The replicative intermediate molecule of bovine viral diarrhoea virus contains multiple nascent strands

Summary.  The replication of bovine viral diarrhoea virus (BVDV) RNA is considered to involve replicative intermediates (RI) and replicative forms (RF) of virus RNA. These RNA species were radiolabelled metabolically by ³H-uridine in BVDV-infected cells and separated by sucrose gradient centrifugation. RNA in the fractions was then digested with RNase A in high salt (2 × SSC) and the RNase-resistance was determined. Using the Baltimore formula, this led to the calculation that the RI of BVDV contained 6–7 nascent strands on the template. This suggests that the structure of the BVDV RI is similar to that of poliovirus and dengue 2 virus. Accepted September 15, 1997 Received May 26,1997     

Nucleotide sequence and genome organization of Dweet mottle virus and its relationship to members of the family Betaflexiviridae

The nucleotide sequence of Dweet mottle virus (DMV) was determined and compared to sequences of members of the families Alphaflexiviridae and Betaflexiviridae. The DMV genome has 8,747 nucleotides (nt) excluding the 3′ poly-(A) tail. DMV genomic RNA contains three putative open reading frames (ORFs) and untranslated regions of 73 nt at the 5′ and 541 nt at 3′ termini. ORF1 potentially encoding a 227.48-kDa polyprotein, which has methyltransferase, oxygenase, endopeptidase, helicase, and RNA-dependent RNA polymerase (RdRP) domains. ORF2 encodes a movement protein of 40.25 kDa, while ORF3 encodes a coat protein of 40.69 kDa. Protein database searches showed 98–99% matches of DMV ORFs with citrus leaf blotch virus (CLBV) sequences. Phylogenetic analysis based on the RdRP core domain revealed that DMV is closely related to CLBV as a member of the genus Citrivirus. DMV did not satisfy the molecular criteria for demarcation of an independent species within the genus Citrivirus, family Betaflexiviridae, and hence, DMV can be considered a CLBV isolate.     

Identification and characterisation of tomato torrado virus,a new plant picorna-like virus from tomato

Summary. A new virus was isolated from tomato plants from the Murcia region in Spain which showed symptoms of ‘torrado disease’; very distinct necrotic, almost burn-like symptoms on leaves of infected plants. The virus particles are isometric with a diameter of approximately 28 nm. The viral genome consists of two (+)ssRNA molecules of 7793 (RNA1) and 5389 nts (RNA2). RNA1 contains one open reading frame (ORF) encoding a predicted polyprotein of 241 kDa that shows conserved regions with motifs typical for a protease-cofactor, a helicase, a protease and an RNA-dependent RNA polymerase. RNA2 contains two, partially overlapping ORFs potentially encoding proteins of 20 and 134 kDa. These viral RNAs are encapsidated by three proteins with estimated sizes of 35, 26 and 23 kDa. Direct protein sequencing mapped these coat proteins to ORF2 on RNA2. Phylogenetic analyses of nucleotide and derived amino acid sequences showed that the virus is related to but distinct from viruses belonging to the genera Sequivirus, Sadwavirus and Cheravirus. This new virus, for which the name tomato torrado virus is proposed, most likely represents a member of a new plant virus genus.     

Properties of the bovine viral diarrhoea virus replicase in extracts of infected MDBK cells

Summary.   An assay for the bovine viral diarrhoea virus (BVDV) replicase was developed using extracts from BVDV-infected cells. The replicase activity was maximal approximately 8 h post-infection as measured by the generation of a genomic length radiolabelled RNA. Using a semi-denaturing gel system, three virus-specific in vitro radiolabelled nascent RNA species were identified. A fast-migrating RNA was demonstrated to be the double-stranded replicative form (RF). A second form was shown to be a partially single-stranded/partially double-stranded RNA, characteristic of the replicative intermediate (RI). A third form, which was often undetectable, migrated between the RF and RI and was probably genomic viral RNA. The optimal replicase activity was dependent on 5–10 mM Mg²⁺ and although it was also active in 1–2 mM Mn²⁺ it was inhibited at higher concentrations. The optimum KCl concentration for labelling of the RI and RF were different, suggestive of at least two distinct replicase activities. These results are supportive of a semi-conservative model of BVDV RNA replication. Received November 26, 1999 Accepted February 4, 2000     

Tomato marchitez virus, a new plant picorna-like virus from tomato related to tomato torrado virus

Summary A new virus was isolated from a tomato plant from the state of Sinaloa in Mexico. This plant showed symptoms locally known as ‘marchitez disease’: severe leaf necrosis, beginning at the base of the leaflets, and necrotic rings on the fruits. A virus was isolated from the infected plant consisting of isometric particles with a diameter of approximately 28 nm. The viral genome consists of two (+)ssRNA molecules of 7221 (RNA1) and 4898 nts (RNA2). The viral capsid contains three coat proteins of 35, 26 and 24 kDa, respectively. The abovementioned characteristics: symptoms, morphology, number and size of coat proteins, and number of RNAs are similar to those of the previously described tomato torrado virus (ToTV). Sequence analysis of the entire viral genome shows that this new virus is related to, but distinct from, ToTV and that these members of two obviously new virus species belong to the recently proposed plant virus genus Torradovirus. For this new virus, the name tomato marchitez virus (ToMarV) is proposed. Correspondence: Martin Verbeek, Plant Research International BV, P.O. Box 16, NL-6700 AA Wageningen, The Netherlands     

Indian citrus ringspot virus: a proposed new species with some affinities to potex-, carla-, fovea- and allexiviruses

Summary.  An isolate of Indian citrus ringspot virus from Kinnow mandarin in northern India had flexuous particles with evident cross-banding and a modal length of 650 nm. It was mechanically transmitted to five herbaceous hosts including Phaseolus vulgaris cv Saxa, in which it became systemic. In thin sections, virus particles were observed in the cytoplasm of parenchyma cells but no specific inclusions were seen. The virus was purified from infected Saxa bean leaves and an antiserum prepared. There was no serological cross-reaction with representative allexi-, capillo-, potex- and trichoviruses, except a faint one-way reaction with Potato virus X. Purified virus yielded a major band, the presumed coat protein (CP), of about 34 kDa, and a single ssRNA of about 7.5 kb, which was infectious. Two ORFs encoding putative proteins of 34 kDa and 23 kDa were located in the 3′ part of the RNA. The product of the 34 kDa ORF was confirmed as the CP by expression in E. coli. The derived amino acid sequence of the CP contained some short motifs similar to those of potex-, fovea-, carla- and allexiviruses but otherwise there was no strong similarity to any of these. The 23 kDa ORF contained a zinc finger-like sequence, as in similar ORFs in carla- and allexiviruses but overall amino acid homology with these was low. The virus does not appear to fall into any known genus. A new species is proposed. Serological and molecular diagnostic reagents were prepared. Received July 14, 1999/Accepted February 10, 2000     

Synthesis of genomic and subgenomic RNAs by a membrane-bound RNA-dependent RNA polymerase isolated from oat plants infected with cereal yellow dwarf virus

Summary. A membrane-bound RNA-dependent RNA polymerase (RdRp) complex was isolated by differential sedimentation from oat plants infected with cereal yellow dwarf virus (CYDV). When incubated with ³²P-labelled UTP, unlabelled ATP, CTP and GTP, and Mg²⁺ ions, the RdRp preparation catalysed the synthesis of double-stranded (ds) RNAs corresponding in size to the virus genomic RNA (5.7 kbp) and two putative subgenomic RNAs (2.8 and 0.7 kbp). Hybridisation using strand-specific hybridization targets showed that the 5.7-kbp dsRNA was labelled mainly in the plus strand, whereas the 2.8- and 0.7-kbp dsRNAs were labelled only in the minus strand. Genomic-length single-stranded, plus-strand RNA of 5.7 kb and single-stranded, plus-strand subgenomic RNAs of 2.8 and 0.7 kbp were detected in RNA isolated from oat plants infected with CYDV. Mapping experiments were consistent with the genomic and subgenomic RNAs having common 3′ ends, but different 5′ ends, whether produced in vitro or in vivo. The RdRp-encoding region of the CYDV genome was cloned and expressed in Escherichia coli, and the purified protein was used to raise antibodies in a rabbit. In immunoblots, the antibodies detected a protein of about 68 kDa in RdRp preparations from CYDV-infected oat plants, but not from equivalent preparations from healthy oats. As far as we are aware, this is the first report of an in vitro RNA synthesis system for a phloem-limited virus.     

Identification and characterization of a novel tospovirus species using a new RT-PCR approach

Summary.  A novel tospovirus serologically distinct from all established tospo- virus species was found in Thailand in Physalis minima L. The S RNA of this virus was cloned by a new RT-PCR approach revealing a nucleotide sequence of 3257 nucleotides. The ambisense RNA segment encoded a nonstructural protein (NSs) of 469 amino acids, with a predicted Mr of 53.2 kDa, and a nucleoprotein (N) of 279 amino acids and a Mr of 31.0 kDa, so far the largest N protein known for any tospovirus species. N protein sequence comparisons revealed closest relationship to the species Watermelon bud necrosis virus (58% identity), Watermelon silver mottle virus and Peanut bud necrosis virus (57%) and a distant relationship to Peanut yellow spot virus (23%) and Peanut chlorotic fanspot virus (22%). Received March 27, 2000 Accepted July 27, 2000     

Molecular characterization and interviral relationships of a flexuous filamentous virus causing mosaic disease of sugarcane (Saccharum officinarum L.) in India

Summary.  A virus isolate causing mosaic disease of commercial sugarcane was purified to homogeneity. Electron microscopy revealed flexuous filamentous virus particles of ca 890 × 15 nm. The virus isolate reacted positively with heterologous antiserum to narcissus latent virus form UK, but failed to react with potyvirus group specific antiserum. N-terminal sequencing of the intact coat protein (CP) and the tryptic peptides indicated that the virus was probably a potyvirus but distinct from several reported potyviruses. Comparison of the 3′-terminal 1084 nucleotide sequence of the RNA genome of this virus revealed 93.6% sequence identity in the coat protein coding region with the recently described sugarcane streak mosaic virus (Pakistani isolate). The molecular weight of the coat protein (40 kDa) was higher than that deduced from the amino acid sequence (34 kDa). The apparent increase in size was shown to be due to glycosylation of the coat protein which has not been reported thus far in the family, Potyviridae. This is the first report on the molecular characterization of a virus causing mosaic disease of sugarcane in India and the results demonstrate that the virus is a strain of sugarcane streak mosaic virus, a member of the Tritimovirus genus of the Potyviridae. We have named it sugarcane streak mosaic virus – Andhra Pradesh isolate (SCSMV-AP). Received October 14, 1997 Accepted August 7, 1998     

Molecular characterization and detection of Vicia cryptic virus in different Vicia faba cultivars

Summary After extraction of double-stranded (ds) RNAs from Vicia faba, dsRNA1 and dsRNA2 of Vicia cryptic virus (VCV), a member of the genus Alphacryptovirus (family Partitiviridae), were detected in six out of seven different cultivars by agarose gel electrophoresis. In attempts to sequence the complete VCV genome, the dsRNA1 and dsRNA2 sequences from a total of five different V. faba cultivars were determined. Analysis of these sequences indicated that V. faba cultivars contain almost indistinguishable VCV sequences. The larger dsRNA1 was 2012 bp in length and contained a major open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp). The smaller dsRNA2 was 1779 bp in length and comprised a single ORF on its plus-strand encoding the coat protein (CP). The sequences of the dsRNA1 and dsRNA2 ORFs shared highest amino acid sequence identities (84 and 56%, respectively) with the corresponding gene products of the alphacryptovirus white clover cryptic virus 1 (WCCV-1). The 5′-terminal untranslated regions of dsRNA1 and dsRNA2 of VCV were highly conserved and were strikingly similar to the corresponding regions of WCCV-1. RdRp amino acid sequence alignments revealed conserved motifs, which correlate with the phylogenetic clustering of the family Partitiviridae.     

Characterization and in vitro translation analysis of pelargonium flower break virus

Summary.  Pelargonium flower break virus (PFBV) is one of the common viruses in the glasshouses of Western Europe and has been assigned to the genus Carmovirus. A Spanish isolate obtained from nursery-grown Pelargonium zonale plants (PFBV-m) has been characterized. The molecular weight of genomic RNA and coat protein of PFBV-m were determined to be 1.36 × 10⁶ (corresponding to approximately 4 kb) and 36,000, respectively. Only genomic-size RNA was encapsidated in PFBV virions; making necessary to purify double-stranded RNA from infected tissue in order to detect putative PFBV subgenomic RNAs. PFBV RNA directed the synthesis of a major polypeptide of 34 kDa and three other relevant polypeptides of estimated sizes 88–90 kDa, 42 kDa and 35–36 kDa. Antisera specific to PFBV immunoprecipitated the in vitro translated 35–36 kDa polypeptide indicating that this polypeptide is the PFBV coat protein. The PFBV in vitro translation pattern was very similar to that of CarMV although the relative levels of translated coat protein differed dramatically between the two viruses, most probably due to the lack of encapsidation of subgenomic PFBV. In vitro translation studies with a different biological clone obtained from the same PFBV-m isolate revealed a prominent additional polypeptide which is postulated to be a truncation of the 5′ proximal ORF. Received November 27, 1998 Accepted March 24, 1999     

The genome organization of the broad bean necrosis virus (BBNV)

Summary.  The genome of the broad bean necrosis virus Oita-isolate (BBNV-O) [RNA1 (6.0 kb), RNA2 (2.8 kb) and RNA3 (2.4 kb)] was cloned and sequenced. Computer analysis indicates that methyltransferase, helicase and RNA-dependent RNA polymerase (RdRp) motifs are present in RNA1. The viral capsid protein (CP) cistron is located at the 5′ terminal end of RNA2 and the Mr of CP (20 K) is close to that determined by SDS-PAGE analysis. An ochre codon (UAA) in the CP cistron is thought to be partially suppressed to produce a large readthrough protein. RNA3 possesses typical motifs of triple gene block proteins, which are also reported in several other plant viruses. The furovirus genome organization and phylogenetic analysis using RdRp and CP amino acid sequences suggest that BBNV is closely related to potato mop-top virus (PMTV), but is relatively distantly related to other furoviruses. The data also suggest that the genus Furovirus should be separated into several genera: the prototypical genus Furovirus, which excludes the following viruses: the PMTV group including BBNV; the beet necro- tic yellow vein virus (BNYVV) group; and the peanut clump virus (PCV) group. Received November 14, 1997 Accepted Febuary 12,1998     

Narcissus symptomless virus: a new carlavirus of daffodils

Summary. A filamentous virus, with particles 600–650 nm long, was purified from Narcissus pseudonarcissus (daffodil) in Hangzhou and an antiserum prepared. After mechanical inoculation, the virus could be detected serologically in Narcissus species but not in some commonly used virus indicators. Infection was symptomless. The complete sequence of the genomic RNA (8281 nt) showed six predicted ORFs typical of carlaviruses. Pairwise comparisons of gene sequences and phylogenetic analysis demonstrated that the new virus should be classified as a carlavirus but that it was not closely related to members of any current species. We propose the name Narcissus symptomless virus (NSV).     

Mutation of the herpes simplex virus 1 KOS UL45 gene reveals dose dependent effects on central nervous system growth

Summary.  The herpes simplex virus type 1 (HSV-1) UL45 gene encodes an 18 kDa virion envelope protein whose function remains unknown. Previous studies using a UL45 null mutant, UL45Δ, demonstrated that deletion of the UL45 gene altered plaque size in Vero and HeLa cells, but was not essential for replication in these cell types. The goal of this study was to determine if mutation of the UL45 gene influenced virus growth in the CNS. Two UL45 mutants, as well as a repaired revertant virus, were constructed and tested for their ability to cause encephalitis and replicate in the CNS. The UL45 mutants were not lethal when 1 × 10³ pfu were injected intracerebrally into Balb/c mice. In contrast, at inocula greater than 1 × 10³, the UL45 mutants were lethal. In vivo growth curves derived from mice inoculated intracerebrally with 1 × 10³ pfu of virus revealed that the mutants grew poorly compared to wild type or revertant viruses. These results suggest that the 18 kDa UL45 gene product is required for efficient growth in the central nervous system at low doses. We propose that the UL45 gene may play an important role under the conditions of a naturally acquired infection. Received June 23, 2001 Accepted November 1, 2001     

Complementary DNA cloning and hybridization analysis of maize stripe virus RNAs

Cloned cDNAs were used to assess the relationships of the RNAs isolated from maize stripe virus (MStV) virion-like nucleoproteins. Northern blot hybridization analysis showed no detectable sequence homology between the five different sized RNAs; however, cDNAs which hybridized with a specific ssRNA also hybridized with a specific dsRNA. Hybridization analysis of denatured MStV RNAs using ssRNA riboprobes of opposite polarities showed that for each of the five MStV RNAs, opposite, complementary polarity RNAs were present. However, unequal amounts of complementary polarities for each size RNA were detected, and the polarity of the RNA in excess was primarily detectable as ssRNA.     

Synergism in replication of cymbidium mosaic potexvirus (CymMV) and odontoglossum ringspot tobamovirus (ORSV) RNA in orchid protoplasts

Summary.  An in vitro orchid protoplast isolation method to study replication kinetics of CymMV and ORSV was developed. This method allows the isolation of viable and raphid-free petal protoplasts from an orchid hybrid, {\it Dendrobium} Sonia (Dendrobium Caesar × Dendrobium Tomie Drake). The optimum field strength for both viral RNA to achieve good efficiency of electroporation was 750 V/cm and the optimum viral RNA concentration required was 1 μg and 4 μg per 2 × 10⁶ protoplasts for CymMV and ORSV, respectively. Autoradiographs of Northern blots depicting the viral genomic and subgenomic RNA in the extracts, referred to as the “Replication Footprint Profiles” (RFP) of specific CymMV/ORSV virus were prepared at different time intervals. Viral RNA synthesis reached a maximum at 18 h for CymMV and 24 h for ORSV. When CymMV and ORSV viral RNA were electroporated into the protoplasts simultaneously, detection signals of both the positive and negative strand viral RNA increased as compared to the singly infected protoplasts. Thus, synergism in replication of CymMV and ORSV was observed in orchid protoplasts. Received November 20, 1997 Accepted February 25, 1998     

The genome organisation and taxonomy of Sugarcane striate mosaic associated virus

Summary.  Sugarcane striate mosaic associated virus (SCSMaV) has slightly flexuous 950 nm × 15 nm filamentous particles and is associated with sugarcane striate mosaic disease in central Queensland, Australia. We report the full sequence of its RNA genome, which comprises 5 open reading frames representing the polymerase, movement function proteins encoded in a triple gene block and coat protein. Phylogenetic analyses based on either the full nucleotide sequence, the polymerase protein, or the coat protein all placed SCSMaV in an intermediate position between the genera Foveavirus and Carlavirus, but outside both genera. In addition, the absence of a sixth open reading frame excludes it from the genus Carlavirus, and the coat protein is approximately half the size of the type member for the genus Foveavirus. Although SCSMaV was most closely allied to Cherry green ring mottle virus by genome analysis, the two viruses are morphologically and biologically dissimilar. SCSMaV may therefore represent a new plant virus taxon. Received January 30, 2001/Accepted May 29, 2001     

Rapid detection and differentiation of Newcastle disease virus by real-time PCR with melting-curve analysis

Summary. In order to rapidly detect and differentiate Newcastle disease virus (NDV) isolates, a method based on real-time PCR SYBR Green I melting-curve analysis of the fusion (F) protein gene was developed. The detection limit of real-time PCR was 9 × 10² plasmid copies and was 100 times more sensitive than conventional PCR. Thirty eight reference NDV strains were rapidly identified by their distinctive melting temperatures (T_ms): 89.23 ± 0.27 °C for velogenic strains, 90.17 ± 0.35 °C for pigeon mesogenic strains, 91.25 ± 0.14 °C for two lentogenic strains (B1 and Ishii). No amplification was detected from unrelated RNA samples by this method. This real-time PCR directly detected NDV from infected tissues and eliminated the gel electrophoretic step for analyzing PCR product using ethidium bromide. The total time for a PCR run was less than 1 hour. The results obtained in this study showed that the real-time PCR presented here is a good screening test for the identification of NDV.     

Electrophoretic separation of dsRNA genome segments from maize wallaby ear virus and its relationship to other phytoreoviruses

Partially purified maize wallaby ear virus (MWEV) preparations were shown to contain 10 double-stranded (ds) RNA segments. Electrophoretic mobilities of the dsRNAs of MWEV and of other phytoreoviruses have been compared in two buffers. The total genome molecular weight of maize wallaby ear virus was ～18.92 × 10⁶ and ～19.33 × 10⁶ in PTE and Loening's buffer, respectively. Extracts from the virus-free leafhopper vector, Cicadulina bimaculata, contained two dsRNA segments of molecular weight 1.15 × 10⁶ and 1.08 × 10⁶ in PTE buffer. Extracts from viruliferous insects also contained these same 2 dsRNA segments in addition to the 10 segments of maize wallaby ear virus. The electrophoretic pattern of dsRNA components of maize wallaby ear virus was similar to those of maize rough dwarf virus and Fiji disease virus suggesting a relationship between them. The degrees of relationship among these viruses and rice black-streaked dwarf virus, wound tumor virus, and rice dwarf virus were indicated by the electrophoretic patterns of their genome segments in the two buffers.