scholarly journals Characterization of Ti Ringspot-Associated Virus, a Novel Emaravirus Associated with an Emerging Ringspot Disease of Cordyline fruticosa

Plant Disease ◽  
2019 ◽  
Vol 103 (9) ◽  
pp. 2345-2352 ◽  
Author(s):  
Alejandro Olmedo-Velarde ◽  
Adam C. Park ◽  
Jari Sugano ◽  
Janice Y. Uchida ◽  
Michael Kawate ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
High Plains ◽  
Virus Species ◽  
Sequence Analyses ◽  
Sequence Identity ◽  
Reverse Transcription Pcr ◽  
Eriophyid Mites ◽  
Cordyline Fruticosa ◽  
Novel Virus

Ti ringspot is an emerging foliar disease of the ti plant (Cordyline fruticosa) in Hawaii that is quickly spreading throughout the islands. Symptoms include small chlorotic ringspots on leaves that often coalesce to form larger lesions. Although several virus species have been discovered in symptomatic plants, none have been associated with these symptoms. Here, we report and characterize a novel virus closely associated with ti ringspot symptoms in Hawaii. The presence of double membrane bodies approximately 85 nm in diameter in symptomatic cells and sequence analyses of five genomic RNA segments obtained by high-throughput sequencing indicate that this virus is most closely related to members of the plant virus genus Emaravirus. Phylogenetic and sequence homology analyses place this virus on a distinct clade within the Emaravirus genus along with High Plains wheat mosaic emaravirus, blue palo verde broom virus, and Raspberry leaf blotch emaravirus. Sequence identity values with taxonomically relevant proteins indicate that this represents a new virus species, which we are tentatively naming ti ringspot-associated virus (TiRSaV). TiRSaV-specific reverse transcription PCR assays detected the virus in several experimental herbaceous host species following mechanical inoculation. TiRSaV was also detected in eriophyid mites collected from symptomatic ti plants, which may represent a putative arthropod vector of the virus.

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 Discovery and Survey of a New Mandarivirus Associated with Leaf Yellow Mottle Disease of Citrus in Pakistan

Plant Disease ◽  
2020 ◽  
Vol 104 (6) ◽  
pp. 1593-1600 ◽  
Author(s):  
Jiaxing Wu ◽  
Song Zhang ◽  
Sagheer Atta ◽  
Caixia Yang ◽  
Yan Zhou ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Biological Data ◽  
High Sequence Identity ◽  
Reverse Transcription Pcr ◽  
Punjab Province ◽  
Transmission Electron ◽  
Genome Features ◽  
Yellow Mottle ◽  
Novel Virus ◽  
Citrus Trees

During biological indexing for viruses in citrus trees, in a collection of Symons sweet orange (SSO) (Citrus sinensis L. Osbeck) graft inoculated with bark tissues of citrus trees from the Punjab Province in Pakistan, several SSO trees exhibited leaf symptoms of vein yellowing and mottle. High-throughput sequencing by Illumina of RNA preparation depleted of ribosomal RNAs from one symptomatic tree, followed by BLAST analyses, allowed identification of a novel virus, tentatively named citrus yellow mottle-associated virus (CiYMaV). Genome features of CiYMaV are typical of members of the genus Mandarivirus (family Alphaflexiviridae). Virus particles with elongated flexuous shape and size resembling those of mandariviruses were observed by transmission electron microscopy. The proteins encoded by CiYMaV share high sequence identity, conserved motifs, and phylogenetic relationships with the corresponding proteins encoded by Indian citrus ringspot virus (ICRSV) and citrus yellow vein clearing virus (CYVCV), the two current members of the genus Mandarivirus. Although CYVCV is the virus most closely related to CiYMaV, the two viruses can be serologically and biologically discriminated from each other. A reverse-transcription PCR method designed to specifically detect CiYMaV revealed high prevalence (62%) of this virus in 120 citrus trees from the Punjab Province, Pakistan, where the novel virus was found mainly in mixed infection with CYVCV and citrus tristeza virus. However, a preliminary survey on samples from 200 citrus trees from the Yunnan Province, China failed to detect CiYMaV in this region, suggesting that the molecular, serological, and biological data provided here are timely and can help to prevent the spread of this virus in citrus-producing countries.

scholarly journals Discovery and Characterization of Bukakata orbivirus (Reoviridae:Orbivirus), a Novel Virus from a Ugandan Bat

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 209 ◽  
Author(s):  
Anna Fagre ◽  
Justin Lee ◽  
Robert Kityo ◽  
Nicholas Bergren ◽  
Eric Mossel ◽  
...  
Keyword(s):  
Virus Species ◽  
Preliminary Screening ◽  
Fruit Bat ◽  
In Vitro Characterization ◽  
Archived Samples ◽  
Additional Testing ◽  
Novel Virus ◽  
Ongoing Surveillance

While serological and virological evidence documents the exposure of bats to medically-important arboviruses, their role as reservoirs or amplifying hosts is less well-characterized. We describe a novel orbivirus (Reoviridae:Orbivirus) isolated from an Egyptian fruit bat (Rousettus aegyptiacus leachii) trapped in 2013 in Uganda and named Bukakata orbivirus. This is the fifth orbivirus isolated from a bat, however genetic information had previously only been available for one bat-associated orbivirus. We performed whole-genome sequencing on Bukakata orbivirus and three other bat-associated orbiviruses (Fomede, Ife, and Japanaut) to assess their phylogenetic relationship within the genus Orbivirus and develop hypotheses regarding potential arthropod vectors. Replication kinetics were assessed for Bukakata orbivirus in three different vertebrate cell lines. Lastly, qRT-PCR and nested PCR were used to determine the prevalence of Bukakata orbivirus RNA in archived samples from three populations of Egyptian fruit bats and one population of cave-associated soft ticks in Uganda. Complete coding sequences were obtained for all ten segments of Fomede, Ife, and Japanaut orbiviruses and for nine of the ten segments for Bukakata orbivirus. Phylogenetic analysis placed Bukakata and Fomede in the tick-borne orbivirus clade and Ife and Japanaut within the Culicoides/phlebotomine sandfly orbivirus clade. Further, Bukakata and Fomede appear to be serotypes of the Chobar Gorge virus species. Bukakata orbivirus replicated to high titers (106–107 PFU/mL) in Vero, BHK-21 [C-13], and R06E (Egyptian fruit bat) cells. Preliminary screening of archived bat and tick samples do not support Bukakata orbivirus presence in these collections, however additional testing is warranted given the phylogenetic associations observed. This study provided complete coding sequence for several bat-associated orbiviruses and in vitro characterization of a bat-associated orbivirus. Our results indicate that bats may play an important role in the epidemiology of viruses in the genus Orbivirus and further investigation is warranted into vector-host associations and ongoing surveillance efforts.

scholarly journals A novel emaravirus comprising five RNA segments is associated with ringspot disease in oak

2021 ◽  
Vol 166 (3) ◽  
pp. 987-990
Author(s):  
Marius Rehanek ◽  
Susanne von Bargen ◽  
Martina Bandte ◽  
David G. Karlin ◽  
Carmen Büttner
Keyword(s):  
High Throughput Sequencing ◽  
Bioinformatic Analysis ◽  
High Plains ◽  
Rt Pcr ◽  
Viral Origin ◽  
Complete Sequences ◽  
Novel Virus ◽  
Rapid Amplification ◽  
Full Length Genome ◽  
Common Oak

AbstractWe report the complete nucleotide sequence of the genome of a novel virus in ringspot-diseased common oak (Quercus robur L.). The newly identified pathogen is associated with leaf symptoms such as mottle, chlorotic spots and ringspots on diseased trees. High-throughput sequencing (HTS, Illumina RNASeq) was used to explore the virome of a ringspot-diseased oak that had chlorotic ringspots of suspected viral origin on leaves for several years. Bioinformatic analysis of the HTS dataset followed by RT-PCR enabled us to determine complete sequences of four RNA genome segments of a novel virus. These sequences showed high similarity to members of the genus Emaravirus, which includes segmented negative-stranded RNA viruses of economic importance. To verify the ends of each RNA, we conducted rapid amplification of cDNA ends (RACE). We identified an additional genome segment (RNA 5) by RT-PCR using a genus-specific primer (PDAP213) to the conserved 3´ and 5´termini in order to amplify full-length genome segments. RNA 5 encodes a 21-kDa protein that is homologous to the silencing suppressor P8 of High Plains wheat mosaic virus. The five viral RNAs were consistently detected by RT-PCR in ringspot-diseased oaks in Germany, Sweden, and Norway. We conclude that the virus represents a new member of the genus Emaravirus affecting oaks in Germany and in Scandinavia, and we propose the name “common oak ringspot-associated emaravirus” (CORaV).

scholarly journals Grapevine virus L: a Novel Vitivirus in Grapevine

2018 ◽  
Author(s):  
Humberto Debat ◽  
Diego Zavallo ◽  
Reid Soltero Brisbane ◽  
Darko Vončina ◽  
Rodrigo P.P. Almeida ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Phylogenetic Analyses ◽  
Protein A ◽  
Virus Species ◽  
Nucleic Acid Binding ◽  
Grapevine Virus ◽  
Rnaseq Data ◽  
Virus Sequence ◽  
Novel Virus

AbstractVitivirus are ssRNA(+) viruses in the family Betaflexiviridae (subfamily Trivirinae). There are currently ten ICTV recognized virus species in the genus; nevertheless, the extended use of NGS technologies is rapidly expanding their diversity and six more have been proposed recently. Here, we present the characterization of a novel virus from grapevines, which fits the genomic architecture and evolutionary constraints to be classifiable within the Vitivirus genus. The detected virus sequence is 7,607 nt long, including a typical genome organization of ORFs encoding a replicase (RP), a 22 kDa protein, a movement protein, a coat protein (CP) and a nucleic acid binding protein. Here, we present the characterization of a novel virus from grapevines. Phylogenetic analyses based on the predicted RP and CP protein unequivocally places the new virus within the Vitivirus genus. Multiple independent RNAseq data confirmed the presence of the detected virus in berries at diverse developmental stages. Additionally, we detected, confirmed, and assembled virus sequences from grapevine samples of distinct cultivars from America, Europe, Asia and Oceania, sharing 74.9%-97.9% nt identity, suggesting that the identified virus is widely distributed and diverse. We propose the name grapevine virus L (GVL) to the detected Vitivirus.

scholarly journals Characterization of Baculovirus Repeated Open Reading Frames (bro) in Bombyx moriNucleopolyhedrovirus

1999 ◽  
Vol 73 (12) ◽  
pp. 10339-10345 ◽  
Author(s):  
Wonkyung Kang ◽  
Masataka Suzuki ◽  
Evgueni Zemskov ◽  
Keiju Okano ◽  
Susumu Maeda
Keyword(s):  
Immunohistochemical Analysis ◽  
Immunoblot Analysis ◽  
Open Reading Frames ◽  
Start Codon ◽  
Sequence Analyses ◽  
Reverse Transcription Pcr ◽  
Double Deletion ◽  
Viral Factor ◽  
Reading Frames

ABSTRACT The baculovirus Bombyx mori nucleopolyhedrovirus (BmNPV) contains five related open reading frames (ORFs). Recent sequence analyses of several other baculovirus genomes reveal that these ORFs belong to a unique multigene family called the baculovirus repeated ORFs (bro) family. Here we have characterized these five genes from BmNPV at the transcriptional and translational levels. Reverse transcription-PCR and primer extension analyses indicated that transcription of all bro genes occurs by 2 to 4 h postinfection (p.i.) and reaches maximal levels between at 8 and 12 h p.i. Transcription of all genes is initiated between 50 and 70 nucleotides upstream of the start codon, at a characteristic C(T)AGT motif. Expression of a cat reporter gene under the control of each bro promoter provides evidence that a viral factor(s) is required for the transcription of all brogenes. Immunoblot analysis indicated that a population of BRO proteins is produced vigorously between at 8 and 14 h p.i. Immunohistochemical analysis by confocal microscopy showed that BRO proteins are localized in both the nucleus and the cytoplasm at 8 h p.i. Four BmNPV mutants, in which the bro-a,bro-b, bro-c, and bro-e genes were individually inactivated, were successfully isolated. However, exhaustive efforts failed to isolate a bro-d-deficient mutant. Similarly, it was not possible to isolate a double-deletionbro-a bro-c mutant. The bro-d gene may play an irreplaceable functional role(s) during viral infection, whilebro-a and bro-c may functionally complement each other.

scholarly journals Full genome characterization of Laem Singh virus (LSNV) in shrimp Penaeus monodon

2020 ◽  
Author(s):  
Suparat Taengchaiyaphum ◽  
Jiraporn Srisala ◽  
Piyachat Sanguanrut ◽  
Chalermporn Ongvarrasopone ◽  
Timothy W. Flegel ◽  
...  
Keyword(s):  
Penaeus Monodon ◽  
Plant Viruses ◽  
Virus Species ◽  
Full Genome ◽  
Cloning And Sequencing ◽  
Genome Characterization ◽  
Sequence Identity ◽  
The Family ◽  
Shrimp Virus

ABSTRACTLaem Singh virus (LSNV) was discovered in 2006 and proposed as a necessary but insufficient cause of retarded growth in the giant tiger shrimp Penaeus monodon. Its closest relatives were plant viruses including an unassigned Sobemovirus and viruses in the family Luteoviridae. During succeeding years, attempts to obtain the full LSNV genome sequence by genome walking failed. However, recent publication of the full sequence of Wenzhou shrimp virus 9 (WZSV 9) at GenBank revealed that LSNV sequences in our database shared 99% sequence identity with it. Thus, we hypothesized that LSNV and WZSV 9 were different isolates of the same virus species. Here we confirm that hypothesis by cloning and sequencing of the full genome of LSNV from P. monodon and by showing that it consists of two fragments each with 99% identity to the matching fragments of WZSV.

scholarly journals Discovery of Viruses and Virus-Like Pathogens in Pistachio using High-Throughput Sequencing

Plant Disease ◽  
2018 ◽  
Vol 102 (7) ◽  
pp. 1419-1425 ◽  
Author(s):  
Maher Al Rwahnih ◽  
Adib Rowhani ◽  
Nathaniel Westrick ◽  
Kristian Stevens ◽  
Alfredo Diaz-Lara ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Amino Acid Sequence Identity ◽  
Sequence Similarity ◽  
Sequence Information ◽  
Virus Species ◽  
Significant Sequence Similarity ◽  
Novel Virus ◽  
Polymerase Chain ◽  
Multiple Samples

Pistachio (Pistacia vera L.) trees from the National Clonal Germplasm Repository (NCGR) and orchards in California were surveyed for viruses and virus-like agents by high-throughput sequencing (HTS). Analyses of sequence information from 60 trees identified a novel virus, provisionally named “Pistachio ampelovirus A” (PAVA), in the NCGR that showed low amino acid sequence identity (approximately 42%) compared with members of the genus Ampelovirus (family Closteroviridae). A putative viroid, provisionally named “Citrus bark cracking viroid-pistachio” (CBCVd-pis), was also found in the NCGR and showed approximately 87% similarity to Citrus bark cracking viroid (CBCVd, genus Cocadviroid, family Pospiviroidae). Both PAVA and CBCVd-pis were graft transmissible to healthy UCB-1 hybrid rootstock seedlings (P. atlantica × P. integerrima). A field survey of 123 trees from commercial orchards found no incidence of PAVA but five (4%) samples were infected with CBCVd-pis. Of 675 NCGR trees, 16 (2.3%) were positive for PAVA and 172 (25.4%) were positive for CBCVd-pis by reverse-transcription polymerase chain reaction. Additionally, several contigs across multiple samples exhibited significant sequence similarity to a number of other plant virus species in different families. These findings require further study and confirmation. This study establishes the occurrence of viral and viroid populations infecting pistachio trees.

scholarly journals Molecular Characterization of Bovine Enteric Caliciviruses: a Distinct Third Genogroup of Noroviruses (Norwalk-Like Viruses) Unlikely To Be of Risk to Humans

2003 ◽  
Vol 77 (4) ◽  
pp. 2789-2798 ◽  
Author(s):  
S. L. Oliver ◽  
A. M. Dastjerdi ◽  
S. Wong ◽  
L. El-Attar ◽  
C. Gallimore ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Orf3 Gene ◽  
Sequence Analyses ◽  
Animal Reservoir ◽  
Reading Frame ◽  
Reverse Transcription Pcr ◽  
The United Kingdom ◽  
Enteric Caliciviruses ◽  
Relationship Of

ABSTRACT Bovine enteric caliciviruses (BoCVs) have been classified in the Norovirus (Norwalk-like virus) genus of the Caliciviridae, raising questions about zoonotic transmission and an animal reservoir for the human Norwalk-like viruses (NLVs), an important cause of nonbacterial gastroenteritis in humans. We examined the genetic relationship of human NLVs to BoCVs that were identified by using reverse transcription-PCR with primer pairs originally designed to detect human NLVs. Polymerase, capsid, and open reading frame 3 (ORF3) gene sequence analyses of BoCVs that were identified from 1976 to 2000 from throughout the United Kingdom showed that BoCVs formed a distinct third genogroup of closely related viruses distinct from the human genogroup I and II NLVs. Evidence was not obtained to support the concept that BoCVs are circulating in humans and pose a threat to human health.

scholarly journals Graft-transmissible diseases of Ribes – pathogens, impact and control

Plant Disease ◽  
2020 ◽  
Author(s):  
Josef Spak ◽  
Igor Koloniuk ◽  
Ioannis Emmanouil Tzanetakis
Keyword(s):  
New Species ◽  
High Throughput Sequencing ◽  
Control Measures ◽  
Mixed Infections ◽  
Virus Species ◽  
New Era ◽  
Ribes Spp ◽  
And Control ◽  
Propagation Material

This article provides an up-to-date review of disease causing viruses and phytoplasmas of currants including symptoms, transmission, detection, economic impact and control measures. Currants are widely cultivated in more than 30 countries in the temperate zones of Europe, Asia, South America, Australia and New Zealand. Ribes spp. can be infected by more than 20 virus species and four Ca. Phytoplasma species, with more to be described in the future. High-throughput sequencing opened a new era of deciphering virus variants and mixed infections, leading to the characterization of several new species. The use of clean propagation material is the basis for control of Ribes graft-transmissible diseases, but this has become a challenging task given the ever-growing number of newly discovered pathogens.

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