A. A. Zaidi

Molecular characterization of a distinct bipartite begomovirus species infecting tomato in India

A distinct bipartite begomovirus was found associated with tomato plants showing yellowing, curling, and crumpling of the leaves, in a sub-temperate region in India. The complete DNA-A and DNA-B components were amplified through rolling circle amplification (RCA) using Φ-29 DNA polymerase and characterized. The DNA-A of the isolate was comprised of 2,756 nucleotides, encoding six open reading frames (ORFs) and DNA-B that of 2,725 nucleotides, encoding two ORFs. Genome organization of the isolate was typical of an old world bipartite begomovirus. Comparisons showed that DNA-A and its intergenic region (IR) have the highest sequence identity (86% and 84%, respectively) with the Tomato leaf curl New Delhi virus (ToLCNDV; DQ116885) and some other begomoviruses (>84%) reported from cucurbits and tomato. This data suggested that the isolate is a distinct begomovirus species for which a name Tomato leaf curl Palampur virus (ToLCPMV) is proposed. DNA-B showed the maximum sequence identity (73%) with Tomato leaf curl New Delhi virus-India-[Pakistan:Dargai:T5/6:2001] (AY150305). The common region (CR) of DNA-A and DNA-B showed 94% sequence similarity with each other. In the present study, phylogenetic relationship of this new species was also established with different begomoviruses reported from tomato and other begomoviruses showing highest homologies with complete DNA-A and DNA-B sequences. ToLCPMV is being reported from a sub-temperate region in India which was previously unaffected by begomoviruses and its whitefly vector.

An overview of diagnostics for viruses infecting gladiolus

Abstract In order to improve the crop productivity, quality of germplasm and minimise infection in different cultivars of gladiolus, its proper diagnosis and control is essential. In addition, diagnosis also helps in exporting planting material to countries wherein strict quarantine conditions have been imposed. During the last two decades much advance has been made in diagnostics for the detection of viral diseases, but incidence of viral infection is increasing. In plants, emphasis has always been given to the diagnosis of viral infection in different parts of plants, particularly in the propagating material as it indirectly helps in the control of the infection. As well as Immuno-diagnostics, molecular biology has also provided techniques like the use of DNA/RNA probes, the polymerase chain reaction, etc. to detect the viruses. These techniques have shown great potential as far as specificity and sensitivity are concerned. The aim of this review is to discuss immuno-diagnostics and molecular-diagnostics used in the field of disease diagnosis of gladiolus, most particularly to diagnose Bean Yellow Mosaic Virus (BYMV) and Cucumber Mosaic Virus (CMV). DAS-ELISA, DTBIA, ISEM and RT-PCR are found to be the most suitable techniques to detect the various BYMV and CMV infecting gladiolus. These tests not only provide information for epidemiological purposes, but also to develop disease-free stock of gladiolus, which ultimately helps to control the infection.

Coat protein sequence shows that Cucumber mosaic virus isolate from geraniums (Pelargonium spp.) belongs to subgroup II

A viral disease was identified on geraniums (Pelargonium spp.) grown in a greenhouse at the Institute of Himalayan Bioresource Technology (IHBT), Palampur, exhibiting mild mottling and stunting. The causal virus (Cucumber mosaic virus, CMV) was identified and characterized on the b0asis of host range, aphid transmission, enzyme linked immunosorbent assay (ELISA), DNA-RNA hybridization and reverse transcription polymerase chain reaction (RT-PCR). A complete coat protein (CP) gene was amplified using degenerate primers and sequenced. The CP gene showed nucleotide and amino acid homology up to 97%–98% and 96%–99%, respectively with the sequences of CMV subgroup II. The CP gene also showed homologies of 75%–97% in nucleotide and 77%–96% in amino acid with the CMV Indian isolates infecting various crops. On the basis of sequence homology, it was concluded that CMV-infecting geraniums in India belong to subgroup II

Detection and characterization of Ageratum enation virus and a nanovirus-like satellite DNA1 from zinnia causing leaf curl symptoms in India.

Leaf curl in Zinnia elegans was observed in a subtemperate region in northern India, and the causal organism was identified as Ageratum enation virus (AEV). The virus appeared to be monopartite and associated with nanovirus-like satellite DNA1. The whole genome was amplified by rolling circle amplification, cloned, and sequenced using a primer walking strategy. The genome (FN543099) was composed of 2753 nucleotides (nt) and that of DNA1 (FN543100) of 1374 nt. DNA-β was not detected from any of the infected samples. The study presents the first report of a begomovirus from Zinnia spp. in India and the complete nucleotide sequence characterization of AEV associated with nanovirus-like satellite DNA1.

Complete nucleotide sequence analysis of Cymbidium mosaic virus Indian isolate: further evidence for natural recombination among potexviruses

The complete nucleotide sequence of an Indian strain of Cymbidium mosaic virus (CymMV) was determined and compared with other potexviruses. Phylogenetic analyses on the basis of RNA-dependent RNA polymerase (RdRp), triple gene block protein and coat protein (CP) amino acid sequences revealed that CymMV is closely related to the Narcissus mosaic virus (NMV), Scallion virus X (SVX), Pepino mosaic virus (PepMV) and Potato aucuba mosaic virus (PAMV). Different sets of primers were used for the amplification of different regions of the genome through RT-PCR and the amplified genes were cloned in a suitable vector. The full genome of the Indian isolate of CymMV from Phaius tankervilliae shares 96–97% similarity with isolates reported from other countries. It was found that the CP gene of CymMV shares a high similarity with each other and other potexviruses. One of the Indian isolates seems to be a recombinant formed by the intermolecular recombination of two other CymMV isolates. The phylogenetic analyses, Recombination Detection Program (RDP2) analyses and sequence alignment survey provided evidence for the occurrence of a recombination between an Indian isolate (AM055720) as the major parent, and a Korean type-2 isolate (AF016914) as the minor parent. Recombination was also observed between a Singapore isolate (U62963) as the major parent, and a Taiwan CymMV (AY571289) as the minor parent.

A potyvirus in Cymbidium spp. in northern India

A potyvirus was isolated from diseased Cymbidium pendulum and C. tigrinum epiphytic orchids collected from Sikkim in northern India. ELISA, RT-PCR and Northern blot analysis revealed the association of potyvirus infection with disease symptoms. The sequencing of a RT-PCR-amplified amplicon using potyvirus group-specific primers showed that this virus is distinct but most closely related to Calanthe mild mosaic virus. This paper reports the occurrence of potyvirus in wild orchids especially in Cymbidium spp.

Molecular variability analyses of Apple chlorotic leaf spot virus capsid protein.

The complete sequences of the coat protein (CP) gene of 26 isolates of Apple chlorotic leaf spot virus (ACLSV) from India were determined. The isolates were obtained from various pome (apple, pear and quince) and stone (plum, peach, apricot, almond and wild Himalayan cherry) fruit trees. Other previously characterized ACLSV isolates and Trichoviruses were used for comparative analysis. Indian ACLSV isolates among themselves and with isolates from elsewhere in the world shared 91–100% and 70–98% sequence identities at the amino acid and nucleotide levels, respectively. The highest degree of variability was observed in the middle portion with 9 amino acid substitutions in contrast to the N-terminal and C-terminal ends, which were maximally conserved with only 4 amino acid substitutions. In phylogenetic analysis no reasonable correlation between host species and/or geographic origin of the isolates was observed. Alignment with capsid protein genes of other Trichoviruses revealed the TaTao ACLSV peach isolate to be phylogenetically closest to Peach mosaic virus, Apricot pseudo chlorotic leaf spot virus and Cherry mottle leaf virus. Recombination analysis (RDP3 ver.2.6) done for all the available ACLSV complete CP sequences of the world and Indian isolates indicate no significant evidence of recombination. However, one recombination event among Indian ACLSV-CP isolates was detected. To the best of our knowledge, this is the first report of complete CP sequence variability study from India and also the first evidence of homologous recombination in ACLSV.

Genomic sequence analysis of four new chrysanthemum virus B isolates: evidence of RNA recombination

Chrysanthemums worldwide suffer from a high incidence of infection with chrysanthemum virus B (CVB), a member of the genus Carlavirus, family Betaflexiviridae. Three major lineages or strains of this virus have been found in India, but none have been characterized beyond the genetic variation they display in their coat protein genes. Here, we describe the analysis of four near-complete genome sequences (from the three lineages) representing the genetic diversity of these strains. Ranging in size from 8815 to 8855 nucleotides (excluding the polyA tail), these four isolates have a genome organization very similar to that of the recently reported Japanese isolate of CVB, with which they share between 70 and 73% genome-wide sequence identity. We present further evidence that recombination may feature quite prominently in the evolution of CVB.

First report of Ageratum enation virus infecting Crassocephalum crepidioides (Benth.) S. Moore and Ageratum conyzoides L. in India

In October 2009, vein yellowing disease was observed on the weeds Crassocephalum crepidioides and Ageratum conyzoides in a subtemperate region in northern India. Ageratum enation virus (AEV), along with a nanovirus like satellite DNA 1, was found to be associated with both weeds. The isolates had 99% identity with each other and with an isolate of AEV reported from Zinnia elegans from this region. To the best of our knowledge, this report is the first of any begomovirus infection in C. crepidioides in India and the first on AEV infecting C. crepidioides worldwide and A. conyzoides in India.

Determination of Major Viral and Sub Viral Pathogens Incidence in Apple Orchards in Himachal Pradesh

Apple is the major commercial horticulture crop in Himachal Pradesh and other hill states of Jammu & Kashmir, Uttarakhand and some parts of Northeastern states of India. In order to gather data on health status and incidence of virus and virus-like pathogens in apple orchards, survey was conducted in the month of June and September, 2010 in Hatkoti, Rohru, Kuthara, Jubbal and Khadapathar areas of major apple producing Shimla district of Himachal Pradesh. A total of 250 samples were collected and analyzed by DAS-ELISA, NASH and RT-PCR. NASH results indicated that a total of 117 samples were infected with Apple chlorotic leaf spot virus (ACLSV), Apple mosaic virus (ApMV), Apple stem grooving virus (ASGV), Apple stem pitting virus (ASPV) and Apple scar skin viroid (ASSVd). Results showed that ASSVd is predominant in these areas with highest infection rate of 27.6% followed by ASPV (17.2%), ACLSV (16.8%), ApMV (15.2%) and ASGV (12%). Mixed infection of these viruses and viroid was frequently detected in apple trees in Himachal Pradesh. The trees, which were positive for viruses and viroids, showed a variety of fruit deformation and rusting symptoms besides leaf deformation, mosaic and chlorosis.