Characterization of a New Tymovirus Causing Stunting and Chlorotic Mosaic in Naranjilla (Solanum quitoense)

Naranjilla (“little orange”), also known as lulo (Solanum quitoense Lam.), is a perennial shrub species cultivated in the Andes for fresh fruit and juice production. In 2015, a naranjilla plant exhibiting stunting, mosaic, and chlorotic spots was sampled in the Pastaza province of Ecuador and maintained under greenhouse conditions. An infectious agent was mechanically transmitted to indicator plants and was subjected to biological and molecular characterization. Spherical particles approximately 30 nm in diameter, composed of a single 20-kDa capsid protein, were observed under an electron microscope in infected naranjilla plants. High-throughput sequencing conducted on inoculated Nicotiana benthamiana plants produced a single sequence contig sharing the closest relationship with several tymoviruses. The entire 6,245-nucleotide genome of a new tymovirus was amplified using reverse-transcription polymerase chain reaction and resequenced with the Sanger methodology. The genome had three open reading frames typical of tymoviruses, and displayed a whole-genome nucleotide identity level with the closest tymovirus, Eggplant mosaic virus, at 71% (90% coverage). This tymovirus from naranjilla was able to systemically infect eggplant, tamarillo, N. benthamiana, and naranjilla. In naranjilla, it produced mosaic, chlorotic spots, and stunting, similar to the symptoms observed in the original plant. The virus was unable to infect potato and tobacco and unable to systemically infect pepper plants, replicating only in inoculated leaves. We concluded that this virus represented a new tymovirus infecting naranjilla, and proposed the tentative name Naranjilla chlorotic mosaic virus (NarCMV).

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Partial Molecular Characterization of Dahlia mosaic virus and Its Detection by PCR

Plant Disease ◽

10.1094/pdis.2003.87.8.945 ◽

2003 ◽

Vol 87 (8) ◽

pp. 945-948 ◽

Cited By ~ 16

Author(s):

M. Nicolaisen

Keyword(s):

Nucleotide Sequence ◽

Mosaic Virus ◽

Real Time ◽

Real Time Pcr ◽

Open Reading Frames ◽

Dahlia Mosaic Virus ◽

Polymerase Chain ◽

Pcr Assays

Dahlia mosaic virus (DMV) is the causal agent of one of the most important diseases of Dahlia pinnata. The nucleotide sequence of a 1,195-bp fragment of its genome was amplified and characterized. Based on this sequence, polymerase chain reaction (PCR) assays were developed for detection of DMV. The nucleotide sequence confirmed the classification of DMV as a member of genus Caulimovirus since it was similar to a region covering partly open reading frames (ORFs) IV and V found in caulimoviruses. The two most closely related viruses on the basis of comparison of ORF V fragments were shown to be Figwort mosaic virus and Mirabilis mosaic virus with 66.6 and 68.1% identity, respectively. Two PCR assays were developed using identical primer pairs: a real-time PCR based on SYBR green chemistry and a conventional PCR. Both methods clearly discriminated DMV-infected and healthy dahlia. The real-time PCR assay detected DMV-infected material that was diluted 105-fold in healthy material.

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Identification and Characterization of a Novel Robigovirus Species from Sweet Cherry in Turkey

Pathogens ◽

10.3390/pathogens8020057 ◽

2019 ◽

Vol 8 (2) ◽

pp. 57 ◽

Cited By ~ 5

Author(s):

Kadriye Çağlayan ◽

Vahid Roumi ◽

Mona Gazel ◽

Eminur Elçi ◽

Mehtap Acioğlu ◽

...

Keyword(s):

High Throughput Sequencing ◽

Sweet Cherry ◽

Prunus Avium ◽

Open Reading Frames ◽

Cherry Tree ◽

Coding Regions ◽

Sweet Cherries ◽

Identification And Characterization ◽

Reading Frames

High throughput sequencing of total RNA isolated from symptomatic leaves of a sweet cherry tree (Prunus avium cv. 0900 Ziraat) from Turkey identified a new member of the genus Robigovirus designated cherry virus Turkey (CVTR). The presence of the virus was confirmed by electron microscopy and overlapping RT-PCR for sequencing its whole-genome. The virus has a ssRNA genome of 8464 nucleotides which encodes five open reading frames (ORFs) and comprises two non-coding regions, 5′ UTR and 3′ UTR of 97 and 296 nt, respectively. Compared to the five most closely related robigoviruses, RdRp, TGB1, TGB2, TGB3 and CP share amino acid identities ranging from 43–53%, 44–60%, 39–43%, 38–44% and 45–50%, respectively. Unlike the four cherry robigoviruses, CVTR lacks ORFs 2a and 5a. Its genome organization is therefore more similar to African oil palm ringspot virus (AOPRV). Using specific primers, the presence of CVTR was confirmed in 15 sweet cherries and two sour cherries out of 156 tested samples collected from three regions in Turkey. Among them, five samples were showing slight chlorotic symptoms on the leaves. It seems that CVTR infects cherry trees with or without eliciting obvious symptoms, but these data should be confirmed by bioassays in woody and possible herbaceous hosts in future studies.

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Genotype 1 of human parvovirus B19 in clinical cases

Revista da Associação Médica Brasileira ◽

10.1590/1806-9282.63.03.224 ◽

2017 ◽

Vol 63 (3) ◽

pp. 224-228 ◽

Cited By ~ 1

Author(s):

Maria Isabel de Oliveira ◽

Ana Maria Sardinha Afonso ◽

Suely Pires Curti ◽

Patrícia Evelin Silva ◽

Tamyris Fernanda Barbosa ◽

...

Keyword(s):

Parvovirus B19 ◽

Infectious Agent ◽

Immunoglobulin M ◽

Human Parvovirus B19 ◽

Genotype 1 ◽

Serum Samples ◽

Chronic Anemia ◽

Virus Surveillance ◽

Polymerase Chain

Summary Introduction: Virus surveillance strategies and genetic characterization of human parvovirus B19 (B19V) are important tools for regional and global control of viral outbreak. In São Paulo, Brazil, we performed a study of B19V by monitoring the spread of this virus, which is an infectious agent and could be mistakenly reported as a rash and other types of infection. Method: Serum samples were subjected to enzyme immunoassay, real time polymerase chain reaction, and sequencing. Results: From the 462 patients with suspected cases of exanthematic infections, the results of the 164 serum samples were positive for B19V immunoglobulin M. Among these cases, there were 38 patients with erythema infections and B19-associated with other infections such as encephalitis, hydrops fetalis, chronic anemia, hematological malignancies. These samples were sequenced and identified as genotype 1. Conclusion: This study showed patients with infections caused by B19V and sequencing genotype 1. Continuous monitoring is necessary to detect all known genotypes, and the emergence of new genotypes of these viruses for case management in public health control activities.

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Characterization of an isolate of Lettuce big-vein associated virus (LBVaV) detected in naturally infected tomato (Solanum lycopersicum L.) in Slovakia

Plant Protection Science ◽

10.17221/56/2021-pps ◽

2021 ◽

Vol 57 (No. 4) ◽

pp. 344-348

Author(s):

Lukáš Predajňa ◽

Daniel Mihálik ◽

Michaela Mrkvová ◽

Pavel Cejnar ◽

Katarína Šoltys ◽

...

Keyword(s):

Solanum Lycopersicum ◽

High Throughput Sequencing ◽

Illumina Miseq ◽

Reference Sequence ◽

Solanum Lycopersicum L ◽

Original Plant ◽

Infected Tomato ◽

Miseq Platform

A tomato plant (Solanum lycopersicum Linnaeus, labelled KVE) displaying virus-like symptoms, tested negative for common tomato viruses, was subjected to high-throughput sequencing (HTS) on the Illumina MiSeq platform using ribosomal RNA-depleted total RNA as a template. The analysis has revealed the contigs mapping to Lettuce big-vein associated virus (LBVaV). The near complete LBVaV-KVE sequence of RNA1 and RNA2 revealed 95.0 and 94.9% identity with the reference sequence, the same length of translated products and a typical varicosavirus genome organisation. After initial long-term maintenance of LBVaV-KVE in the original plant, the virus could be detected by RT-PCR or nanoLC-ESI-Q-TOF in new plants generated from lateral shoot cuttings or inoculated by stem chips, although not uniformly. So far, LBVaV was reported to infect lettuce and related species. Our study expands the natural host range of the LBVaV to tomato.

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Double-Stranded RNA High-Throughput Sequencing Reveals a New Cytorhabdovirus in a Bean Golden Mosaic Virus-Resistant Common Bean Transgenic Line

Viruses ◽

10.3390/v11010090 ◽

2019 ◽

Vol 11 (1) ◽

pp. 90 ◽

Cited By ~ 8

Author(s):

Dione M. T. Alves-Freitas ◽

Bruna Pinheiro-Lima ◽

Josias C. Faria ◽

Cristiano Lacorte ◽

Simone G. Ribeiro ◽

...

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Mosaic Virus ◽

High Throughput ◽

Transgenic Line ◽

High Throughput Sequencing ◽

Open Reading Frames ◽

Virus Species ◽

Homologous Proteins ◽

Bean Golden Mosaic Virus

Using double-strand RNA (dsRNA) high-throughput sequencing, we identified five RNA viruses in a bean golden mosaic virus (BGMV)-resistant common bean transgenic line with symptoms of viral infection. Four of the identified viruses had already been described as infecting common bean (cowpea mild mottle virus, bean rugose mosaic virus, Phaseolus vulgaris alphaendornavirus 1, and Phaseolus vulgaris alphaendornavirus 2) and one is a putative new plant rhabdovirus (genus Cytorhabdovirus), tentatively named bean-associated cytorhabdovirus (BaCV). The BaCV genome presented all five open reading frames (ORFs) found in most rhabdoviruses: nucleoprotein (N) (ORF1) (451 amino acids, aa), phosphoprotein (P) (ORF2) (445 aa), matrix (M) (ORF4) (287 aa), glycoprotein (G) (ORF5) (520 aa), and an RNA-dependent RNA polymerase (L) (ORF6) (114 aa), as well as a putative movement protein (P3) (ORF3) (189 aa) and the hypothetical small protein P4. The predicted BaCV proteins were compared to homologous proteins from the closest cytorhabdoviruses, and a low level of sequence identity (15–39%) was observed. The phylogenetic analysis shows that BaCV clustered with yerba mate chlorosis-associated virus (YmCaV) and rice stripe mosaic virus (RSMV). Overall, our results provide strong evidence that BaCV is indeed a new virus species in the genus Cytorhabdovirus (family Rhabdoviridae), the first rhabdovirus to be identified infecting common bean.

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A New Tymovirus Isolated From Solanum quitoense: Characterization and Prevalence in Two Solanaceous Crops in Ecuador

Plant Disease ◽

10.1094/pdis-01-19-0113-re ◽

2019 ◽

Vol 103 (9) ◽

pp. 2246-2251 ◽

Cited By ~ 1

Author(s):

Juan F. Cornejo-Franco ◽

Robert A. Alvarez-Quinto ◽

Samuel Grinstead ◽

Dimitre Mollov ◽

Alexander V. Karasev ◽

...

Keyword(s):

Mosaic Virus ◽

Open Reading Frames ◽

Yellow Mosaic Virus ◽

Enzyme Linked Immunosorbent Assay ◽

Mild Mosaic ◽

Fresh Market ◽

Certification Programs ◽

Mild Mosaic Virus ◽

Polymerase Chain ◽

Production Areas

Naranjilla (Solanum quitoense Lam.) and tamarillo (S. betaceum Cav.) are two important perennial solanaceous crops grown in Ecuador for the fresh market and juice production. Viruses infecting tamarillo and naranjilla are currently poorly studied, and no clean stock program exists in Ecuador. Here, we report a new virus, provisionally named as naranjilla mild mosaic virus (NarMMV) (genus Tymovirus, family Tymoviridae), isolated from naranjilla grown in an orchard in Pichincha Province, Ecuador. The complete genome of the virus consists of 6,348 nucleotides and encodes three open reading frames typical for members of the genus Tymovirus. Phylogenetically, Chiltepin yellow mosaic virus, Eggplant mosaic virus, and the recently characterized naranjilla chlorotic mosaic virus (NarCMV) were found to be the closest relatives of NarMMV. Unlike NarCMV, the new virus induced mild mosaic in naranjilla and more severe symptoms in tamarillo. Similar to NarCMV, NarMMV was unable to systemically infect potato. Virus surveys found NarMMV prevalent in naranjilla production areas of two provinces of Ecuador, especially where hybrid cultivars of naranjilla were cultivated. NarMMV was also found in field-grown tamarillo. The new virus cross-reacted with antibodies developed against NarCMV. Hence, this antibody will be useful for its field diagnosis using enzyme-linked immunosorbent assay or immunocapture reverse transcription polymerase chain reaction in future virus-free certification programs.

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Molecular Characterization, Phylogenetic Relationships, and Specific Detection of Peach mosaic virus

Phytopathology ◽

10.1094/phyto-96-0137 ◽

2006 ◽

Vol 96 (2) ◽

pp. 137-144 ◽

Cited By ~ 12

Author(s):

D. James ◽

A. Varga ◽

H. Croft ◽

H. Rast ◽

D. Thompson ◽

...

Keyword(s):

Mosaic Virus ◽

Open Reading Frames ◽

Nucleic Acid Binding ◽

Specific Detection ◽

Deletion Event ◽

Polymerase Chain ◽

Similar Genome Organization ◽

Leaf Virus

Peach mosaic virus (PcMV) and Cherry mottle leaf virus (CMLV) are serologically related viruses that cause distinct diseases, have a different host range, and are vectored by different eriophyid mites. Sequence analysis of the genome of PcMV indicates that it is closely related genetically to CMLV but distinct, with similar genome organization and a member of the genus Trichovirus. The genome of PcMV consists of 7,988 nucleotides, excluding a poly(A) tail at the 3′ end of the genome. Four putative open reading frames (ORF1 to 4) were identified coding for proteins of 216.3, 47.2, 21.7, and 15.7 kDa, respectively. Also, three noncoding regions were identified, including an intergenic region separating ORF3 and ORF4. The complete nucleotide sequence of PcMV shares 73% identity with CMLV. The CP amino acid sequence identity between isolates of PcMV ranged from 97 to 99% versus 83% identity when compared with the CP of CMLV. In vitro expression and subsequent western blot analysis confirmed ORF3 as encoding the CP gene of PcMV. Phylogenetic analysis supports classification of PcMV and CMLV as members of the genus Trichovirus. They are unique members of this genus with an extra ORF (ORF4). PcMV ORF4 appears to code for a putative nucleic acid-binding (NB) protein which has identity with the NB protein of CMLV and members of the genera Allexivirus, Carlavirus, and Vitivirus. PcMV and CMLV appear to be the products of recombination between members of the genus Trichovirus and a virus group containing the putative NB protein. Alternatively, PcMV and CMLV may represent the intact genome, with a deletion event producing members that lack ORF4. A reverse transcription-polymerase chain reaction procedure was developed for reliable and specific detection of PcMV. This will be an asset for stone fruit virus certification.

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Detection and molecular characterization of the Iris severe mosaic virus-Ir isolate from Iran

Journal of Plant Protection Research ◽

10.1515/jppr-2015-0032 ◽

2015 ◽

Vol 55 (3) ◽

pp. 235-240 ◽

Cited By ~ 3

Author(s):

Masoud Nateqi ◽

Mina Koohi Habibi ◽

Akbar Dizadji ◽

Shirin Parizad

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Mosaic Virus ◽

Ornamental Plants ◽

Rt Pcr ◽

Chain Reaction ◽

C Terminus ◽

Coated Plate ◽

Polymerase Chain

AbstractIris belongs to the Iridaceae family. It is one of the most important pharmaceutical and ornamental plants in the world. To assess the potyvirus incidence in natural resources of iris plants in Iran, Antigen Coated-Plate ELISA (ACP-ELISA) was performed on 490 symptomatic rhizomatous iris leaf samples, which detected the potyvirus in 36.7% of the samples. Genomic 3′ end of one mechanically non-transmitted potyvirus isolate, comprising a 3′ untranslated region (390 bp) and C-terminus of the coat protein (CP) gene (459 bp), was amplified by reverse transcription polymerase chain reaction (RT-PCR), which was ligated into pTG19-T vector. The nucleotide sequence of amplicons was compared with related sequences, using Blastn software available at NCBI GenBank, and showed the highest similarity withIris severe mosaic virus(ISMV) isolates. The nucleotide and deduced amino acid sequence of the CP C-terminus region was more than 83% identical with other ISMV isolates, therefore this isolate was designated as ISMV-Ir. This new ISMV isolate is closely related to the Chinese ISMV-PHz in phylogenetic analysis, based on the partial nucleotide and deduced amino acid sequence of the CP region. This is the first report of ISMV occurrence onIrisspp. in Iran.

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High-Throughput Sequencing Facilitates Characterization of a “Forgotten” Plant Virus: The Case of a Henbane Mosaic Virus Infecting Tomato

Frontiers in Microbiology ◽

10.3389/fmicb.2018.02739 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 1

Author(s):

Anja Pecman ◽

Denis Kutnjak ◽

Nataša Mehle ◽

Magda Tušek Žnidarič ◽

Ion Gutiérrez-Aguirre ◽

...

Keyword(s):

Mosaic Virus ◽

High Throughput ◽

Plant Virus ◽

High Throughput Sequencing

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Molecular Characterization of the Complete Coding Sequence of Olive Leaf Yellowing-Associated Virus

Plants ◽

10.3390/plants9101272 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1272

Author(s):

Ana Belén Ruiz-García ◽

Thierry Candresse ◽

Celia Canales ◽

Félix Morán ◽

Carlos Machado de Oliveira ◽

...

Keyword(s):

High Throughput Sequencing ◽

Genomic Sequence ◽

Olive Tree ◽

Open Reading Frames ◽

Olive Leaf ◽

Coding Sequence ◽

The Family ◽

Leaf Yellowing ◽

Yellowing Disease

Genome organization and phylogenetic relationships of olive leaf yellowing-associated virus (OLYaV) with other members of the Closteroviridae family were determined. The complete coding sequence of OLYaV was obtained by high throughput sequencing of total RNA from a 35-year-old olive tree (cv. Zarzaleña) from Brazil, showing olive leaf yellowing disease and deformations in the wood. This represents the first report of OLYaV in this country. A genomic sequence of 16,700 nt containing 11 open reading frames (ORFs) was recovered, representing the complete virus coding capacity. The knowledge of the nucleotide sequence of the genome including the gene that codes the coat protein will facilitate the development of diagnostic tests, which are limited so far to PCR-based methods targeting the HSP70h gene. Interestingly, a thaumatin-like protein (ORF2), previously reported in other unassigned viruses in the Closteroviridae family, persimmon virus B and actidinia virus 1, was identified in the OLYaV genome. Phylogenetic analysis of shared proteins (ORF1a, ORF1b, HSP70h, HSP90h and CP) with all members of the Closteroviridae family provides new insight into the taxonomic position of these three closteroviruses and suggests they could represent a new genus in the family.

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