Characterization of a begomovirus causing horsegram yellow mosaic disease in India

The virus causing horsegram (Macrotyloma uniflorum) yellow mosaic disease has been shown to be a typical Old World bipartite begomovirus. The viral origin of the disease has been established through agroinoculation of horsegram using partial tandem repeat clones of both DNA-A and DNA-B. The DNA-A genome shows less than 89% identity with the corresponding sequences of all the begomoviruses in the databases earlier to this sequence submission (AJ627904). Therefore Horsegram yellow mosaic virus (HgYMV-[IN:Coi]) can be considered to be a new species of the genus Begomovirus (family Geminiviridae). Phylogenetic analysis shows that this virus is part of the cluster of mungbean yellow mosaic viruses of legumes from South and South East Asia.     

Occurrence of a new recombinant begomovirus species infecting tomato in the Al‐Batinah region of Oman

Whitefly‐transmitted begomoviruses are the most important limiting factor for tomato cultivation in Oman, particularly in the Al‐Batinah region, the major agricultural area of the country. Commercial farms in the Al‐Batinah region were surveyed during January–March 2013. Samples of tomato showing leaf curl disease symptoms typical of begomoviruses were collected and analysed. Full‐length sequences of five clones were shown to have relatively low percentage identity values to known begomoviruses, with the highest (88·6%) to isolates of Tomato leaf curl Oman virus (ToLCOMV), a begomovirus previously reported in Oman, indicating that these represent a newly identified species, for which the name Tomato leaf curl Barka virus (ToLCBrV) is proposed. Four isolates of ToLCBrV were found associated with Tomato leaf curl betasatellite (ToLCB). The five isolates of ToLCBrV characterized in this study were shown to be recombinants, with ToLCOMV as the major parent, and a fragment of Croton yellow vein virus (CrYVV) spanning the 3′ half of the replication‐associated protein. The significance of these findings is discussed.     

Evidence for two predominant viral lineages,recombination and subpopulation structure in begomoviruses associated with yellow vein mosaic disease of okra in India

Yellow vein mosaic disease (YVMD) caused by whitefly‐transmitted begomoviruses is an economically significant viral disease of okra. In this study, a survey of begomoviruses associated with YVMD was carried out in eight states and two union territories of India. A total of 92 full‐length DNA‐A components were sequenced and characterized. Sequence comparisons and population structure analysis revealed the existence of four begomovirus species. Two novel species were detected with several recombinationally derived genome fragments that probably originated from begomoviruses known to infect malvaceous and non‐malvaceous hosts. Among the four species, Bhendi yellow vein Maharastra virus (BYVMaV) and Bhendi yellow vein Madurai virus (BYVMV) were found to be predominant in okra, with BYVMV having a pan‐India distribution. There was evidence for a high degree of genetic variability and subpopulation structure within these four species. Neutrality tests suggested the occurrence of purifying selection acting upon these populations. The results of the current study have uncovered the diversity and genetic structure of okra‐infecting begomoviruses in India and generated potentially useful information for developing management strategies for YVMD.     

Characterization of Passionfruit severe leaf distortion virus,a novel begomovirus infecting passionfruit in Brazil,reveals a close relationship with tomato‐infecting begomoviruses

Molecular and biological characterization of the begomovirus isolate BR:LNS2:Pas:01, obtained from yellow passionfruit plants in Livramento de Nossa Senhora, Bahia state, Brazil, was carried out. Sequence analysis demonstrated that the BR:LNS2:Pas:01 DNA‐A had highest nucleotide sequence identity with Tomato chlorotic mottle virus (77%) and had five ORFs corresponding to the genes cp, rep, trap, ren and ac4. The DNA‐B had highest nucleotide sequence identity with Tomato yellow spot virus (74%) and two ORFs corresponding to the genes mp and nsp. These identity values indicate that this isolate represents a new begomovirus species, for which the name Passionfruit severe leaf distortion virus (PSLDV), is proposed. Phylogenetic analysis clustered the PSLDV DNA‐A and ‐B in a monophyletic branch with Brazilian tomato‐infecting begomoviruses. The isolate’s host range was restricted to species from the Passifloraceae and Solanaceae. PSLDV‐[BR:LNS2:Pas:01] was capable of forming pseudorecombinants with tomato‐infecting begomoviruses, reinforcing its close relationship with these viruses and suggesting a possible common origin. However, the virus was not capable of infecting tomato.     

Occurrence of Honeysuckle Yellow Vein Virus (HYVV) containing a monopartite DNA-A genome in Korea

Two newly emerged begomoviruses were isolated from naturally infected tomato (Solanum lycopersicum) plants grown in greenhouses at Jeju Island and Dangjin in Korea and their genomes were characterized. These viruses-infected plants had very small leaves that curled upward, yellow margins and a leathery appearance, and a bushy and stunted appearance with short internodes. Nucleotide (nt) sequence analysis of their genomes showed that they have a DNA-A component of a monopartite begomovirus. Their genomes comprised 2763 and 2764 nucleotides with six open reading frames. The results of nt sequence similarity analysis of DNA-A genome between the two Korean isolates and isolates of Tobacco leaf curl Japan virus (TbLCJV), Honeysuckle yellow vein virus (HYVV), Honeysuckle yellow vein mosaic virus (HYVMV), and Eupatorium yellow vein virus in Japan (EpYVV) showed that they are likely similar to HYVV-[Masuda] (89.4–92.8% nt identity). Consequently, we tentatively propose the two isolates’ names as HYVV-Jeju and -DJ according to the ICTV geminivirus rules. Phylogenetic relationship analysis of 33 DNA-A genome sequences using PAUP* 4.0b10 and MrBayes revealed that HYVV-Jeju and -DJ belong to the Far East Asian begomovirus species complex. Within the Far East Asian begomovirus species complex, HYVV-Jeju and -DJ are distantly related to EpYVV, HYVMV, and TbLCJV groups. Based on the presence of a recombination fragment spanning the C3 ORF, a recombinant origin was suggested for both HYVV-Jeju and –DJ, with parents close to Japanese isolates HYVMV-[SP1:00] and Eupatorium yellow vein virus (EpYVV)-[Suya]. In addition, the presence of a further recombination fragment spanning the IR suggested the parents of HYVV-DJ were close to HYVV-Jeju and EpYVV-[Suya].     

Species diversity,phylogeny and genetic variability of begomovirus populations infecting leguminous weeds in northeastern Brazil

A survey of begomoviruses infecting leguminous weeds (family Fabaceae) was carried out in four states of northeastern Brazil. A total of 26 full‐length begomovirus components (19 DNA‐A and seven DNA‐B, with three pairs of cognate A and B components) were amplified using rolling‐circle amplification, then cloned and sequenced. Sequence analysis indicated the presence of six species, four of them novel. In phylogenetic analysis five of the viruses clustered with other Brazilian begomoviruses, but one of them (Euphorbia yellow mosaic virus, EuYMV) clustered with viruses from other countries in Central and South America. Evidence of recombination was found among isolates of Macroptilium yellow spot virus (MaYSV). The MaYSV population had a high degree of genetic variability. Macroptilium lathyroides was revealed as a common host for several of these viruses, and could act as a mixing vessel from which recombinant viruses could emerge. The results indicate that leguminous weeds are reservoirs of several begomoviruses in Brazil, and could play a significant role in begomovirus epidemics, both as inoculum sources and as sources of emerging novel viruses.     

Occurrence and incidence of viruses infecting green beans in south-eastern Spain

A study was conducted to determine the identity and prevalence of viruses in 455 greenhouses in the main Spanish green bean growing area. Directed surveys were conducted in 422 crops from 2000–2004 to collect samples from diseased plants displaying symptoms that could be attributed to viruses. The samples were analysed to detect any virus by means of dsRNA extraction, mechanical inoculation to test plants, as well as ELISA and/or RT-PCR tests to detect potyviruses, geminiviruses and viruses previously known to infect beans in Spain. Random surveys were conducted in the years 2002 and 2005 (in 21 and 12 greenhouses, respectively) to study the actual incidence of known viruses in the area. Symptoms were recorded in 23,108 plants from which 664 plants were collected and analysed by ELISA or RT-PCR. The results of the directed surveys showed that all the analyzed crops carried the cryptic virus Phaseolus vulgaris endornavirus (PVuV), whereas phytopathogenic viruses appeared in smaller percentages of the crops: Tomato yellow leaf curl virus (TYLCV) 20.4%, Southern bean mosaic virus (SBMV) 9.0%, Tomato spotted wilt virus (TSWV) 4.0%, and the new species Bean yellow disorder virus (BnYDV) that broke out in 2004 with occurrence values higher than 34.3% that year. From 2000–2004 an important decrease in TYLCV was observed, along with a slight increase in SBMV and a consistently low occurrence of TSWV. The results of the random surveys confirmed the increased occurrence of virus detected during the directed surveys, and furthermore demonstrated the percentage of incidence for each virus.     

Characterization of a New Begomovirus from Egypt Infecting Hollyhock (Althea Rosea)

A viral isolate from Egypt associated with symptoms of enations and leaf curling on hollyhock (Althea rosea) was characterized at the cytopathological and molecular levels. Microscopic observations showed that enations resulted from a reorganization of the vascular tissues, including activation of a cambial activity in the phloem, the development of a palisade parenchyma in place of a spongy one and the differentiation of minor vascular tissues. From this isolate, the full-length DNA-A of a begomovirus (family Geminiviridae) was cloned and sequenced. This genome exhibited a genetic organization similar to that of other old-world begomoviruses like Tomato yellow leaf curl virus from Israel and Ageratum yellow vein virus from Singapore. However, its sequence was significantly distinct (similarity < 69%) from any other geminivirus. This begomovirus was thus considered as representative of a new viral species named Althea rosea enation virus (AREV). AREV was agroinfectious on Nicotiana benthamiana, on which it induced a severe leaf-curling and vein distortion, but could not re-establish infection on A. rosea. To determine if AREV was also associated with a similar disease affecting okra in Upper-Egypt, the partial sequence of the coat protein gene of an isolate was determined. It exhibited 90% nt identity with the hollyhock isolate (97% amino acid), suggesting a genetic heterogeneity in the begomovirus population associated with the enation diseases.     

Occurrence of aphidborne viruses in southernmost South American populations of Fragaria chiloensis ssp. chiloensis

Wild and cultivated Fragaria chiloensis ssp. chiloensis (Fcc) plants were collected at different locations in southern Chile in order to determine the current viral status of this native strawberry. The following aphidborne viruses (ABVs): Strawberry mild yellow edge virus (SMYEV), Strawberry mottle virus (SMoV), Strawberry crinkle virus (SCV) and Strawberry vein banding virus (SVBV), were found in wild and cultivated Fcc plants, but severe symptoms were not associated with viral infection. Furthermore, partial gene sequences of these ABV isolates were determined and displayed a high degree of conservation with virus isolates reported previously. In addition, partial gene sequences of SCV and SVBV from southernmost South American populations of Fcc are described for the first time. High‐throughput parallel sequencing (Illumina) of double‐stranded RNA was used to provide viral profiles of Fcc from different locations. Although strong evidence of novel viruses affecting Fcc was not found, it was confirmed that ABVs are the most frequent viruses affecting this subspecies. The information provided will help in the development of high‐quality molecular tools for virus detection and control in Fcc.     

南疆温室番茄黄化曲叶病病毒种类的分子鉴定

为明确南疆温室番茄黄化曲叶病的病毒种类,利用双生病毒的兼并引物通过PCR扩增,对采集的20个番茄病株进行了分子检测.从20个病株中均扩增到约500 bp的目标片段,对其中4株进行克隆和测序,其相互间序列同源性为97.1％ ～99.3％,与番茄黄化曲叶病毒(Tomato yellow leaf curl virus,TYLCV)的同源性较高,为98.6％ ～ 99.5％.随机选取莎车分离物KS2-5进行全基因组的克隆和测序,KS2-5 DNA全长为2781 nt(序列号:JQ807735),具有典型的双生病毒基因组特征,与TYLCV其它分离物同源性达到98.9％～99.5％,而与其它粉虱传双生病毒的序列同源性较低,为68.3％ ～75.5％,表明危害南疆温室番茄的病毒种类为番茄黄化曲叶病毒TYLCV.     

Tomato leaf curl Guangxi virus is a distinct monopartite begomovirus species

Three begomovirus isolates were obtained from tomato plants showing leaf curl symptoms in Guangxi province of China. Typical begomovirus DNA components representing the three isolates (GX-1, GX-2 and GX-3) were cloned and their full-length sequences were determined to be 2752 nucleotides. Nucleotide identities among the three viral sequences were 98.9–99.7%, but all shared <86.7% nucleotide sequence identity with other reported begomoviruses. The sequence data indicated that GX-1, GX-2 and GX-3 are isolates of a distinct begomovirus species for which the name Tomato leaf curl Guangxi virus (ToLCGXV) is proposed. Further analysis indicated that ToLCGXV probably originated through recombination among viruses related to Ageratum yellow vein virus, Tomato leaf curl China virus and Euphorbia leaf curl virus. PCR and Southern blot analyses demonstrated that isolates GX-1 and GX-2 were associated with DNAβ components, but not isolate GX-3. Sequence comparisons revealed that GX-1 and GX-2 DNAβ components shared the highest sequence identity (86.2%) with that of Tomato yellow leaf curl China virus (TYLCCNV). An infectious construct of ToLCGXV isolate GX-1 (ToLCGXV-GX) was produced and determined to be highly infectious in Nicotiana benthamiana, N. glutinosa, tobacco cvs. Samsun and Xanthi, tomato and Petunia hybrida plants inducing leaf curl and stunting symptoms. Co-inoculation of tomato plants with ToLCGXV-GX and TYLCCNV DNAβ resulted in disease symptoms similar to that caused by ToLCGXV-GX alone or that observed in infected field tomato plants.     

复合侵染水茄的两种菜豆金色花叶病毒属病毒基因组结构特征分析

为明确水茄Solanum torvum植株叶片邹缩、褪绿是否由菜豆金色花叶病毒属病毒侵染引起,从云南省西双版纳傣族自治州田间采集具有疑似感染症状的水茄植株叶片样品,应用菜豆金色花叶病毒属病毒简并引物和特异性引物进行PCR扩增、克隆和测序,通过生物信息软件分析比较其核苷酸序列特征,并对其进行系统发育分析。结果显示,从采集的疑似病叶中共克隆获得了5条菜豆金色花叶病毒属病毒DNA-A全序列和3条DNA-B全序列,经全序列分析发现,侵染水茄的2种菜豆金色花叶病毒属病毒分离物分别属于中国南瓜曲叶病毒(squash leaf curl China virus,SLCCNV)和野茼蒿黄脉病毒(Crassocephalum yellow vein virus,CraYVV)。SLCCNV水茄分离物的基因组具有典型的菜豆金色花叶病毒属病毒双组分结构特征,与来自泰国的SLCCNV分离物(AB330078)亲缘关系最近,相似性最高达到99.0%;CraYVV水茄分离物的基因组具有典型的菜豆金色花叶病毒属病毒单组分结构特征,与来自云南省景洪市的CraYVV分离物(EF165536)亲缘关系最近,相似性最高达到97.6%。表明水茄是这2种菜豆金色花叶病毒属病毒的新寄主,并首次发现双组分和单组分菜豆金色花叶病毒属病毒可复合侵染水茄。     

A new Badnavirus species detected in Bougainvillea in Brazil

Badnavirus in Bougainvillea spectabilis showing virus-like symptoms was identified by the presence of bacilliform particles, measuring 125–130 × 30–40 nm in leaf-dip preparations and by analysis of its putative open reading frame 3 sequence. The virus, tentatively named Bougainvillea bacilliform virus (BBV), had the highest identities (up to 60%) with Spiraea yellow leaf spot virus, Gooseberry vein banding associated virus, Taro bacilliform virus, and Citrus yellow mosaic virus. In phylogenetic analysis, BBV clustered with Badnavirus putative species. Attempts to transmit the virus to several hosts failed. This is the first report of a new Badnavirus detected in Bougainvillea.     

Evidence for Lettuce big‐vein associated virus as the causal agent of a syndrome of necrotic rings and spots in lettuce

Lettuce big‐vein associated virus (LBVaV, genus Varicosavirus) was shown to be responsible for characteristic necrotic symptoms observed in combination with big‐vein symptoms in lettuce breeding lines when tested for their susceptibility to lettuce big‐vein disease (BVD) using viruliferous Olpidium virulentus spores in a nutrient film technique (NFT) system. Lettuce plants showing BVD are generally infected by two viruses: Mirafiori lettuce big‐vein virus (MiLBVV, genus Ophiovirus) and LBVaV. New mechanical inoculation methods were developed to separate the two viruses from each other and to transfer both viruses to indicator plants and lettuce. After mechanical inoculation onto lettuce plants MiLBVV induced vein‐band chlorosis, which is the characteristic symptom of BVD. LBVaV caused a syndrome of necrotic spots and rings which was also observed earlier in lettuce plants inoculated in the NFT system, resembling symptoms described for lettuce ring necrosis disease (RND). This observation is in contrast with the idea that LBVaV only causes latent infections in lettuce. De novo next‐generation sequencing demonstrated that LBVaV was the only pathogen present in a mechanically inoculated lettuce plant with symptoms, providing evidence that LBVaV was the causal agent of the observed necrotic syndrome and thus fulfilling Koch’s postulates for this virus. The necrotic syndrome caused by LBVaV in lettuce is referred to as LBVaV‐associated necrosis (LAN).     

Ageratum yellow vein China virus Is a Distinct Begomovirus Species Associated with a DNAbeta Molecule

ABSTRACT Ageratum conyzoides plants exhibiting yellow vein symptoms, collected near Haikou, Hainan Province, China, contained begomoviral DNA-A-like molecules. The complete sequences of the molecules from two samples, Hn2 and Hn2-19, were shown to consist of 2,768 and 2,748 nucelotides (nt), respectively. These sequences have more than 97% nucleotide sequence identity, but less than 86% identity with other reported begomovirus sequences. In line with the taxonomic convention for begomoviruses, Hn2 and Hn2-19 are therefore considered to represent isolates of a distinct begomovirus species, for which the name Ageratum yellow vein China virus (AYVCNV) is proposed. Sequence alignment shows AYVCNV has arisen by recombination among viruses related to Ageratum yellow vein virus, Papaya leaf curl China virus, and an unidentified begomovirus. Southern blot analyses revealed that all plants sampled contained molecules resembling DNAbeta. DNAbeta molecules from three samples were 1,323 or 1,324 nt long and had >98% sequence identity but <81% identity with previously reported DNAbeta sequences. Infectious clones of Hn2 and its associated DNAbeta were constructed and agroinoculated to plants. Hn2 alone caused sporadic asymptomatic systemic infection of Nicotiana benthamiana, N. glutinosa, Lycopersicon esculentum, Petunia hybrida, and A. conyzoides but its accumulation was much enhanced in plants co-inoculated with DNAbeta. The co-inoculated N. benthamiana, N. glutinosa, P. hybrida, and L. esculentum plants developed leaf curling or leaf crinkling symptom; those in A. conyzoides were typical of ageratum yellow vein disease. When the DNAbeta molecules associated with four other Chinese begomoviruses were coinoculated with Hn2 to N. benthamiana and N. glutinosa, the DNAbeta molecules were replicated, and the plants developed systemic symptoms of types that were specific for each DNAbeta. This illustrates that there is less specific interaction between monopartite begomovirus and DNAbeta than between the DNA-A and DNA-B of begomoviruses with bipartite genomes.     

Infectivity analysis of a soybean isolate of Mungbean yellow mosaic India virus by agroinoculation

Yellow mosaic disease (YMD) of legumes endemic to South Asia are caused by begomoviruses transmitted by whiteflies. Based on molecular characterization, two distinct viruses – Mungbean yellow mosaic India virus (MYMIV) and Mungbean yellow mosaic virus (MYMV) – were found previously to be the etiological agents of YMD in legumes. Here, host range studies with a soybean isolate of MYMIV (MYMIV-[Sb]) were carried out by both whitefly transmission and agroinoculation. MYMIV-[Sb] was similar to a cowpea isolate of MYMIV (MYMIV-[Cp]) in its ability to infect cowpea, thus differing from blackgram (MYMIV) and mungbean (MYMIV-[Mg]) isolates, which do not infect cowpea. Genomic analysis of DNA A and DNA B components of these MYMIV isolates show characteristic differences in complete DNA B nucleotide sequence correlating with host range differences.     

Molecular characterisation of <Emphasis Type="Italic">Rice stripe necrosis virus</Emphasis> as a new species of the genus <Emphasis Type="Italic">Benyvirus</Emphasis>

The complete nucleotide sequences of RNAs 1 and 2 of Rice stripe necrosis virus (RSNV) were determined and compared to the corresponding genomes of all sequenced, rod-shaped plant viruses. The genome organisation of RSNV RNA1 and RNA2 is nearly identical to that of Beet necrotic yellow vein virus (BNYVV) and Beet soil-borne mosaic virus (BSBMV), definitive species of the genus Benyvirus. As demonstrated for BNYVV and BSBMV, the RNA1 of RSNV also encodes a single ORF with putative replicase-associated motifs, which distinguishes benyviruses from all other viruses possessing rod-shaped particles. As described for BNYVV, RNSV RNA-2 also contains six ORFs: the capsid protein gene, the read-through protein gene, a triple gene block gene that codes for three different proteins, and a 17 kDa cysteine-rich protein. RNAs 3 and 4 (or 5 in the case of BNYVV), identified in natural infections of BNYVV and BSBMV, were not detected in any of the 44 RSNV cDNA clones obtained in this investigation. Nevertheless, phylogenetic and amino comparative acid sequence analyses demonstrated that RSNV is more closely related to BNYVV and BSBMV than to any other rod-shaped plant virus characterised to date.     

Biomolecular relationships among isolates of<Emphasis Type="Italic">Tomato Yellow Leaf Curl Tanzania Virus</Emphasis>

An investigation of the biological properties of the virus causing tomato yellow leaf curl disease in Tanzania was initiated to compare it with other known tomato yellow leaf curl viruses. Properties relating to acquisition and inoculation feeding time, persistence, mechanical inoculation, seed transmission and host range were studied. Results obtained indicate that the virus was transmitted persistently byBemisia tabaci Genn., but it was not mechanically, sap- or seed-transmissible. Minimum acquisition and inoculation feeding time was 30 min.Capsicum annuum, Datura stramonium, Nicotiana glutinosa, N. tabacum andLycopersicon esculentum were found to be hosts of the virus among the plant species tested, whereasPhaseolus vulgaris was not. It is concluded that the properties of the agent causing yellow leaf curl symptoms in tomato plants from different regions in Tanzania are similar to those ofTomato yellow leaf curl Sardinia virus species studied elsewhere. http://www.phytoparasitica.org posting Feb. 20, 2003.