The use of reverse transcriptase for efficient first- and second-strand cDNA synthesis from single- and double-stranded RNA templates

Development of Rapid and Affordable Virus-Mimicking Artificial Positive Controls

A major bottleneck in the development of detection assays is the availability of positive controls. Their acquisition can be problematic, their maintenance is expensive, and without them, assays cannot be validated. Herein, we present a novel strategy for the development of virus-mimicking artificial positive controls (ViMAPCs). The time between design and application is less than 5 days, unlike alternatives which normally take several weeks to obtain and implement. The ViMAPCs provide a realistic representation of natural infection unlike alternatives and allow for an effortless recognition of laboratory-based contamination. The feasibility and adaptability of the strategy was evaluated using several RNA and DNA plant viruses. ViMAPCs can be used in diagnostics laboratories but also in the monitoring of pathogen outbreaks where rapid response is of utmost importance.

Transcriptomic profiling of Indian breast cancer patients revealed subtype-specific mRNA and lncRNA signatures

Breast cancer (BC) is one of the leading causes of cancer-associated death in women. Despite the progress in therapeutic regimen, resistance and recurrence of breast cancer have affected the overall survival of patients. The present signatures, such as PAM50 and Oncotype DX, do not segregate the Indian breast samples based on molecular subtypes. This study aims at finding signatures of long noncoding RNA (lncRNA) and mRNA in Indian breast cancer patients using RNA-seq. We have analyzed the survival based on the menopausal and hormone status of 380 Indian breast cancer patients, and of these, we have sequenced and analyzed matched tumor–normal transcriptome of 17 (pre- and postmenopausal) Indian breast cancer patients representing six different subtypes, namely, four patients in triple-positive, three patients in estrogen receptor–positive (ER+ve), three patients in estrogen and progesterone receptors–positive (ER+ve, PR+ve), two patients in human epidermal growth factor receptor (Her2+ve), three patients in triple-negative, and one patient in ER+ve and Her2+ve subtypes. We have identified a 25 mRNA–27 lncRNA gene set, which segregated the subtypes in our data. A pathway analysis of the differentially expressed genes revealed downregulated ECM interaction and upregulated immune regulation, cell cycle, DNA damage response and repair, and telomere elongation in premenopausal women. Postmenopausal women showed downregulated metabolism, innate immune system, upregulated translation, sumoylation, and AKT2 activation. A Kaplan–Meier survival analysis revealed that menopausal status, grade of the tumor, and hormonal status displayed statistically significant effects (p < 0.05) on the risk of mortality due to breast cancer. Her2+ve patients showed low overall survival. One of the unique lncRNA-mRNA pairs specific to the EP-subtype, SNHG12 and EPB41, showed interaction, which correlates with their expression level; SNHG12 is downregulated and EPB41 is upregulated in EP samples.

Integrated Transcriptome and Metabolomic Analysis Reveal Anti-Angiogenic Properties of Disarib, a Novel Bcl2-Specific Inhibitor

Transcriptomic profiling of several drugs in cancer cell lines has been utilised to obtain drug-specific signatures and guided combination therapy to combat drug resistance and toxicity. Global metabolomics reflects changes due to altered activity of enzymes, environmental factors, etc. Integrating transcriptomics and metabolomics can provide genotype-phenotype correlation, providing meaningful insights into alterations in gene expression and its outcome to understand differential metabolism and guide therapy. This study uses a multi-omics approach to understand the global gene expression and metabolite changes induced by Disarib, a novel Bcl2-specific inhibitor in the Ehrlich adenocarcinoma (EAC) breast cancer mouse model. RNAseq analysis was performed on EAC mouse tumours treated with Disarib and compared to the controls. The expression of 6 oncogenes and 101 tumour suppressor genes interacting with Bcl2 and Bak were modulated upon Disarib treatment. Cancer hallmark pathways like DNA repair, Cell cycle, angiogenesis, and mitochondrial metabolism were downregulated, and programmed cell death platelet-related pathways were upregulated. Global metabolomic profiling using LC-MS revealed that Oncometabolites like carnitine, oleic acid, glycine, and arginine were elevated in tumour mice compared to normal and were downregulated upon Disarib treatment. Integrated transcriptomic and metabolomic profiles identified arginine metabolism, histidine, and purine metabolism to be altered upon Disarib treatment. Pro-angiogenic metabolites, arginine, palmitic acid, oleic acid, and myristoleic acid were downregulated in Disarib-treated mice. We further validated the effect of Disarib on angiogenesis by qRT-PCR analysis of genes in the VEGF pathway. Disarib treatment led to the downregulation of pro-angiogenic markers. Furthermore, the chorioallantoic membrane assay displayed a reduction in the formation of the number of secondary blood vessels upon Disarib treatment. Disarib reduces tumours by reducing oncometabolite and activating apoptosis and downregulating angiogenesis.

A new, sensitive and efficient method for taxonomic placement in the Eriophyoidea and virus detection in individual eriophyoids

Eriophyoids affect crops around the globe directly or indirectly as virus vectors. Eriophyoid systematics initiated over a century ago, yet more than 90% of their fauna remain undescribed. Morphological identification is challenging because of a limited number of traits, cryptic speciation and complex life cycle reported for many species in the group. Nucleic acids extraction for mite identification is challenging due to their microscopic size with researchers using pooled samples leading to polymorphisms and inconclusive results. Identification of mite virus vectors is a tiresome task that could be simplified with a protocol that allows for the detection of viruses in the individual specimen. This communication describes an innovative, highly efficient extraction and detection pipeline. Direct Reverse Transcriptase - Polymerase Chain Reaction (Drt-PCR) assays were implemented in the molecular identification of eriophyoids and detection of viruses present in their bodies. The reverse transcription step allows for amplification from a single mite or egg, as in addition to the genomic DNA, it incorporates the abundant transcripts of targeted genes, whereas it also allows for the amplification of viruses. This communication provides an efficient, sensitive and cost-effective alternative that can be implemented in pest identification and detection as well as biological and ecological studies.

Molecular detection of watermelon mosaic virus associated with a serious mosaic disease on Cucurbita pepo L. in Shanxi, China

With continued expansion of Cucurbita pepo L. cultivation, viral diseases affecting the crop have become more serious in recent years, causing enormous losses in yield and quality. A virus sample was obtained from Wenshui in Shanxi province, China. Double-stranded RNA technology and sequence-independent amplification (SIA) were used to identify the virus that induced C. pepo L. mosaic disease. SIA and sequencing results showed the presence of watermelon mosaic virus (WMV) in diseased C. pepo L. leaves. The complete sequence of WMV from the Shanxi isolate (i.e., WMV-WS) was cloned and analyzed for further characterization. The genomic RNA of WMV-WS is 10,040 nucleotides in length and encodes a putative polyprotein of 3218 amino acids. Phylogenetic analysis indicate that all WMV isolates were divided into four groups and WMV-WS isolate belong to Group 4. Further analysis showed that these WMV isolates were not only to a certain degree related to the host, but also related to geographical origin of isolates. Our results provide information for a better understanding of the genetic diversity of WMV isolates infecting C. pepo L. in Shanxi, China.

Genetic characterization of Blueberry necrotic ring blotch virus, a novel RNA virus with unique genetic features

A new disorder was observed on southern highbush blueberries in several south-eastern states in the USA. Symptoms included irregularly shaped circular spots or blotches with green centres on the upper and lower surfaces of leaves. Double-stranded RNA was extracted from symptomatic leaves suggesting the presence of virus(es) possibly involved in the disease. Sequencing revealed the presence of a novel RNA virus with a ~14 kb genome divided into four RNA segments. Sequence analyses showed that the virus, for which we propose the name Blueberry necrotic ring blotch virus (BNRBV), possesses protein domains conserved across RNA viruses in the alpha-virus-like supergroup. Phylogenetic inferences using different genes placed BNRBV in a clade that includes the Bromoviridae, the genus Cilevirus (CiLV) and the recently characterized Hibiscus green spot virus (HGSV). Despite the strong genetic relationships found among BNRBV, Cilevirus and HGSV, the genome of BNRBV contains three features that distinguish it significantly from its closest relatives: (i) the presence of two helicase domains with different evolutionary pathways, (ii) the existence of three conserved nucleotide stretches located at the 3' non-coding regions of each RNA segment and (iii) the conservation of terminal nucleotide motifs across each segment. Furthermore, CiLV and HGSV possess poly(A)-tailed bipartite and tripartite genomes, respectively, whereas BNRBV has a quadra-partite genome lacking a poly(A) tail. Based on these genetic features a new genus is proposed for the classification of BNRBV.

Raspberry leaf blotch virus, a putative new member of the genus Emaravirus, encodes a novel genomic RNA

A new, segmented, negative-strand RNA virus with morphological and sequence similarities to other viruses in the genus Emaravirus was discovered in raspberry plants exhibiting symptoms of leaf blotch disorder, a disease previously attributed to the eriophyid raspberry leaf and bud mite (Phyllocoptes gracilis). The virus, tentatively named raspberry leaf blotch virus (RLBV), has five RNAs that each potentially encode a single protein on the complementary strand. RNAs 1, 2 and 3 encode, respectively, a putative RNA-dependent RNA polymerase, a glycoprotein precursor and the nucleocapsid. RNA4 encodes a protein with sequence similarity to proteins of unknown function that are encoded by the genomes of other emaraviruses. When expressed transiently in plants fused to green or red fluorescent protein, the RLBV P4 protein localized to the peripheral cell membrane and to punctate spots in the cell wall. These spots co-localized with GFP-tagged tobacco mosaic virus 30K cell-to-cell movement protein, which is itself known to associate with plasmodesmata. These results suggest that the P4 protein may be a movement protein for RLBV. The fifth RLBV RNA, encoding the P5 protein, is unique among the sequenced emaraviruses. The amino acid sequence of the P5 protein does not suggest any potential function; however, when expressed as a GFP fusion, it localized as small aggregates in the cytoplasm near to the periphery of the cell.

Molecular characterization of a new Tospovirus infecting soybean

A new, widespread disease was recently observed in soybean in the United States. The disease, named Soybean vein necrosis, is manifested by intraveinal chlorosis and necrosis, and has been found in almost all of the 50 fields visited over a period of 3 years in the midwest and midsouth part of the United States. A virus was isolated from symptomatic material, and detection protocols were developed. More than 150 symptomatic specimens collected from seven US States were tested, and all were found positive for the virus unlike 75 asymptomatic samples, revealing the absolute association between virus and disease. Protein pairwise comparisons coupled with phylogenetic analyses indicate that the virus is a new member of the genus Tospovirus.

Complete sequence and genetic characterization of Raspberry latent virus, a novel member of the family Reoviridae

A new virus isolated from red raspberry plants and detected in the main production areas in northern Washington State, USA and British Columbia, Canada was fully sequenced and found to be a novel member of the family Reoviridae. The virus was designated as Raspberry latent virus (RpLV) based on the fact that it is symptomless when present in single infections in several Rubus virus indicators and commercial raspberry cultivars. RpLV genome is 26,128 nucleotides (nt) divided into 10 dsRNA segments. The length of the genomic segments (S) was similar to those of other reoviruses ranging from 3948 nt (S1) to 1141 nt (S10). All of the segments, except S8, have the conserved terminal sequences 5'-AGUU----GAAUAC-3'. A point mutation at each terminus of S8 resulted in the sequences 5'-AGUA----GAUUAC-3'. Inverted repeats adjacent to each conserved terminus as well as stem loops and extended pan handles were identified by analyses of secondary structures of the non-coding sequences. All segments, except S3 and S10, contained a single open reading frame (ORF) on the positive sense RNAs. Two out-of-frame overlapping ORFs were identified in segments S3 (ORF S3a and S3b) and S10 (ORF S10a and S10b). Amino acid (aa) alignments of the putative proteins encoded by the main ORF in each segment revealed a high identity to several proteins encoded by reoviruses from different genera including Oryzavirus, Cypovirus, and Dinovernavirus. Alignments of the polymerase, the most conserved protein among reoviruses, revealed a 36% aa identity between RpLV and Rice ragged stunt virus (RRSV), the type member of the genus Oryzavirus, indicating that these two viruses are closely related. Phylogenetic analyses showed that RpLV clusters with members of the genera Oryzavirus, Cypovirus, Dinovernavirus and Fijivirus. These genera belong to the subfamily Spinareovirinae which includes reoviruses with spiked core particles ('turreted' reoviruses). In addition, two nucleotide binding motifs, regarded as 'signature' sequences among turreted reoviruses, were also found in RpLV P8, suggesting that RpLV is a novel dicot-infecting reovirus in the subfamily Spinareovirinae.

Blueberry latent virus: an amalgam of the Partitiviridae and Totiviridae

A new, symptomless virus was identified in blueberry. The dsRNA genome of the virus, provisionally named Blueberry latent virus (BBLV), codes for two putative proteins, one without any similarities to virus proteins and an RNA-dependent RNA polymerase. More than 35 isolates of the virus from different cultivars and geographic regions were partially or completely sequenced. BBLV, found in more than 50% of the material tested, has high degree of homogeneity as isolates show more than 99% nucleotide identity between them. Phylogenetic analysis clearly shows a close relationship between BBLV and members of the Partitiviridae, although its genome organization is related more closely to members of the Totiviridae. Transmission studies from three separate crosses showed that the virus is transmitted very efficiently by seed. These properties suggest that BBLV belongs to a new family of plant viruses with unique genome organization for a plant virus but signature properties of cryptic viruses including symptomless infection and very efficient vertical transmission.

A New Potyvirus sp. Infects Verbena Exhibiting Leaf Mottling Symptoms

Verbena 'Taylortown Red' plants showed virus-like mottling symptoms. Virus purifications disclosed the presence of elongated and spherical particles, evidence of mixed virus infections, whereas double-stranded RNA analysis revealed the presence of several bands absent in healthy plants. After shotgun cloning, three viruses were identified in 'Taylortown Red': Broad bean wilt virus-1, Coleus vein necrosis virus, and a previously undescribed potyvirus. Given the importance of verbena to the ornamental industry, we studied the viruses found in 'Taylortown Red' and, in this article, we present our findings on the new potyvirus, provisionally named Verbena virus Y (VVY). VVY belongs to the Potato virus Y subgroup in the genus Potyvirus, has solanaceous plants, including potato, as alternative hosts, and can be transmitted by a ubiquitous pest in the ornamental industry, the green peach aphid.

The genome of Beet cryptic virus 1 shows high homology to certain cryptoviruses present in phylogenetically distant hosts

This study determined the complete nucleotide sequence of Beet cryptic virus 1 (BCV1). As expected by analogy to previously sequenced alphacryptoviruses, dsRNA1 (2008 bp) encodes a 72.5-kDa protein containing sequence motifs characteristic for RNA-dependent RNA polymerases (RdRp). In addition to the full-length dsRNA1, a truncated form was also detected in dsRNA extracts. dsRNA2 (1783 bp) codes for the viral coat protein (CP) as proven by the identity of the predicted CP sequence to peptide sequences of the purified virion protein. The amino acid sequence of BCV1 RdRp as well as the 5'- and 3'-UTRs show 81-85% identity to the corresponding regions of Vicia cryptic virus (VCV), White clover cryptic virus 1 (WCCV1) and Carrot cryptic virus (CaCV). The amino acid sequence identity of the CP is about 55-62%, moreover, a strong conservation of predicted alpha-helical regions was observed. The high degree of similarity of these seed- and pollen-transmitted viruses persisting in phylogenetically distant hosts, together with their high similarity to fungal partitiviruses strongly supports the hypothesis that horizontal transfer by a fungus played a role in the emergence of the present cryptovirus species. The change in the distribution of cryptic viruses may also be due to human influence: While earlier BCV1 occurred frequently in sugar beet cultivars, it is very rare in cultivars currently used in agricultural practice and was detected in only one of the 28 cultivars investigated in our experiments.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (doi:10.1007/s11262-009-0432-4) contains supplementary material, which is available to authorized users.

A tymovirus with an atypical 3'-UTR illuminates the possibilities for 3'-UTR evolution

We report the complete genome sequence of Dulcamara mottle virus (DuMV), confirming its membership within the Tymovirus genus, which was previously based on physical and pathology evidence. The 5'-untranslated region (UTR) and coding region of DuMV RNA have the typical characteristics of tymoviral RNAs. In contrast, the 3'-UTR is the longest and most unusual yet reported for a tymovirus, possessing an internal poly(A) tract, lacking a 3'-tRNA-like structure (TLS) and terminating at the 3'-end with -UUC instead of the typical -CC(A). An expressible cDNA clone was constructed and shown to be capable of producing infectious DuMV genomic RNAs with -UUC 3'-termini. A chimeric Turnip yellow mosaic virus (TYMV) genome bearing the DuMV 3'-UTR in place of the normal TLS was constructed in order to investigate the ability of the TYMV replication proteins to amplify RNAs with -UUC instead of -CC(A) 3'-termini. The chimeric genome was shown to be capable of replication and systemic spread in plants, although amplification was very limited. These experiments suggest the way in which DuMV may have evolved from a typical tymovirus, and illuminate the ways in which viral 3'-UTRs in general can evolve.

'Kwanzan Stunting' syndrome: detection and molecular characterization of an Italian isolate of Little cherry virus 1

Evident stunting was observed for the first time on Prunus serrulata 'Kwanzan' indicator trees in Southern Italy during the indexing of two sour cherry accessions from cultivars 'Marasca di Verona' and 'Spanska'. Bud break and shooting were delayed and the developing leaves remained small. During the third year many Kwanzan plants died, regardless of the indexed cultivar. Electrophoretic analysis showed the presence of dsRNA pattern in extracts of stunted Kwanzan with a similar size to that of viruses of the family Closteroviridae. An identical pattern of more abundant dsRNA bands was obtained from GF305 seedlings grafted with the same sour cherry accessions. Observations by electron microscopy revealed the presence of long flexuous virus particles in both indicators (Kwanzan and GF305), characteristic of closteroviruses. Subsequent cloning work, starting from the dsRNA extracts of cultivar Marasca di Verona grafted on GF305 indicator, yielded 7 different clones, all showing high identity to the Little cherry virus 1 genome. Full sequencing of this virus isolate (ITMAR) was then done resulting in a complete genome composed of 16,936nt. Primers designed on the obtained sequences for RT-PCR detection confirmed the presence of Little cherry virus 1 in Kwanzan and GF305 trees, inoculated with both sour cherry cultivars. Phylogenetic analysis of the minor coat protein grouped virus isolates into two clusters: one including Italian isolates of sweet cherry, Japanese plum, peach and almond, together with German sweet cherry UW1 isolate, and a second one containing the Italian isolates of sour cherry (ITMAR and ITSPA), that were found associated with strong symptoms of 'Kwanzan Stunting'.

The complete nucleotide sequence of the RNA2 of the crinivirus tomato infectious chlorosis virus: isolates from North America and Europe are essentially identical

The complete nucleotide sequences of the RNA2 of two isolates of Tomato infectious chlorosis virus (TICV, genus Crinivirus, family Closteroviridae) from the United States and Spain, respectively, were determined. The sequences of both isolates were found to be nearly identical. TICV RNA2 consisted of 7,914 nucleotides in both isolates and contains eight open reading frames that encompass the Closteroviridae hallmark gene array represented by a heat shock protein 70 family homologue, a protein of 59 kDa, the major coat protein, and a divergent copy of the coat protein. Phylogenetic analysis suggested that TICV is most similar to Lettuce infectious yellows virus (LIYV), the type species of the genus Crinivirus.

Southern tomato virus: The link between the families Totiviridae and Partitiviridae

A dsRNA virus with a genome of 3.5 kb was isolated from field and greenhouse-grown tomato plants of different cultivars and geographic locations in North America. Cloning and sequencing of the viral genome showed the presence of two partially overlapping open reading frames (ORFs), and a genomic organization resembling members of the family Totiviridae that comprises fungal and protozoan viruses, but not plant viruses. The 5'-proximal ORF codes for a 377 amino acid-long protein of unknown function, whereas the product of ORF2 contains typical motifs of an RNA-dependant RNA-polymerase and is likely expressed by a +1 ribosomal frame shift. Despite the similarity in the genome organization with members of the family Totiviridae, this virus shared very limited sequence homology with known totiviruses or with other viruses. Repeated attempts to detect the presence of an endophytic fungus as the possible host of the virus failed, supporting its phytoviral nature. The virus was efficiently transmitted by seed but not mechanically and/or by grafting. Phylogenetic analyses revealed that this virus, for which the name Southern tomato virus (STV) is proposed, belongs to a partitivirus-like lineage and represents a species of a new taxon of plant viruses.

A new method for extraction of double-stranded RNA from plants

The occurrence of high molecular weight double-stranded RNA (dsRNA) in plants is associated with the presence of RNA viruses. DsRNA is stable, can be extracted easily from the majority of plant species and provides an excellent tool for characterization of novel viruses that are recalcitrant to purification. Several protocols have been developed for dsRNA purification, the majority of which are based on extraction with phenol and chloroform. We have developed a protocol for dsRNA extraction based on a lithium salts buffer that does not require organic solvents other than alcohols. The method yields comparable amount of dsRNA to protocols described previously and yields consistently dsRNA from Vaccinium hosts that have been recalcitrant to dsRNA purification using traditional protocols. The quality of the dsRNA purified is such that it can be used for downstream enzymatic reactions including reverse transcription-polymerase chain reaction and cloning.

RNA interference of Schistosoma mansoni cathepsin D, the apical enzyme of the hemoglobin proteolysis cascade

The aspartic protease cathepsin D (Clan AA, Family A1) is expressed in the schistosome gut where it plays an apical role in the digestion of hemoglobin released from ingested erythrocytes. In this report, RNA interference approaches were employed to investigate the effects of knockdown of schistosome cathepsin D. Cultured schistosomules of Schistosoma mansoni were exposed by square wave electroporation to double stranded RNA (dsRNA) specific for cDNA encoding S. mansoni cathepsin D. RNAi-mediated reductions in transcript levels led to phenotypic changes including significant growth retardation in vitro and suppression of aspartic protease enzyme activity. In addition, black-pigmented heme, the end point by-product of normal hemoglobin proteolysis that accumulates in the schistosome gut, was not apparent within the guts of the treated schistosomules. Their guts appeared to be red in color, rather than black, apparently indicating the presence of intact rather than digested host hemoglobin. These phenotypic effects were apparent when either of two forms of dsRNA, a long form spanning the entire target transcript or a short form specific for the 3'-region was employed. Off-target effects were not apparent in transcript levels of the gut-localized cysteine protease cathepsin B1. Finally, cathepsin D may be an essential enzyme in the mammal-parasitic stages of schistosomes because schistosomules treated with dsRNA did not survive to maturity after transfer into Balb/c mice. These and earlier findings suggest that, given its essential function in parasite nutrition, schistosome cathepsin D could be developed as a target for novel anti-schistosomal interventions.

Identification, detection and transmission of a new vitivirus from Mentha

Mentha x gracilis 'Variegata' is an ornamental clone with a phenotype caused by virus infection. Several clones were ordered from mail-order nurseries in an attempt to identify a virus consistently associated with symptoms. One of these clones did not exhibit typical 'Variegata' symptoms, and steps were taken to identify any agents causing the 'off-type' symptoms. One of the viruses identified in the atypical 'Variegata' clone is a previously unknown virus, a member of the family Flexiviridae. Sequence and phylogenetic analysis indicate that the virus, designated as mint virus-2, is related to members of the species Grapevine virus A, Grapevine virus B and Heracleum latent virus, placing it in the genus Vitivirus. A detection protocol for the virus has been developed, and the mint aphid (Ovatus crataegarius) was able to transmit the virus in the presence of a helper virus but not from single infected plants.

Identification and characterization of Raspberry mottle virus, a novel member of the Closteroviridae

Raspberry mosaic is one of the most important viral diseases of raspberry. Four virus and virus-like agents, two of which are poorly characterized, have been implicated in the disease complex based on symptom development in Rubus indicators. Three novel viruses were identified in a red raspberry plant that caused typical raspberry mosaic symptoms when grafted onto indicators. This communication focuses on one of these viruses, Raspberry mottle virus (RMoV), a new member of the family Closteroviridae. The complete nucleotide sequence of RMoV has been determined and exceeds 17 kilobases encoding 10 genes. The genome organization of RMoV is similar to that of Beet yellows virus, the type member of the Closterovirus genus, and phylogenetic analysis using the polymerase conserved motifs and the heat shock protein 70 homolog revealed a close relationship of RMoV with Strawberry chlorotic fleck associated virus and Citrus tristeza virus, which suggests the possibility of an aphid vector. The virus was detected in symptomatic raspberry plants in production areas in mixed infections with several other viruses, indicating that RMoV may impact raspberry production.

Macroarray Detection of Plant RNA Viruses Using Randomly Primed and Amplified Complementary DNAs from Infected Plants

ABSTRACT Membrane-based macroarrays provide a relatively inexpensive technology with the potential to detect hundreds of pathogens in a single assay. For the simultaneous detection of a large number of pathogens, it is necessary to obtain sufficient nucleic acids for labeling, and any amplification reactions need to be performed using unbiased, pathogen-non-specific primers. A nonradioactive macroarray system is described to test for plant RNA viruses using 70-mer oligonucleotide probes immobilized on nylon membranes. Starting with a total plant RNA extract, complementary DNA (cDNA) and second-strand syntheses were carried out using an anchor primer sequence with random pentamers coupled at the 3' end. Subsequent synthesis by polymerase chain reaction using the anchor primer alone resulted in a relatively unbiased amplification of plant and viral RNAs. These cDNAs were chemically labeled and the product used as a target in hybridization analyses. The system was validated using RNA extracts from plants infected with Cucumber mosaic virus, Potato virus Y, and Potato leaf roll virus (PLRV). Despite the relative excess of host-derived nonviral sequences, viral RNAs were amplified between 100- and 1,000-fold and were detected in single and mixed infections. The macroarray sensitivity was comparable to that of double-antibody sandwich enzyme-linked immunosorbent assay, with PLRV being detected in sap dilutions of 1:100. The potential for the development of a relatively inexpensive multipathogen detection system is discussed.

Strawberry chlorotic fleck: identification and characterization of a novel Closterovirus associated with the disease

Chlorotic fleck, a strawberry disease caused by a graft and aphid transmissible agent, was identified more than 45 years ago in Louisiana. Since its discovery there has been no additional information on the agent that causes the disease. The mode of transmission implies that a virus is the causal agent of chlorotic fleck. We identified four closteroviruses in the single chlorotic fleck infected strawberry clone known to exist in the United States. Sequence analysis indicated that two of the viruses are novel and one of them is closely related to members of the Closterovirus genus, the aphid-transmitted viruses in the family Closteroviridae, a feature that is in accordance with the aphid transmissibility of the chlorotic fleck agent. The genome of the novel Closterovirus, designated as Strawberry chlorotic fleck associated virus exceeds 17 kilobases and encodes 10 open reading frames, including the signature closterovirus genes as well as a gene without obvious homologs in the family. RNA folding predicted a pseudoknot structure near the 3' terminus of the virus that may be involved in template recognition by the viral polymerase. Phylogenetic analysis indicates that Strawberry chlorotic fleck associated virus is most closely related to Citrus tristeza virus among sequenced members of the family. Detection protocols have been developed and the virus was detected in several strawberry plants from production fields.

A virus between families: nucleotide sequence and evolution of Strawberry latent ringspot virus

Several clones of golden ginger mint (Mentha x gracilis, 'Variegata') were found infected with Strawberry latent ringspot virus (SLRSV). The virus was purified and cloned and the complete nucleotide sequence of a mint isolate was obtained. RNA 1 consists of 7,496 nucleotides excluding the poly-A tail and encodes a polyprotein with signature enzymatic motifs found in other picorna-like plant viruses. RNA 2 consists of 3,842 nucleotides excluding the poly-A tail, encoding a polyprotein that is processed to a putative movement protein and the two coat proteins of the virus. A satellite RNA of 1,117 nucleotides was associated with this isolate encoding for a putative protein of 31 kDa. Phylogenetic analysis revealed that SLRSV shares characteristics with members of the Cheravirus, Fabavirus, Comovirus and Sadwavirus genera indicative of the uniqueness of SLRSV. The close relationship of SLRSV with these genera led to the examination of aphid and beetle transmission of the virus with, however, negative results.

Nucleotide sequence of Blackberry yellow vein associated virus, a novel member of the Closteroviridae

The complete nucleotide sequence of a novel member of the genus Crinivirus (family Closteroviridae), isolated from blackberry and tentatively named Blackberry yellow vein associated virus, was determined. The virus possesses a bipartite genome. RNA 1 is 7,801 nucleotides in length and papain-like protease, methyltransferase, RNA helicase and RNA-dependent RNA polymerase motifs have been identified in the proteins coded for by this molecule. The polymerase is probably expressed via a +1 ribosomal frameshift, a common feature among members of the Closteroviridae. RNA 2 is 7,917 nucleotides long and encodes nine open reading frames, similar in size and position to orthologous genes of other criniviruses with the exception of a second hydrophobic peptide found near the 5' terminus of the molecule. Phylogenetic analysis revealed a close relationship between Blackberry yellow vein associated virus and Beet pseudo yellows virus, another crinivirus that infects small fruit crops.

Characterization of a Novel Member of the Family Closteroviridae from Mentha spp

ABSTRACT While characterizing the agents involved in symptomatology of a variegated mint, Mentha x gracilis 'Variegata', a nursery plant with atypical symptoms was examined. This plant, unlike 'Variegata', did not exhibit yellow vein banding symptoms but instead had distorted and crinkled leaves. Molecular tests for the three viruses found in 'Variegata' clones failed to detect any of these viruses in the plant. Double-stranded RNA was extracted and cloned, disclosing the presence of two unknown viruses. One of the viruses was a novel member of the family Closteroviridae. The complete nucleotide sequence of the virus, designated as Mint virus 1, has been obtained. A detection test was developed, and revealed the presence of the virus in several other mint clones and species. Genomic regions from three additional isolates were examined to investigate the genetic diversity of the virus. Genome and phylogenetic analysis placed Mint virus 1 in the genus Closterovirus and transmission studies have identified the mint aphid, Ovatus crataegarius, as a vector for this new member of the genus Closterovirus.

New features in the genus Ilarvirus revealed by the nucleotide sequence of Fragaria chiloensis latent virus

Fragaria chiloensis latent virus (FClLV), a member of the genus Ilarvirus was first identified in the early 1990s. Double-stranded RNA was extracted from FClLV infected plants and cloned. The complete nucleotide sequence of the virus has been elucidated. RNA 1 encodes a protein with methyltransferase and helicase enzymatic motifs while RNA 2 encodes the viral RNA dependent RNA polymerase and an ORF, that shares no homology with other Ilarvirus genes. RNA 3 codes for movement and coat proteins and an additional ORF, making FClLV possibly the first Ilarvirus encoding a third protein in RNA 3. Phylogenetic analysis reveals that FClLV is most closely related to Prune dwarf virus, the type member of subgroup 4 of the Ilarvirus genus. FClLV is also closely related to Alfalfa mosaic virus (AlMV), a virus that shares many properties with Ilarviruses . We propose the reclassification of AlMV as a member of the Ilarvirus genus instead of being a member of a distinct genus.

Mint virus X: a novel potexvirus associated with symptoms in ‘Variegata’ mint

Mentha x gracilis 'Variegata', an ornamental mint clone first described about 200 years ago, exhibits virus-like vein banding symptoms. Double-stranded RNA and virion isolations revealed the presence of three viruses in a 'Variegata' plant. Cloning and sequencing disclosed that one of the viruses was a previously unidentified species with similarities to members of the Flexiviridae family, designated as Mint virus X (MVX). The complete nucleotide sequence of the virus was determined. Phylogenetic analysis divulged the close relationship of the virus with lily virus X and strawberry mild yellow edge virus, members of the Potexvirus genus. A reverse transcription-polymerase chain reaction protocol was developed and used for detection of MVX in other 'Variegata' plants. All clones tested, obtained from nurseries around the United States were infected with MVX, making the virus a possible causal agent of the variegated symptoms.

A Member of the Closteroviridae from Mint with Similarities to All Three Genera of the Family

Mentha × gracilis 'Variegata', described more than 200 years ago, is still being used as an ornamental. The bright vein-banding symptoms that confer the ornamental value to 'Variegata' clones are graft transmissible and can be eliminated after heat therapy and apical meristem culture. This observation led us to investigate the possibility that symptoms are virus-induced. Double-stranded RNA extracted from a 'Variegata' clone was cloned. One of the viruses identified was a member of the Closteroviridae family. This virus, designated Mint vein-banding associated virus, shares sequence similarities with all three genera of the family, making it an important link among the genera of the Closteroviridae. A detection protocol has been developed that readily detects the virus in other mint clones that exhibit vein-banding symptoms.