Identification and Characterization of a Novel Cytorhabdovirus Associated with Pear (P. communis 'Bartlett') Through RNA-seq.

Novel viruses in plants can be detected through transcriptome data mining. In this study, a novel cytorhabdovirus, pear rhabdovirus 1 (PRV-1) was identified through reanalysis of RNA-seq data of pear (P. communis 'Bartlett').

Novel genetic variants of banana streak MY virus and banana streak IM virus naturally infecting banana in Northeast India.

Divergent banana streak viruses (BSV) were characterized from banana plants exhibiting diverse symptoms in the Northeast region (NER) of India. Using rolling circle amplification (RCA), the complete genome sequences of seven episomal banana streak MY virus (BSMYV) isolates, including two novel variants, and two new banana streak IM virus (BSIMV) isolates were characterized. The novel BSMYV genetic variants were associated with conspicuous necrosis on newly emerged leaves, peduncle distortion, pseudostem internal necrosis, in addition to common streak symptoms.

Evidence of true seed transmissible nature of turnip mosaic virus in mustard species.

Mustard is a commercial oilseed crop worldwide infected by a highly infectious turnip mosaic virus (TuMV). In the experimental field at ICAR-IARI, New Delhi, in 2022, a 100% incidence of TuMV infection was observed in brown, black and yellow mustard. A very low aphid population suggested the possibility of seed transmission.

Complete genome sequence of grapevine yellow speckle viroid 3, a novel apscaviroid infecting grapevine, characterized by high-throughput sequencing.

A novel grapevine viroid was discovered in an asymptomatic grapevine of Indian rootstocks. The whole genome sequence of the viroid (370 nt) was determined by high-throughput sequencing as well as RT-PCR followed by cloning and Sanger sequencing. The terminal conserved region (TCR), central conserved region (CCR) upper strand, and CCR lower strand are conserved regions found in the viroid that are unique to the members of the genus Apscaviroid.

Identification of a novel mitovirus in grapevine through high-throughput sequencing.

Background: Transcriptome data from a plant sample frequently include numerous reads originating from RNA virus genomes that were concurrently isolated during RNA preparation. These high-throughput sequencing reads from the virus can be assembled to form a new sequence for the plant RNA genome.

Methods And Results: Here, we identify putative novel mitovirus, grapevine mitovirus 1 (GMV1) through high-throughput sequencing (HTS) of grapevine rootstocks (Vitis spp.

Mixed infection of two mandariviruses identified by high-throughput sequencing in Kinnow mandarin and development of their specific detection using duplex RT-PCR.

Unlabelled: In the current study, high-throughput sequencing (HTS) was used to identify viruses associated with the Kinnow mandarin () plants exhibiting yellow vein clearing, mottling, and chlorosis symptoms at experimental farm of ICAR-Indian Agricultural Research Institute, New Delhi, India. During November 2022, leaf samples of symptomatic and asymptomatic Kinnow mandarin trees were collected, subjected to HTS and one of the representative symptomatic samples was subjected to leaf-dip electron microscopy (EM). In the EM results, flexuous virus particles typical of mandarivirus were observed.

Development of Simplified Recombinase Polymerase Amplification Assay for Rapid and Robust Detection of Citrus Yellow Vein Clearing Virus.

Citrus is an economically important fruit crop, belongs to family Rutaceae, cultivated commercially in over 130 countries, which holds a leading profitable position in the international market. The most important citrus varieties are mandarins, oranges, lemons, sweet limes, grapefruits and pomelos. Citrus yellow vein clearing virus (CYVCV) is an important graft transmissible plant pathogen known to reduce productivity of citrus fruits due to its predominant association and widespread occurrence.

Development and application of crude sap-based recombinase polymerase amplification assay for the detection and occurrence of grapevine geminivirus A in Indian grapevine cultivars.

Geminiviruses are known to infect several fields and horticultural crops around the globe. Grapevine geminivirus A (GGVA) was reported in the United States in 2017, and since then, it has been reported in several countries. The complete genome recovered through high-throughput sequencing (HTS)-based virome analysis in Indian grapevine cultivars had all of the six open reading frames (ORFs) and a conserved nonanucleotide sequence 5'-TAATATTAC-3' similar to all other geminiviruses.

A Simplified Multiplex PCR Assay for Simultaneous Detection of Six Viruses Infecting Diverse Chilli Species in India and Its Application in Field Diagnosis.

Chilli is infected by at least 65 viruses globally, with a mixed infection of multiple viruses leading to severe losses being a common occurrence. A simple diagnostic procedure that can identify multiple viruses at once is required to track their spread, initiate management measures and manage them using virus-free planting supplies. The present study, for the first time, reports a simplified and robust multiplex PCR (mPCR) assay for the simultaneous detection of five RNA viruses, capsicum chlorosis orthotospovirus (CaCV), chilli veinal mottle virus (ChiVMV), large cardamom chirke virus (LCCV), cucumber mosaic virus (CMV), and pepper mild mottle virus (PMMoV), and a DNA virus, chilli leaf curl virus (ChiLCV) infecting chilli.

Complete Genomic RNA Sequence of Tuberose Mild Mosaic Virus and Tuberose Mild Mottle Virus Acquired by High-Throughput Sequencing.

Tuberose () is an ornamental flowering crop of the family. Tuberose mild mosaic virus (TuMMV) and tuberose mild mottle virus (TuMMoV), members of the genus , are ubiquitously distributed in most tuberose growing countries worldwide with low biological incidence. Here, we report the first coding-complete genomic RNA of TuMMV and TuMMoV obtained through high-throughput sequencing (HTS) and further, the presence of both the viruses were confirmed using virus-specific primers in RT-PCR assays.

High-throughput RNA sequencing and genetic structure studies of turnip mosaic virus infecting black and yellow mustard revealing emergence of world-B3 pathotype in India.

Unlabelled: The RNA viruses are marked by high genetic diversity, which allows them to quickly adapt to new and resistant hosts. The pathogenic turnip mosaic virus (TuMV) infects Brassicaceae plant species all over the world.

Aim: To study the evolution and host expansion of a TuMV for the first time in India using molecular population genetic framework.

Dwarf polish wheat hosts a novel closterovirus: Revelation by transcriptome data-mining.

losteroviruses are positive sense single-stranded RNA genome-containing plant viruses with narrow natural host range and wide distribution. In the present study, a putative novel closterovirus, Triticum polonicum closterovirus (TriPCV) was identified in the transcriptome assembled contigs of dwarf polish wheat available in public domain. The genome of TriPCV (15.

Development of a Polymerase Spiral Reaction-Based Isothermal Assay for Rapid Identification of .

Thrips cause considerable economic losses to a wide range of food, feed, and forest crops. They also transmit several plant viruses. Being cryptic, it is often difficult to distinguish thrips species in crops and large consignments by conventional methods.

Transcriptomic Changes of Asia II 1 Induced by Chilli Leaf Curl Virus Trigger Infection and Circulation in Its Vector.

(Hemiptera: Aleyrodidae) is a highly efficient vector in the spread of chilli leaf curl virus (ChiLCV, ) which is a major constraint in the production of chilli in South Asia. Transcriptome analysis of post-6 h acquisition of ChiLCV showed differential expression of 80 (29 upregulated and 51 downregulated) genes. The maximum number of DEGs are categorized under the biological processes category followed by cellular components and molecular functions.

Identification and Characterization of a Garlic Virus E Genome in Garlic ( L.) Using High-Throughput Sequencing from India.

Garlic ( L.) plants exhibiting mosaics, deformation, and yellow stripes symptoms were identified in Meerut City, Uttar Pradesh, India. To investigate the viruses in the garlic samples, the method of high-throughput sequencing (HTS) was used.

Development of polyclonal antibodies using bacterially expressed recombinant coat protein for the detection of (OYDV) and identification of virus free onion genotypes.

Onion yellow dwarf virus (OYDV) belonging to the genus , family is one of the widely distributed viruses of species worldwide. It causes dwarfing, yellow striping, crinkling and flaccidity of the leaves of onion and garlic. To see the occurrence and incidence of OYDV on crop, an attempt was made to develop antibody based diagnostic assay which would be useful for routine indexing and screening of the germplasm.

Molecular characterization of chickpea chlorotic dwarf virus and peanut witches' broom phytoplasma associated with chickpea stunt disease and identification of new host crops and leafhopper vectors in India.

An investigation was carried out to identify and characterize the phytoplasma and viruses associated with the chickpea varieties showing severe stunting, leaf reddening, yellowing and phyllody symptoms during the summer season of 2018-2019 and 2019-2020 in eight states of India. The average disease incidence was recorded from 3 to 32% in different states. The presence of chickpea chlorotic dwarf virus (CpCDV) was confirmed in thirty-seven chickpea samples by amplification of CpCDV coat protein gene and sequence comparison analysis.

Liberibacter asiaticus manipulates the expression of vitellogenin, cytoskeleton, and endocytotic pathway-related genes to become circulative in its vector, (Hemiptera: Psyllidae).

Unlabelled: Citrus greening disease or huanglongbing (HLB) caused by Liberibacter asiaticus (Las) limits citrus production worldwide. Las is transmitted by the Asian citrus psyllid (ACP), (Hemiptera: Psyllidae) in a persistent-propagative manner. Understanding the molecular interaction between Las and ACP and interrupting the interrelationship can provide an alternative to insecticides for managing citrus greening disease.

Genetic Variability Based on Tandem Repeat Numbers in a Genomic Locus of ' Liberibacter asiaticus' Prevalent in North East India.

The genetic variability of ' Liberibacter asiaticus' (CLas) population associated with huanglongbing (HLB) disease of citrus in North Eastern (NE) region of India, a geographically locked region, and home for the diversity of many citrus species was analyzed on the basis of tandem repeat numbers (TRN) in variable CLIBASIA_01645 genomic loci. Fifty-five CLas strains sampled from different groves of NE Hill (NEH) region of India were in single amplicon group, but there was remarkable genetic variability in TRNs. The TRN in HLB-associated CLas strains varied from 0-21 and two novel repeat motifs were also identified.

Efficient immunodiagnosis of using polyclonal antibodies with an expressed recombinant virion-associated protein.

(CYMV) is a member of genus of the family . It is the causal agent of citrus yellow mosaic disease in citrus and causes reduction in yield. As the virus is vegetative propagated by grafting, development of high-throughput diagnosis methods based on serological techniques is a prerequisite for production of healthy virus-free planting material.

Development of a recombinase polymerase amplification assay for the diagnosis of banana bunchy top virus in different banana cultivars.

Recombinase polymerase amplification (RPA) is a rapid, isothermal amplification method with high specificity and sensitivity. In this study, an assay was developed and evaluated for the detection of banana bunchy top virus (BBTV) in infected banana plants. Three oligonucleotide primer pairs were designed from the replicase initiator protein gene sequences of BBTV to function both in RPA as well as in polymerase chain reaction (PCR).

Immunodiagnosis of episomal Banana streak MY virus using polyclonal antibodies to an expressed putative coat protein.

A cryptic Badnavirus species complex, known as banana streak viruses (BSV) poses a serious threat to banana production and genetic improvement worldwide. Due to the presence of integrated BSV sequences in the banana genome, routine detection is largely based on serological and nucleo-serological diagnostic methods which require high titre specific polyclonal antiserum. Viral structural proteins like coat protein (CP) are the best target for in vitro expression, to be used as antigen for antiserum production.