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Jeong DE, Sundrani S, Hall RN, Krupovic M, Koonin EV, Fire AZ. DNA Polymerase Diversity Reveals Multiple Incursions of Polintons During Nematode Evolution. Mol Biol Evol 2023; 40:msad274. [PMID: 38069639 DOI: 10.1093/molbev/msad274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/01/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023] Open
Abstract
Polintons are double-stranded DNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family but encode a distinct protein-primed DNA polymerase B (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda. Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting interphylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of an HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.
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Affiliation(s)
- Dae-Eun Jeong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sameer Sundrani
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Present address: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
| | - Eugene V Koonin
- National National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
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2
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Jeong DE, Sundrani S, Hall RN, Krupovic M, Koonin EV, Fire AZ. DNA polymerase diversity reveals multiple incursions of Polintons during nematode evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554363. [PMID: 37662302 PMCID: PMC10473752 DOI: 10.1101/2023.08.22.554363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Polintons are dsDNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family, but encode a distinct protein-primed B family DNA polymerase (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda . Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting inter-phylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of a HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.
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3
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A Novel Rhabdovirus Associated with the Idaho Population of Potato Cyst Nematode Globodera pallida. Viruses 2022; 14:v14122718. [PMID: 36560722 PMCID: PMC9783950 DOI: 10.3390/v14122718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Globodera pallida, a potato cyst nematode (PCN), is a quarantine endoparasitic pest of potato (Solanum tuberosum) in the US due to its effects on yield and quality of potato tubers. A new rhabdovirus, named potato cyst nematode rhabdovirus (PcRV), was revealed and characterized in the G. pallida populations collected in Idaho through use of high-throughput sequencing (HTS) and RT-PCR and found to be most closely related to soybean cyst nematode rhabdovirus (ScRV). PcRV has a 13,604 bp long, single-stranded RNA genome encoding five open reading frames, including four rhabdovirus-specific genes, N, P, G, and L, and one unknown gene. PcRV was found present in eggs, invasive second-stage juveniles, and parasitic females of G. pallida, implying a vertical transmission mode. RT-PCR and partial sequencing of PcRV in laboratory-reared G. pallida populations maintained over five years suggested that the virus is highly persistent and genetically stable. Two other Globodera spp. reproducing on potato and reported in the US, G. rostochiensis and G. ellingtonae, tested negative for PcRV presence. To the best of our knowledge, PcRV is the first virus experimentally found infecting G. pallida. Based on their similar genome organizations, the phylogeny of their RNA-dependent RNA polymerase domains (L gene), and relatively high identity levels in their protein products, PcRV and ScRV are proposed to form a new genus, provisionally named "Gammanemrhavirus", within the family Rhabdoviridae.
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Abstract
Echinoderms are a phylum of marine invertebrates that include model organisms, keystone species, and animals commercially harvested for seafood. Despite their scientific, ecological, and economic importance, there is little known about the diversity of RNA viruses that infect echinoderms compared to other invertebrates. We screened over 900 transcriptomes and viral metagenomes to characterize the RNA virome of 38 echinoderm species from all five classes (Crinoidea, Holothuroidea, Asteroidea, Ophiuroidea and Echinoidea). We identified 347 viral genome fragments that were classified to genera and families within nine viral orders - Picornavirales, Durnavirales, Martellivirales, Nodamuvirales, Reovirales, Amarillovirales, Ghabrivirales, Mononegavirales, and Hepelivirales. We compared the relative viral representation across three life stages (embryo, larvae, adult) and characterized the gene content of contigs which encoded complete or near-complete genomes. The proportion of viral reads in a given transcriptome was not found to significantly differ between life stages though the majority of viral contigs were discovered from transcriptomes of adult tissue. This study illuminates the biodiversity of RNA viruses from echinoderms, revealing the occurrence of viral groups in natural populations.
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Affiliation(s)
- Elliot W Jackson
- Department of Microbiology, Cornell University, Ithaca, NY, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla CA, USA
| | - Roland C Wilhelm
- School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, NY, USA
| | - Daniel H Buckley
- Department of Microbiology, Cornell University, Ithaca, NY, USA.,School of Integrative Plant Science, Bradfield Hall, Cornell University, Ithaca, NY, USA
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY, USA
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5
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Vieira P, Subbotin SA, Alkharouf N, Eisenback J, Nemchinov LG. Expanding the RNA virome of nematodes and other soil-inhabiting organisms. Virus Evol 2022; 8:veac019. [PMID: 35371560 PMCID: PMC8967085 DOI: 10.1093/ve/veac019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/02/2022] [Accepted: 03/10/2022] [Indexed: 07/25/2023] Open
Abstract
In recent years, several newly discovered viruses infecting free-living nematodes, sedentary plant-parasitic nematodes, and migratory root lesion nematodes have been described. However, to the best of our knowledge, no comprehensive research focusing exclusively on metagenomic analysis of the soil nematode community virome has thus far been carried out. In this work, we have attempted to bridge this gap by investigating viral communities that are associated with soil-inhabiting organisms, particularly nematodes. This study demonstrates a remarkable diversity of RNA viruses in the natural soil environment. Over 150 viruses were identified in different soil-inhabiting hosts, of which more than 139 are potentially new virus species. Many of these viruses belong to the nematode virome, thereby enriching our understanding of the diversity and evolution of this complex part of the natural ecosystem.
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Affiliation(s)
- Paulo Vieira
- USDA-ARS Mycology & Nematology Genetic Diversity & Biology Laboratory, Beltsville, MD 20705, USA
| | - Sergei A Subbotin
- Plant Pest Diagnostics Branch, California Department of Food & Agriculture, Sacramento, CA 95832, USA
- Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow 117071, Russia
| | - Nadim Alkharouf
- Department of Computer & Information Sciences Faculty, Towson University, Towson, MD 21204, USA
| | - Jonathan Eisenback
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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6
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Wang S, Ahmed I, Li X, Nie J, Guo L. Evidence for a novel partitivirus isolated from the entomopathogenic nematode Steinernema ceratophorum. Arch Virol 2022; 167:969-972. [PMID: 35112200 DOI: 10.1007/s00705-021-05314-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/12/2021] [Indexed: 12/26/2022]
Abstract
Nematodes are abundant, but little is known about their viruses. In this study, we report a novel partitivirus isolated from the entomopathogenic nematode species Steinernema ceratophorum, named "Steinernema ceratophorum partitivirus 1" (ScPV-1). The complete genome of ScPV-1 comprises two dsRNA segments, dsRNA1 (2352 bp) and dsRNA2 (2196 bp). Each dsRNA contains a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp) and a coat protein (CP), respectively. The sequences of the RdRp and CP showed the highest similarity (47% and 33% identity, respectively) to Plasmopara viticola associated partitivirus 7 (PvAP-7). A multiple sequence alignment and phylogenetic analysis of the RdRp of ScPV-1 and other selected viruses indicated that ScPV-1 is a new member of the genus Betapartitivirus in the family Partitiviridae.
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Affiliation(s)
- Shuangchao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Irfan Ahmed
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianhui Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianhua Nie
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lihua Guo
- 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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Dilweg IW, Bouabda A, Dalebout T, Gultyaev AP, Bredenbeek PJ, Olsthoorn RCL. Xrn1-resistant RNA structures are well-conserved within the genus flavivirus. RNA Biol 2021; 18:709-717. [PMID: 33064973 PMCID: PMC8078501 DOI: 10.1080/15476286.2020.1830238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/18/2022] Open
Abstract
Subgenomic RNAs are produced by several RNA viruses through incomplete degradation of their genomic RNA by the exoribonuclease Xrn1, and have been shown to be essential for viral growth and pathogenicity. Within the flavivirus genus of the Flaviviridae family, two distinct classes of Xrn1-resistant RNA motifs have been proposed; one for mosquito-borne and insect-specific flaviviruses, and one for tick-borne flaviviruses and no-known-vector flaviviruses. We investigated tick-borne and no-known-vector flavivirus Xrn1-resistant RNA motifs through systematic in vitro mutational analysis and showed that both classes actually possess very similar structural configurations, including a double pseudoknot and a base-triple at identical, conserved locations. For the no-known-vector flavivirus Modoc virus, we show that in vivo generation of subgenomic flaviviral RNA was affected by mutations targeted at nucleotides involved in the structural features of flaviviral Xrn1-resistant RNA motifs that were defined in this work. Our results suggest that throughout the genus flavivirus Xrn1-resistant RNA motifs adopt the same topologically conserved structure.
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Affiliation(s)
- Ivar W. Dilweg
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Assia Bouabda
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tim Dalebout
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander P. Gultyaev
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden, The Netherlands
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Peter J. Bredenbeek
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - R. C. L. Olsthoorn
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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Paraskevopoulou S, Käfer S, Zirkel F, Donath A, Petersen M, Liu S, Zhou X, Drosten C, Misof B, Junglen S. Viromics of extant insect orders unveil the evolution of the flavi-like superfamily. Virus Evol 2021; 7:veab030. [PMID: 34026271 PMCID: PMC8129625 DOI: 10.1093/ve/veab030] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insects are the most diversified and species-rich group of animals and harbor an immense diversity of viruses. Several taxa in the flavi-like superfamily, such as the genus Flavivirus, are associated with insects; however, systematic studies on insect virus genetic diversity are lacking, limiting our understanding of the evolution of the flavi-like superfamily. Here, we examined the diversity of flavi-like viruses within the most complete and up-to-date insect transcriptome collection comprising 1,243 insect species by employing a Flaviviridae RdRp profile hidden Markov model search. We identified seventy-six viral sequences in sixty-one species belonging to seventeen insect, one entognathan, and one arachnidan orders. Phylogenetic analyses revealed that twenty-seven sequences fell within the Flaviviridae phylogeny but did not group with established genera. Despite the large diversity of insect hosts studied, we only detected one virus in a blood-feeding insect, which branched within the genus Flavivirus, indicating that this genus likely diversified only in hematophagous arthropods. Nine new jingmenviruses with novel host associations were identified. One of the jingmenviruses established a deep rooting lineage additional to the insect- and tick-associated clades. Segment co-segregation phylogenies support the separation of tick- and insect-associated groups within jingmenviruses, with evidence for segment reassortment. In addition, fourteen viruses grouped with unclassified flaviviruses encompassing genome length of up to 20 kb. Species-specific clades for Hymenopteran- and Orthopteran-associated viruses were identified. Forty-nine viruses populated three highly diversified clades in distant relationship to Tombusviridae, a plant-infecting virus family, suggesting the detection of three previously unknown insect-associated families that contributed to tombusvirus evolution.
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Affiliation(s)
- Sofia Paraskevopoulou
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany
| | - Simon Käfer
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany
| | - Florian Zirkel
- Institute of Virology, University of Bonn Medical Center, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Malte Petersen
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, 17 Qinghua E Rd, Haidian District, Beijing, China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, 17 Qinghua E Rd, Haidian District, Beijing, China
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany.,German Center for Infection Research (DZIF), partner site Charité, Chariteplatz 1, 10117 Berlin, Germany
| | - Bernhard Misof
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany.,German Center for Infection Research (DZIF), partner site Charité, Chariteplatz 1, 10117 Berlin, Germany
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9
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Szucs MJ, Nichols PJ, Jones RA, Vicens Q, Kieft JS. A New Subclass of Exoribonuclease-Resistant RNA Found in Multiple Genera of Flaviviridae. mBio 2020; 11:mBio.02352-20. [PMID: 32994331 DOI: 10.1101/2020.06.26.172668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
Viruses have developed innovative strategies to exploit the cellular machinery and overcome the antiviral defenses of the host, often using specifically structured RNA elements. Examples are found in the Flavivirus genus (in the family Flaviviridae), where during flaviviral infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) accumulate in the cell. These sfRNAs are formed when a host cell 5' to 3' exoribonuclease degrades the viral genomic RNA but is blocked by an exoribonuclease-resistant RNA structure (xrRNA) located in the viral genome's 3' untranslated region (UTR). Although known to exist in several Flaviviridae genera, the full distribution and diversity of xrRNAs in this family were unknown. Using the recently solved high-resolution structure of an xrRNA from the divergent flavivirus Tamana bat virus (TABV) as a reference, we used bioinformatic searches to identify xrRNAs in the remaining three genera of Flaviviridae: Pegivirus, Pestivirus, and Hepacivirus We biochemically and structurally characterized several examples, determining that they are genuine xrRNAs with a conserved fold. These new xrRNAs look superficially similar to the previously described xrRNAs but possess structural differences making them distinct from previous classes of xrRNAs. Overall, we have identified the presence of xrRNA in all four genera of Flaviviridae, but not in all species. Our findings thus require adjustments of previous xrRNA classification schemes and expand the previously known distribution of xrRNA in Flaviviridae.IMPORTANCE The members of the Flaviviridae comprise one of the largest families of positive-sense single-stranded RNA (+ssRNA) and are divided into the Flavivirus, Pestivirus, Pegivirus, and Hepacivirus genera. The genus Flavivirus contains many medically relevant viruses such as Zika virus, dengue virus, and Powassan virus. In these, a part of the RNA of the virus twists up into a distinct three-dimensional shape called an exoribonuclease-resistant RNA (xrRNA) that blocks the ability of the cell to "chew up" the viral RNA. Hence, part of the RNA of the virus remains intact, and this protected part is important for viral infection. These xrRNAs were known to occur in flaviviruses, but whether they existed in the other members of the family was not known. In this study, we identified a new subclass of xrRNA found not only in flaviviruses but also in the remaining three genera. The fact that these structured viral RNAs exist throughout the Flaviviridae family suggests they are important parts of the infection strategy of diverse pathogens, which could lead to new avenues of research.
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Affiliation(s)
- Matthew J Szucs
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Rachel A Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
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Abstract
The members of the Flaviviridae comprise one of the largest families of positive-sense single-stranded RNA (+ssRNA) and are divided into the Flavivirus, Pestivirus, Pegivirus, and Hepacivirus genera. The genus Flavivirus contains many medically relevant viruses such as Zika virus, dengue virus, and Powassan virus. In these, a part of the RNA of the virus twists up into a distinct three-dimensional shape called an exoribonuclease-resistant RNA (xrRNA) that blocks the ability of the cell to “chew up” the viral RNA. Hence, part of the RNA of the virus remains intact, and this protected part is important for viral infection. These xrRNAs were known to occur in flaviviruses, but whether they existed in the other members of the family was not known. In this study, we identified a new subclass of xrRNA found not only in flaviviruses but also in the remaining three genera. The fact that these structured viral RNAs exist throughout the Flaviviridae family suggests they are important parts of the infection strategy of diverse pathogens, which could lead to new avenues of research. Viruses have developed innovative strategies to exploit the cellular machinery and overcome the antiviral defenses of the host, often using specifically structured RNA elements. Examples are found in the Flavivirus genus (in the family Flaviviridae), where during flaviviral infection, pathogenic subgenomic flaviviral RNAs (sfRNAs) accumulate in the cell. These sfRNAs are formed when a host cell 5′ to 3′ exoribonuclease degrades the viral genomic RNA but is blocked by an exoribonuclease-resistant RNA structure (xrRNA) located in the viral genome’s 3′ untranslated region (UTR). Although known to exist in several Flaviviridae genera, the full distribution and diversity of xrRNAs in this family were unknown. Using the recently solved high-resolution structure of an xrRNA from the divergent flavivirus Tamana bat virus (TABV) as a reference, we used bioinformatic searches to identify xrRNAs in the remaining three genera of Flaviviridae: Pegivirus, Pestivirus, and Hepacivirus. We biochemically and structurally characterized several examples, determining that they are genuine xrRNAs with a conserved fold. These new xrRNAs look superficially similar to the previously described xrRNAs but possess structural differences making them distinct from previous classes of xrRNAs. Overall, we have identified the presence of xrRNA in all four genera of Flaviviridae, but not in all species. Our findings thus require adjustments of previous xrRNA classification schemes and expand the previously known distribution of xrRNA in Flaviviridae.
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11
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Bejerman N, Roumagnac P, Nemchinov LG. High-Throughput Sequencing for Deciphering the Virome of Alfalfa ( Medicago sativa L.). Front Microbiol 2020; 11:553109. [PMID: 33042059 PMCID: PMC7518122 DOI: 10.3389/fmicb.2020.553109] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/12/2020] [Indexed: 12/22/2022] Open
Abstract
Alfalfa (Medicago sativa L.), also known as lucerne, is a major forage crop worldwide. In the United States, it has recently become the third most valuable field crop, with an estimated value of over $9.3 billion. Alfalfa is naturally infected by many different pathogens, including viruses, obligate parasites that reproduce only inside living host cells. Traditionally, viral infections of alfalfa have been considered by breeders, growers, producers and researchers to be diseases of limited importance, although they are widespread in all major cultivation areas. However, over the past few years, due to the rapid development of high-throughput sequencing (HTS), viral metagenomics, bioinformatics tools for interpreting massive amounts of HTS data and the increasing accessibility of public data repositories for transcriptomic discoveries, several emerging viruses of alfalfa with the potential to cause serious yield losses have been described. They include alfalfa leaf curl virus (family Geminiviridae), alfalfa dwarf virus (family Rhabdoviridae), alfalfa enamovirus 1 (family Luteoviridae), alfalfa virus S (family Alphaflexiviridae) and others. These discoveries have called into question the assumed low economic impact of viral diseases in alfalfa and further suggested their possible contribution to the severity of complex infections involving multiple pathogens. In this review, we will focus on viruses of alfalfa recently described in different laboratories on the basis of the above research methodologies.
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Affiliation(s)
| | - Philippe Roumagnac
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Université Montpellier, Montpellier, France
| | - Lev G Nemchinov
- Molecular Plant Pathology Laboratory, USDA-ARS-BARC, Beltsville, MD, United States
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12
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de Bernadi Schneider A, Jacob Machado D, Guirales S, Janies DA. FLAVi: An Enhanced Annotator for Viral Genomes of Flaviviridae. Viruses 2020; 12:E892. [PMID: 32824044 PMCID: PMC7472247 DOI: 10.3390/v12080892] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Responding to the ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and Zika, demands a greater understanding of how these viruses emerge and spread. Updated phylogenies are central to this understanding. Most cladograms of Flaviviridae focus on specific lineages and ignore outgroups, hampering the efficacy of the analysis to test ingroup monophyly and relationships. This is due to the lack of annotated Flaviviridae genomes, which has gene content variation among genera. This variation makes analysis without partitioning difficult. Therefore, we developed an annotation pipeline for the genera of Flaviviridae (Flavirirus, Hepacivirus, Pegivirus, and Pestivirus, named "Fast Loci Annotation of Viruses" (FLAVi; http://flavi-web.com/), that combines ab initio and homology-based strategies. FLAVi recovered 100% of the genes in Flavivirus and Hepacivirus genomes. In Pegivirus and Pestivirus, annotation efficiency was 100% except for one partition each. There were no false positives. The combined phylogenetic analysis of multiple genes made possible by annotation has clear impacts over the tree topology compared to phylogenies that we inferred without outgroups or data partitioning. The final tree is largely congruent with previous hypotheses and adds evidence supporting the close phylogenetic relationship between dengue and Zika.
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Affiliation(s)
- Adriano de Bernadi Schneider
- AntiViral Research Center, Department of Medicine, University of California San Diego, San Diego, CA 92103, USA;
| | - Denis Jacob Machado
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; (S.G.); (D.A.J.)
| | - Sayal Guirales
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; (S.G.); (D.A.J.)
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; (S.G.); (D.A.J.)
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Kondo H, Fujita M, Hisano H, Hyodo K, Andika IB, Suzuki N. Virome Analysis of Aphid Populations That Infest the Barley Field: The Discovery of Two Novel Groups of Nege/Kita-Like Viruses and Other Novel RNA Viruses. Front Microbiol 2020; 11:509. [PMID: 32318034 PMCID: PMC7154061 DOI: 10.3389/fmicb.2020.00509] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Aphids (order Hemiptera) are important insect pests of crops and are also vectors of many plant viruses. However, little is known about aphid-infecting viruses, particularly their diversity and relationship to plant viruses. To investigate the aphid viromes, we performed deep sequencing analyses of the aphid transcriptomes from infested barley plants in a field in Japan. We discovered virus-like sequences related to nege/kita-, flavi-, tombus-, phenui-, mononega-, narna-, chryso-, partiti-, and luteoviruses. Using RT-PCR and sequence analyses, we determined almost complete sequences of seven nege/kitavirus-like virus genomes; one of which was a variant of the Wuhan house centipede virus (WHCV-1). The other six seem to belong to four novel viruses distantly related to Wuhan insect virus 9 (WhIV-9) or Hubei nege-like virus 4 (HVLV-4). We designated the four viruses as barley aphid RNA virus 1 to 4 (BARV-1 to -4). Moreover, some nege/kitavirus-like sequences were found by searches on the transcriptome shotgun assembly (TSA) libraries of arthropods and plants. Phylogenetic analyses showed that BARV-1 forms a clade with WHCV-1 and HVLV-4, whereas BARV-2 to -4 clustered with WhIV-9 and an aphid virus, Aphis glycines virus 3. Both virus groups (tentatively designated as Centivirus and Aphiglyvirus, respectively), together with arthropod virus-like TSAs, fill the phylogenetic gaps between the negeviruses and kitaviruses lineages. We also characterized the flavi/jingmen-like and tombus-like virus sequences as well as other RNA viruses, including six putative novel viruses, designated as barley aphid RNA viruses 5 to 10. Interestingly, we also discovered that some aphid-associated viruses, including nege/kita-like viruses, were present in different aphid species, raising a speculation that these viruses might be distributed across different aphid species with plants being the reservoirs. This study provides novel information on the diversity and spread of nege/kitavirus-related viruses and other RNA viruses that are associated with aphids.
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Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Miki Fujita
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Hiroshi Hisano
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Kiwamu Hyodo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki, Japan
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14
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Garry CE, Garry RF. Proteomics Computational Analyses Suggest That the Envelope Glycoproteins of Segmented Jingmen Flavi-Like Viruses are Class II Viral Fusion Proteins (b-Penetrenes) with Mucin-Like Domains. Viruses 2020; 12:v12030260. [PMID: 32120884 PMCID: PMC7150890 DOI: 10.3390/v12030260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 12/27/2022] Open
Abstract
Jingmen viruses are newly described segmented flavi-like viruses that have a worldwide distribution in ticks and have been associated with febrile illnesses in humans. Computational analyses were used to predict that Jingmen flavi-like virus glycoproteins have structural features of class II viral fusion proteins, including an ectodomain consisting of beta-sheets and short alpha-helices, a fusion peptide with interfacial hydrophobicity and a three-domain architecture. Jingmen flavi-like virus glycoproteins have a sequence enriched in serine, threonine, and proline at the amino terminus, which is a feature of mucin-like domains. Several of the serines and threonines are predicted be modified by the addition of O-linked glycans. Some of the glycoproteins are predicted to have an additional mucin-like domain located prior to the transmembrane anchor, whereas others are predicted to have a stem consisting of two alpha-helices. The flavivirus envelope protein and Jingmen flavi-virus glycoproteins may have diverged from a common class II precursor glycoprotein with a mucin-like domain or domains acquired after divergence.
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Affiliation(s)
- Courtney E. Garry
- School of Nursing, Johns Hopkins University, Baltimore, MD 21205, USA;
| | - Robert F. Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Zalgen Labs, Germantown, MD 20876, USA
- Correspondence: ; Tel.: +1-504-988-2027
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15
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Ruark-Seward CL, Davis EL, Sit TL. Localization of viral and host RNA within soybean cyst nematode via fluorescence in situ hybridization. Exp Parasitol 2020; 211:107866. [PMID: 32113861 DOI: 10.1016/j.exppara.2020.107866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/19/2019] [Accepted: 02/23/2020] [Indexed: 10/24/2022]
Abstract
Nematode-infecting RNA viruses have recently been discovered via transcriptome sequencing. In soybean cyst nematode (SCN; Heterodera glycines), seven single-stranded RNA viruses have been identified from transcriptome data and experimentally confirmed with qRT-PCR and Sanger sequencing. Presently, there is still much unknown about the relationship between these viruses and the nematode host. In this study, we localize three viruses within the soybean cyst nematode: SCN socyvirus-1 (SbCNV-1), SCN nyami-like virus (NLV), and SCN bunya-like virus (BLV). To visually locate the viruses, whole-mount fluorescence in situ hybridization (FISH) methodology was developed for SCN pre-parasitic second-stage juveniles (ppJ2s). Two SCN populations with differing viral titers (LY1 and MM21) were used as a comparison for viral probe fluorescence intensity. Viral RNAs for all three viruses were abundant in cells throughout the SCN ppJ2 body of the high titer (LY1) population but absent within the majority of the intestinal tract. A significant reduction in viral fluorescence intensity was observed in a similar body pattern in ppJ2 of the low-titer (MM21) SCN, highlighting the specificity of the FISH method. As controls, viral RNAs were colocalized with host mRNA glyceraldehyde 3-phosphate dehydrogenase (GAPDH) for full body localization and a secretory ubiquitin protein (4G06) expressed specifically within the subventral esophageal glands. In addition, viral replication was confirmed in SCN eggs and ppJ2s via qRT-PCR detection of the anti-genomic RNA strands.
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Affiliation(s)
- Casey L Ruark-Seward
- Department of Entomology and Plant Pathology, North Carolina State University, 1575 Varsity Drive, Raleigh, NC, 27606, USA.
| | - Eric L Davis
- Department of Entomology and Plant Pathology, North Carolina State University, 1575 Varsity Drive, Raleigh, NC, 27606, USA
| | - Tim L Sit
- Department of Entomology and Plant Pathology, North Carolina State University, 1575 Varsity Drive, Raleigh, NC, 27606, USA
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16
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Jo WK, van Elk C, van de Bildt M, van Run P, Petry M, Jesse ST, Jung K, Ludlow M, Kuiken T, Osterhaus A. An evolutionary divergent pestivirus lacking the N pro gene systemically infects a whale species. Emerg Microbes Infect 2020; 8:1383-1392. [PMID: 31526243 PMCID: PMC6758615 DOI: 10.1080/22221751.2019.1664940] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Pestiviruses typically infect members of the order Artiodactyla, including ruminants and pigs, although putative rat and bat pestiviruses have also been described. In the present study, we identified and characterized an evolutionary divergent pestivirus in the toothed whale species, harbour porpoise (Phocoena phocoena). We tentatively named the virus Phocoena pestivirus (PhoPeV). PhoPeV displays a typical pestivirus genome organization except for the unique absence of Npro, an N-terminal autoprotease that targets the innate host immune response. Evolutionary evidence indicates that PhoPeV emerged following an interspecies transmission event from an ancestral pestivirus that expressed Npro. We show that 9% (n = 10) of stranded porpoises from the Dutch North Sea coast (n = 112) were positive for PhoPeV and they displayed a systemic infection reminiscent of non-cytopathogenic persistent pestivirus infection. The identification of PhoPeV extends the host range of pestiviruses to cetaceans (dolphins, whales, porpoises), which are considered to have evolved from artiodactyls (even-toed ungulates). Elucidation of the pathophysiology of PhoPeV infection and Npro unique absence will add to our understanding of molecular mechanisms governing pestivirus pathogenesis.
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Affiliation(s)
- Wendy K Jo
- Research Center Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover , Hannover , Germany
| | - Cornelis van Elk
- Department Viroscience, Erasmus MC Rotterdam , Rotterdam , The Netherlands
| | - Marco van de Bildt
- Department Viroscience, Erasmus MC Rotterdam , Rotterdam , The Netherlands
| | - Peter van Run
- Department Viroscience, Erasmus MC Rotterdam , Rotterdam , The Netherlands
| | - Monique Petry
- Research Center Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover , Hannover , Germany
| | - Sonja T Jesse
- Research Center Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover , Hannover , Germany
| | - Klaus Jung
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover , Hannover , Germany
| | - Martin Ludlow
- Research Center Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover , Hannover , Germany
| | - Thijs Kuiken
- Research Center Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover , Hannover , Germany
| | - Albert Osterhaus
- Research Center Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover , Hannover , Germany
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17
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Vieira P, Peetz A, Mimee B, Saikai K, Mollov D, MacGuidwin A, Zasada I, Nemchinov LG. Prevalence of the root lesion nematode virus (RLNV1) in populations of Pratylenchus penetrans from North America. J Nematol 2020; 52:1-10. [PMID: 32421266 PMCID: PMC7266026 DOI: 10.21307/jofnem-2020-045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Indexed: 11/11/2022] Open
Abstract
Root lesion nematode virus 1 (RLNV1) was discovered in the migratory endoparasitic nematode species Pratylenchus penetrans. It was found in a P. penetrans population collected from soil samples in Beltsville, Maryland, USA. In this study, the distribution of the RLNV1 in 31 geographically distinct P. penetrans populations obtained from different crops was examined. The results demonstrate that RLNV1 is widespread in North American populations of P. penetrans and exhibits low genetic variability in the helicase and RNA-dependent RNA polymerase regions of the genome.
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Affiliation(s)
- Paulo Vieira
- Molecular Plant Pathology Laboratory , USDA-ARS , Beltsville, MD 20705 ; School of Plant Environmental Science , Virginia Tech , Blacksburg, VA 24061
| | - Amy Peetz
- Horticultural Crops Research Laboratory , USDA-ARS , Corvallis, OR 97330
| | - Benjamin Mimee
- St-Jean-sur-Richelieu Research and Development Center , Agriculture and Agri-Food Canada , St-Jean-sur-Richelieu , Canada
| | - Kanan Saikai
- Department of Plant Pathology, University of Wisconsin-Madison , Madison, WI 53706
| | - Dimitre Mollov
- National Germplasm Resources Laboratory , USDA-ARS , Beltsville, MD 20705
| | - Ann MacGuidwin
- Department of Plant Pathology, University of Wisconsin-Madison , Madison, WI 53706
| | - Inga Zasada
- Horticultural Crops Research Laboratory , USDA-ARS , Corvallis, OR 97330
| | - Lev G Nemchinov
- Molecular Plant Pathology Laboratory , USDA-ARS , Beltsville, MD 20705
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18
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Jiang P, Shao J, Nemchinov LG. Identification of emerging viral genomes in transcriptomic datasets of alfalfa (Medicago sativa L.). Virol J 2019; 16:153. [PMID: 31818304 PMCID: PMC6902351 DOI: 10.1186/s12985-019-1257-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022] Open
Abstract
Background Publicly available transcriptomic datasets have become a valuable tool for the discovery of new pathogens, particularly viruses. In this study, several coding-complete viral genomes previously not found or experimentally confirmed in alfalfa were identified in the plant datasets retrieved from the NCBI Sequence Read Archive. Methods Publicly available Medicago spp. transcriptomic datasets were retrieved from the NCBI SRA database. The raw reads were first mapped to the reference genomes of Medicago sativa and Medigago truncatula followed by the alignment of the unmapped reads to the NCBI viral genome database and de novo assembly using the SPAdes tool. When possible, assemblies were experimentally confirmed using 5′/3′ RACE and RT-PCRs. Results Twenty three different viruses were identified in the analyzed datasets, of which several represented emerging viruses not reported in alfalfa prior to this study. Among them were two strains of cnidium vein yellowing virus, lychnis mottle virus and Cactus virus X, for which coding-complete genomic sequences were obtained by a de novo assembly. Conclusions The results improve our knowledge of the diversity and host range of viruses infecting alfalfa, provide essential tools for their diagnostics and characterization and demonstrate the utility of transcriptomic datasets for the discovery of new pathogens.
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Affiliation(s)
- Peng Jiang
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA
| | - Jonathan Shao
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA
| | - Lev G Nemchinov
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA.
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19
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Abstract
Caenorhabditis elegans has long been a laboratory model organism with no known natural pathogens. In the past ten years, however, natural viruses have been isolated from wild-caught C. elegans (Orsay virus) and its relative Caenorhabditis briggsae (Santeuil virus, Le Blanc virus, and Melnik virus). All are RNA positive-sense viruses related to Nodaviridae; they infect intestinal cells and are horizontally transmitted. The Orsay virus capsid structure has been determined and the virus can be reconstituted by transgenesis of the host. Recent use of the Orsay virus has enabled researchers to identify evolutionarily conserved proviral and antiviral genes that function in nematodes and mammals. These pathways include endocytosis through SID-3 and WASP; a uridylyltransferase that destabilizes viral RNAs by uridylation of their 3′ end; ubiquitin protein modifications and turnover; and the RNA interference pathway, which recognizes and degrades viral RNA.
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Affiliation(s)
- Marie-Anne Félix
- Institute of Biology of the École Normale Supérieure, CNRS UMR8197, INSERM U1024, 75230 Paris CEDEX 05, France
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
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20
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Williams SH, Che X, Oleynik A, Garcia JA, Muller D, Zabka TS, Firth C, Corrigan RM, Briese T, Jain K, Lipkin WI. Discovery of two highly divergent negative-sense RNA viruses associated with the parasitic nematode, Capillaria hepatica, in wild Mus musculus from New York City. J Gen Virol 2019; 100:1350-1362. [PMID: 31513008 PMCID: PMC7363305 DOI: 10.1099/jgv.0.001315] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Recent advances in high-throughput sequencing technology have led to a rapid expansion in the number of viral sequences associated with samples from vertebrates, invertebrates and environmental samples. Accurate host identification can be difficult in assays of complex samples that contain more than one potential host. Using unbiased metagenomic sequencing, we investigated wild house mice (Mus musculus) and brown rats (Rattus norvegicus) from New York City to determine the aetiology of liver disease. Light microscopy was used to characterize liver disease, and fluorescent microscopy with in situ hybridization was employed to identify viral cell tropism. Sequences representing two novel negative-sense RNA viruses were identified in homogenates of wild house mouse liver tissue: Amsterdam virus and Fulton virus. In situ hybridization localized viral RNA to Capillaria hepatica, a parasitic nematode that had infected the mouse liver. RNA from either virus was found within nematode adults and unembryonated eggs. Expanded PCR screening identified brown rats as a second rodent host for C. hepatica as well as both nematode-associated viruses. Our findings indicate that the current diversity of nematode-associated viruses may be underappreciated and that anatomical imaging offers an alternative to computational host assignment approaches.
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Affiliation(s)
- Simon H Williams
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Xiaoyu Che
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Alexandra Oleynik
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Joel A Garcia
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Dorothy Muller
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Tanja S Zabka
- Development Sciences Safety Assessment, Genentech, Inc., South San Francisco, California
| | - Cadhla Firth
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
| | | | - Thomas Briese
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Komal Jain
- Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Columbia University, New York, NY, USA
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21
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Vieira P, Nemchinov LG. A novel species of RNA virus associated with root lesion nematode Pratylenchus penetrans. J Gen Virol 2019; 100:704-708. [DOI: 10.1099/jgv.0.001246] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Paulo Vieira
- 1Molecular Plant Pathology Laboratory, Agricultural Research Service, USA Department of Agriculture, Beltsville, USA
- 2School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, USA
| | - Lev G. Nemchinov
- 1Molecular Plant Pathology Laboratory, Agricultural Research Service, USA Department of Agriculture, Beltsville, USA
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22
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Virus discovery reveals frequent infection by diverse novel members of the Flaviviridae in wild lemurs. Arch Virol 2018; 164:509-522. [PMID: 30460488 DOI: 10.1007/s00705-018-4099-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022]
Abstract
Lemurs are highly endangered mammals inhabiting the forests of Madagascar. In this study, we performed virus discovery on serum samples collected from 84 wild lemurs and identified viral sequence fragments from 4 novel viruses within the family Flaviviridae, including members of the genera Hepacivirus and Pegivirus. The sifaka hepacivirus (SifHV, two genotypes) and pegivirus (SifPgV, two genotypes) were discovered in the diademed sifaka (Propithecus diadema), while other pegiviral fragments were detected in samples from the indri (Indri indri, IndPgV) and the weasel sportive lemur (Lepilemur mustelinus, LepPgV). Although data are preliminary, each viral species appeared host species-specific and frequent infection was detected (18 of 84 individuals were positive for at least one virus). The complete coding sequence and partial 5' and 3' untranslated regions (UTRs) were obtained for SifHV and its genomic organization was consistent with that of other hepaciviruses, with one unique polyprotein and highly structured UTRs. Phylogenetic analyses showed the SifHV belonged to a clade that includes several viral species identified in rodents from Asia and North America, while SifPgV and IndPgV were more closely related to pegiviral species A and C, that include viruses found in humans as well as New- and Old-World monkeys. Our results support the current proposed model of virus-host co-divergence with frequent occurrence of cross-species transmission for these genera and highlight how the discovery of more members of the Flaviviridae can help clarify the ecology and evolutionary history of these viruses. Furthermore, this knowledge is important for conservation and captive management of lemurs.
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23
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Anderson S, Soman C, Bekal S, Domier L, Lambert K, Bhalerao K. An Agent-Based Metapopulation Model Simulating Virus-Based Biocontrol of Heterodera Glycines. J Nematol 2018; 50:79-90. [PMID: 30451429 DOI: 10.21307/jofnem-2018-002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
With recently discovered soybean cyst nematode (SCN) viruses, biological control of the nematodes is a theoretical possibility. This study explores the question of what kinds of viruses would make useful biocontrol agents, taking into account evolutionary and population dynamics. An agent-based model, Soybean Cyst Nematode Simulation (SCNSim), was developed to simulate within-host virulence evolution in a virus-nematode-soybean ecosystem. SCNSim was used to predict nematode suppression under a range of viral mutation rates, initial virulences, and release strategies. The simulation model suggested that virus-based biocontrol worked best when the nematodes were inundated with the viruses. Under lower infection prevalence, the viral burden thinned out rapidly due to the limited mobility and high reproductive rate of the SCN. In accordance with the generally accepted trade-off theory, SCNSim predicted the optimal initial virulence for the maximum nematode suppression. Higher initial virulence resulted in shorter lifetime transmission, whereas viruses with lower initial virulence values evolved toward avirulence. SCNSim also indicated that a greater viral mutation rate reinforced the virulence pathotype, suggesting the presence of a virulence threshold necessary to achieve biocontrol against SCN.
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Affiliation(s)
- Safyre Anderson
- School of Information, University of California at Berkeley, Berkeley, CA
| | - Chinmay Soman
- Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Sadia Bekal
- Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Leslie Domier
- Agricultural Research Service, United States Department of Agriculture, Beltsville, MD ; Crop Science, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Kris Lambert
- Crop Science, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Kaustubh Bhalerao
- Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL
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24
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Lin J, Ye R, Thekke-Veetil T, Staton ME, Arelli PR, Bernard EC, Hewezi T, Domier LL, Hajimorad MR. A novel picornavirus-like genome from transcriptome sequencing of sugar beet cyst nematode represents a new putative genus. J Gen Virol 2018; 99:1418-1424. [PMID: 30156527 DOI: 10.1099/jgv.0.001139] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Analysis of transcriptome sequence data from eggs and second-stage juveniles (J2s) of sugar beet cyst nematode (SBCN, Heterodera schachtii) identified the full-length genome of a positive-sense single-stranded RNA virus, provisionally named sugar beet cyst nematode virus 1 (SBCNV1). The SBCNV1 sequence was detected in both eggs and J2s, indicating its possible vertical transmission. The 9503-nucleotide genome sequence contains a single long open reading frame, which was predicted to encode a polyprotein with conserved domains for picornaviral structural proteins proximal to its amino terminus and RNA helicase, cysteine proteinase and RNA-dependent RNA polymerase (RdRp) conserved domains proximal to its carboxyl terminus, hallmarks of viruses belonging to the order Picornavirales. Phylogenetic analysis of the predicted SBCNV1 RdRp amino acid sequence indicated that the SBCNV1 sequence is most closely related to members of the family Secoviridae, which includes genera of nematode-transmitted plant-infecting viruses. SBCNV1 represents the first fully sequenced viral genome from SBCN.
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Affiliation(s)
- Jingyu Lin
- 1Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Rongjian Ye
- 1Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA.,†Present address: Life Science and Technology Center, China National Seed Group Company Limited, Wuhan 430075, PR China
| | | | - Margaret E Staton
- 1Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Prakash R Arelli
- 3Crop Genetics Research Unit, USDA-ARS, 605 Airways Blvd., Jackson, TN 38301, USA
| | - Ernest C Bernard
- 1Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Tarek Hewezi
- 4Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
| | - Leslie L Domier
- 2Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.,5Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, USDA-ARS, Urbana, IL 61801, USA
| | - M R Hajimorad
- 1Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
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25
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Han Z, Thapa S, Reuter-Carlson U, Reed H, Gates M, Lambert KN, Schroeder NE. Immobility in the sedentary plant-parasitic nematode H. glycines is associated with remodeling of neuromuscular tissue. PLoS Pathog 2018; 14:e1007198. [PMID: 30114260 PMCID: PMC6095618 DOI: 10.1371/journal.ppat.1007198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/05/2018] [Indexed: 12/22/2022] Open
Abstract
The sedentary plant-parasitic nematodes are considered among the most economically damaging pathogens of plants. Following infection and the establishment of a feeding site, sedentary nematodes become immobile. Loss of mobility is reversed in adult males while females never regain mobility. The structural basis for this change in mobility is unknown. We used a combination of light and transmission electron microscopy to demonstrate cell-specific muscle atrophy and sex-specific renewal of neuromuscular tissue in the sedentary nematode Heterodera glycines. We found that both females and males undergo body wall muscle atrophy and loss of attachment to the underlying cuticle during immobile developmental stages. Male H. glycines undergo somatic muscle renewal prior to molting into a mobile adult. In addition, we found developmental changes to the organization and number of motor neurons in the ventral nerve cord correlated with changes in mobility. To further examine neuronal changes associated with immobility, we used a combination of immunohistochemistry and molecular biology to characterize the GABAergic nervous system of H. glycines during mobile and immobile stages. We cloned and confirmed the function of the putative H. glycines GABA synthesis-encoding gene hg-unc-25 using heterologous rescue in C. elegans. We found a reduction in gene expression of hg-unc-25 as well as a reduction in the number of GABA-immunoreactive neurons during immobile developmental stages. Finally, we found evidence of similar muscle atrophy in the phylogenetically diverged plant-parasitic nematode Meloidogyne incognita. Together, our data demonstrate remodeling of neuromuscular structure and function during sedentary plant-parasitic nematode development.
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Affiliation(s)
- Ziduan Han
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Sita Thapa
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Ursula Reuter-Carlson
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Hannah Reed
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Michael Gates
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Kris N. Lambert
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Nathan E. Schroeder
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
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26
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Abstract
Viruses are an important but sequence-diverse and often understudied component of the phytobiome. We succinctly review current information on how plant viruses directly affect plant health and physiology and consequently have the capacity to modulate plant interactions with their biotic and abiotic environments. Virus interactions with other biota in the phytobiome, including arthropods, fungi, and nematodes, may also impact plant health. For example, viruses interact with and modulate the interface between plants and insects. This has been extensively studied for insect-vectored plant viruses, some of which also infect their vectors. Other viruses have been shown to alter the impacts of plant-interacting phytopathogenic and nonpathogenic fungi and bacteria. Viruses that infect nematodes have also recently been discovered, but the impact of these and phage infecting soil bacteria on plant health remain largely unexplored.
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Affiliation(s)
- James E Schoelz
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Lucy R Stewart
- Corn, Soybean and Wheat Quality Research Unit, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Wooster, Ohio 44691, USA;
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27
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Showmaker KC, Walden KKO, Fields CJ, Lambert KN, Hudson ME. Genome Sequence of the Soybean Cyst Nematode (Heterodera glycines) Endosymbiont "Candidatus Cardinium hertigii" Strain cHgTN10. GENOME ANNOUNCEMENTS 2018; 6:e00624-18. [PMID: 29954916 PMCID: PMC6025951 DOI: 10.1128/genomea.00624-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/02/2018] [Indexed: 02/01/2023]
Abstract
In this study, we present the genome sequence of the "Candidatus Cardinium hertigii" strain cHgTN10, an endosymbiotic bacterium of the plant-parasitic nematode Heterodera glycines This is the first genome assembly reported for an endosymbiont directly sequenced from a tylenchid nematode.
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Affiliation(s)
- Kurt C Showmaker
- Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kimberly K O Walden
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J Fields
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kris N Lambert
- Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Matthew E Hudson
- Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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28
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Ruark CL, Gardner M, Mitchum MG, Davis EL, Sit TL. Novel RNA viruses within plant parasitic cyst nematodes. PLoS One 2018; 13:e0193881. [PMID: 29509804 PMCID: PMC5839581 DOI: 10.1371/journal.pone.0193881] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/20/2018] [Indexed: 02/06/2023] Open
Abstract
The study of invertebrate-and particularly nematode-viruses is emerging with the advancement of transcriptome sequencing. Five single-stranded RNA viruses have now been confirmed within the economically important soybean cyst nematode (SCN; Heterodera glycines). From previous research, we know these viruses to be widespread in greenhouse and field populations of SCN. Several of the SCN viruses were also confirmed within clover (H. trifolii) and beet (H. schachtii) cyst nematodes. In the presented study, we sequenced the transcriptomes of several inbred SCN populations and identified two previously undiscovered viral-like genomes. Both of these proposed viruses are negative-sense RNA viruses and have been named SCN nyami-like virus (NLV) and SCN bunya-like virus (BLV). Finally, we analyzed publicly available transcriptome data of two potato cyst nematode (PCN) species, Globodera pallida and G. rostochiensis. From these data, a third potential virus was discovered and called PCN picorna-like virus (PLV). PCN PLV is a positive-sense RNA virus, and to the best of our knowledge, is the first virus described within PCN. The presence of these novel viruses was confirmed via qRT-PCR, endpoint PCR, and Sanger sequencing with the exception of PCN PLV due to quarantine restrictions on the nematode host. While much work needs to be done to understand the biological and evolutionary significance of these viruses, they offer insight into nematode ecology and the possibility of novel nematode management strategies.
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Affiliation(s)
- Casey L. Ruark
- Department of Entomology and Plant Pathology, North Carolina State University, Thomas Hall, Raleigh, North Carolina, United States of America
| | - Michael Gardner
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, 371H Bond Life Sciences Center, Columbia, Missouri, United States of America
| | - Melissa G. Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, 371H Bond Life Sciences Center, Columbia, Missouri, United States of America
| | - Eric L. Davis
- Department of Entomology and Plant Pathology, North Carolina State University, Thomas Hall, Raleigh, North Carolina, United States of America
| | - Tim L. Sit
- Department of Entomology and Plant Pathology, North Carolina State University, Thomas Hall, Raleigh, North Carolina, United States of America
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29
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Gardner M, Dhroso A, Johnson N, Davis EL, Baum TJ, Korkin D, Mitchum MG. Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines. Sci Rep 2018; 8:2505. [PMID: 29410430 PMCID: PMC5802810 DOI: 10.1038/s41598-018-20536-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 01/12/2018] [Indexed: 11/08/2022] Open
Abstract
Soybean cyst nematode (SCN) Heterodera glycines is an obligate parasite that relies on the secretion of effector proteins to manipulate host cellular processes that favor the formation of a feeding site within host roots to ensure its survival. The sequence complexity and co-evolutionary forces acting upon these effectors remain unknown. Here we generated a de novo transcriptome assembly representing the early life stages of SCN in both a compatible and an incompatible host interaction to facilitate global effector mining efforts in the absence of an available annotated SCN genome. We then employed a dual effector prediction strategy coupling a newly developed nematode effector prediction tool, N-Preffector, with a traditional secreted protein prediction pipeline to uncover a suite of novel effector candidates. Our analysis distinguished between effectors that co-evolve with the host genotype and those conserved by the pathogen to maintain a core function in parasitism and demonstrated that alternative splicing is one mechanism used to diversify the effector pool. In addition, we confirmed the presence of viral and microbial inhabitants with molecular sequence information. This transcriptome represents the most comprehensive whole-nematode sequence currently available for SCN and can be used as a tool for annotation of expected genome assemblies.
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Affiliation(s)
- Michael Gardner
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Andi Dhroso
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, USA
| | - Nathan Johnson
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, USA
| | - Eric L Davis
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, USA
| | - Dmitry Korkin
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, USA.
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, USA.
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30
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Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer. Virus Res 2017; 244:36-52. [PMID: 29103997 PMCID: PMC5801114 DOI: 10.1016/j.virusres.2017.10.020] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/22/2022]
Abstract
Virus metagenomics is a young research filed but it has already transformed our understanding of virus diversity and evolution, and illuminated at a new level the connections between virus evolution and the evolution and ecology of the hosts. In this review article, we examine the new picture of the evolution of RNA viruses, the dominant component of the eukaryotic virome, that is emerging from metagenomic data analysis. The major expansion of many groups of RNA viruses through metagenomics allowed the construction of substantially improved phylogenetic trees for the conserved virus genes, primarily, the RNA-dependent RNA polymerases (RdRp). In particular, a new superfamily of widespread, small positive-strand RNA viruses was delineated that unites tombus-like and noda-like viruses. Comparison of the genome architectures of RNA viruses discovered by metagenomics and by traditional methods reveals an extent of gene module shuffling among diverse virus genomes that far exceeds the previous appreciation of this evolutionary phenomenon. Most dramatically, inclusion of the metagenomic data in phylogenetic analyses of the RdRp resulted in the identification of numerous, strongly supported groups that encompass RNA viruses from diverse hosts including different groups of protists, animals and plants. Notwithstanding potential caveats, in particular, incomplete and uneven sampling of eukaryotic taxa, these highly unexpected findings reveal horizontal virus transfer (HVT) between diverse hosts as the central aspect of RNA virus evolution. The vast and diverse virome of invertebrates, particularly nematodes and arthropods, appears to be the reservoir, from which the viromes of plants and vertebrates evolved via multiple HVT events.
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31
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Thekke-Veetil T, McCoppin NK, Domier LL. Strain-specific association of soybean dwarf virus small subgenomic RNA with virus particles. Virus Res 2017; 242:100-105. [PMID: 28893654 DOI: 10.1016/j.virusres.2017.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
Soybean dwarf virus (SbDV) produces a large subgenomic RNA (LsgRNA) for expression of structural and movement proteins and a small subgenomic RNA (SsgRNA) that does not contain an open reading frame. Sucrose gradient-purified SbDV virions from soybean plants systemically infected with SbDV by aphids and Nicotiana benthamiana leaves agroinfiltrated with infectious clones of two red clover SbDV isolates encapsidated genomic RNA and were associated with SsgRNA in a strain-specific manner. The LsgRNA was protected from RNase degradation, but not packaged into virions as indicated by its presence primarily in ELISA-negative fractions near the tops of sucrose gradients even in mutants that did not express coat protein. Nucleotide differences in the SsgRNA region between isolates conferred differential association of SsgRNA with virions.
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Affiliation(s)
| | - Nancy K McCoppin
- United State Department of Agriculture, Agricultural Research Service, Urbana, IL, 61801, USA
| | - Leslie L Domier
- United State Department of Agriculture, Agricultural Research Service, Urbana, IL, 61801, USA.
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32
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Remnant EJ, Shi M, Buchmann G, Blacquière T, Holmes EC, Beekman M, Ashe A. A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations. J Virol 2017; 91:e00158-17. [PMID: 28515299 PMCID: PMC5533899 DOI: 10.1128/jvi.00158-17] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/26/2017] [Indexed: 01/16/2023] Open
Abstract
Understanding the diversity and consequences of viruses present in honey bees is critical for maintaining pollinator health and managing the spread of disease. The viral landscape of honey bees (Apis mellifera) has changed dramatically since the emergence of the parasitic mite Varroa destructor, which increased the spread of virulent variants of viruses such as deformed wing virus. Previous genomic studies have focused on colonies suffering from infections by Varroa and virulent viruses, which could mask other viral species present in honey bees, resulting in a distorted view of viral diversity. To capture the viral diversity within colonies that are exposed to mites but do not suffer the ultimate consequences of the infestation, we examined populations of honey bees that have evolved naturally or have been selected for resistance to Varroa This analysis revealed seven novel viruses isolated from honey bees sampled globally, including the first identification of negative-sense RNA viruses in honey bees. Notably, two rhabdoviruses were present in three geographically diverse locations and were also present in Varroa mites parasitizing the bees. To characterize the antiviral response, we performed deep sequencing of small RNA populations in honey bees and mites. This provided evidence of a Dicer-mediated immune response in honey bees, while the viral small RNA profile in Varroa mites was novel and distinct from the response observed in bees. Overall, we show that viral diversity in honey bee colonies is greater than previously thought, which encourages additional studies of the bee virome on a global scale and which may ultimately improve disease management.IMPORTANCE Honey bee populations have become increasingly susceptible to colony losses due to pathogenic viruses spread by parasitic Varroa mites. To date, 24 viruses have been described in honey bees, with most belonging to the order Picornavirales Collapsing Varroa-infected colonies are often overwhelmed with high levels of picornaviruses. To examine the underlying viral diversity in honey bees, we employed viral metatranscriptomics analyses on three geographically diverse Varroa-resistant populations from Europe, Africa, and the Pacific. We describe seven novel viruses from a range of diverse viral families, including two viruses that are present in all three locations. In honey bees, small RNA sequences indicate that these viruses are processed by Dicer and the RNA interference pathway, whereas Varroa mites produce strikingly novel small RNA patterns. This work increases the number and diversity of known honey bee viruses and will ultimately contribute to improved disease management in our most important agricultural pollinator.
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Affiliation(s)
- Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Mang Shi
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Gabriele Buchmann
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
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33
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Walsh E, Elmore JM, Taylor CG. Root-Knot Nematode Parasitism Suppresses Host RNA Silencing. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:295-300. [PMID: 28402184 DOI: 10.1094/mpmi-08-16-0160-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Root-knot nematodes damage crops around the world by developing complex feeding sites from normal root cells of their hosts. The ability to initiate and maintain this feeding site (composed of individual "giant cells") is essential to their parasitism process. RNA silencing pathways in plants serve a diverse set of functions, from directing growth and development to defending against invading pathogens. Influencing a host's RNA silencing pathways as a pathogenicity strategy has been well-documented for viral plant pathogens, but recently, it has become clear that silencing pathways also play an important role in other plant pathosystems. To determine if RNA silencing pathways play a role in nematode parasitism, we tested the susceptibility of plants that express a viral suppressor of RNA silencing. We observed an increase in susceptibility to nematode parasitism in plants expressing viral suppressors of RNA silencing. Results from studies utilizing a silenced reporter gene suggest that active suppression of RNA silencing pathways may be occurring during nematode parasitism. With these studies, we provide further evidence to the growing body of plant-biotic interaction research that suppression of RNA silencing is important in the successful interaction between a plant-parasitic animal and its host.
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Affiliation(s)
- E Walsh
- 1 Department of Plant Pathology, The Ohio State University, OARDC, Wooster, OH 44691, U.S.A.; and
| | - J M Elmore
- 2 Department of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - C G Taylor
- 1 Department of Plant Pathology, The Ohio State University, OARDC, Wooster, OH 44691, U.S.A.; and
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34
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Ruark CL, Koenning SR, Davis EL, Opperman CH, Lommel SA, Mitchum MG, Sit TL. Soybean cyst nematode culture collections and field populations from North Carolina and Missouri reveal high incidences of infection by viruses. PLoS One 2017; 12:e0171514. [PMID: 28141854 PMCID: PMC5283738 DOI: 10.1371/journal.pone.0171514] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/20/2017] [Indexed: 11/18/2022] Open
Abstract
Five viruses were previously discovered infecting soybean cyst nematodes (SCN; Heterodera glycines) from greenhouse cultures maintained in Illinois. In this study, the five viruses [ScNV, ScPV, ScRV, ScTV, and SbCNV-5] were detected within SCN greenhouse and field populations from North Carolina (NC) and Missouri (MO). The prevalence and titers of viruses in SCN from 43 greenhouse cultures and 25 field populations were analyzed using qRT-PCR. Viral titers within SCN greenhouse cultures were similar throughout juvenile development, and the presence of viral anti-genomic RNAs within egg, second-stage juvenile (J2), and pooled J3 and J4 stages suggests active viral replication within the nematode. Viruses were found at similar or lower levels within field populations of SCN compared with greenhouse cultures of North Carolina populations. Five greenhouse cultures harbored all five known viruses whereas in most populations a mixture of fewer viruses was detected. In contrast, three greenhouse cultures of similar descent to one another did not possess any detectable viruses and primarily differed in location of the cultures (NC versus MO). Several of these SCN viruses were also detected in Heterodera trifolii (clover cyst) and Heterodera schachtii (beet cyst), but not the other cyst, root-knot, or reniform nematode species tested. Viruses were not detected within soybean host plant tissue. If nematode infection with viruses is truly more common than first considered, the potential influence on nematode biology, pathogenicity, ecology, and control warrants continued investigation.
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Affiliation(s)
- Casey L. Ruark
- Department of Entomology and Plant Pathology, North Carolina State University, 2510 Thomas Hall, Raleigh, North Carolina, United States of America
| | - Stephen R. Koenning
- Department of Entomology and Plant Pathology, North Carolina State University, 2510 Thomas Hall, Raleigh, North Carolina, United States of America
| | - Eric L. Davis
- Department of Entomology and Plant Pathology, North Carolina State University, 2510 Thomas Hall, Raleigh, North Carolina, United States of America
| | - Charles H. Opperman
- Department of Entomology and Plant Pathology, North Carolina State University, 2510 Thomas Hall, Raleigh, North Carolina, United States of America
| | - Steven A. Lommel
- Department of Entomology and Plant Pathology, North Carolina State University, 2510 Thomas Hall, Raleigh, North Carolina, United States of America
| | - Melissa G. Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, 371H Bond Life Sciences Center, Columbia, Missouri, United States of America
| | - Tim L. Sit
- Department of Entomology and Plant Pathology, North Carolina State University, 2510 Thomas Hall, Raleigh, North Carolina, United States of America
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35
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Complete Genome Sequence of the Largest Known Flavi-Like Virus, Diaphorina citri flavi-like virus, a Novel Virus of the Asian Citrus Psyllid, Diaphorina citri. GENOME ANNOUNCEMENTS 2016; 4:4/5/e00946-16. [PMID: 27609921 PMCID: PMC5017226 DOI: 10.1128/genomea.00946-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A novel flavi-like virus tentatively named Diaphorina citri flavi-like virus (DcFLV) was identified in field populations of Diaphorina citri through small RNA and transcriptome sequencing followed by reverse transcription (RT)-PCR. We report here the complete nucleotide sequence and genome organization of DcFLV, the largest flavi-like virus identified to date.
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36
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Teixeira M, Sela N, Ng J, Casteel CL, Peng HC, Bekal S, Girke T, Ghanim M, Kaloshian I. A novel virus from Macrosiphum euphorbiae with similarities to members of the family Flaviviridae. J Gen Virol 2016; 97:1261-1271. [PMID: 26822322 DOI: 10.1099/jgv.0.000414] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A virus with a large genome was identified in the transcriptome of the potato aphid (Macrosiphum euphorbiae) and was named Macrosiphum euphorbiae virus 1 (MeV-1). The MeV-1 genome is 22 780 nt in size, including 3' and 5' non-coding regions, with a single large ORF encoding a putative polyprotein of 7333 aa. The C-terminal region of the predicted MeV-1 polyprotein contained sequences with similarities to helicase, methyltransferase and RNA-dependent RNA polymerase (RdRp) motifs, while the N-terminal region lacked any motifs including structural proteins. Phylogenetic analysis of the helicase placed MeV-1 close to pestiviruses, while the RdRp region placed it close to pestiviruses and flaviviruses, suggesting MeV-1 has a positive-polarity ssRNA genome and is a member of the family Flaviviridae. Since the MeV-1 genome is predicted to contain a methyltransferase, a gene present typically in flaviviruses but not pestiviruses, MeV-1 is likely a member of the genus Flavivirus. MeV-1 was present in nymphal and adult stages of the aphid, aphid saliva and plant tissues fed upon by aphids. However, the virus was unable to multiply and spread in tomato plants. In addition, dsRNA, the replication intermediate of RNA viruses, was isolated from virus-infected M. euphorbiae and not from tomato plants infested with the aphid. Furthermore, nymphs laid without exposure to infected plants harboured the virus, indicating that MeV-1 is an aphid-infecting virus likely transmitted transovarially. The virus was present in M. euphorbiae populations from Europe but not from North America and was absent in all other aphid species tested.
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Affiliation(s)
- Marcella Teixeira
- Department of Nematology,University of California, Riverside, California,USA
| | - Noa Sela
- Department of Plant Pathology and Weed Research,Volcani Center, Bet Dagan,Israel
| | - James Ng
- Plant Pathology and Microbiology,University of California, Riverside, California,USA.,Institute of Integrative Genome Biology,University of California, Riverside, California,USA
| | - Clare L Casteel
- Department of Plant Pathology,University of California, Davis, California,USA
| | - Hsuan-Chieh Peng
- Plant Pathology and Microbiology,University of California, Riverside, California,USA
| | - Sadia Bekal
- Department of Agricultural and Biological Engineering,University of Illinois, Urbana, IL,USA
| | - Thomas Girke
- Institute of Integrative Genome Biology,University of California, Riverside, California,USA.,Department of Botany and Plant Sciences,University of California, Riverside, California,USA
| | - Murad Ghanim
- Department of Entomology,Volcani Center, Bet Dagan,Israel
| | - Isgouhi Kaloshian
- Institute of Integrative Genome Biology,University of California, Riverside, California,USA.,Department of Nematology,University of California, Riverside, California,USA
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37
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Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses. J Virol 2015; 90:659-69. [PMID: 26491167 DOI: 10.1128/jvi.02036-15] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/13/2015] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED Viruses of the family Flaviviridae are important pathogens of humans and other animals and are currently classified into four genera. To better understand their diversity, evolutionary history, and genomic flexibility, we used transcriptome sequencing (RNA-seq) to search for the viruses related to the Flaviviridae in a range of potential invertebrate and vertebrate hosts. Accordingly, we recovered the full genomes of five segmented jingmenviruses and 12 distant relatives of the known Flaviviridae ("flavi-like" viruses) from a range of arthropod species. Although these viruses are highly divergent, they share a similar genomic plan and common ancestry with the Flaviviridae in the NS3 and NS5 regions. Remarkably, although these viruses fill in major gaps in the phylogenetic diversity of the Flaviviridae, genomic comparisons reveal important changes in genome structure, genome size, and replication/gene regulation strategy during evolutionary history. In addition, the wide diversity of flavi-like viruses found in invertebrates, as well as their deep phylogenetic positions, suggests that they may represent the ancestral forms from which the vertebrate-infecting viruses evolved. For the vertebrate viruses, we expanded the previously mammal-only pegivirus-hepacivirus group to include a virus from the graceful catshark (Proscyllium habereri), which in turn implies that these viruses possess a larger host range than is currently known. In sum, our data show that the Flaviviridae infect a far wider range of hosts and exhibit greater diversity in genome structure than previously anticipated. IMPORTANCE The family Flaviviridae of RNA viruses contains several notorious human pathogens, including dengue virus, West Nile virus, and hepatitis C virus. To date, however, our understanding of the biodiversity and evolution of the Flaviviridae has largely been directed toward vertebrate hosts and their blood-feeding arthropod vectors. Therefore, we investigated an expanded group of potential arthropod and vertebrate host species that have generally been ignored by surveillance programs. Remarkably, these species contained diverse flaviviruses and related viruses that are characterized by major changes in genome size and genome structure, such that these traits are more flexible than previously thought. More generally, these data suggest that arthropods may be the ultimate reservoir of the Flaviviridae and related viruses, harboring considerable genetic and phenotypic diversity. In sum, this study revises the traditional view on the evolutionary history, host range, and genomic structures of a major group of RNA viruses.
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38
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Abstract
Pestiviruses are among the economically most important pathogens of livestock. The biology of these viruses is characterized by unique and interesting features that are both crucial for their success as pathogens and challenging from a scientific point of view. Elucidation of these features at the molecular level has made striking progress during recent years. The analyses revealed that major aspects of pestivirus biology show significant similarity to the biology of human hepatitis C virus (HCV). The detailed molecular analyses conducted for pestiviruses and HCV supported and complemented each other during the last three decades resulting in elucidation of the functions of viral proteins and RNA elements in replication and virus-host interaction. For pestiviruses, the analyses also helped to shed light on the molecular basis of persistent infection, a special strategy these viruses have evolved to be maintained within their host population. The results of these investigations are summarized in this chapter.
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Affiliation(s)
- Norbert Tautz
- Institute for Virology and Cell Biology, University of Lübeck, Lübeck, Germany
| | - Birke Andrea Tews
- Institut für Immunologie, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Gregor Meyers
- Institut für Immunologie, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany.
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39
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Koonin EV, Dolja VV, Krupovic M. Origins and evolution of viruses of eukaryotes: The ultimate modularity. Virology 2015; 479-480:2-25. [PMID: 25771806 PMCID: PMC5898234 DOI: 10.1016/j.virol.2015.02.039] [Citation(s) in RCA: 321] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 02/19/2015] [Accepted: 02/20/2015] [Indexed: 01/04/2023]
Abstract
Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order "Megavirales" that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
| | - Mart Krupovic
- Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Paris 75015, France.
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Clarke BD, Roby JA, Slonchak A, Khromykh AA. Functional non-coding RNAs derived from the flavivirus 3' untranslated region. Virus Res 2015; 206:53-61. [PMID: 25660582 DOI: 10.1016/j.virusres.2015.01.026] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/28/2015] [Accepted: 01/29/2015] [Indexed: 12/25/2022]
Abstract
Flaviviruses are single-stranded positive sense RNA enveloped viruses. The flavivirus genus includes important human pathogens such as dengue virus (DENV), West Nile virus (WNV), yellow fever virus (YFV), Japanese encephalitis virus (JEV), tick-borne encephalitis virus (TBEV), and Murray Valley encephalitis virus (MVEV). In addition to the viral proteins and viral genomic RNA, flaviviruses produce at least two functional non-coding RNAs derived from the 3' untranslated region (3'UTR), the subgenomic flavivirus RNA (sfRNA) and a putative WNV miRNA (KUN-miR-1). In this review we summarize published data from studies with WNV, YFV, DENV, JEV, and MVEV on sfRNA production following incomplete degradation of the viral genomic RNA by the cellular 5'-3' exoribonuclease 1 (XRN1), RNA structural elements involved in stalling XRN1 to generate sfRNA, and functions of sfRNA in modulating cellular mRNA decay and RNAi pathways as well as in modulating anti-viral type I interferon response. In addition, we also summarize data on the mechanisms of biogenesis of 3'UTR-derived KUN-miR-1 and its function in WNV replication in mosquito host, along with recent findings on a discovery of a second potential flaviviral miRNA vsRNA5, derived from the 3'UTR of DENV. This review thus summarizes the known mechanisms of generation and the functions of flaviviral 3'UTR-derived non-coding RNAs.
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Affiliation(s)
- B D Clarke
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - J A Roby
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - A Slonchak
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - A A Khromykh
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia.
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