwald R, Dufkova L, Dundon WG, Duprex WP, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Fernandes J, Fooks AR, Formenty PBH, Forth LF, Fouchier RAM, Freitas-Astúa J, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gbakima A, Goldstein T, Gonzalez JPJ, Griffiths A, Groschup MH, Günther S, Guterres A, Hall RA, Hammond J, Hassan M, Hepojoki J, Hepojoki S, Hetzel U, Hewson R, Hoffmann B, Hongo S, Höper D, Horie M, Hughes HR, Hyndman TH, Jambai A, Jardim R, Jiāng D, Jin Q, Jonson GB, Junglen S, Karadağ S, Keller KE, Klempa B, Klingström J, Kobinger G, Kondō H, Koonin EV, Krupovic M, Kurath G, Kuzmin IV, Laenen L, Lamb RA, Lambert AJ, Langevin SL, Lee B, Lemos ERS, Leroy EM, Li D, Lǐ J, Liang M, Liú W, Liú Y, Lukashevich IS, Maes P, Marciel de Souza W, Marklewitz M, Marshall SH, Martelli GP, Martin RR, Marzano SYL, Massart S, McCauley JW, Mielke-Ehret N, Minafra A, Minutolo M, Mirazimi A, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki T, Navarro B, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Nylund A, Økland AL, Oliveira RC, Palacios G, Pallas V, Pályi B, Papa A, Parrish CR, Pauvolid-Corrêa A, Pawęska JT, Payne S, Pérez DR, Pfaff F, Radoshitzky SR, Rahman AU, Ramos-González PL, Resende RO, Reyes CA, Rima BK, Romanowski V, Robles Luna G, Rota P, Rubbenstroth D, Runstadler JA, Ruzek D, Sabanadzovic S, Salát J, Sall AA, Salvato MS, Sarpkaya K, Sasaya T, Schwemmle M, Shabbir MZ, Shí X, Shí Z, Shirako Y, Simmonds P, Širmarová J, Sironi M, Smither S, Smura T, Song JW, Spann KM, Spengler JR, Stenglein MD, Stone DM, Straková P, Takada A, Tesh RB, Thornburg NJ, Tomonaga K, Tordo N, Towner JS, Turina M, Tzanetakis I, Ulrich RG, Vaira AM, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, Wahl V, Walker PJ, Wang H, Wang J, Wang X, Wang LF, Wèi T, Wells H, Whitfield AE, Williams JV, Wolf YI, Wú Z, Yang X, Yáng X, Yu X, Yutin N, Zerbini FM, Zhang T, Zhang YZ, Zhou G, Zhou X. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2020; 165:3023-3072. [PMID: 32888050 PMCID: PMC7606449 DOI: 10.1007/s00705-020-04731-2] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/04/2020] [Indexed: 12/13/2022]
Abstract
In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
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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, Fort Detrick, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Daniela Alioto
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Simon J Anthony
- Mailman School of Public Health, Columbia University, New York, NY, USA
- EcoHealth Alliance, New York, NY, USA
| | | | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Justin Bahl
- Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Tomáš Bartonička
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Christopher Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- Edge BioInnovation Consulting and Mgt, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dennis A Bente
- Galveston National Laboratory, The University of Texas, Medical Branch at Galveston, Galveston, TX, USA
| | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian H Bird
- School of Veterinary Medicine, One Health Institute, University of California, Davis, CA, USA
| | - Carol Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Steven B Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rachel Breyta
- US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - Thomas Briese
- Department of Epidemiology, Mailman School of Public Health, Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Paul A Brown
- Laboratory of Ploufragan-Plouzané-Niort, French Agency for Food, Environmental and Occupational Heath Safety ANSES, Ploufragan, France
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas, Medical Branch at Galveston, Galveston, TX, USA
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service, University of the Free State, Bloemfontein, Republic of South Africa
| | - Nihal Buzkan
- Department of Plant Protection, Faculty of Agriculture, Kahramanmaras Sütçü Imam University, Avsar Campus, 46060, Kahramanmaras, Turkey
| | | | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - John Chamberlain
- Virology and Pathogenesis Group, National Infection Service, Public Health England, Porton Down, UK
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Biao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Il-Ryong Choi
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | | | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John V da Graça
- Texas A&M University-Kingsville Citrus Center, Weslaco, TX, USA
| | - Elena Dal Bó
- CIDEFI. Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Alberto M R Dávila
- Laboratório de Biologia Computacional e Sistemas, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Rik L de Swart
- Department Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Patrick L Di Bello
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Michael A Drebot
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | | | - William G Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Jorlan Fernandes
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | | | | | - Leonie F Forth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Ron A M Fouchier
- Department Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | | | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Aiah Gbakima
- Metabiota, Inc. Sierra Leone, Freetown, Sierra Leone
| | - Tracey Goldstein
- One Health Institute, Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, 20057, USA
- Centaurus Biotechnologies, CTP, Manassas, VA, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Martin H Groschup
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - John Hammond
- United States Department of Agriculture, Agricultural Research Service, USNA, Floral and Nursery Plants Research Unit, Beltsville, MD, USA
| | - Mohamed Hassan
- Department of Agricultural Botany, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Satu Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Mobidiag Ltd, Espoo, Finland
| | - Udo Hetzel
- Institute of Veterinary Pathology, University of Zuerich, Zurich, Switzerland
| | - Roger Hewson
- Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Bernd Hoffmann
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Seiji Hongo
- Department of Infectious Diseases, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - Amara Jambai
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Rodrigo Jardim
- Laboratório de Biologia Computacional e Sistemas, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qi Jin
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Gilda B Jonson
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Serpil Karadağ
- Republic Of Turkey Ministry Of Agriculture And Forestry, Pistachio Research Institute, Gaziantep, Turkey
| | - Karen E Keller
- United States Department of Agriculture, Agricultural Research Service, Horticulture Crops Research Unit, Corvallis, OR, USA
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gary Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Ivan V Kuzmin
- US Department of Agriculture, Animal and Plant Health Inspection, National Veterinary Services Laboratories, Diagnostic Virology Laboratory, Ames, USA
| | - Lies Laenen
- Zoonotic Infectious Diseases Unit, KU Leuven, Rega Institute, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Robert A Lamb
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
| | - Amy J Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elba R S Lemos
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Eric M Leroy
- MIVEGEC (IRD-CNRS-Montpellier university) Unit, French National Research Institute for Sustainable Development (IRD), Montpellier, France
| | - Dexin Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Mifang Liang
- Key Laboratory for Medical Virology, NHFPC, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Wénwén Liú
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yàn Liú
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Igor S Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, The Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Piet Maes
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | | | - Marco Marklewitz
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Giovanni P Martelli
- Department of Plant, Soil and Food Sciences, University "Aldo Moro", Bari, Italy
| | - Robert R Martin
- United States Department of Agriculture, Horticultural Crops Research Unit, Corvallis, OR, USA
| | - Shin-Yi L Marzano
- Department of Biology and Microbiology, Department of Plant Sciences, South Dakota State University, Brookings, SD, USA
| | - Sébastien Massart
- Gembloux Agro-Bio Tech, TERRA, Plant Pathology Laboratory, Liège University, Liège, Belgium
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | | | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Maria Minutolo
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | | | | | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, Japan
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Are Nylund
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Arnfinn L Økland
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Renata C Oliveira
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever Viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Colin R Parrish
- College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrated Biosciences and Department of Entomology, Texas A&M University, College Station, USA
| | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Susan Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Sheli R Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Aziz-Ul Rahman
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | | | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, Centro Cientifico Technológico-La Plata, Consejo Nacional de Investigaciones Científico Tecnológico-Universidad Nacional de La Plata, La Plata, Argentina
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA, 01536, USA
| | - Daniel Ruzek
- Veterinary Research Institute, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Jiří Salát
- Veterinary Research Institute, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | | | - Maria S Salvato
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kamil Sarpkaya
- Department of Forestry Engineering, Faculty of Forestry, Karabuk University (UNIKA), Karabük, Turkey
| | - Takahide Sasaya
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Japan
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Muhammad Z Shabbir
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Xiǎohóng Shí
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Zhènglì Shí
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Yukio Shirako
- Asian Center for Bioresources and Environmental Sciences, University of Tokyo, Tokyo, Japan
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - Sophie Smither
- CBR Division, Dstl, Porton Down, Salisbury, Wiltshire, UK
| | - Teemu Smura
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten M Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | | | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur, Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV and CCHFV, Paris, France
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Ioannis Tzanetakis
- Division of Agriculture, Department of Entomology and Plant Pathology, University of Arkansas System, Fayetteville, AR, 72701, USA
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Südufer 10, 17493, Greifswald-Insel Riems, Germany
- German Center of Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 73 Strada delle Cacce, 10135, Turin, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Hui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB-Fondation Mérieux, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Tàiyún Wèi
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Heather Wells
- Mailman School of Public Health, Center for Infection and Immunity, Columbia University, New York, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - John V Williams
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Zhìqiáng Wú
- MOH Key Laboratory of Systems Biology of Pathogens, IPB, CAMS, Beijing, China
| | - Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Xīnglóu Yáng
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Xuejie Yu
- Wuhan University School of Health Sciences, Wuhan, China
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
- Shanghai Public Health Clinical Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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45
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Hutchings RSG, Hutchings RW, Menezes IS, Sallum MAM. Mosquitoes (Diptera: Culicidae) From the Southwestern Brazilian Amazon: Liberdade and Gregório Rivers. JOURNAL OF MEDICAL ENTOMOLOGY 2020; 57:1793-1811. [PMID: 32597474 DOI: 10.1093/jme/tjaa100] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Indexed: 06/11/2023]
Abstract
The mosquito community from remote locations toward the southern border of the Brazilian State of Amazonas, in four localities along the Liberdade and Gregório Rivers, was sampled using CDC and Malaise traps, complemented with net sweeping and immature collections. During May 2011, 190 collections yielded 13,012 mosquitoes, from 15 genera and 112 different species, together with 10 morphospecies, which may represent new undescribed taxa. Among the species collected, there are two new geographical distribution records for the State of Amazonas. Culex, the most abundant genus, also had the highest number of species. Both Aedes and Uranotaenia had the second highest number of species, although they were the second and seventh most abundant, respectively. The most abundant species were Aedes (Ochlerotatus) fulvus (Wiedemann), Aedes (Ochlerotatus) nubilus (Theobald), Culex (Culex) mollis Dyar & Knab, Nyssorhynchus (Nyssorhynchus) oswaldoi sensu lato, Culex (Melanoconion) pedroi Sirivanakarn & Belkin, and Culex (Melanoconion) gnomatos Sallum, Hutchings & Ferreira. The epidemiological implications of mosquito species are discussed and compared with other mosquito inventories from the Amazon region. These results represent the first standardized mosquito inventories of the Liberdade and Gregório Rivers, with the identification of 112 species and 10 morphospecies, within the municipalities of Ipixuna and Eirunepé, from which we have only few records in the published literature.
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Affiliation(s)
- Rosa Sá Gomes Hutchings
- Laboratório de Bionomia e Sistemática de Culicidae, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Roger William Hutchings
- Laboratório de Bionomia e Sistemática de Culicidae, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Isis Sá Menezes
- Laboratório de Bionomia e Sistemática de Culicidae, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Maria Anice Mureb Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brazil
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46
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Abstract
Recombinant viruses are the workhorse of modern neuroscience. Whether one would like to understand a neuron's morphology, natural activity patterns, molecular composition, connectivity or behavioural and physiologic function, most studies begin with the injection of an engineered virus, often an adeno-associated virus or herpes simplex virus, among many other types. Recombinant viruses currently enable some combination of cell type-specific, circuit-selective, activity-dependent and spatiotemporally resolved transgene expression. Viruses are now used routinely to study the molecular and cellular functions of a gene within an identified cell type in the brain, and enable the application of optogenetics, chemogenetics, calcium imaging and related approaches. These advantageous properties of engineered viruses thus enable characterization of neuronal function at unprecedented resolution. However, each virus has specific advantages and disadvantages, which makes viral tool selection paramount for properly designing and executing experiments within the central nervous system. In the current Review, we discuss the key principles and uses of engineered viruses and highlight innovations that are needed moving forward.
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Affiliation(s)
- Alexander R Nectow
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA.
| | - Eric J Nestler
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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47
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Revisiting the Classification of Percid Perhabdoviruses Using New Full-Length Genomes. Viruses 2020; 12:v12060649. [PMID: 32560066 PMCID: PMC7354598 DOI: 10.3390/v12060649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 11/16/2022] Open
Abstract
Perhabdoviruses are a threat to some freshwater fish species raised in aquaculture farms in Europe. Although the genetic diversity of these viruses is suspected to be high, the classification of isolates is still in its infancy, with just one full-length genome available and only partial sequences for a limited number of others. Here, we characterized a series of viruses isolated from percids in France from 1999 to 2009 by sequencing the nucleoprotein (N) gene. Four main clusters were distinguished, all related at varying levels of similarity to one of the two already-recognized species, namely Perch perhabdovirus and Sea trout perhabdovirus. Furthermore, we obtained the complete genome of five isolates, including one belonging to Sea trout rhabdovirus. The analysis of the complete L genes and the concatenated open reading frames confirmed the existence of four main genetic clusters, sharing 69 to 74% similarity. We propose the assignation of all these viral isolates into four species, including two new ones: Perch perhabdovirus 1, Perch perhabdovirus 2, Sea trout perhabdovirus 1 and Sea trout perhabdovirus 2. In addition, we developed new primers to readily amplify specific portions of the N gene of any isolate of each species by conventional PCR. The presence of such genetically diverse viruses in France is likely due to divergent viral populations maintained in the wild and then introduced to experimental facilities or farms, as well as via trade between farms across the European continent. It is now urgent to improve the identification tools for this large group of viruses to prevent their unchecked dissemination.
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48
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Blasdell KR, Davis SS, Voysey R, Bulach DM, Middleton D, Williams S, Harmsen MB, Weir RP, Crameri S, Walsh SJ, Peck GR, Tesh RB, Boyle DB, Melville LF, Walker PJ. Hayes Yard virus: a novel ephemerovirus isolated from a bull with severe clinical signs of bovine ephemeral fever is most closely related to Puchong virus. Vet Res 2020; 51:58. [PMID: 32349781 PMCID: PMC7191811 DOI: 10.1186/s13567-020-00781-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/06/2020] [Indexed: 01/05/2023] Open
Abstract
Bovine ephemeral fever is a vector-borne disease of ruminants that occurs in tropical and sub-tropical regions of Africa, Asia and Australia. The disease is caused by a rhabdovirus, bovine ephemeral fever virus (BEFV), which occurs as a single serotype globally. Although several other closely related ephemeroviruses have been isolated from cattle and/or arthropods, only kotonkan virus from Nigeria and (tentatively) Mavingoni virus from Mayotte Island in the Indian Ocean have been previously associated with febrile disease. Here, we report the isolation of a novel virus (Hayes Yard virus; HYV) from blood collected in February 2000 from a bull (Bos indicus) in the Northern Territory of Australia. The animal was suffering from a severe ephemeral fever-like illness with neurological involvement, including recumbency and paralysis, and was euthanised. Histological examination of spinal cord and lung tissue identified extensive haemorrhage in the dura mata with moderate perineuronal oedema and extensive emphysema. HYV displayed cone-shaped morphology, typical of rhabdoviruses, and was found to be most closely related antigenically to Puchong virus (PUCV), isolated in 1965 from mosquitoes in Malaysia. Analysis of complete genome sequences of HYV (15 025 nt) and PUCV (14 932 nt) indicated that each has a complex organisation (3' N-P-M-G-GNS-α1-α2-β-γ-L 5') and expression strategy, similar to that of BEFV. Based on an alignment of complete L protein sequences, HYV and PUCV cluster with other rhabdoviruses in the genus Ephemerovirus and appear to represent two new species. Neutralising antibody to HYV was also detected in a retrospective survey of cattle sera collected in the Northern Territory.
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Affiliation(s)
- Kim R Blasdell
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.
| | - Steven S Davis
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Darwin, NT, Australia.,Timor-Leste Office, Menzies School of Health Research, Dili, Timor-Leste
| | - Rhonda Voysey
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Dieter M Bulach
- Melbourne Bioinformatics, The University of Melbourne, Carlton, VIC, 3053, Australia
| | - Deborah Middleton
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Sinead Williams
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Margaret B Harmsen
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Darwin, NT, Australia
| | - Richard P Weir
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Darwin, NT, Australia
| | - Sandra Crameri
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Susan J Walsh
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Darwin, NT, Australia
| | - Grantley R Peck
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Robert B Tesh
- Center for Biodefense and Emerging Infectious Diseases, Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - David B Boyle
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia
| | - Lorna F Melville
- Berrimah Veterinary Laboratories, Department of Primary Industry and Fisheries, Darwin, NT, Australia
| | - Peter J Walker
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, VIC, 3220, Australia.,School of Chemistry and Biomolecular Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
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49
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Characterization of viruses in a tapeworm: phylogenetic position, vertical transmission, and transmission to the parasitized host. ISME JOURNAL 2020; 14:1755-1767. [PMID: 32286546 PMCID: PMC7305300 DOI: 10.1038/s41396-020-0642-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 12/19/2022]
Abstract
Parasitic flatworms (Neodermata) infect all vertebrates and represent a significant health and economic burden worldwide due to the debilitating diseases they cause. This study sheds light for the first time into the virome of a tapeworm by describing six novel RNA virus candidate species associated with Schistocephalus solidus, including three negative-strand RNA viruses (order Jingchuvirales, Mononegavirales, and Bunyavirales) and three double-stranded RNA viruses. Using in vitro culture of S. solidus, controlled experimental infections and field sampling, we demonstrate that five of these viruses are vertically transmitted, and persist throughout the S. solidus complex life cycle. Moreover, we show that one of the viruses, named Schistocephalus solidus rhabdovirus (SsRV1), is excreted by the parasite and transmitted to parasitized hosts indicating that it may impact S. solidus-host interactions. In addition, SsRV1 has a basal phylogenetic position relative to vertebrate rhabdoviruses suggesting that parasitic flatworms could have contributed to virus emergence. Viruses similar to four of the S. solidus viruses identified here were found in geographically distant S. solidus populations through data mining. Further studies are necessary to determine if flatworm viruses can replicate in parasitized hosts, how they contribute to parasite infection dynamics and if these viruses could be targeted for treatment of parasitic disease.
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50
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Bejerman N, Acevedo RM, de Breuil S, Ruiz OA, Sansberro P, Dietzgen RG, Nome C, Debat H. Molecular characterization of a novel cytorhabdovirus with a unique genomic organization infecting yerba mate (Ilex paraguariensis) in Argentina. Arch Virol 2020; 165:1475-1479. [PMID: 32246285 DOI: 10.1007/s00705-020-04609-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/10/2020] [Indexed: 01/02/2023]
Abstract
The genome of a novel rhabdovirus was detected in yerba mate (Ilex paraguariensis St. Hil.). The newly identified virus, tentatively named "yerba mate virus A" (YmVA), has a genome of 14,961 nucleotides. Notably, eight open reading frames were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, including two novel accessory genes, in the order 3'-N-P-3-4-M-G-L-8-5'. Sequence comparisons of the encoded proteins as well as phylogenetic analysis suggest that YmVA is a new member of the genus Cytorhabdovirus, family Rhabdoviridae. YmVA's unique genomic organization and phylogenetic relationships indicate that this virus likely represents a distinct evolutionary lineage among the cytorhabdoviruses.
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Affiliation(s)
- Nicolás Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, (X5020ICA), Córdoba, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina.
| | - Raúl Maximiliano Acevedo
- Laboratorio de Biotecnología Aplicada y Genómica Funcional. Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (IBONE-CONICET), Universidad Nacional del Nordeste, W3402BKG, Corrientes, Argentina
| | - Soledad de Breuil
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, (X5020ICA), Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
| | - Oscar A Ruiz
- INTECH (UNSAM-CONICET), Unidad de Biotecnología 1, B7130IWA, Chascomús, Argentina
| | - Pedro Sansberro
- Laboratorio de Biotecnología Aplicada y Genómica Funcional. Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (IBONE-CONICET), Universidad Nacional del Nordeste, W3402BKG, Corrientes, Argentina
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Claudia Nome
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, (X5020ICA), Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
| | - Humberto Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5, (X5020ICA), Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
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