scholarly journals Two Novel Negative-Sense RNA Viruses Infecting Grapevine Are Members of a Newly Proposed Genus within the Family Phenuiviridae

Viruses ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 685 ◽  
Author(s):  
Alfredo Diaz-Lara ◽  
Beatriz Navarro ◽  
Francesco Di Serio ◽  
Kristian Stevens ◽  
Min Sook Hwang ◽  
...  
Keyword(s):  
Nucleocapsid Protein ◽  
High Throughput Sequencing ◽  
Movement Protein ◽  
Rna Viruses ◽  
Rt Pcr ◽  
Rna Dependent Rna Polymerase ◽  
Sequence Identity ◽  
The Family ◽  
Putative Movement Protein ◽  
Negative Sense

Two novel negative-stranded (ns)RNA viruses were identified by high throughput sequencing in grapevine. The genomes of both viruses, named grapevine Muscat rose virus (GMRV) and grapevine Garan dmak virus (GGDV), comprise three segments with each containing a unique gene. Based on sequence identity and presence of typical domains/motifs, the proteins encoded by the two viruses were predicted to be: RNA-dependent RNA polymerase (RdRp), nucleocapsid protein (NP), and putative movement protein (MP). These proteins showed the highest identities with orthologs in the recently discovered apple rubbery wood viruses 1 and 2, members of a tentative genus (Rubodvirus) within the family Phenuiviridae. The three segments of GMRV and GGDV share almost identical sequences at their 5′ and 3′ termini, which are also complementary to each other and may form a panhandle structure. Phylogenetics based on RdRp, NP and MP placed GMRV and GGDV in the same cluster with rubodviruses. Grapevine collections were screened for the presence of both novel viruses via RT-PCR, identifying infected plants. GMRV and GGDV were successfully graft-transmitted, thus, they are the first nsRNA viruses identified and transmitted in grapevine. Lastly, different evolutionary scenarios of nsRNA viruses are discussed.

scholarly journals Reassortment of Genome Segments Creates Stable Lineages Among Strains of Orchid Fleck Virus Infecting Citrus in Mexico

2020 ◽  
Vol 110 (1) ◽  
pp. 106-120 ◽  
Author(s):  
Avijit Roy ◽  
Andrew L. Stone ◽  
Gabriel Otero-Colina ◽  
Gang Wei ◽  
Ronald H. Brlansky ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sensu Stricto ◽  
Genome Segment ◽  
Rt Pcr ◽  
Sequence Comparisons ◽  
Orchid Fleck Virus ◽  
Reverse Transcription Pcr ◽  
Sequencing Technologies ◽  
Negative Sense

The genus Dichorhavirus contains viruses with bipartite, negative-sense, single-stranded RNA genomes that are transmitted by flat mites to hosts that include orchids, coffee, the genus Clerodendrum, and citrus. A dichorhavirus infecting citrus in Mexico is classified as a citrus strain of orchid fleck virus (OFV-Cit). We previously used RNA sequencing technologies on OFV-Cit samples from Mexico to develop an OFV-Cit–specific reverse transcription PCR (RT-PCR) assay. During assay validation, OFV-Cit–specific RT-PCR failed to produce an amplicon from some samples with clear symptoms of OFV-Cit. Characterization of this virus revealed that dichorhavirus-like particles were found in the nucleus. High-throughput sequencing of small RNAs from these citrus plants revealed a novel citrus strain of OFV, OFV-Cit2. Sequence comparisons with known orchid and citrus strains of OFV showed variation in the protein products encoded by genome segment 1 (RNA1). Strains of OFV clustered together based on host of origin, whether orchid or citrus, and were clearly separated from other dichorhaviruses described from infected citrus in Brazil. The variation in RNA1 between the original (now OFV-Cit1) and the new (OFV-Cit2) strain was not observed with genome segment 2 (RNA2), but instead, a common RNA2 molecule was shared among strains of OFV-Cit1 and -Cit2, a situation strikingly similar to OFV infecting orchids. We also collected mites at the affected groves, identified them as Brevipalpus californicus sensu stricto, and confirmed that they were infected by OFV-Cit1 or with both OFV-Cit1 and -Cit2. OFV-Cit1 and -Cit2 have coexisted at the same site in Toliman, Queretaro, Mexico since 2012. OFV strain-specific diagnostic tests were developed.

scholarly journals Trimeric Hantavirus Nucleocapsid Protein Binds Specifically to the Viral RNA Panhandle

2004 ◽  
Vol 78 (15) ◽  
pp. 8281-8288 ◽  
Author(s):  
M. A. Mir ◽  
A. T. Panganiban
Keyword(s):  
Nucleocapsid Protein ◽  
Rna Binding ◽  
Rna Viruses ◽  
Sin Nombre Virus ◽  
Viral Capsid ◽  
Genomic Rna ◽  
Rna Molecules ◽  
N Protein ◽  
High Affinity ◽  
Negative Sense

ABSTRACT Hantaviruses are tripartite negative-sense RNA viruses and members of the Bunyaviridae family. The nucleocapsid (N) protein is encoded by the smallest of the three genome segments (S). N protein is the principal structural component of the viral capsid and is central to the hantavirus replication cycle. We examined intermolecular N-protein interaction and RNA binding by using bacterially expressed Sin Nombre virus N protein. N assembles into di- and trimeric forms. The mono- and dimeric forms exist transiently and assemble into a trimeric form. In contrast, the trimer is highly stable and does not efficiently disassemble into the mono- and dimeric forms. The purified N-protein trimer is able to discriminate between viral and nonviral RNA molecules and, interestingly, recognizes and binds with high affinity the panhandle structure composed of the 3′ and 5′ ends of the genomic RNA. In contrast, the mono- and dimeric forms of N bind RNA to form a complex that is semispecific and salt sensitive. We suggest that trimerization of N protein is a molecular switch to generate a protein complex that can discriminate between viral and nonviral RNA molecules during the early steps of the encapsidation process.

scholarly journals A Plum Marbling Conundrum: Identification of a New Viroid Associated with Marbling and Corky Flesh in Japanese Plums

2020 ◽  
Vol 110 (8) ◽  
pp. 1476-1482
Author(s):  
Rachelle Bester ◽  
Sophia S. Malan ◽  
Hans J Maree
Keyword(s):  
High Throughput Sequencing ◽  
Fruit Size ◽  
Circular Rna ◽  
Structural Features ◽  
Fruit Tree ◽  
Rt Pcr ◽  
Field Surveys ◽  
Sequence Identity ◽  
The Past ◽  
Fruit Skin

Over the past 2 decades, fruit symptoms resembling a marbling pattern on the fruit skin or corking of the fruit flesh were observed on Japanese plums in South Africa, resulting in unmarketable fruit. The ability of high-throughput sequencing (HTS) to detect known and unknown pathogens was exploited by assaying affected and unaffected fruit tree accessions to identify the potential aetiological agent of marbling and/or corky flesh disease. In this study, it is shown that the disease is associated with a previously undescribed small RNA with typical viroid structural features. The potential viroid was the only pathological agent consistently detected in all symptomatic trees by HTS, and the association with the symptoms was confirmed in field surveys over two seasons. To date, this RNA was not detectable by RT-PCR in seedlings raised from seeds collected from infected trees. Although the autonomous replication of this viroid-like RNA was not proven, it was shown to be transmissible by grafting and associated with a range of symptoms that include marbling on the fruit skin, corky flesh, reduced fruit size, irregular shape, and uneven fruit surface depending on the cultivar. Moreover, the circular RNA genome, consisting of 317 nucleotides, strongly supports that this viroid-like RNA is most likely a viroid for which the name plum viroid I (PVd-I) is proposed. The primary structure of this viroid showed a less than 90% nucleotide sequence identity to viroids of the genus Apscaviroid, with which it has close phylogenetic relationships and shares conserved structural motifs.

scholarly journals Rice Stripe Tenuivirus Has a Greater Tendency To Use the Prime-and-Realign Mechanism in Transcription of Genomic than in Transcription of Antigenomic Template RNAs

2017 ◽  
Vol 92 (1) ◽  
Author(s):  
Xiaojuan Liu ◽  
Jing Jin ◽  
Ping Qiu ◽  
Fangluan Gao ◽  
Wenzhong Lin ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Rna Viruses ◽  
Viral Mrnas ◽  
Viral Pathogens ◽  
Promising Target ◽  
Cellular Mrnas ◽  
Sequencing Strategy ◽  
First Time ◽  
Negative Sense

ABSTRACTMost segmented negative-sense RNA viruses employ a process termed cap snatching, during which they snatch capped RNA leaders from host cellular mRNAs and use the snatched leaders as primers for transcription, leading to the synthesis of viral mRNAs with 5′ heterogeneous sequences (HSs). With traditional methods, only a few HSs can be determined, and identification of their donors is difficult. Here, the mRNA 5′ ends ofRice stripe tenuivirus(RSV) andRice grassy stunt tenuivirus(RGSV) and those of their host rice were determined by high-throughput sequencing. Millions of tenuiviral HSs were obtained, and a large number of them mapped to the 5′ ends of corresponding host cellular mRNAs. Repeats of the dinucleotide AC, which are complementary to the U1G2of the tenuiviral template 3′-U1G2U3G4UUUCG, were found to be prevalent at the 3′ termini of tenuiviral HSs. Most of these ACs did not match host cellular mRNAs, supporting the idea that tenuiviruses use the prime-and-realign mechanism during cap snatching. We previously reported a greater tendency of RSV than RGSV to use the prime-and-realign mechanism in transcription with leaders cap snatched from a coinfecting reovirus. Besides confirming this observation in natural tenuiviral infections, the data here additionally reveal that RSV has a greater tendency to use this mechanism in transcribing genomic than in transcribing antigenomic templates. The data also suggest that tenuiviruses cap snatch host cellular mRNAs from translation- and photosynthesis-related genes, and capped RNA leaders snatched by tenuiviruses base pair with U1/U3or G2/G4of viral templates. These results provide unprecedented insights into the cap-snatching process of tenuiviruses.IMPORTANCEMany segmented negative-sense RNA viruses (segmented NSVs) are medically or agriculturally important pathogens. The cap-snatching process is a promising target for the development of antiviral strategies against this group of viruses. However, many details of this process remain poorly characterized. Tenuiviruses constitute a genus of agriculturally important segmented NSVs, several members of which are major viral pathogens of rice. Here, we for the first time adopted a high-throughput sequencing strategy to determine the 5′ heterogeneous sequences (HSs) of tenuiviruses and mapped them to host cellular mRNAs. Besides providing deep insights into the cap snatching of tenuiviruses, the data obtained provide clear evidence to support several previously proposed models regarding cap snatching. Curiously and importantly, the data here reveal that not only different tenuiviruses but also the same tenuivirus synthesizing different mRNAs use the prime-and-realign mechanism with different tendencies during their cap snatching.

Electron microscopy of frozen, hydrated lacrosse virus

1986 ◽  
Vol 44 ◽  
pp. 104-105
Author(s):  
Y. Talmon ◽  
B. V. V. Prasad ◽  
J. P. M. Clerx ◽  
W. Chiu ◽  
M. J. Hewlett
Keyword(s):  
Electron Microscopy ◽  
Ionic Strength ◽  
Nucleocapsid Protein ◽  
Rna Viruses ◽  
High Sensitivity ◽  
Bilayer Membrane ◽  
Viral Rna ◽  
California Serogroup ◽  
Viral Nucleocapsid ◽  
Negative Sense

LaCrosse (LAC) virus is a member of the California serogroup of the Bunyaviridae. The bunyaviruses are all negative-sense, RNA viruses whose genome consists of three segments of single stranded RNA. LAC virions are composed of multiple viral RNA strands complexed with viral nucleocapsid protein surrounded by a bilayer membrane embedded with 2 glycoproteins.Staining and drying of LAC virus samples produce images in which the virions are collapsed and distorted (Figure 1). Fixation prior to staining, also gives disappointing results, probably due to the high sensitivity of the LAC virus to changes in the ionic strength and composition of the solution in which it is suspended.

Bunyaviridae

2020 ◽  
pp. 852-862
Author(s):  
James W. Le Duc ◽  
D.A. Bente
Keyword(s):  
Small Mammal ◽  
Rna Viruses ◽  
Seasonal Distribution ◽  
Transovarial Transmission ◽  
Human Pathogens ◽  
The Family ◽  
The World ◽  
Vertebrate Hosts ◽  
Adverse Environmental Conditions ◽  
Negative Sense

Viruses of the family Bunyaviridae are the largest family of RNA viruses with more than 350 named isolated. They contain a three-segmented, single-stranded, negative-sense RNA genome. They are divided into five genera, of which four are known to include human pathogens—Orthobunyavirus, Phlebovirus, Hantavirus, and Nairovirus. These viruses are found throughout the world and are transmitted between vertebrate hosts and to humans through the bite of infected arthropod vectors (mosquitoes, ticks, others), or from infectious excreta of rodents and other small mammals, and rarely person to person. Many are transmitted from infected arthropod vector females to the next generation by transovarial transmission, thereby surviving adverse environmental conditions and leading to marked seasonal distribution of disease. There are few vaccines or drugs available to protect against infection. Prevention is by avoidance of exposure to potentially infected arthropod and small mammal vectors.

scholarly journals Armillaria root rot fungi host single-stranded RNA viruses

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Riikka Linnakoski ◽  
Suvi Sutela ◽  
Martin P. A. Coetzee ◽  
Tuan A. Duong ◽  
Igor N. Pavlov ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Rna Viruses ◽  
Virus Infections ◽  
New Members ◽  
Armillaria Root Rot ◽  
Host Growth ◽  
Dsrna Viruses ◽  
Ornamental Trees ◽  
Vegetative Spread ◽  
Negative Sense

AbstractSpecies of Armillaria are distributed globally and include some of the most important pathogens of forest and ornamental trees. Some of them form large long-living clones that are considered as one of the largest organisms on earth and are capable of long-range spore-mediated transfer as well as vegetative spread by drought-resistant hyphal cords called rhizomorphs. However, the virus community infecting these species has remained unknown. In this study we used dsRNA screening and high-throughput sequencing to search for possible virus infections in a collection of Armillaria isolates representing three different species: Armillaria mellea from South Africa, A. borealis from Finland and Russia (Siberia) and A. cepistipes from Finland. Our analysis revealed the presence of both negative-sense RNA viruses and positive-sense RNA viruses, while no dsRNA viruses were detected. The viruses included putative new members of virus families Mymonaviridae, Botourmiaviridae and Virgaviridae and members of a recently discovered virus group tentatively named “ambiviruses” with ambisense bicistronic genomic organization. We demonstrated that Armillaria isolates can be cured of viruses by thermal treatment, which enables the examination of virus effects on host growth and phenotype using isogenic virus-infected and virus-free strains.

scholarly journals Novel picornavirus (family Picornaviridae) from freshwater fishes (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) in Hungary

2021 ◽  
Author(s):  
Renáta Hargitai ◽  
Péter Pankovics ◽  
Ákos Boros ◽  
Róbert Mátics ◽  
Eda Altan ◽  
...  
Keyword(s):  
Amino Acid Sequence Identity ◽  
Perca Fluviatilis ◽  
Viral Metagenomics ◽  
Rt Pcr ◽  
Sander Lucioperca ◽  
Sequence Identity ◽  
Faecal Samples ◽  
The Family ◽  
Unassigned Genus ◽  
Ameiurus Melas

AbstractIn this study, a novel picornavirus (perchPV/M9/2015/HUN, GenBank accession no. MW590713) was detected in eight (12.9%) out of 62 faecal samples collected from three (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) out of 13 freshwater fish species tested and genetically characterized using viral metagenomics and RT-PCR methods. The complete genome of perchPV/M9/2015/HUN is 7,741 nt long, excluding the poly(A) tail, and has the genome organization 5’UTRIRES-?/P1(VP0-VP3-VP1)/P2(2A1NPG↓P-2A2H-box/NC-2B-2C)/P3(3A-3BVPg-3CPro-3DPol)/3’UTR-poly(A). The P1, 2C, and 3CD proteins had 41.4%, 38.1%, and 47.3% amino acid sequence identity to the corresponding proteins of Wenling lepidotrigla picornavirus (MG600079), eel picornavirus (NC_022332), and Wenling pleuronectiformes picornavirus (MG600098), respectively, as the closest relatives in the genus Potamipivirus. PerchPV/M9/2015/HUN represents a potential novel fish-origin species in an unassigned genus in the family Picornaviridae.

scholarly journals Prevalence and Detection of Flaviviruses Occurring in Slovakia

2017 ◽  
Vol 61 (3) ◽  
pp. 5-11 ◽  
Author(s):  
Z. Mojžišová ◽  
P. Drzewnioková ◽  
E. Bocková ◽  
B. Vargová ◽  
V. Majláthová ◽  
...  
Keyword(s):  
Rt Pcr ◽  
Chain Reaction ◽  
Rna Dependent Rna Polymerase ◽  
Tick Borne Encephalitis ◽  
The Family ◽  
Polymerase Chain ◽  
General Signs ◽  
Tick Borne Encephalitis Virus ◽  
The Village ◽  
Pooled Samples

AbstractThe tick-borne encephalitis virus (TBEV) and West Nile virus (WNV) are arboviruses of the genusFlavivirusin the familyFlaviviridae. Their hosts are vertebratesof which rodents are the reservoirs of TBEV and birds are the reservoirs of WNV. Both viruses are transmitted from reservoirs to mammals by vectors. TBEV is transmitted by ticks (mostlyIxodesspp.) and WNV by mosquitoes (mostlyCulexspp.). Both viruses are capable of infecting mammals, including man. TBEV and WNV are neurotropic, however infection is, in most cases, subclinical or accompanied by only moderate general signs. However, in some cases they can cause serious disturbances of the CNS. Our study focused on the detection of the genomes of TBEV and WNV in vectors by means of the reverse-transcription polymerase chain reaction (RT-PCR). The flavivirus genome was detected by means of oligonucleotides delineating the sequence in NS5 gene that encodes viral RNA-dependent RNA-polymerase. For the detection of TBEV, we used the oligonucleotide pair detecting the structural envelope protein. The positive samples were subjected to the sequence and phylogenetic analysis. The WNV was not detected in any of the pooled samples prepared from 616 mosquitoes captured in the vicinity of the village Drienovec, district Košice-surroundings. The investigation of 676 ticks demonstrated the presence of one strain of TBEV. One blood-fedI. ricinusfemale was obtained from a goat grazing in a pasture in the Dúbrava area close to Prešov. The genetic analysis revealed the presence of a strain close to the endemic strainsof TBEV Hypr and Neudörfl. The results of our study can become a motivation for additional studies in model locations oriented on ecology and circulation of these important zoonotic flaviviruses.

scholarly journals The family Rhabdoviridae: mono- and bipartite negative-sense RNA viruses with diverse genome organization and common evolutionary origins

2017 ◽  
Vol 227 ◽  
pp. 158-170 ◽  
Author(s):  
Ralf G. Dietzgen ◽  
Hideki Kondo ◽  
Michael M. Goodin ◽  
Gael Kurath ◽  
Nikos Vasilakis
Keyword(s):  
Genome Organization ◽  
Rna Viruses ◽  
Evolutionary Origins ◽  
The Family ◽  
Negative Sense ◽  
Family Rhabdoviridae
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