Genome organization of ageratum yellow vein virus, a monopartite whitefly-transmitted geminivirus isolated from a common weed

Functional role of geminivirus encoded proteins in the host: Past and present

During plant-pathogen interaction, plant exhibits a strong defense system utilizing diverse groups of proteins to suppress the infection and subsequent establishment of the pathogen. However, in response, pathogens trigger an anti-silencing mechanism to overcome the host defense machinery. Among plant viruses, geminiviruses are the second largest virus family with a worldwide distribution and continue to be production constraints to food, feed, and fiber crops. These viruses are spread by a diverse group of insects, predominantly by whiteflies, and are characterized by a single-stranded DNA (ssDNA) genome coding for four to eight proteins that facilitate viral infection. The most effective means to managing these viruses is through an integrated disease management strategy that includes virus-resistant cultivars, vector management, and cultural practices. Dynamic changes in this virus family enable the species to manipulate their genome organization to respond to external changes in the environment. Therefore, the evolutionary nature of geminiviruses leads to new and novel approaches for developing virus-resistant cultivars and it is essential to study molecular ecology and evolution of geminiviruses. This review summarizes the multifunctionality of each geminivirus-encoded protein. These protein-based interactions trigger the abrupt changes in the host methyl cycle and signaling pathways that turn over protein normal production and impair the plant antiviral defense system. Studying these geminivirus interactions localized at cytoplasm-nucleus could reveal a more clear picture of host-pathogen relation. Data collected from this antagonistic relationship among geminivirus, vector, and its host, will provide extensive knowledge on their virulence mode and diversity with climate change.

Impact of leaf trichomes of tomatoes and weeds on the host selection and developmental bioassays of Bemisia tabaci Q and A cryptic species

The whiteflies of Bemisia tabaci complex, composed of >44 cryptic species, are economically important pests of tomatoes for their direct feeding and virus transmission. The present study aimed to evaluate the impact of leaf trichomes on the host selection and development of whitefly; comparative invasiveness between B. tabaci Q and A cryptic species; and the ability of weeds as hosts of the population of insect whitefly. We carried out our investigation through adult host selection and oviposition in multi-choice conditions, immature development and survival, and adult survival and oviposition in no-choice conditions. We investigated leaf trichomes type and densities on the leaves of four tomato varieties and two weed species. Results showed that the leaf trichomes of tomatoes and weeds impact the host selection and immature development differently on the cryptic species B. tabaci Q and A. In the multi-choice case, B. tabaci Q adults preferred tomato varieties Ao-Ni-Er and He-Fen for both settling and oviposition whereas B. tabaci A preferred Ao-Ni-Er, He-Fen, and Billy-Goat-Weed for settling but oviposited more eggs on both weed species Billy-Goat-Weed and False-Mallow. Both B. tabaci Q and A adults refused Ye-Sheng either settling or oviposition. In the case of immature development, B. tabaci Q developed faster than B. tabaci A. Concerning plant, B. tabaci Q developed faster on Ao-Ni-Er, He-Fen and Billy-Goat-Weed but B. tabaci A on Billy-Goat-Weed, False-Mallow and Ao-Ni-Er. The immature survival of Q was higher than that of A. Immature of B. tabaci Q survived well (68.6-86.8%) on all plants except Ye-Sheng (49.3%) but B. tabaci A survived very less (0-17.6%) on any tomatoes where 70.4% on Billy-Goat-Weed and 60.5% on False-Mallow. After seven days of adult infestation, both B. tabaci Q and A died on Ye-Sheng where 52.5-78.1% survivorships were observed on other plants. In seven days, B. tabaci Q laid more eggs compared to B. tabaci A. Considering the plants, both species laid more eggs on Ao-Ni-Er, He-Fen and False-Mallow, whereas the lowest number was laid on Ye-Sheng. The highest number of glandular trichome Type IV was observed on Ye-Sheng which showed resistance against both B. tabaci Q and A cryptic species. The cryptic species B. tabaci Q showed a wider range adaptation ability on plants than that of A. Weeds can play a significant role as an infestation source of whiteflies to tomatoes and other crops. These findings suggest that glandular trichomes may be used in plant breeding programmes for the development of whitefly-resistant crop cultivars.

Complete genome sequence of a novel bipartite begomovirus infecting the legume weed Macroptilium erythroloma

The natural occurrence of mixed infections and large populations of the polyphagous vector (Bemisia tabaci) are the main factors associated with the intensification of the genetic flow among begomoviruses in Neotropical areas, contributing to the emergence of novel recombinants. Here, high-throughput sequencing and metagenomic analyses were employed to discover and characterize a novel recombinant bipartite begomovirus, tentatively named "macroptilium bright yellow interveinal virus" (MaBYIV) in the weed Macroptilium erythroloma (Fabaceae). Recombination signals were detected in MaBYIV, involving bean golden mosaic virus (BGMV) and tomato mottle leaf curl virus (ToMoLCV) genome components. All of the original MaBYIV-infected M. erythroloma plants were found to have mixed infections with BGMV. MaBYIV was transmitted to bean and soybean cultivars via B. tabaci MEAM 1, indicating that M. erythroloma may play a role as a year-round reservoir of a potential new viral pathogen of economically important legume crops.

Complete Genome Sequences of Tomato Leaf Curl Guam Virus, a Novel Tomato-Infecting Begomovirus from Guam, USA

Genome sequences of a novel begomovirus infecting tomato on Guam were obtained using primer-walking and sequencing. The complete genome sequences are 2,750 nucleotides long with a typical monopartite organization and display less than 91% nucleotide sequence identity to other begomoviruses. A provisional name, tomato leaf curl Guam virus (ToLCGuV), is proposed.

Requirements for the Packaging of Geminivirus Circular Single-Stranded DNA: Effect of DNA Length and Coat Protein Sequence

Geminivirus particles, consisting of a pair of twinned isometric structures, have one of the most distinctive capsids in the virological world. Until recently, there was little information as to how these structures are generated. To address this, we developed a system to produce capsid structures following the delivery of geminivirus coat protein and replicating circular single-stranded DNA (cssDNA) by the infiltration of gene constructs into plant leaves. The transencapsidation of cssDNA of the Begomovirus genus by coat protein of different geminivirus genera was shown to occur with full-length but not half-length molecules. Double capsid structures, distinct from geminate capsid structures, were also generated in this expression system. By increasing the length of the encapsidated cssDNA, triple geminate capsid structures, consisting of straight, bent and condensed forms were generated. The straight geminate triple structures generated were similar in morphology to those recorded for a potato-infecting virus from Peru. These finding demonstrate that the length of encapsidated DNA controls both the size and stability of geminivirus particles.

Identification and characterization of Ageratum yellow vein Malaysia virus (AYVMV) and an associated betasatellite among begomoviruses infecting Solanum lycopersicum in Malaysia

The study describes results of a survey of tomato fields for the presence of begomoviruses from different regions of Peninsular Malaysia. An ORF-based (C2 and C3) study was performed to determine the distribution of begomoviruses associated with a severe leaf curl disease in tomato-growing areas of Peninsular Malaysia. Viral DNA was isolated from symptomatic tomato plants, and begomovirus association was confirmed by PCR using DNA-A degenerate primers. The C2 and C3 sequences of the putative begomoviruses were similar to two corresponded ORFs of different geographically separated strains of begomoviruses: Pepper yellow leaf curl Indonesia virus and Tomato yellow leaf curl Kanchanaburi virus. The present study also identified a unique isolate, Ageratum yellow vein Malaysia virus (AYVMV) among above mentioned survey. It has a single-stranded DNA component and its associated betasatellite. The single-stranded DNA component is consisting of 2750 nt with six open reading frames and an organization resembling that of monopartite geminiviruses. The full length of viral single-stranded DNA component genome obtained using next generation sequencing (NGS) showed the highest sequence identity (99%) with Ageratum yellow vein virus (AYVV-BA). The betasatellite component genome obtained by NGS has 1342 nt and showed the highest sequence identity (91%) with the Pepper yellow leaf curl betasatellite. Following ICTV guidelines, Ageratum yellow vein Malaysia virus was assigned the abbreviation AYVMV with sequence and phylogenetic analysis indicating that it might have evolved by recombination of two or more viral ancestors.

African Basil (Ocimum gratissimum) Is a Reservoir of Divergent Begomoviruses in Uganda

Begomoviruses are plant viruses that cause major losses to many economically important crops. Although they are poorly understood, begomoviruses infecting wild plants may have an important role as reservoirs in the epidemiology of viral diseases. This study reports the discovery and genomic characterization of three novel bipartite begomoviruses from wild and cultivated African basil (Ocimum gratissimum) plants collected in Uganda, East Africa. Based on the symptoms shown by the infected plants, the names proposed for these viruses are Ocimum yellow vein virus (OcYVV), Ocimum mosaic virus (OcMV), and Ocimum golden mosaic virus (OcGMV). Genome and phylogenetic analyses suggest that DNA-A of OcGMV is mostly related to begomoviruses infecting tomato in Africa, whereas those of OcYVV and OcMV are closely related to one another and highly divergent within the Old World begomoviruses. The DNA-A of all characterized begomovirus isolates are of a recombinant nature, revealing the role of recombination in the evolution of these begomoviruses. The viruses characterized here are the first identified in O. gratissimum and the first in Ocimum spp. in the African continent and could have important epidemiological consequences for cultivated basils and other important crops.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Multifaceted role of geminivirus associated betasatellite in pathogenesis

Begomoviruses have emerged as a group of plant pathogens that cause devastating diseases in a wide range of crops in tropical and subtropical regions of the world. Betasatellites, the circular single-stranded DNA molecules with the size of almost half of that of the associated helper begomoviruses, are often essential for the production of typical disease symptoms in several virus-host systems. Association of betasatellites with begomoviruses results in more severe symptoms in the plants and affects the yield of numerous crops leading to huge agroeconomic losses. βC1, the only protein encoded by betasatellites, plays a multifaceted role in the successful establishment of infection. This protein counteracts the innate defence mechanisms of the host, like RNA silencing, ubiquitin-proteasome system and defence responsive hormones. In the last two decades, the molecular aspect of betasatellite pathogenesis has attracted much attention from the researchers worldwide, and reports have shown that βC1 protein aggravates the helper begomovirus disease complex by modulating specific host factors. This review discusses the molecular aspects of the pathogenesis of betasatellites, including various βC1-host factor interactions and their effects on the suppression of defence responses of the plants.

The 3.3 Å structure of a plant geminivirus using cryo-EM

Geminiviruses are major plant pathogens that threaten food security globally. They have a unique architecture built from two incomplete icosahedral particles, fused to form a geminate capsid. However, despite their importance to agricultural economies and fundamental biological interest, the details of how this is realized in 3D remain unknown. Here we report the structure of Ageratum yellow vein virus at 3.3 Å resolution, using single-particle cryo-electron microscopy, together with an atomic model that shows that the N-terminus of the single capsid protein (CP) adopts three different conformations essential for building the interface between geminate halves. Our map also contains density for ~7 bases of single-stranded DNA bound to each CP, and we show that the interactions between the genome and CPs are different at the interface than in the rest of the capsid. With additional mutagenesis data, this suggests a central role for DNA binding-induced conformational change in directing the assembly of geminate capsids.

Identification of amino acid residues of the coat protein of Sri Lankan cassava mosaic virus affecting symptom production and viral titer in Nicotiana benthamiana

Sri Lankan cassava mosaic virus (SLCMV) is bipartite begomovirus infecting cassava in India and Sri Lanka. Interestingly, the DNA-A component of the SLCMV alone is able to infect Nicotiana benthamiana causing symptoms of upward leaf rolling and stunting. One of the differences between monopartite and bipartite begomoviruses is the requirement of Coat Protein (CP) for infectivity; CP being essential for the former, but dispensable in the latter. This investigation was aimed to determine the importance of CP in the infectivity of the bipartite SLCMV, behaving as a monopartite virus in N. benthamiana. We tested CP-null mutants, single amino acid replacement mutants and double, triple and quadruple combinations of the above in SLCMV DNA-A, for infectivity, symptom development and viral DNA accumulation in N. benthamiana. While CP-null mutants were non-infectious, a majority of the single amino acid replacement mutants and their combinations retained infectivity, some with attenuated symptoms and reduced viral titers. Some of the combined mutations restored the attenuated symptoms to wild type levels. Some of the mutations were predicted to cause changes in the secondary structure of the CP, which roughly correlated with the attenuation of symptoms and the reduction in viral titers.

Molecular Characterization of a Begomovirus and Betasatellite Causing Yellow Vein Net Disease of Ageratum houstonianum

Ageratum houstonianum was introduced in India as an annual ornamental plant and is grown in beds for blue head flowers. Yellow vein net disease was observed on A. houstonianum plants with about 9.0% disease incidence during a survey in February 2012 at gardens of NBRI, Lucknow, India. Association of a begomovirus and betasatellite with the disease was characterized based on sequence analyses of their cloned full length genome isolated from diseased A. houstonianum. Sequence analysis of the begomovirus showed presence of the six open reading frames in its genome, similar to the arrangement of Old World begomoviruses. The begomoviral genome shared 95 to 97% sequence identities with various strains of Ageratum enation virus (AEV); however, it showed distinct phylogenetic relationships with them, and hence was identified as a variant of AEV based on more than 94% sequence homology, the criteria defined by ICTV. The sequence analysis of associated betasatellite revealed highest 93% sequence identity and close phylogenetic relationships with Ageratum leaf curl betasatellite (ALCB) molecules; therefore, it was identified as an isolate of ALCB (based on 93% sequence homology). Agroinfiltration of partial dimers of the AEV variant and ALCB induced similar systemic yellow vein net and leaf curl symptoms on A. houstonianum when infiltrated in combination, fulfilling Koch's postulates. Characterization of AEV and ALCB causing yellow vein net disease of A. houstonianum is being reported for the first time.

Organellar mechanosensitive channels involved in hypo-osmoregulation in fission yeast

MscS and MscL, bacterial mechanosensitive channels, play crucial roles in the hypo-osmotic shock response. However, only MscS has homologs in eukaryotes. These homologs are called MscS-like proteins or MSL proteins. MSL proteins have changed both structurally and functionally during evolution and are now localized not only to the membrane of the chloroplast, which is thought to be a descendant of an ancient, free-living bacterium, but also the cell membrane and the endoplasmic reticulum (ER) membrane, suggesting that the role of MSL proteins has diverged. In this brief review, we mainly focus on two MSL proteins in the fission yeast Schizosaccharomyces pombe that are localized in the ER membrane and protect cells from hypo-osmotic shock-induced death by regulating intracellular Ca(2+) concentrations. We also discuss Arabidopsis thaliana MSL proteins and other yeast ion channels in terms of osmoregulation in eukaryotes.

Generation of marker-free transgenic plants concurrently resistant to a DNA geminivirus and a RNA tospovirus

Global threats of ssDNA geminivirus and ss(-)RNA tospovirus on crops necessitate the development of transgenic resistance. Here, we constructed a two-T DNA vector carrying a hairpin of the intergenic region (IGR) of Ageratum yellow vein virus (AYVV), residing in an intron inserted in an untranslatable nucleocapsid protein (NP) fragment of Melon yellow spot virus (MYSV). Transgenic tobacco lines highly resistant to AYVV and MYSV were generated. Accumulation of 24-nt siRNA, higher methylation levels on the IGR promoters of the transgene, and suppression of IGR promoter activity of invading AYVV indicate that AYVV resistance is mediated by transcriptional gene silencing. Lack of NP transcript and accumulation of corresponding siRNAs indicate that MYSV resistance is mediated through post-transcriptional gene silencing. Marker-free progenies with concurrent resistance to both AYVV and MYSV, stably inherited as dominant nuclear traits, were obtained. Hence, we provide a novel way for concurrent control of noxious DNA and RNA viruses with less biosafety concerns.

Identification and characterisation of a highly divergent geminivirus: evolutionary and taxonomic implications

During a large scale "non a priori" survey in 2010 of South African plant-infecting single stranded DNA viruses, a highly divergent geminivirus genome was isolated from a wild spurge, Euphorbia caput-medusae. In addition to being infectious in E. caput-medusae, the cloned viral genome was also infectious in tomato and Nicotiana benthamiana. The virus, named Euphorbia caput-medusae latent virus (EcmLV) due to the absence of infection symptoms displayed by its natural host, caused severe symptoms in both tomato and N. benthamiana. The genome organisation of EcmLV is unique amongst geminiviruses and it likely expresses at least two proteins without any detectable homologues within public sequence databases. Although clearly a geminivirus, EcmLV is so divergent that we propose its placement within a new genus that we have tentatively named Capulavirus. Using a set of highly divergent geminiviruses genomes, it is apparent that recombination has likely been a primary process in the genus-level diversification of geminiviruses. It is also demonstrated how this insight, taken together with phylogenetic analyses of predicted coat protein and replication associated protein (Rep) amino acid sequences indicate that the most recent common ancestor of the geminiviruses was likely a dicot-infecting virus that, like modern day mastreviruses and becurtoviruses, expressed its Rep from a spliced complementary strand transcript.

Identification and molecular characterization of begomovirus and associated satellite DNA molecules infecting Cyamopsis tetragonoloba

Monopartite begomoviruses comprise DNA-A as the main genome and associated satellite DNAs. Viral DNA extracted from guar (Cyamopsis tetragonoloba) showing leaf curl symptoms exhibited positive amplification of coat protein (CP) gene of DNA-A component, suggesting the presence of begomovirus. Full length DNA-A was amplified by primer pair re-designed from CP gene nucleotide sequence. The associated alphasatellite and betasatellite DNA molecules were amplified and sequenced, confirming the presence of monopartite begomovirus. Sequence comparisons showed 89% identity with other begomoviruses. The Neighbor-Joining tree based on full length DNA-A nucleotide sequence showed that the guar infecting begomovirus clustered separately from other known begomoviruses. The betasatellite shared a high (96%) nucleotide identity to Cotton leaf curl Multan betasatellites. The alphasatellite showed 91% nucleotide identity to alphasatellite associated with begomovirus infecting Okra. Recombination analyses showed three recombinant fragments in DNA-A, two in betasatellite, and four in alphasatellite. The results suggest that the begomovirus identified in this study was a new recombinant virus. Its name was proposed as Cyamopsis tetragonoloba leaf curl virus (CyTLCuV).

Identification and molecular characterization of begomovirus and associated satellite DNA molecules infecting Cyamopsis tetragonoloba

Monopartite begomoviruses comprise DNA-A as the main genome and associated satellite DNAs. Viral DNA extracted from guar (Cyamopsis tetragonoloba) showing leaf curl symptoms exhibited positive amplification of coat protein (CP) gene of DNA-A component, suggesting the presence of begomovirus. Full length DNA-A was amplified by primer pair re-designed from CP gene nucleotide sequence. The associated alphasatellite and betasatellite DNA molecules were amplified and sequenced, confirming the presence of monopartite begomovirus. Sequence comparisons showed 89% identity with other begomoviruses. The Neighbor-Joining tree based on full length DNA-A nucleotide sequence showed that the guar infecting begomovirus clustered separately from other known begomoviruses. The betasatellite shared a high (96%) nucleotide identity to Cotton leaf curl Multan betasatellites. The alphasatellite showed 91% nucleotide identity to alphasatellite associated with begomovirus infecting Okra. Recombination analyses showed three recombinant fragments in DNA-A, two in betasatellite, and four in alphasatellite. The results suggest that the begomovirus identified in this study was a new recombinant virus. Its name was proposed as Cyamopsis tetragonoloba leaf curl virus (CyTLCuV).

Replication promiscuity of DNA-beta satellites associated with monopartite begomoviruses; deletion mutagenesis of the Ageratum yellow vein virus DNA-beta satellite localizes sequences involved in replication

Pseudorecombination studies in Nicotiana benthamiana demonstrate that Ageratum yellow vein virus (AYVV) and Eupatorium yellow vein virus (EpYVV) can functionally interact with DNA-beta satellites associated with AYVV, EpYVV, cotton leaf curl Multan virus (CLCuMV) and honeysuckle yellow vein virus (HYVV). In contrast, CLCuMV shows some specificity in its ability to interact with distinct satellites and HYVV is able to interact only with its own satellite. Using an N. benthamiana leaf disk assay, we have demonstrated that HYVV is unable to trans-replicate other satellites. To investigate the basis of trans-replication compatibility, deletion mutagenesis of AYVV DNA-beta has been used to localize the origin of replication to approximately 360 nt, encompassing the ubiquitous nonanucleotide/stem-loop structure, satellite conserved region (SCR) and part of the intergenic region immediately upstream of the SCR. Additional deletions within this intergenic region have identified a region that is essential for replication. The capacity for DNA-beta satellites to functionally interact with distinct geminivirus species and its implications for disease diversification are discussed.

Recommendations for the classification and nomenclature of the DNA-beta satellites of begomoviruses

The symptom-modulating, single-stranded DNA satellites (known as DNA-beta) associated with begomoviruses (family Geminiviridae) have proven to be widespread and important components of a large number of plant diseases across the Old World. Since they were first identified in 2000, over 260 full-length sequences (approximately 1,360 nucleotides) have been deposited with databases, and this number increases daily. This has highlighted the need for a standardised, concise and unambiguous nomenclature for these components, as well as a meaningful and robust classification system. Pairwise comparisons of all available full-length DNA-beta sequences indicate that the minimum numbers of pairs occur at a sequence identity of 78%, which we propose as the species demarcation threshold for a distinct DNA-beta. This threshold value divides the presently known DNA-beta sequences into 51 distinct satellite species. In addition, we propose a naming convention for the satellites that is based upon the system already in use for geminiviruses. This maintains, whenever possible, the association with the helper begomovirus, the disease symptoms and the host plant and provides a logical and consistent system for referring to already recognised and newly identified satellites.

Deletion and recombination events between the DNA-A and DNA-B components of Indian cassava-infecting geminiviruses generate defective molecules in Nicotiana benthamiana

Cloned DNA-B components, belonging to the bipartite begomoviruses Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosaic virus (SLCMV), family Geminiviridae, when co-inoculated along with previously cloned DNA-A components of the respective viruses onto the experimental host Nicotiana benthamiana, generated defective DNAs (def-DNA) ranging in size from 549 to 1555 nucleotides. All the cloned def-DNAs contained the common region (CR) as well as portions of either DNA-A or DNA-B and, in a few cases, both DNA-A and DNA-B, representing recombinant products, the junction points of which correspond to repeats of 2-11 bases found in the parental molecules. The DNA-B-derived def-DNAs were, in some cases, associated with a decrease in levels of DNA-B, with a concomitant change in the symptoms from downward leaf curling in the older leaves to upward leaf-rolling in newly emerging leaves, more typical of monopartite begomoviruses.

Molecular characterization of a new begomovirus infecting Sida cordifolia and its associated satellite DNA molecules

Two virus isolates Hn57 and Hn60 were obtained from Sida cordifolia showing mild upward leaf-curling symptoms in Hainan province of China. Comparison of partial sequences of DNA-A like molecule confirmed the existence of a single type of begomovirus. The complete nucleotide sequence of DNA-A of Hn57 was determined to be 2757 nucleotides, with a genomic organization typical of begomoviruses. Complete sequence comparison with other reported begomoviruses revealed that Hn57 DNA-A has the highest sequence identity (71.0%) with that of Tobacco leaf curl Yunnan virus. Consequently, Hn57 was considered to be a new begomovirus species, for which the name Sida leaf curl virus (SiLCV) is proposed. In addition to DNA-A molecule, two additional circular single-stranded satellite DNA molecules corresponding to DNAbeta and DNA1 were found to be associated with SiLCV isolates. Both DNAbeta and DNA1 were approximately half the size of their cognate genomic DNA. Sequence analysis shows that DNAbeta of Hn57 and Hn60 share 93.8% nucleotide sequence identity, and they have the highest sequence identity (58.5%) with DNAbeta associated with Ageratum leaf curl disease (AJ316027). The nucleotide sequence identity between DNA1 of Hn57 and that of Hn60 was 83.8%, they share 58.2-79.3% nucleotide sequence identities in comparison with other previously reported DNAl.

Serological investigation and genomic characterization of PCV2 isolates from different geographic regions of Zhejiang province in China

Sera collected from 46 swine farms in Zhejiang province were evaluated for the presence of antibodies to PCV2 using an indirect-fluorescent antibody procedure. In addition PCV2 isolated from superficial inguinal lymph node samples collected from 40-to 90-day-old pigs with clinical signs of post-weaning multisystemic wasting syndrome (PMWS) using the PK-15 cell line were sequenced and compared. Overall seroprevalence of PCV2 antibody averaged 58.34% for all samples. Breakdown of serology by groups was as follows: 59.38% for sows, 57.41% for post-weaning piglets, 44.83% for Landrace sows and 64.28% for Landrace piglets. The seroprevalence of Landrace sows was higher than that of Yorkshire and Duroc sows, but non-significant (p > 0.05). Serological analysis also showed that seroprevalence of PCV2 antibody was a negative correlation to that of PRRSV antibody. The complete genomes of five PCV2 isolates identified in the herds with PMWS consisted of 1767nt, containing the 11 potential ORFs. Genome of the virus isolates shared 93.8% to 99.8% identity with PCV2 reference strains from GenBank, 76.6% to 77.9% identity with PCV1. Phylogenetic analysis indicated that there were two subgenotypes within PCV2: subgenotype I (1767 nt) and subgenotype II (1768 nt).

The Natural Occurrence of Two Distinct Begomoviruses Associated with DNAbeta and a Recombinant DNA in a Tomato Plant from Indonesia

ABSTRACT Two begomoviruses (Java virus-1 and Java virus-2), two satellite DNAs (DNAbeta01 and DNAbeta02), and a recombinant DNA (recDNA) were cloned from a single tomato plant from Indonesia with leaf curl symptoms, and the role of these satellite DNAs in the etiology of begomovirus disease was investigated. The genome organizations of the two viruses were similar to those of other Old World monopartite begomoviruses. Comparison of the sequences with other begomoviruses revealed that Java virus-1 was a newly described virus for which the name Tomato leaf curl Java virus (ToLCJAV) is proposed. Java virus-2 was a strain of Ageratum yellow vein virus (AYVV) (AYVV-[Java]). ToLCJAV or AYVV-[Java] alone did not induce leaf curl symptoms in tomato plants. However, in the presence of DNAbeta02, both ToLCJAV and AYVV-[Java] induced leaf curl symptoms in tomato plants. In the presence of DNAbeta01, these viruses induced mild leaf curl symptoms in tomato plants. The recDNA had a chimeric sequence, which arose from recombination among ToLCJAV, AYVV-[Java], DNAbeta01, and DNAbeta02; it was replicated only in the presence of AYVV-[Java] in tomato plants.

Subviral agents associated with plant single-stranded DNA viruses

Begomoviruses (family Geminiviridae) are responsible for many economically important crop diseases worldwide. The majority of these diseases are caused by bipartite begomovirus infections, although a rapidly growing number of diseases of the Old World are associated with monopartite begomoviruses. With the exception of several diseases of tomato, most of these are caused by a monopartite begomovirus in association with a recently discovered essential satellite component (DNA-beta). These begomovirus/satellite disease complexes are widespread and diverse and collectively infect a wide variety of crops, weeds and ornamental plants. Non-essential subviral components (DNA-1) originating from nanoviruses are frequently associated with these disease complexes, and there are tantalizing hints that further novel satellites may also be associated with some begomovirus diseases. DNA-beta components can be maintained in permissive plants by more than one distinct begomovirus, reflecting less stringent requirements for trans-replication that will undoubtedly encourage diversification and adaptation as a consequence of component exchange and recombination. In view of their impact on agriculture, there is a pressing need to develop a more comprehensive picture of the diversity and distribution of the disease complexes. A greater understanding of how they elicit the host response may provide useful information for their control as well as an insight into plant developmental processes.

Cotton leaf curl Gezira virus-satellite DNAs represent a divergent, geographically isolated Nile Basin lineage: predictive identification of a satDNA REP-binding motif

Cotton leaf curl Gezira virus (CLCuGV), a species of the genus Begomovirus (family Geminiviridae), was recently cloned from cotton, okra, and Sida alba plants exhibiting leaf-curling and vein-thickening symptoms in Sudan. Here, we describe a previously unknown lineage of single-stranded DNA satellite (satDNA) molecules, which are associated with CLCuGV, and are required for development of characteristic disease symptoms. Co-inoculation of cotton and Nicotiana benthamiana plants with satDNAs cloned from cotton, okra, and S. alba, together with CLCuGV as the 'helper virus' resulted in the development of characteristic leaf-curling and vein-thickening symptoms in both hosts. An anatomical study of symptomatic, virus-infected cotton leaves revealed that spongy parenchyma cells had developed instead of collenchyma cells at the sites of vein thickening. Phylogenetically, the CLCuGV-associated satDNAs from Sudan, together with their closest relatives from Egypt, form a new satDNA lineage comprising only satDNAs from the Upper and Lower Nile Basins. Analysis of satellites and their helper virus sequences identified a predicted REP-binding site consisting of the directly repeated sequence, 'CGGTACTCA', and an inverted repeated sequence, 'TGAGTACCG', which occur in the context of a 17-nucleotide motif. The conserved REP-binding motif identified herein, together with strict geographic isolation, and apparent host-restriction, may be the collective hallmark of these new satDNA-begomovirus lineages, extant in the Nile Basin.

Molecular Cloning of Coat Protein Gene of an Indian Cotton Leaf Curl Virus (CLCuV-HS2) Isolate and its Phylogenetic Relationship with others Members of Geminiviridae

Cotton leaf curl geminivirus is a whitefly (Bemisia tabaci Genn.) transmitted Begomovirus (Family Geminiviridae) causing a serious disease of cotton in northern India. The very typical symptoms of present isolate (CLCuV-HS2) showed thickened veins, dark green discoloration of the leaves with upward curling and leaf like structure known as enation (one in number), which develops into cup-shaped on the reverse side of leaves. The polymerase chain reaction (PCR) based technique can detect the viral DNA in samples stored upto 3 days after the collection and have wide application for the field diagnosis. The complete nucleotide sequence of the Indian isolate of cotton leaf curl geminivirus (CLCuV-HS2) coat protein (CP) gene component was determined using CP specific primers through PCR amplification from field infected cotton plants growing in Haryana, India. Comparison of the amino acid sequence of the putative CP with some other mono and bipartite geminiviruses revealed a maximum of 97.3% identity with Pakistan cotton leaf curl virus (CLCuV-62). A nuclear localization signal located close to the N-terminal of CP gene was determined.

Diversity of DNA 1: a satellite-like molecule associated with monopartite begomovirus-DNA beta complexes

DNA 1 components are satellite-like, single-stranded DNA molecules associated with begomoviruses (family Geminiviridae) that require the satellite molecule DNA beta to induce authentic disease symptoms in some hosts. They have been shown to be present in the begomovirus-DNA beta complexes causing cotton leaf curl disease (CLCuD) and okra leaf curl disease (OLCD) in Pakistan as well as Ageratum yellow vein disease (AYVD) in Singapore. We have cloned and sequenced a further 17 DNA 1 molecules from a diverse range of plant species and geographical origins. The analysis shows that DNA 1 components are associated with the majority of begomovirus-DNA beta complexes, being absent from only two of the complexes examined, both of which have their origins in Far East Asia. The sequences showed a high level of conservation as well as a common organization consisting of a single open reading frame (ORF) in the virion sense, a region of sequence rich in adenine and a predicted hairpin structure. In phylogenetic analyses, there was some evidence of grouping of DNA 1 molecules according to geographic origin, but less evidence for grouping according to host plant origin. The possible origin and function of DNA 1 components are discussed in light of these findings.

The DNA beta satellite component associated with ageratum yellow vein disease encodes an essential pathogenicity protein (betaC1)

Ageratum yellow vein disease (AYVD) is caused by the geminivirus ageratum yellow vein virus (AYVV) and an associated DNA beta satellite. We have mapped a DNA beta transcript to a highly conserved open reading frame (betaC1 ORF). The most abundant transcript 5'-terminus is located 8 bases upstream of the betaC1 ORF putative initiation codon while the transcript terminates at multiple sites downstream from the putative termination codon. Disruption of betaC1 protein expression by the introduction of an internal nonsense codon prevented infection of the AYVV-satellite complex in ageratum and altered the phenotype in Nicotiana benthamiana to that produced by AYVV alone although the mutant was maintained in systemically infected tissues. Modification of the putative initiation codon to a nonsense codon produced an intermediate phenotype in N. benthamiana and a mild yellow vein phenotype in ageratum, suggesting that betaC1 protein expression could be initiated from an alternative site. N. benthamiana plants containing a dimeric DNA beta transgene produced severe developmental abnormalities, vein-greening, and cell proliferation in the vascular bundles. Expression of betaC1 protein from a potato virus X (PVX) vector also induced abnormal plant growth. Our results demonstrate that the satellite encodes at least one protein that plays a major role in symptom development and is essential for disease progression in ageratum, the natural host of the AYVD complex.

Subviral DNAs associated with geminivirus disease complexes

Ageratum conyzoides (ageratum) is a common and widespread weed species that may act as a reservoir host for geminivirus diseases. Ageratum plants growing in Singapore and exhibiting yellow vein disease are infected with a complex mixture of viral, subviral and recombinant DNA components. This whitefly-transmitted disease is caused by the monopartite begomovirus ageratum yellow vein virus (AYVV) in association with a recently discovered satellite component referred to as DNA beta. Diseased plants also contain a subviral component, referred to as DNA 1, that has probably become associated with the begomovirus and adapted to whitefly transmission during mixed infection with an aphid-transmitted nanovirus. Unlike DNA beta, the nanovirus-like component is not essential for the disease. Recombination between the viral and subviral DNAs occurs frequently and may play an important evolutionary role by generating component diversity. The identification of a similar complex associated with cotton leaf curl disease (CLCuD), a serious constraint to cotton growing in Pakistan, and the isolation of DNA beta homologues from diverse plant species growing in widespread geographical locations suggests that such disease complexes are common and may have a significant impact on agriculture in the eastern hemisphere.

Diversity of DNA beta, a satellite molecule associated with some monopartite begomoviruses

DNA beta molecules are symptom-modulating, single-stranded DNA satellites associated with monopartite begomoviruses (family Geminiviridae). Such molecules have thus far been shown to be associated with Ageratum yellow vein virus from Singapore and Cotton leaf curl Multan virus from Pakistan. Here, 26 additional DNA beta molecules, associated with diverse plant species obtained from different geographical locations, were cloned and sequenced. These molecules were shown to be widespread in the Old World, where monopartite begomoviruses are known to occur. Analysis of the sequences revealed a highly conserved organization for DNA beta molecules consisting of a single conserved open reading frame, an adenine-rich region, and a region of high sequence conservation [the satellite conserved region (SCR)]. The SCR contains a potential hairpin structure with the loop sequence TAA/GTATTAC; similar to the origins of replication of geminiviruses and nanoviruses. Two major groups of DNA beta satellites were resolved by phylogenetic analyses. One group originated from hosts within the Malvaceae and the second from a more diverse group of plants within the Solanaceae and Compositae. Within the two clusters, DNA beta molecules showed relatedness based both on host and geographic origin. These findings strongly support coadaptation of DNA beta molecules with their respective helper begomoviruses.

Bhendi yellow vein mosaic disease in India is caused by association of a DNA Beta satellite with a begomovirus

Yellow vein mosaic disease is the major limitation in the production of bhendi or okra (Abelmoschus esculentus), an important vegetable crop of India. This disease is caused by a complex consisting of the monopartite begomovirus Bhendi yellow vein mosaic virus (BYVMV, family: Geminiviridae) and a small satellite DNA beta component. BYVMV can systemically infect bhendi upon agroinoculation but produces only mild leaf curling in this host. DNA beta induces typical symptoms of bhendi yellow vein mosaic disease (BYVMD) when co-agroinoculated with the begomovirus to bhendi. The DNA beta component associated with BYVMD has a number of features in common with those reported for ageratum yellow vein disease and cotton leaf curl disease. BYVMV represents a new member of the emerging group of monopartite begomoviruses requiring a satellite component for symptom induction.

Adaptation from whitefly to leafhopper transmission of an autonomously replicating nanovirus-like DNA component associated with ageratum yellow vein disease

Ageratum yellow vein disease is caused by the whitefly-transmitted monopartite begomovirus Ageratum yellow vein virus and a DNA beta satellite component. Naturally occurring symptomatic plants also contain an autonomously replicating nanovirus-like DNA 1 component that relies on the begomovirus and DNA beta for systemic spread and whitefly transmission but is not required for maintenance of the disease. Here, we show that systemic movement of DNA 1 occurs in Nicotiana benthamiana when co-inoculated with the bipartite begomovirus Tomato golden mosaic virus and the curtovirus Beet curly top virus (BCTV), but not with the mastrevirus Bean yellow dwarf virus. BCTV also mediates the systemic movement of DNA 1 in sugar beet, and the nanovirus-like component is transmitted between plants by the BCTV leafhopper vector Circulifer tenellus. We also describe a second nanovirus-like component, referred to as DNA 2, that has only 47% nucleotide sequence identity with DNA 1. The diversity and adaptation of nanovirus components are discussed.

Mutation of three cysteine residues in Tomato yellow leaf curl virus-China C2 protein causes dysfunction in pathogenesis and posttranscriptional gene-silencing suppression

The nuclear localized C2 protein of the monopartite begomovirus Tomato yellow leaf curl virus-China (TYLCV-C) contributes to viral pathogenicity. Here, we have investigated TYLCV-C C2 protein domains that play a role in the phenotype. Alignment of the C2 protein with 67 homologues from monopartite and bipartite begomoviruses revealed that a putative zinc-finger motif C36-X1-C38-X7-C46-X6-H53-X4-H58C59 and four potential phosphorylation sites (T52, S61, Y68, and S74) are highly conserved. When expressed from a Potato virus X (PVX) vector, TYLCV-C C2 protein mutants C2-T52M, C2-H58S, C2-C59S, C2-S61R, and C2-S74D, like the wild-type C2 protein, induced local necrotic ringspots and systemic necrosis in Nicotiana benthamiana plants. Mutants C2-H53P and C2-Y68D produced irregular necrotic lesions on inoculated leaves that were distinct from the wild-type phenotype. In contrast, mutants C2-C36R, C2-C38N, and C2-C46I induced chlorosis and mosaic symptoms rather than necrosis. We demonstrate that TYLCV-C C2, like its counterpart in the bipartite begomovirus African cassava mosaic virus, mediates suppression of posttranscriptional gene silencing (PTGS). Moreover, the individual mutations C36R, C38N, and C46I abolished the ability of C2 protein to suppress PTGS. These results suggest that the three cysteine residues within the putative zinc-finger motif are essential for C2 protein to induce necrosis and to act as a suppressor of PTGS.

Characterisation of Sri Lankan cassava mosaic virus and Indian cassava mosaic virus: evidence for acquisition of a DNA B component by a monopartite begomovirus

Two bipartite begomoviruses, Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosaic virus (SLCMV), have been isolated from mosaic-diseased cassava originating from central India and Sri Lanka, respectively. ICMV was transmitted with low efficiency from cassava to Nicotiana benthamiana by sap inoculation to give leaf curl symptoms. SLCMV was much more virulent in this host, producing severe stunting, leaf curl, and chlorosis. These symptoms were reproduced when their cloned genomic components (DNAs A and B) were introduced into N. benthamiana by either mechanical or Agrobacterium-mediated inoculation (agroinoculation). SLCMV is more closely related to ICMV (DNA A, 84%; DNA B, 94% nucleotide identity) than African cassava mosaic virus (ACMV) (DNA A, 74%; DNA B, 47% nucleotide identity). Sequence comparisons suggest that SLCMV DNA B originated from ICMV DNA B by a recombination event involving the SLCMV DNA A intergenic region. Pseudorecombinants produced by reassortment of the cloned components of ICMV and ACMV were not infectious in N. benthamiana, emphasising their status as distinct virus species. In contrast, a pseudorecombinant between ACMV DNA A and SLCMV DNA B was infectious. Consistent with these observations, iteron motifs located within the intergenic region that may be involved in the initiation of viral DNA replication are conserved between SLCMV and ACMV but not ICMV. When introduced into N. benthamiana by agroinoculation, SLCMV DNA A alone produced a severe upward leaf roll symptom, reminiscent of the phenotype associated with some monopartite begomoviruses. Furthermore, coinoculation of SLCMV DNA A and the satellite DNA beta associated with ageratum yellow vein virus (AYVV) produced severe downward leaf curl in N. glutinosa and yellow vein symptoms in Ageratum conyzoides, resembling the phenotypes associated with AYVV DNA A and DNA beta infection in these hosts. Thus, SLCMV DNA A has biological characteristics of a monopartite begomovirus, and the virus probably evolved by acquisition of a DNA B component from ICMV.

Tomato yellow leaf curl China virus: monopartite genome organization and agroinfection of plants

The complete DNA sequence (2734 nucleotides) of the monopartite genome of tomato yellow leaf curl China virus (TYLCCNV), a begomovirus transmitted by the whitefly Bemisia tabaci, was determined. The circular genomic DNA contains six open reading frames (ORFs) encoding proteins of molecular weights >10 kDa, of which two (V1 and V2) are located on the virion-sense strand and four (C1, C2, C3 and C4) on the complementary-sense strand. The ORFs are comparable to those of other whitefly-transmitted begomoviruses with a monopartite genome and to those encoded by DNA-A of bipartite begomoviruses. Sequence comparisons with other geminiviruses showed that TYLCCNV belongs to Begomovirus from the Old World. No putative DNA-B genome was found. Nicotiana species and tomato plants agroinoculated with the TYLCCNV monopartite genome developed typical yellowing and leaf-curling symptoms. The cloned molecule carried all the information needed for virus replication and systemic infection of plants.

Gene C2 of the monopartite geminivirus tomato yellow leaf curl virus-China encodes a pathogenicity determinant that is localized in the nucleus

Expression of the Tomato yellow leaf curl virus-China (TYLCV-C) C2 protein and green fluorescent protein (GFP) fused to the C2 protein (C2-GFP) in Nicotiana benthamiana from a Potato virus X (PVX) vector induced necrotic ringspots on inoculated leaves as well as necrotic vein banding and severe necrosis on systemically infected leaves. The localization of GFP fluorescence in plant cells infected with PVX/C2-GFP and in insect cells transfected with Baculovirus expressing C2-GFP indicates that the TYLCV-C C2 protein is capable of shuttling GFP into plant and insect cell nuclei. Our data demonstrate that the TYLCV-C C2 protein may contribute to viral pathogenicity in planta and is nuclear localized.

Genome sequence determinations and analyses of novel circoviruses from goose and pigeon

The genomes of novel circoviruses from goose and pigeon, which were isolated using degenerate primer and inverse primer PCR methods, were cloned and sequenced. Comparative nucleotide (nt) sequence analyses showed that the goose circovirus (GCV) and pigeon circovirus (PiCV) possessed genomes which were 1821 and 2037 or 2036 nt, respectively, and which had features in common with the genomes of porcine circoviruses types 1 and 2 (PCV1, PCV2) and psittacine beak and feather disease virus (BFDV), such that they can now be assigned to the genus Circovirus of the family Circoviridae. Common features include the possession of (i) a potential stem-loop/nonanucleotide motif with which the initiation of rolling circle replication of the virus DNA is associated; (ii) two major ORFs, located on the virus (V1 ORF) and complementary (C1 ORF) strands, which encode the replication-associated protein (Rep) and capsid protein, respectively; (iii) high levels of amino acid identity (41.2--58.2%) shared with other circovirus Rep proteins; and (iv) direct/inverted repeat sequences within the putative intergenic region. On the basis of nt and amino acid sequence identities, GCV is substantially less closely related to BFDV than PiCV is to BFDV.

Pathogenicity of a natural recombinant associated with ageratum yellow vein disease: implications for geminivirus evolution and disease aetiology

Yellow vein disease of Ageratum conyzoides is caused by a viral DNA complex consisting of the genomic component (DNA A) of the monopartite begomovirus Ageratum yellow vein virus (AYVV, family: Geminiviridae) and a small satellite-like DNA beta component. AYVV DNA A is unable to induce symptoms in this host alone but can systemically infect A. conyzoides in which it accumulates to low levels. Here, we demonstrate that the yellow vein phenotype can also be produced by co-inoculating A. conyzoides with AYVV DNA A and recDNA-Abeta17, a naturally occurring recombinant of approximately the same size as DNA beta that contains sequences from both DNA A and DNA beta. Symptoms induced by DNA A and recDNA-Abeta17 in A. conyzoides and Nicotiana glutinosa are qualitatively similar to those associated with DNA A and DNA beta although milder. Recombination between DNA A and DNA beta to produce a chimera resembling recDNA-Abeta17 was observed after whitefly transmission of the disease in A. conyzoides. Hence, such recombination events are likely to occur frequently, implying that recombinants will normally be associated with this type of disease complex in the field. Possible implications of these findings for the evolution of begomoviruses and the aetiology of their diseases are discussed.

Genetic diversity of beak and feather disease virus detected in psittacine species in Australia

The complete nucleotide (nt) sequence of eight isolates of beak and feather disease virus (BFDV) obtained from a range of psittacine species with psittacine beak and feather disease (PBFD) from throughout Australia were compared with the sequences of two BFDV isolates previously reported from Australia (BFDV-AUS) and America (BFDV-USA), respectively. All isolates had the same basic structure including the position of the open reading frames, the hairpin structure between ORF1 and ORF2, the nonanucleotide motif (TAGTATTAC) therein, the three motifs of Rep protein encoded from ORF1 and involved in rolling circle replication, and the P-loop motif previously described, but the genome size of the eight isolates ranged from 1992 to 2018 nt. Overall nt identity of the isolates compared to BFDV-AUS ranged from 84 to 97%; the variation was due to a combination of point mutations and a number of deletions and insertions ranging from 1 to 17 nt in size detected in both coding and noncoding regions. The identity of the nt sequence of ORF2 compared to BFDV-AUS varied from 80 to 99%, while the identity of the deduced amino acid sequences varied from 73 to 99%. Phylogenetic analysis grouped the isolates into four clusters but there were no apparent regional differences or differences related to the psittacine species of origin. While seven ORFs with the potential to encode proteins greater than 8.7 kDa were detected in the BFDV-AUS isolate described previously, only three of these ORFs were detected in all 10 BFDV isolates for which sequence data were available. The three ORFs were ORF1 that presumably encodes the Rep protein, ORF2 presumably the major capsid protein, and the ORF previously designated ORF5. The ORF5 was of two size classes in different isolates, 303 and 474 nt, and only the first 303 nt of the viruses with an ORF of 474 nt were common to the other isolates.

Cotton leaf curl virus disease

Cotton is one of the most important crops of Pakistan, accounting for over 60% of foreign exchange earnings. The present epidemic of cotton leaf curl disease (CLCuD) originated in the Punjab region near the city of Multan and was first reported in 1985, although it was noted in this region as early as 1967. By the early 1990s, CLCuD had become the major limitation to cotton production in Pakistan and it has now spread into India and, more recently, south and west into other provinces of Pakistan. The very characteristic symptoms include leaf curling, darkened veins, vein swelling and enations that frequently develop into cup-shaped, leaf-like structures on the undersides of leaves. Identification of the vector of CLCuD as the whitefly Bemisia tabaci (Genn.) quickly led to the suggestion that the causative agent of the disease is a geminivirus. Researchers soon confirmed the presence of such a virus that is currently ascribed to the genus Begomovirus of the family Geminiviridae, However, in 1999, the aetiology of the disease was shown to be more complex than was originally assumed. Despite the identification of both a begomovirus and a so-called nanovirus-like component, the precise causal agent of CLCuD remains uncertain.

Clones of cotton leaf curl geminivirus induce symptoms atypical of cotton leaf curl disease

The causative agent of cotton leaf curl disease has previously been shown to be transmissible by the whitefly Bemisia tabaci (Gennadius) and a begomovirus (Geminiviridae) was shown to be associated with the disease. This virus was provisionally called cotton leaf curl virus (CLCuV) although no causal relationship between virus and disease was shown. In the present study full-length clones of CLCuV, equivalent to the DNA A component of bipartite begomoviruses, were obtained. The clones of CLCuV were systemically infectious to both Nicotiana benthamiana and cotton. Infected plants did not exhibit symptoms characteristic of cotton leaf curl disease, producing mild leaf curling, yellowing and some stunting. Efforts to identify a second genomic component were not successful. These findings suggest that the begomovirus, CLCuV, is not or not the sole cause of cotton leaf curl disease. The transmission of cotton leaf curl disease by B. tabaci, however, may indicate that the begomovirus plays a part in the transmission of the disease. The implications of these findings are discussed.

A unique virus complex causes Ageratum yellow vein disease

Ageratum conyzoides L., a weed species widely distributed throughout southeast Asia, frequently exhibits striking yellow vein symptoms associated with infection by Ageratum yellow vein virus (AYVV), a member of the Geminiviridae (genus Begomovirus). Most begomoviruses have bipartite genomes (DNAs A and B), but only a DNA A has been identified for AYVV. We demonstrate that yellow vein disease of A. conyzoides results from co-infection by AYVV DNA A (2,741 nt) and a circular DNA that is approximately half its size (1,347 nt) that we designate DNA beta. Apart from the sequence TAATATTAC, common to all geminiviruses and containing the initiation site of rolling circle replication, DNA beta shows negligible sequence homology either to AYVV DNA A or to DNA B associated with bipartite begomoviruses. DNA beta depends on DNA A for replication and is encapsidated by DNA A-encoded coat protein and so has characteristics of a DNA satellite. However, systemic infection of A. conyzoides by DNA A alone is sporadic and asymptomatic, and DNA A accumulation is reduced to 5% or less of its accumulation in the presence of DNA beta. Therefore, DNA A and DNA beta together form a previously unrecognized disease-inducing complex. Our data also demonstrate that the nanovirus-like DNA 1 component associated with infected A. conyzoides plays no essential role in the disease and represents a satellite-like DNA. Furthermore, the satellite DNA previously found associated with tomato leaf curl virus is probably a defective DNA beta homologue.

Watermelon chlorotic stunt virus from the Sudan and Iran: Sequence Comparisons and Identification of a Whitefly-Transmission Determinant

ABSTRACT The genomes of two Watermelon chlorotic stunt virus (WmCSV) isolates, one from the Sudan and one from Iran, were cloned and sequenced. Sequence relationship with other geminiviruses characterizes WmCSV as a typical Eastern Hemisphere geminivirus with a bipartite genome. The two geographically distant WmCSV isolates from Africa and the Middle East share a very high overall sequence similarity: 98% between their DNA-A and 96% between their DNA-B components, and their respective capsid proteins are identical. A single amino acid change in the capsid protein (N131D) renders WmCSV whitefly nontransmissible. This region of the capsid is also implicated in transmission by Bemisia tabaci of Tomato yellow leaf curl virus.

A nanovirus-like DNA component associated with yellow vein disease of Ageratum conyzoides: evidence for interfamilial recombination between plant DNA viruses

Yellow vein disease of Ageratum conyzoides, a weed species that is widely distributed throughout Asia, has been attributed to infection by the geminivirus Ageratum yellow vein virus (AYVV). In addition to a single AYVV genomic component (DNA A), we have previously demonstrated that infected plants contain chimeric defective viral components, comprising DNA A and nongeminiviral sequences, that act as defective interfering DNAs. A database search has revealed that the nongeminiviral sequences of one such defective component (def19) show significant homology with sequences of nanovirus components that encode replication-associated proteins (Reps). Primers designed to hybridise to the nongeminiviral DNA were used to PCR-amplify a full-length nanovirus-like component, referred to as DNA 1, from an extract of infected A. conyzoides. DNA 1 is unrelated to AYVV DNA A but resembles nanovirus components that encode Reps and is most closely related (73% identity) to a nanovirus-like DNA recently isolated from geminivirus-infected cotton. DNA 1 is dependent on AYVV DNA A for systemic infection of A. conyzoides and Nicotiana benthamiana and can systemically infect N. benthamiana in the presence of the bipartite geminivirus African cassava mosaic virus. A. conyzoides plants coinfected with AYVV DNA A and DNA 1 remain asymptomatic, indicating that additional factors are required to elicit yellow vein disease. Our results provide direct evidence for recombination between distinct families of plant single-stranded DNA viruses and suggest that coinfection by geminivirus and nanovirus-like pathogens may be a widespread phenomenon. The ability of plant DNA viruses to recombine in this way may greatly increase their scope for diversification.

Identification of a novel circular single-stranded DNA associated with cotton leaf curl disease in Pakistan

Recent reports have suggested that cotton leaf curl virus (CLCuV), a geminivirus of the genus Begomovirus, may be responsible for cotton leaf curl disease in Pakistan. However, the causal agent of the disease remains unclear as CLCuV genomic components resembling begomovirus DNA A are unable to induce typical disease symptoms when reintroduced into plants. All attempts to isolate a genomic component equivalent to begomovirus DNA B have been unsuccessful. Here, we describe the isolation and characterisation of a novel circular single-stranded (ss) DNA associated with naturally infected cotton plants. In addition to a component resembling DNA A, purified geminate particles contain a smaller unrelated ssDNA that we refer to as DNA 1. DNA 1 was cloned from double-stranded replicative form of the viral DNA isolated from infected cotton plants. Blot hybridisation using probes specific for either CLCuV DNA or DNA 1 was used to demonstrate that both DNAs co-infect naturally infected cotton plants from different geographical locations. DNA 1 was detected in viruliferous Bemisia tabaci and in tobacco plants infected under laboratory conditions using B. tabaci, indicating that it is transmitted by whiteflies. Sequence analysis showed that DNA 1 is approximately half the size of CLCuV DNA but shares no homology, indicating that it is not a defective geminivirus component. DNA 1 has some homology to a genomic component of members of Nanoviridae, a family of DNA viruses that are normally transmitted by aphids or planthoppers. DNA 1 encodes a homologue of the nanovirus replication-associated protein (Rep) and has the capacity to autonomously replicate in tobacco. The data suggest that a nanovirus-like DNA has become whitefly-transmissible as a result of its association with a geminivirus and that cotton leaf curl disease may result from a mutually dependent relationship that has developed between members of two distinct DNA virus families that share a similar replication strategy.

Bean yellow dwarf virus RepA, but not rep, binds to maize retinoblastoma protein, and the virus tolerates mutations in the consensus binding motif

It has previously been reported that complementary-sense gene products of wheat dwarf virus (WDV), a geminivirus of the genus Mastrevirus that infects monocotyledonous plants, bind to human and maize retinoblastoma (Rb) protein. Rb proteins control cell-cycle progression by sequestering transcription factors required for entry into S-phase, suggesting that the virus modifies the cellular environment to produce conditions suitable for viral DNA replication. Using a yeast two-hybrid assay, we have investigated whether the complementary-sense gene products of bean yellow dwarf virus, a mastrevirus that is adapted to dicotyledonous plants, also bind maize Rb protein. We demonstrate that whereas RepA binds to Rb protein, Rep does not, suggesting that RepA alone regulates host gene expression and progression of cells to S-phase. RepA mutants containing L --> I, C --> S, C --> G, and E --> Q mutations within the consensus Rb protein binding motif LXCXE retained the ability to bind to Rb, but with reduced efficiency. Most notably, the E --> Q mutation reduced binding by approximately 95%. Nonetheless, all LXCXE mutants were able to replicate in tobacco protoplasts and to systemically infect Nicotiana benthamiana and bean, in which they produced wild-type symptoms.

Psittacine beak and feather disease virus nucleotide sequence analysis and its relationship to porcine circovirus, plant circoviruses, and chicken anaemia virus

Cloning and sequencing of the circular, single-stranded DNA of one isolate of psittacine beak and feather disease virus (BFDV) demonstrate a genome composed of a circular molecule of 1993 nucleotide bases. An analysis of the assembled replicative form demonstrated seven open reading frames (ORFs) (three in the virion strand and four in the complementary strand), potentially encoding seven viral proteins of >8.7 kDa. High amino acid sequence similarity was demonstrated between a potential 33.3-kDa protein product of ORF1 of BFDV and the replicase-associated protein of porcine circovirus (PCV), subterranean clover stunt virus, and faba bean necrotic yellows virus. However, significant similarity in nucleotide or amino acid sequences was not present between BFDV and chicken anaemia virus. A potential stem-loop structure similar to that found in PCV and plant circoviruses was present in the putative encapsidated strand of the BFDV genome. At the top of this structure, a nonanucleotide motif (TAGTATTAC) similar to that of PCV, plant circoviruses, and geminiviruses also was recognised. Comparison of the deduced amino acid sequences of ORF2 of BFDV and PCV demonstrated 29.1% identity, and in both viruses, ORF2 is located on the complementary strand, beginning close to or within the hairpin stem. Our findings provide further evidence of a close relationship among BFDV, PCV, and plant circoviruses but not chicken anaemia virus.