Molecular characterization of a new badnavirus associated with streak symptoms on enset (Ensete ventricosum,Musaceae)

Electron microscopy of leaf samples displaying streak symptoms from enset (Ensete ventricosum), a banana‐like plant widely cultivated in Ethiopia, showed the presence of bacilliform shaped virions as known for badnaviruses. DNA extracts subjected to rolling circle amplification (RCA), polymerase chain reaction (PCR) and cloning and sequence analysis revealed that the virus has a circular double‐stranded DNA genome of 7,163 nucleotides encoding predicted proteins of 21.5 kDa, 14.5 kDa and 202.5 kDa, a genome organization known for badnaviruses. The virus is phylogenetically most closely related to Sugarcane bacilliform Guadeloupe D virus with a nucleotide sequence identity of 77.2% at the conserved RT/RNase‐H region and 73.6% for the whole genome. Following the current species demarcation criteria, the virus should be considered as an isolate of a new species in the genus Badnavirus for which the name Enset leaf streak virus (ELSV) is suggested. Leaf samples from enset and banana were screened using virus‐specific primers, and ELSV was detected in six of 40 enset but not found in any of 61 banana samples. On the other hand, Banana streak OL virus (BSOLV) was detected from the majority (60%) of symptomatic banana samples but not from enset samples. This paper reports the first full‐genome sequence of a putative new badnavirus species infecting plants in the genus Ensete. In addition, this is the first report of the occurrence of BSOLV in Ethiopia.     

Identification of Rubus yellow net virus as a distinct badnavirus and its detection by PCR in Rubus species and in aphids

Rubus yellow net virus (RYNV) infects Rubus species and cultivars worldwide and is an essential component of raspberry veinbanding mosaic (RVBMD), a virus disease complex that causes serious decline in plant vigour and productivity. The virus is transmitted, probably in a semi‐persistent manner, by the large raspberry aphid, Amphorophora idaei in Europe, and A. agathonica in North America. The particles of RYNV are bacilliform in shape and measure 80–150 × 25–30 nm, similar to those of badnaviruses. A1.7 kb fragment of the viral DNA was amplified by PCR and then directly sequenced. Analysis of this sequence suggests that RYNV is possibly a distinct species in the genus Badnavirus and is most closely related to Gooseberry vein banding associated virus (GVBAV) and Spiraea yellow leaf spot virus, two other badnaviruses described recently. Using the sequence derived from the PCR‐amplified viral DNA fragment, RYNV‐specific primers were designed and used in PCR to assay for RYNV in a range of Rubus germplasm infected with RYNV, with other unrelated viruses and virus‐like diseases found in Rubus, and in healthy plants. RYNV was detected in all glasshouse cultures of RYNV‐infected plants, whether alone or in complex infections with other viruses, but not from healthy Rubus plants, nor from plants infected with other viruses. It was also detected in field‐grown raspberry plants with and without symptoms of RVBMD and in raspberry plants infected with RYNV by viruliferous A. idaei. RYNV was also detected by PCR in A. idaei following access feeds on RYNV‐infected plants of 1 h or more. PCR failed to amplify DNA from gooseberry infected with GVBAV confirming the specificity of the RYNV analysis. PCR detection of RYNV in dormant raspberry buds allows assays to be made outside the natural growing season, providing a useful application for plant introduction and quarantine programmes.     

Particle purification and properties of cassava Ivorian bacilliform virus

A virus found in cassava from the north-west of the Ivory Coast was transmitted by inoculation with sap extracts to herbaceous species in six plant families. Chenopodium quinoa was used as a propagation host and C. murale was used for local lesion assays. The virus particles are bacilliform, c. 18 nm in diameter, with predominant lengths of 42,49 and 76 nm and a structure apparently similar to that found in alfalfa mosaic virus. Purified preparations of virus particles had A₂₆₀/A₂₈₀ of 1.7 ±0.05, contained one protein of M_rc. 22 000, and yielded three species of RNA with M_r (× 10^-6) of c. 0.7, 0.8 and 1.2. Although the virus particles were poorly immunogenic, an antiserum was produced and the virus was detected by enzyme-linked immunosorbent assay (DAS-ELISA) in leaf extracts at concentrations down to c. 6 ng/ml. Four other field isolates were also detected, including a strain which caused only mild systemic symptoms in C. quinoa instead of necrosis. The naturally infected cassava source plants were also infected with African cassava mosaic virus (ACMV) but when the new virus was cultured in Nicotiana benthamiana, either separately or together with ACMV, its concentration was the same. The new virus did not react with antisera to several plant viruses with small bacilliform or quasi-bacilliform particles, and alfalfa mosaic virus reacted only weakly and inconsistently with antiserum to the cassava virus. The new virus, for which the name cassava Ivorian bacilliform virus is proposed, is tentatively classified as the second member of the alfalfa mosaic virus group.     

Identification and detection of Bougainvillea spectabilis chlorotic vein‐banding virus in different bougainvillea cultivars in Taiwan

A new virus disease of bougainvillea occurred in Taiwan and proved to be caused by a Badnavirus, which is similar to the pathogen tentatively named ‘Bougainvillea spectabilis chlorotic vein‐banding virus (BsCVBV)’ in Brazil according to pathological and molecular results. In electron microscopic observations, typical bacilliform virions measuring 130–158 × 27–42 nm were observed in infected bougainvillea tissues. The transmission tests demonstrated that the virus could be easily transmitted among different bougainvillea cultivars by bud grafting but not by mechanical inoculation. BsCVBV showed different pathogenicity to various bougainvillea cultivars in our inoculation tests. The Taipei‐Red and Thimma cultivars showed the apparent foliar symptoms of chlorosis, chlorotic spots, wrinkling and leaf‐distortion; the original species of Bougainvillea glabra produced chlorotic spots and vein clearing on leaves without wrinkling or leaf distortion; both ‘Mrs. Eva Mauve Variegata’ and Hati Gadis showed mild mottling and faint spots of leaves; Helen Johnson was tolerant to BsCVBV. Our devised PCR‐based assays demonstrated that BsCVBV could replicate and persistently survived in all tested bougainvillea cultivars used in this study although it induced different symptoms in them. The BsCVBV‐1 primer pair devised from our cloned BsCVBV‐specific DNA fragments proved to be efficient in the PCR assays for the rapid and specific detection of BsCVBV in Taiwan, and this PCR‐based method is helpful in the quarantine, inspection and ecological studies for BsCVBV in Taiwan.     

Molecular characterization of <Emphasis Type="Italic">Banana streak virus</Emphasis> isolate from <Emphasis Type="Italic">Musa Acuminata</Emphasis> in China

Banana streak virus (BSV), a member of genus Badnavirus, is a causal agent of banana streak disease throughout the world. The genetic diversity of BSVs from different regions of banana plantations has previously been investigated, but there are relatively few reports of the genetic characteristic of episomal (non-integrated) BSV genomes isolated from China. Here, the complete genome, a total of 7722bp (GenBank accession number DQ092436), of an isolate of Banana streak virus (BSV) on cultivar Cavendish (BSAcYNV) in Yunnan, China was determined. The genome organises in the typical manner of badnaviruses. The intergenic region of genomic DNA contains a large stem-loop, which may contribute to the ribosome shift into the following open reading frames (ORFs). The coding region of BSAcYNV consists of three overlapping ORFs, ORF1 with a non-AUG start codon and ORF2 encoding two small proteins are individually involved in viral movement and ORF3 encodes a polyprotein. Besides the complete genome, a defective genome lacking the whole RNA leader region and a majority of ORF1 and which encompasses 6525bp was also isolated and sequenced from this BSV DNA reservoir in infected banana plants. Sequence analyses showed that BSAcYNV has closest similarity in terms of genome organization and the coding assignments with an BSV isolate from Vietnam (BSAcVNV). The corresponding coding regions shared identities of 88% and ∼95% at nucleotide and amino acid levels, respectively. Phylogenetic analysis also indicated BSAcYNV shared the closest geographical evolutionary relationship to BSAcVNV among sequenced banana streak badnaviruses.     

Ultrastructural changes and small bacilliform particles associated with infection by rubus yellow net virus

A culture of rubus yellow net virus (RYNV) was obtained free from other detectable viruses by heat treatment of red raspberry (Rubus idaeus) cv. Mailing Jewel showing veinbanding mosaic symptoms. Graft inoculated black raspberry (JR. occidentalis) plants showed three kinds of ultrastructural abnormality: (1) cell wall outgrowths in many kinds of cells in the leaf blade and vascular bundles, (2) tubular structures c. 30 nm in diameter and up to 1100 nm long, in groups in the cytoplasm close to the nucleus and (3) small bacilliform virus-like particles c. 80–150 × 25 nm in size randomly distributed in the cytoplasm of many kinds of leaf cells, but especially in the phloem. The bacilliform particles, which in some cells were in large groups associated with lightly staining amorphous material, are considered to be those of RYNV.     

Genetic variability of tobacco streak virus in South India based on the analysis of coat protein gene

Tobacco streak virus (TSV), a member of the genus Ilarvirus, family Bromoviridae is an important viral pathogen in peanut and other crops in South India. Fifteen TSV isolates naturally infecting groundnut, sunflower, onion, black gram, green gram, jute, tagetes, calotropis, pumpkin, watermelon and kenaf plants were collected from fields in different regions of Andhra Pradesh, Tamil Nadu and Karnataka. Virus was identified as TSV by direct antigen coating enzyme linked immunosorbent assay using TSV antiserum. The CP gene from each isolate was amplified using TSV coat protein specific primers. About 700 bp product was amplified, cloned, sequenced and determined its length as 717 nucleotides and codes for 239 amino acids. The sequence analysis revealed that the CP gene shared 91–100% and 91–99% sequence identity with TSV at nucleotide and amino acid level, respectively. The phylogenetic relationship based on the nucleotide sequence of these isolates from different geographical regions was also analysed in this study.     

The genome of African yam (Dioscorea cayenensis‐rotundata complex) hosts endogenous sequences from four distinct badnavirus species

Several endogenous viral elements (EVEs) have been identified in plant genomes, including endogenous pararetroviruses (EPRVs). Here, we report the first characterization of EPRV sequences in the genome of African yam of the Dioscorea cayenensis‐rotundata complex. We propose that these sequences should be termed ‘endogenous Dioscorea bacilliform viruses' (eDBVs). Molecular characterization of eDBVs shows that they constitute sequences originating from various parts of badnavirus genomes, resulting in a mosaic structure that is typical of most EPRVs characterized to date. Using complementary molecular approaches, we show that eDBVs belong to at least four distinct Badnavirus species, indicating multiple, independent, endogenization events. Phylogenetic analyses of eDBVs support and enrich the current taxonomy of yam badnaviruses and lead to the characterization of a new Badnavirus species in yam. The impact of eDBVs on diagnosis, yam germplasm conservation and movement, and breeding is discussed.     

The Occurrence of a Rhabdovirus in Daphne mezereum in the Czech Republic

A virus detected in symptomless Daphne mezereum L. plants in the Czech Republic had bacilliform virions which, in thin sections, measured 162–215 nm by 62–75 nm. They occurred mostly in the parenchymatous cells of vascular bundles and cambium, and were located in perinuclear spaces and within cisternae of the endoplasmic reticulum, either singly or in aggregates; occasionally, isolated particles or particle aggregates were seen within the nuclei. This is the first record of a rhabdovirus occurring in daphne.     

Crimson clover latent virus - a newly recognised seed-borne virus infecting crimson clover (Trigolium incarnatum)

Crimson clover latent virus (CCLV) was detected in five seed lots of crimson clover (Trifolium incarnatum) from Europe and in one from the United States of America. Ninety-seven per cent of all crimson clover plants examined were found to be infected but were without symptoms. Keeping crimson clover plants at 32–38°C for 34 days failed to free them from CCLV. The virus was not transmitted by Myzus persicae, but was transmitted by inoculation of sap to Chenopodium album, C. amaranticolor and C. quinoa. Twenty-four other plant species from seven families were not infected. CCLV was best propagated in C. quinoa in which it caused stunting and systemic chlorosis. Sap from infected C. quinoa was infective after dilution to 10^-2 but not 10^-3, after 10 min at 60°C but not 65°C, and after 20 days at 20°C. In neutral phosphotungstate, CCLV had isometric particles c. 26 nm in diameter with a hexagonal profile. About 20 to 80 A_1cm,260 units of purified virus were obtained from 1 kg of infected C. quinoa or C. amaranticolor leaves by extraction in 0.5 M phosphate buffer, pH 7.5, containing 0.01 M ethylene diamine tetra-acetate and 0.4% 2–mercaptoethanol and clarification with chloroform-butanol followed by two precipitations with polyethylene glycol (mol. wt 6000) and several cycles of differential centrifugation. Purified virus sedimented as three components with sedimentation coefficients (s°_{20, w}) of 52S, 101S and 122S. The 101S and 122S components had buoyant densities in CsCl of 1.438 and 1.495 g/cm³ respectively. From these values the nucleic acid content of the 101S and 122S components was estimated to be 32–35% and 40–41% respectively. The virus contained a single protein with an estimated mol. wt of 52 000 and two single-stranded RNA species of estimated mol. wt 1.6 × 10⁶ and 2.2 × 10⁶. CCLV was serologically unrelated to 31 other morphologically similar viruses. Although its vector is unknown, CCLV seems to have affinities with nepoviruses. The cryptogram of CCLV is R/1:2.2/40–41 + 1.6132–35:S/S:S/*.     

Association of a distinct strain of Chilli veinal mottle virus with mottling and distortion disease of Datura inoxia in India

Association of a distinct strain of Chilli veinal mottle virus (ChiVMV) with severe mottling and distortion disease of Datura inoxia was investigated based on the presence of flexuous filamentous particles of ~800 × 11 nm and sequence analyses of ~1.5 kb amplicons obtained during RT-PCR from two representative samples, designated as GMT (accession JN692501) and JNP (JN624776). Both GMT and JNP isolates contained partial polyprotein gene comprising of partial nuclear inclusion b gene, complete coat protein gene and 3′ un-translated region, a hallmark gene array of genus Potyvirus. The isolates under study shared 99% nucleotide sequence identities with each other and 83–85% identities (marginal value for species demarcation recommended by ICTV) during basic local alignments and distant phylogenetic relationships with strains of ChiVMV, hence identified as isolates of a distinct strain of ChiVMV. Association of ChiVMV strain with mottling and distortion disease of D. inoxia is being reported for the first time from India.     

Sequence Diversity of the Nucleoprotein Gene of Peanut bud necrosis virus Isolates from South India

Peanut bud necrosis virus (PBNV), genus Tospovirus (family Bunyaviridae), is an important virus infecting peanut and other crops in South India. PBNV isolates naturally infecting groundnut, brinjal, tomato, black gram, field bean, cowpea, cotton, jute, taro and Calotropis plants were collected from different regions of South India and characterized. Infection was confirmed by direct antigen‐coating enzyme‐linked immunosorbent assay (DAC‐ELISA) using PBNV‐specific antiserum. The coat protein gene was further amplified using PBNV coat protein‐specific primers. The amplicon (830 bp) was cloned and sequenced; sequence analysis revealed that the N gene shared 93–100% and 95–100% sequence identity with PBNV at the nucleotide and amino acid levels, respectively.     

Pathology, soil transmission and characterization of cymbidium ringspot, a virus from cymbidium orchids and white clover (Trifolium repens)

Two strains of a virus, designated cymbidium ringspot virus (CyRSV), were isolated from cymbidium orchids and from Trifolium repens respectively in Britain. Experimentally infected cymbidiums developed slight chlorotic ring-mottle; T. repens developed flecks and mottling in the leaves, and slight stunting. Of 101 plant species tested, the cymbidium strain infected sixty-one (thirteen systemically) in twenty-three of thirty-five families; the clover strain infected sixty-four species (eighteen systemically) in twenty-two families. Both strains were propagated in Nicotiana clevelandii and assayed in Chenopodium quinoa. CyRSV was readily transmitted by inoculation of sap, and by foliage contact between plants, but not by the aphids Myzus persicae or Acyrtho-siphon pisum, nor through seed of T. incarnatum, Phaseolus vulgaris or N. clevelandii. Highly infective virus was released into soil from roots of infected N. clevelandii, and acquired by bait seedlings planted in such soil. Similar transmission occurred when purified virus was applied to the surface of sterilized soil containing bait plants; there was no evidence for any living soil vector. The virus was eliminated from 96 % of small cuttings taken from infected N. clevelandii plants grown at 35–37 °C for 9 wk. CyRSV was still infective in sap of N. clevelandii after dilution to 10?⁵-io–⁶ (only 2 × 10^_1 in cymbidium sap), or after 10min at 85–90 °C. It survived at least 10 months at c. 20 °C and more than 12 yr at 2 °C. Lyophilized sap was highly infective after over 13 yr at laboratory temperatures under high vacuum. Purified preparations made by clarification with n-butanol, followed by differential centrifugation and exclusion chromatography on controlled-pore glass beads, contained isometric particles c. 30 nm diam., with s°_20W= 137 S, and had a buoyant density in caesium chloride of 1–36 g/ml. The A 260/A 280 ratio was 1–55, and A max(26o)/A min(242) was 1–17. The virus contained c. 15 % of single-stranded RNA of mol. wt 1–7 × 10⁶; the nucleotide base ratios were: G27'8; A24/9; C2I-3; U26-I. There was one capsid polypeptide of mol. wt 43600. The virus was a good immunogen and a strongly reacting antigen in vitro; in Immunoelectrophoresis, each strain migrated as a single antigenic component towards the cathode. The cymbidium and clover strains were serologically closely related, although spurs were produced in immunodiffusion. No serological relationship was found to forty-three other isometric viruses, including eighteen tombusvirus isolates; CyRSV nevertheless shares many properties with tombusviruses, and we assign it provisionally to this group. The cryptogram is: R/r:1:7/15:S/S:S/O.     

Role of the parasporal body in causing toxicity of Bacillus thuringiensis toward Aedes aegypti larvae

A unique type of microorganism has been found causing an unusual disease in larvae of the clover cutworm, Scotogramma trifolii (Lepidoptera; Noctuidae). The organism contains DNA and reproduces exclusively by self-assembly forming enveloped reniform/bacilliform particles which measure 170 × 450 nm in negatively stained preparations. During initial stages of development, the organism apparently reproduces primarily within vesicles in the cytoplasm of a variety of cell types including hemocytes, and epidermal, fat body, and tracheal matrix cells. Most reproduction, however, occurs in vesicles that circulate in the hemolymph. These vesicles, most of which are derived from host cells, measure 2–10 μm in diameter, are highly refractile, reach populations as high as 10⁸/ml of hemolymph, and are diagnostic for the disease. The pathology caused by this organism, its shape and ultrastructure, and reproduction within vesicles indicate it is either a peculiar type of rickettsia, possibly related to those of the genus Rickettsiella, or a new type of invertebrate virus. Among its unusual features are its ability to induce the formation of reproductive vesicles from host cell components, and its apparent control of de novo ribosome and membrane synthesis within these vesicles as it develops. The possible relationship of this organism to baculoviruses and rickettsia is discussed.     

Association of different kinds of bacilliform particle with vein chlorosis and mosaic diseases of raspberry (Rubus idaeus)

Thin sections of diseased raspberry (Rubus idaeus) were examined by electron microscopy. Plants of the cv. Baumforth's B and of an aphid (Amphorophora rubi)-resistant breeding selection (6820/54), both infected with raspberry vein chlorosis virus (RVCV) but not with other detectable viruses, contained large bacilliform particles c. 430 × 65 nm. Particles occurred in the cytoplasm and perinuclear space of a small proportion of xylem parenchyma cells. They had an inner core c. 25–30 nm in diameter with cross-banding of periodicity 4·5 nm, and were bounded by an outer membrane. They are probably the particles of RVCV. Plants of cv. Mailing Jewel and of a selection (M14) both showing symptoms of raspberry mosaic (veinbanding) disease contained smaller bacilliform particles c. 125 × 30 nm, which occurred singly or in clusters in the cytoplasm of a small proportion of vascular parenchyma cells. It is not known which, if any, of the viruses associated with raspberry mosaic are represented by the particles.