Cucumber Mosaic Virus Subgroup Research Articles

Molecular characterization and genetic analysis of Orthotospovirus tomatomaculae (tomato spotted wilt virus) and cucumber mosaic virus infecting tomato and pepper in Türkiye

Many viral diseases threaten the sustainable production of tomato (Solanum lycopersicum) and pepper (Capsicum annuum), which are among the most produced vegetables in the world and Türkiye. Eskişehir province of Türkiye produces a significant amount of vegetables both in the greenhouse and in the open-field. However, there have been no previous comprehensive study on the presence of viruses in tomato and pepper fields. In this study, 123 of 170 samples (72.4%) collected from tomato and pepper fields in Eskişehir in 2019 were infected with different viruses listed. While Orthotospovirus tomatomaculae (tomato spotted wilt virus, TSWV), cucumber mosaic virus (CMV), potato virus Y (PVY), tomato mosaic virus (ToMV), tobacco mosaic virus (TMV) viruses were detected by DAS-ELISA, pepino mosaic virus (PepMV), tomato chlorosis virus (ToCV) and tobacco necrosis virus (TNV) viruses could not be detected in both host plants. To molecularly characterize the selected isolates, the complete nucleocapsid (N) gene region specific to TSWV and a partial capsid protein (CP) gene region specific to CMV were amplified via RT-PCR, followed by sequencing. Phylogenetic trees were constructed with NCBI GenBank isolates and newly sequenced isolates. Genetic structure-related analyses such as genetic diversity, genetic differentiation, gene flow, neutrality tests, selection pressure, and recombination were performed on populations. In the phylogenetic tree of the TSWV N gene, the isolates are divided into three clades of geographical origin. Genetic structure analyses revealed that TSWV populations exhibited genetic diversity. In the phylogenetic tree of the CMV CP gene, the isolates are divided into known subgroups. The analyses indicate the presence of high genetic diversity and suggest that Subgroup IB, one of the clades, may contain subgroups within itself. In addition, there are indications for the existence of different CMV subgroups in Türkiye. Although different approaches were used for both the TSWV N gene and CMV CP gene, no recombination event could be detected. This study, marking the initial identification of viruses in tomatoes and peppers within the Eskişehir region, is believed to hold substantial potential for advancing future research endeavors and enhancing disease management not only within Türkiye but also globally.

Cucumber mosaic virus subgroup IA isolates infect four varieties of Nandina domestica in China

AbstractCucumber mosaic virus (CMV) subgroup IA isolates were first identified from Nandina domestica plants in Zhejiang province of China by small RNA deep sequencing followed by bioinformatics analysis and was confirmed by RT‐PCR amplification, 5′ and 3′ RACE and DNA sequencing. The complete nucleotide sequences of this virus shared the highest sequence similarities (97–98%) with CMV subgroup IA isolate CTL RNA1 and RNA3 (GenBank accession no: EF213023, EF213025) and RP48 RNA2 (KC527727), respectively; and converged with CMV subgroup IA isolates into a branch in phylogenetic tree using full length nucleotide sequences. Pathogenicity test confirmed that this virus can be mechanically transmitted to N. domestica, Nicotiana tabacum and N. benthamiana. All thirty randomly collected samples of four major N. domestica varieties (N. domestica cv. Hong Baoshi, Nana, Fire Power and Xiu Dada) in Lin'an Zhejiang province were positive for CMV subgroup IA. This is the first report of CMV subgroup IA isolate on varieties of N. domestica in China.

Genomic characterization of recombinant cucumber mosaic virus isolates infecting mustard species via HTS in India

AbstractOne of the most pervasive plant viruses, the cucumber mosaic virus (CMV), Bromoviridae: Cucumovirus, infects a variety of plants worldwide and significantly affects production quality and quantity. Viral infection exhibiting severe mosaic and stunting symptoms in plants infected with turnip mosaic virus was observed in experimental fields in IARI. Leaf samples were collected and the virome was identified through high‐throughput sequencing subjecting ribosomal RNA‐depleted mRNA. Here, we unravel for the first time the complete genome sequences of two CMV isolates infecting yellow and black‐seeded mustard in India. The three segments of the viral genome, as well as coat protein cds, were amplified and subjected to Sanger sequencing. The three viral genomic components were 3348 of RNA1, 3032 and 3040 of RNA2, 2260 and 2236 nts of RNA 3, respectively (including the 5′ and 3′ UTR). The two isolates shared high sequence identity and clubbed with the subgroup‐IB isolates in a clade. Recombination signals were detected within all the three RNAs of both New Delhi isolates wherein one of the parent isolates was reported to infect the family Brassicaceae. Recombination was observed throughout the region of RNA2 but the 3′ UTR was observed to be most prone to recombination. This is the first comprehensive depiction of a recombinant CMV subgroup IB isolate from black, yellow and brown‐seeded mustard from India, which has implications for its robust detection and overall management. This study also provides insight into population structuring, host expansions, level of genetic heterogeneity and variability of worldwide prevalent CMV isolates.

Molecular Characterization of Cucumber Mosaic Virus Subgroup IB in Iraq

Molecular Characterization of Cucumber Mosaic Virus Subgroup IB in Iraq

Molecular characterization and differentiation of cucumber mosaic virus subgroups in Serbia by RT-PCR-RFLP

Samples of various host plants from different locations in Serbia showing foliar symptoms resembling those caused by the cucumber mosaic virus (CMV) were collected. Samples were considered CMV-infected after detection by double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA). Fifteen CMV isolates were selected for developing a reverse transcription-polymerase chain reaction (RT-PCR) restriction fragment length polymorphism (RFLP) protocol and a more detailed molecular characterization of all five genes. Based on in silico RFLP, the following restriction enzymes were selected: HindIII, SacII (1a gene), MluI (2a gene), StuI, SalI (2b gene), BaeI (movement protein (MP) gene of CMV), SfcI, and HaeIII (capsid protein (CP) gene), which were capable of distinguishing between subgroups of CMV based on the obtained characteristic restriction patterns. According to in situ RFLP, the predominant haplotype IA; IA, IA; IA, IA was determined in 14, while the distinct haplotype II; II, II; II, II was found in only one isolate. Sequence analyses of two selected Serbian CMV isolates with different restriction patterns and haplotype profiles confirmed the RFLP results, showing that isolates 674-11 and 137-13 belong to subgroups IA and II, respectively. Different restriction patterns after digestion of all five CMV genomic regions proved to be a simple way to investigate the natural population of CMV. This study provides insight into the genetic structure of the CMV population in Serbia.

Molecular characterization of Cucumber mosaic virus subgroup II isolate associated with cucumber in Bangladesh

Molecular characterization of Cucumber mosaic virus subgroup II isolate associated with cucumber in Bangladesh

The Weak Small RNA-Binding Activity of the 2b Proteins of Subgroup II Cucumber Mosaic Virus Strains Is Insufficient for RNA Silencing Suppression.

The 2b proteins encoded by cucumber mosaic virus (CMV) subgroup I strains suppress RNA silencing primarily by competitively binding small RNAs (sRNAs) in the host cell cytoplasm. Interestingly, 2b proteins encoded by CMV subgroup II strains accumulate predominantly in nuclei. Here we determined that whereas the 2b protein (Fny2b) of subgroup IA strain Fny-CMV is highly effective in suppressing both sense RNA-induced and inverted repeat-induced posttranscriptional gene silencing, the 2b protein (LS2b) of the subgroup II strain LS-CMV was not as effective. Reducing nuclear accumulation of LS2b by mutating a residue in its nuclear localization sequence had no effect on RNA silencing suppressor activity, while attenuated viral symptoms. Electrophoretic mobility shift assays showed that the sRNA binding of LS2b was weaker and more selective than that of Fny2b. The domain determining the differential sRNA-binding ability was delimited to the putative helix α1 region. Moreover, LS2b mutants that completely lost suppressor activity still retained their weak sRNA-binding ability, suggesting that sRNA binding is not sufficient for LS2b to suppress RNA silencing. Considering the subgroup I strain-encoded 2b proteins that require sRNA-binding ability for the suppression of RNA silencing, we suggest that in addition to binding sRNA, the 2b proteins of subgroup II CMV strains would require extra biological activities to achieve RNA silencing inhibition.

Genome characterization and host range studies of Cucumber mosaic virus belonging to the Subgroup IB infecting chilli in India and screening of chilli genotypes for identification of resistance.

The online version contains supplementary material available at 10.1007/s13337-021-00713-3.

Molecular analysis of Greek isolates of cucumber mosaic virus from vegetables shows a low prevalence of satellite RNAs and suggests the presence of host-associated virus strains.

Cucumber mosaic virus (CMV) is a generalist pathogen that infects many economically important crops in Greece. The present study was designed to evaluate the genetic variability of Greek CMV isolates in combination with their satellite RNAs (satRNAs). To achieve this goal, 77 CMV isolates were collected from symptomatic Greek vegetables, mainly tomatoes and cucurbits, alongside their neighboring crops, during a four-year period from 2015 to 2018. Phylogenetic analysis of a partial coat protein (CP) gene segment revealed that all of the isolates belong to CMV subgroups IA and IB and that they are closely related to previously reported Greek isolates. It should be noted, however, that the latter mainly included tomato isolates. Network analysis of the evolutionary relationships among the CP sequences of the Greek isolates in comparison to the corresponding sequences obtained from the GenBank database indicated two predominant common ancestors and at least three differentiated peripherals, and possibly host-associated (tomatoes, legumes, cucurbits) haplogroups (strain groups). More specifically, host-adaptive evolution can be postulated regarding the tomato isolates in subgroup IB. Necrogenic or non-necrogenic satRNAs were detected in four samples from tomato and melon, and this is the first report of non-necrogenic satRNAs in CMV in Greece.

Characterization of cucumber mosaic virus (CMV) subgroup IB infecting chilli in Tamil Nadu, India.

CMV (cucumber mosaic virus) is the most primitive virus infecting chilli (Capsicum annuum. L). The mosaic incidence with leaf filiformity, mosaic mottling and stunted growth was observed in major chilli growing regions of Tamil Nadu. CMV sap was inoculated on chilli, cowpea, bitter gourd, bottle gourd, ridge gourd, banana, cucumber, Nicotiana and Chenopodium plants. Host range studies revealed that CMV produced localized infection on Nicotiana and systemic symptoms on most of the test plants. The occurrence of CMV was confirmed through DAC-ELISA and RT-PCR analysis. Host plant samples tested with DAC-ELISA showed strong reaction with 1.7 optical density. For molecular characterization, total RNA isolated from infected plants used in RT-PCR with CMV specific primers. The specific amplicons were cloned and sequenced. The complete genome sequencing depicts CMV-RNA1 consist of 3339 nucleotides (nt), RNA2 and RNA3 with 3052nt and 2027nt respectively. Phylogenetic and nucleotide sequence analysis showed TN CMV isolates closely associated with subgroup IB rather than subgroup IA and II. Comparative sequence analysis indicates replicase protein to be more variable among five genes. CP sequence analysis showed 97-98 per cent identity with subgroup IB strains, 92-93 per cent identity with subgroup IA strains and 81-82 per cent identity with subgroup II strains. CMV-RNA3 was predicted to have recombination with Indian black pepper isolate (KU947031) between 165-505nt and Egyptian tomato isolate (KX014666) between 165-506nt positions.

Analysis of the complete genome sequence of cucumber mosaic virus from Vinca minor and Wisteria sinensis in Iran

We present here the first complete sequence of cucumber mosaic virus (CMV) from RNA sequencing of a dwarf periwinkle (Vinca minor) and a Wisteria sinensis in Iran by de novo assembly and annotation of contigs. The tripartite genome of CMV-Ir-VM and Ir-WS consists of a 3391-nucleotide (nt) RNA1, a 3038-nt RNA2, and a 2197-nt RNA3 segment. The sequence comparisons and phylogenetic analyses revealed that all three RNA segments of these two isolates belonged to the CMV subgroup II. RNA1, RNA2, and RNA3 of these two isolates, respectively shared 97.61–99.06%, 97.83–98.88%, and 97.19–98.86% nucleotide identities to those of CMV subgroup II isolates. In genetic analysis, the 2b gene revealed more genetic variability (π = 0.2614) compared with other regions. Our results indicated that purifying selection pressure was the major force acting upon the CMV genome, although some positively selected sites were identified for all encoded proteins.

Occurrence of cucumber mosaic virus Subgroup I on different plant families in Himachal Pradesh and its infection to new hosts

Cucumber mosaic virus (CMV) has been recorded worldwide, infecting more than 1200 plant species including weeds. In this study, 23 samples of bell pepper, squash, tomato, ornamental (calla lily, French hydrangea, spider lily) and weeds (Arrowleaf dock, Spanish needle) hosts originating from Himachal Pradesh were examined. 20 of 23 samples were identified CMV positive based on electron microscopy, bio-assay, RT-PCR assay and sequence analyses of coat protein (CP) gene. The CMV-CP gene sequences from eight isolates cloned and sequenced in this study shared 96–100% amino acid sequence identities with CMV Subgroup I isolates. This study forms the first report of the natural occurrence of CMV on squash and a weed host, Arrowleaf dock (Rumex hastatus), in India as well as the occurrence of CMV Subgroup I in the cooler hilly regions of India. These findings suggest the expansion of the host range as well as ecological niche of CMV.

The molecular characterization of the coat protein sequence and differentiation of CMV- subgroup I on tobacco from native flora in Turkey

Cucumber mosaic virus (CMV) has a broad plant-host range and a wide ecological zone distribution. Virus-like symptoms were observed on tobacco fields of Adiyaman province (Turkey) showing conspicuous mottling, greenish mosaic patterns and severe malformations of leaves. A total of forty tobacco samples tested positive against CMV by reverse transcription polymerase chain reaction (RT-PCR) using coat protein gene specific primers. Five randomly chosen CMV isolates were cloned into pGEM T-Easy vector and transformed into Escherichia coli JM109 strain. The recombinant bacterial clones containing insert-DNA were further purified and sequenced bidirectionally. In multiplex-RT-PCR studies carried out, it was found that all 40 CMV isolates belong to Subgroup I by resulting a 593 bp long DNA fragments. CMV subgroup IA was found to predominate in 4 out of 5 tobacco samples and CMV subgroup IB was found in 1 out of 5 CMV-positive samples by comparing the isolates with CMV reference isolates in phylogenetic tree. However, no Subgroup II sequences were found by multiplex RT-PCR using discriminating primers. The nucleic acid sequences were analyzed for the investigation of diversity of coat protein (CP) sequences of 5 CMV isolates. The sequence similarity ranged from 94.2-100% with the CMV subgroup I isolates infecting diverse plants in other regions of the world. The evolutionary tree revealed that the CMV IA Adiyaman isolates exhibited a genetic affinity with Australian and Spanish isolates. However, the CMV IB Adiyaman isolate showed a close genetic relationship with only the Australian isolates. To our knowledge, this study shows for the first time the occurrence of CMV IA and IB isolates infecting cultured tobacco plants in Adiyaman province.

A multiplex RT-PCR assay for the simultaneous detection of prevalent viruses infecting pepper (Capsicum annuum L.)

The aim of this work was to create an easy, fast and sensitive method for the simultaneous detection of the most frequent viruses known to infect pepper (Capsicum annuum L.) crops. A multiplex RT-PCR assay was developed that successfully achieved this aim. Using specifically designed primer pairs, the assay could simultaneously amplify the genomes of members of the two subgroups (I and II) of cucumber mosaic virus (CMV), two tobamoviruses, tobacco mosaic virus (TMV) and pepper mild mottle virus (PMMoV), potato virus Y (PVY), and tomato spotted wilt virus (TSWV) in a single assay. The multiplex RT-PCR assay was found to be a sensitive diagnostic tool for the detection of the viruses from the leaves and fruits of naturally infected pepper plants. This assay would provide prompt disease status information for pepper breeders.

Evolutionary timescale and geographical movement of cucumber mosaic virus, with focus on Iranian strains.

Cucumber mosaic virus (CMV) is a geographically widespread plant virus with a very broad host range. The virus has been detected in diverse crops all over Iran. In this study, we estimated the timescale of the evolution of CMV subgroup I and the geographical movement of the virus with a focus on Iranian strains. Analyses using the MP and CP genes and their concatenation revealed that the CMV population within subgroup I had a single ancestor dating back to about 450-550 years ago. The Iranian strains formed three clusters in a maximum-clade-credibility phylogenetic tree. It was found that the most recent common ancestor of the Iranian strains within each cluster dates back to less than 100 years ago. Our results also suggest that both short- and long-distance migration of Iranian CMV strains has occurred in the last 100 years.

First report of cucumber mosaic virus subgroups I and II with satellite RNA infecting Nicotiana glauca in Mexico

First report of cucumber mosaic virus subgroups I and II with satellite RNA infecting Nicotiana glauca in Mexico

First report of cucumber mosaic virus subgroup IB and II isolates infecting tomatoes in Pakistan

First report of cucumber mosaic virus subgroup IB and II isolates infecting tomatoes in Pakistan

Protein 2b of Cucumber mosaic virus strains IA and SD preferentially suppresses RDR6-dependent silencing pathway

The 2b protein of Cucumber mosaic virus (CMV) subgroup IB strain IA (IA2b) suppresses the sense transgene-induced post-transcriptional gene silencing (S-PTGS) but not the inverted repeat-induced post-transcriptional gene silencing (IR-PTGS) of a tobacco microsome-localized α-linolenate synthase gene (NtFAD3). In contrast, the 2b protein of CMV subgroup IB strain SD (SD2b) has been reported to suppress IR-PTGS. We overexpressed the SD2b gene in tobacco, and this transgenic line was crossed with the transgenic plants showing S-PTGS and IR-PTGS of the NtFAD3 gene. The phenotype of offspring showed that SD2b inhibited S-PTGS but not IR-PTGS. Next, we determined the suppressor activity of IA2b and SD2b proteins in a transient IR-PTGS assay. The transient expression of firefly luciferase (LUC) gene was efficiently decreased by IR-PTGS. Co-infiltration of SD2b and IA2b gene partially suppressed IR-PTGS of the LUC gene in the wild-type plants; however, these 2b proteins did not suppress IR-PTGS in the RNA-dependent RNA polymerase6 (RDR6) knockdown plants. It has been reported that RDR6-dependent secondary small interfering RNA synthesis does not occur in the IR-PTGS, when targeting endogenous genes such as NtFAD3, but is efficiently induced in the IR-PTGS of the reporter transgenes. These results indicate that the SD2b and IA2b preferentially suppress the RDR6-dependent silencing pathway but do not suppress the RDR6-independent IR-PTGS pathway.

First report of a cucumber mosaic virus (CMV) subgroup II isolate infecting pea in Pakistan

First report of a cucumber mosaic virus (CMV) subgroup II isolate infecting pea in Pakistan

Occurrence of cucumber mosaic virus subgroup II and its genetic diversity in Sichuan, southwest of China

Twenty-six leaf samples from Capsicum annuum, Solanum lycopersicum, Brassica campestris and Pisum sativum var. saccharatum plants were collected from different locations in Sichuan (China) during 2008–2016. Using RT-PCR and sequencing of the coat protein (CP) genes, 11 cucumber mosaic virus (CMV) subgroup II isolates were detected. The sequences of the 11 isolates compared with each other showed 98.63 to 99.54% identity. Phylogenetic analysis of the CP sequences revealed that all isolates clustered in the subgroup II and showed no host range specificity. This is the first report of the rising frequency of occurrence of CMV subgroup II isolates in Sichuan. The information of host diversity and the epidemic tendency of these CMV isolates presented in this study will provide the basis for disease control.