Peanut bud necrosis tospovirus S RNA: complete nucleotide sequence, genome organization and homology to other tospoviruses

Emerging challenges in the management of Orthotospoviruses in Indian agriculture

Orthotospoviruses, a genera of negative-sense ssRNA viruses transmitted by thrips, have gained significant attention in recent years due to their detrimental impact on diverse crops, causing substantial economic losses and posing threats to food security. Orthotospoviruses are characterised by a wide range of symptoms in plants, including chlorotic/necrotic spots, vein banding, and fruit deformation. Seven species, including four definite and three tentative species in the genus Orthotospovirus, have so far been documented on the crops of the Indian subcontinent. Management of Orthotospoviruses under field conditions is challenging since they have a wide host range, adaptation to versatile environmental conditions, a lack of promising resistance sources, and the ubiquitous nature of thrips and their transmission through a propagative manner. Our present review elucidates the significance, molecular biology and evolutionary relationship of Orthotospoviruses; vector population; and possible management strategies for Orthotospoviruses and their vectors in the scenario of the Indian subcontinent.

Antiviral activity of basidiomycetous fungi against Groundnut bud necrosis virus in tomato

Tomato is an important vegetable crop which is severely affected by Groundnut bud necrosis virus (GBNV). Until now effective antiviral agents have not been reported for the management of necrosis disease caused by GBNV. Therefore, a study was undertaken to manage the necrosis disease caused by GBNV using culture filtrate of basidiomycetous fungi viz., Coprinopsiscinerea, Ganoderma lucidum and Lentinula edodes. In vitro studies were conducted in the indicator host cowpea and primary host tomato in glasshouse under insect proof condition; co-inoculation spraying of culture filtrate of Ganoderma lucidum at 0.1% concentration reduced the lesion numbers and inhibited the virus population build-up when compared to inoculated control in the indicator host cowpea upto 77.83%. DAC-ELISA test was performed to quantify the virus titre, indicated reduced virus titre in co- inoculation spray of culture filtrate of G. lucidum treated cowpea with OD value 0.17 ± 0.01 at 405 nm and in tomato plants 0.14 ± 0.01 respectively. The viral copy numbers were quantified by qPCR. About 2.0 × 10¹ viral copy numbers were observed in tomato plants treated with G. lucidum (co-inoculation) which was lesser than untreated inoculated control plants (2.4 × 10⁸). In order to identify the antiviral properties of G. lucidum, GCMS analysis was carried out and we found the triterpenoid compound Squalene. This is the first study to analyse and confirm the antiviral activity of G. lucidum against a plant virus.

Groundnut bud necrosis virus encoded NSm associates with membranes via its C-terminal domain

Groundnut Bud Necrosis Virus (GBNV) is a tripartite ambisense RNA plant virus that belongs to serogroup IV of Tospovirus genus. Non-Structural protein-m (NSm), which functions as movement protein in tospoviruses, is encoded by the M RNA. In this communication, we demonstrate that despite the absence of any putative transmembrane domain, GBNV NSm associates with membranes when expressed in E. coli as well as in N. benthamiana. Incubation of refolded NSm with liposomes ranging in size from 200–250 nm resulted in changes in the secondary and tertiary structure of NSm. A similar behaviour was observed in the presence of anionic and zwitterionic detergents. Furthermore, the morphology of the liposomes was found to be modified in the presence of NSm. Deletion of coiled coil domain resulted in the inability of in planta expressed NSm to interact with membranes. Further, when the C-terminal coiled coil domain alone was expressed, it was found to be associated with membrane. These results demonstrate that NSm associates with membranes via the C-terminal coiled coil domain and such an association may be important for movement of viral RNA from cell to cell.

Multiple artificial microRNAs targeting conserved motifs of the replicase gene confer robust transgenic resistance to negative-sense single-stranded RNA plant virus

MicroRNAs (miRNAs) regulate the abundance of target mRNAs by guiding cleavage at sequence complementary regions. In this study, artificial miRNAs (amiRNAs) targeting conserved motifs of the L (replicase) gene of Watermelon silver mottle virus (WSMoV) were constructed using Arabidopsis pre-miRNA159a as the backbone. The constructs included six single amiRNAs targeting motifs A, B1, B2, C, D of E, and two triple amiRNAs targeting motifs AB1E or B2DC. Processing of pre-amiRNAs was confirmed by agro-infiltration, and transgenic Nicotiana benthamiana plants expressing each amiRNA were generated. Single amiRNA transgenic lines expressing amiR-LB2 or amiR-LD showed resistance to WSMoV by delaying symptom development. Triple amiRNA lines expressing amiR-LB2, amiR-LD and amiR-LC provided complete resistance against WSMoV, with no indication of infection 28 days after inoculation. Resistance levels were positively correlated with amiRNA expression levels in these single and triple amiRNA lines. The triple amiR-LAB1E line did not provide resistance to WSMoV. Similarly, the poorly expressed amiR-LC and amiR-LE lines did not provide resistance to WSMoV. The amiR-LA- and amiR-LB1-expressing lines were susceptible to WSMoV, and their additional susceptibility to the heterologous Turnip mosaic virus harbouring individual target sequences indicated that these two amiRNAs have no effect in vivo. Transgenic lines expressing amiR-LB2 exhibited delayed symptoms after challenge with Peanut bud necrosis virus having a single mismatch in the target site. Overall, our results indicate that two amiRNAs, amiR-LB2 and amiR-LD, of the six designed amiRNAs confer moderate resistance against WSMoV, and the triple construct including the two amiRNAs provides complete resistance.

Investigations on the RNA binding and phosphorylation of groundnut bud necrosis virus nucleocapsid protein

Groundnut bud necrosis virus belongs to the genus Tospovirus, infects a wide range of crop plants and causes severe losses. To understand the role of the nucleocapsid protein in the viral life cycle, the protein was overexpressed in E. coli and purified by Ni-NTA chromatography. The purified N protein was well folded and was predominantly alpha-helical. Deletion analysis revealed that the C-terminal unfolded region of the N protein was involved in RNA binding. Furthermore, the N protein could be phosphorylated in vitro by Nicotiana benthamiana plant sap and by purified recombinant kinases such as protein kinase CK2 and calcium-dependent protein kinase. This is the first report of phoshphorylation of a nucleocapsid protein in the family Bunyaviridae. The possible implications of the present findings for the viral life cycle are discussed.

Interference in plant defense and development by non-structural protein NSs of Groundnut bud necrosis virus

Groundnut bud necrosis virus (GBNV) infects a large number of leguminous and solanaceous plants. To elucidate the biological function of the non-structural protein encoded by the S RNA of GBNV (NSs), we studied its role in RNA silencing suppression and in viral pathogenesis. Our results demonstrated that GBNV NSs functions as a suppressor of RNA silencing using the agroinfiltration patch assay. An in silico analysis suggested the presence of pro-apoptotic protein Reaper-like sequences in the GBNV NSs, which were known to be present in animal infecting bunyaviruses. Utilizing NSs mutants, we demonstrated that a Leu-rich domain was required for RNA silencing suppression activity, but not the non-overlapping Trp/GH3 motif of the Reaper-like sequence. To investigate the role of NSs in symptom development we generated transgenic tomato expressing the GBNV NSs and showed that the expression of NSs in tomato mimics symptoms induced by infection with GBNV, such as leaf senescence and necrosis. As leaf senescence is controlled by miR319 regulation of the transcription factor TCP1, we assessed the accumulation of both RNAs in transgenic NSs-expressing and GBNV-infected tomato plants. In both types of plants the levels of miR319 decreased, while the levels of TCP1 transcripts increased. We propose that GBNV-NSs affects miRNA biogenesis through its RNA silencing suppressor activity and interferes with TCP1-regulated leaf developmental pathways.

Importance and genetic diversity of vegetable-infecting tospoviruses in India

A survey for Peanut bud necrosis virus (PBNV), Watermelon bud necrosis virus (WBNV), Capsicum chlorosis virus (CaCV), and Iris yellow spot virus (IYSV) was conducted between 2002 and 2009 in the major vegetable-growing areas in India. PBNV was documented widely in tomato and chili peppers in 14 states representing southern, north-western, north-eastern, and central regions and WBNV was predominantly detected in watermelons and cucurbits in all except north-eastern regions. In addition, the expanded host range of PBNV to watermelons and other cucurbits and WBNV to tomato and chili peppers was observed leading to natural mixed infection of the two viruses. IYSV was found in onion in southern, central, and north-eastern regions and CaCV in tomato and chili peppers in northern and southern regions, respectively. Phylogenetic analysis of the nucleocapsid gene revealed segregation of field isolates of PBNV and WBNV into two distinct subclades, whereas isolates of CaCV and IYSV each clustered into a single clade. A proposal for establishing WBNV as a distinct tospovirus species is made based on the molecular characterization of small- (S) and medium- (M) RNA segments.

Tomato necrotic ringspot virus, a new tospovirus isolated in Thailand

A new tospovirus isolated from naturally infected tomato plants grown in Nakhon Pathom province (Thailand) was characterized. Infected plants showed symptoms consisting of necrotic spots, necrotic ringspots and stem necrosis. This virus was detected using general antibodies that could recognize watermelon silver mottle virus (WSMoV), capsicum chlorosis virus (CaCV) and melon yellow spot virus (MYSV). However, it did not react with specific monoclonal antibodies (MAbs) to WSMoV and CaCV or a specific MAb to MYSV. The complete nucleotide sequences of S and M RNAs of the virus were determined. They were 3,023 and 4,716 nucleotides in length, respectively, and contained two ORFs in an ambisense arrangement. Sequence analysis indicated that amino acid sequence of the N protein shared 58.2%, 56.0% and 51.8% identity with those of CaCV, WSMoV and MYSV, respectively. The virus was experimentally transmitted by Thrips palmi and Ceratothripoides claratris. Based on our results, we conclude that this tospovirus isolate should be considered a member of a new species. The name tomato necrotic ringspot virus (TNRV) is proposed for this tospovirus.

Biological and molecular characterization of Capsicum chlorosis virus infecting chilli and tomato in India

Two isolates of Capsicum chlorosis virus (CaCV, genus Tospovirus) from tomato (CaCV-To-Ind) and chilli (CaCV-Ch-Pan), collected from Haryana and Uttar Pradesh states of northern India respectively, were compared. A comparison of the amino acid sequences of their N genes revealed more than 96% identity, confirming that the virus isolates in India have a high degree of sequence conservation and are closely related to Australian isolates. Analysis of the host range of CaCV revealed no biological difference between the isolates, but they differed from CaCV-Australia. The nucleotide sequences of S, M and L RNA of CaCV-Ch-Pan were determined. The S RNA contains 3,105 nucleotides (nt), with NSs and N genes of 1,320 and 828 nt, respectively. The M RNA consists of 4,821 nt, with an NSm gene of 927 nt and a Gn/Gc gene of 3,366 nt. The intergenic regions of S and M RNA contain 824 and 425 nt, respectively. The L RNA consists of 8,912 nt, with an RNA-dependent RNA polymerase gene of 8,634 nt.

NSs encoded by groundnut bud necrosis virus is a bifunctional enzyme

Groundnut bud necrosis virus (GBNV), a member of genus Tospovirus in the family Bunyaviridae, infects a large number of leguminosae and solanaceae plants in India. With a view to elucidate the function of nonstructural protein, NSs encoded by the small RNA genome (S RNA), the NSs protein of GBNV- tomato (Karnataka) [1] was over-expressed in E. coli and purified by Ni-NTA chromatography. The purified rNSs protein exhibited an RNA stimulated NTPase activity. Further, this activity was metal ion dependent and was inhibited by adenosine 5′ (β, γ imido) triphosphate, an ATP analog. The rNSs could also hydrolyze dATP. Interestingly, in addition to the NTPase and dATPase activities, the rNSs exhibited ATP independent 5′ RNA/DNA phosphatase activity that was completely inhibited by AMP. The 5′ α phosphate could be removed from ssDNA, ssRNA, dsDNA and dsRNA thus confirming that rNSs has a novel 5′ α phosphatase activity. K189A mutation in the Walker motif A (GxxxxGKT) resulted in complete loss of ATPase activity, but the 5′ phosphatase activity was unaffected. On the other hand, D159A mutation in the Walker motif B (DExx) resulted in partial loss of both the activities. These results demonstrate for the first time that NSs is a bifunctional enzyme, which could participate in viral movement, replication or in suppression of the host defense mechanism.

Characterization of tomato zonate spot virus, a new tospovirus in China

An isolate of a new tospovirus species, causing concentric zoned ringspots on fruits and necrotic lesions on leaves of infected plants, was characterised based on particle morphology, host range and serological properties. The complete nucleotide sequences of large (L), medium (M), and small (S) RNAs of this virus were found to contain 8919, 4945, and 3279 nts respectively. The L RNA encoded the RNA-dependent RNA polymerase (RdRp) (2885 aa, 332.7 kDa). The M RNA encoded a non-structural (NSm) protein (309 aa, 34.4 kDa) and a viral glycoprotein precursor (Gn/Gc) (1122 aa, 127.4 kDa). The S RNA encoded a non-structural protein (NSs) (459 aa, 51.9 kDa) and the nucleocapsid (N) protein (278 aa, 30.6 kDa). This N protein shared amino acid identities of 80.9% with those of calla lily chlorotic spot virus. Our results suggest that the virus studied here belongs to a new tospovirus species, for which the name tomato zonate spot virus is proposed.

The glycoprotein gene of Chrysanthemum stem necrosis virus and Zucchini lethal chlorosis virus and molecular relationship with other tospoviruses

Two tospoviruses, Chrysanthemum stem necrosis virus (CSNV) and Zucchini lethal chlorosis virus (ZLCV), cause economical losses in several ornamental and vegetable crops in Brazil. The nucleocapsid gene and movement protein sequences had already been reported for both viruses, though the glycoprotein precursor gene sequence was not available. In this study, cDNA fragments (ca. 4 kb) of the M RNA 3' portion of CSNV (isolate Chry-1) and ZLCV (isolate 1038), including the complete glycoprotein precursor gene, partial NSm gene, and the entire intergenic and 3' untranslated regions, were cloned and sequenced. The sequences were assembled with the corresponding 5' region sequence (NSm gene and 5'UTR) of the same isolates to build up the complete sequence of the M RNA segment of both species. The M RNA of CSNV was 4,828 nucleotide-long, while of ZLCV 4,836 nucleotides. Both M RNA molecules comprised two ORFs in an ambisense arrangement. The vcRNA coded for the viral glycoprotein (Gn/Gc) precursor gene of CSNV and ZLCV (both with 127.5 kDa). Comparison of deduced amino acids of the CSNV and ZLCV glycoprotein precursor genes with those of other tospoviruses showed the highest identity with that of Tomato spotted wilt virus (86%) and with that of CSNV (82%), respectively. However, the nucleotide sequence of the intergenic and 3' untranslated regions of CSNV and ZLCV shared lower identities with other tospoviruses. The glycoprotein precursor gene is thought to be a good candidate as additional classification parameter for Tospovirus taxonomy. The presence of the RGD motif in both Gc proteins indicated that they are typical American tospoviruses, which was confirmed by phylogenetic analysis. The membrane topology of both glycoproteins is discussed.

Nucleotide sequence of the S and M RNA segments of a Groundnut bud necrosis virus isolate from Vigna radiata in India

Nucleotide sequence of the S and M RNA segments of a Groundnut bud necrosis virus isolate from Vigna radiata (mungbean isolate, GBNV-MB) was determined and compared with another isolate from Arachis hypogaea (groundnut isolate, GBNV-type). Comparative sequence analysis revealed that the genome organization of the S and M RNA segments of both GBNV-MB and GBNV-type isolates was similar. However, considerable differences were observed in their intergenic regions (IGRs) and the glycoprotein precursors (Gn/Gc) of the M RNA segments. M RNA IGRs of GBNV-MB and GBNV-type isolates differed in size by 14 nucleotides. This difference was of 75 nucleotides in another GBNV isolate from Lycopersicon esculentum (tomato). Sequence comparison of the M RNA IGRs of GBNV isolates from mungbean, groundnut and tomato from India revealed 56-89% sequence identity. The topology of Gn/Gc revealed the presence of both N-glycosylation (5) and O-glycosylation (1) sites in GBNV-MB isolate, whereas only N-glycosylation sites (4) were present in GBNV-type isolate.

Identification of Common Epitopes on a Conserved Region of NSs Proteins Among Tospoviruses of Watermelon silver mottle virus Serogroup

ABSTRACT The NSs protein of Watermelon silver mottle virus (WSMoV) was expressed by a Zucchini yellow mosaic virus (ZYMV) vector in squash. The expressed NSs protein with a histidine tag and an additional NIa protease cleavage sequence was isolated by Ni(2+)-NTA resins as a free-form protein and further eluted after sodium dodecyl sulfate-polyacrylamide gel electrophoresis for production of rabbit antiserum and mouse monoclonal antibodies (MAbs). The rabbit antiserum strongly reacted with the NSs crude antigen of WSMoV and weakly reacted with that of a high-temperature-recovered gloxinia isolate (HT-1) of Capsicum chlorosis virus (CaCV), but not with that of Calla lily chlorotic spot virus (CCSV). In contrast, the MAbs reacted strongly with all crude NSs antigens of WSMoV, CaCV, and CCSV. Various deletions of the NSs open reading frame were constructed and expressed by ZYMV vector. Results indicate that all three MAbs target the 89- to 125-amino-acid (aa) region of WSMoV NSs protein. Two indispensable residues of cysteine and lysine were essential for MAbs recognition. Sequence comparison of the deduced MAbs-recognized region with the reported tospoviral NSs proteins revealed the presence of a consensus sequence VRKPGVKNTGCKFTMHNQIFNPN (denoted WNSscon), at the 98- to 120-aa position of NSs proteins, sharing 86 to 100% identities among those of WSMoV, CaCV, CCSV, and Peanut bud necrosis virus. A synthetic WNSscon peptide reacted with the MAbs and verified that the epitopes are present in the 98- to 120-aa region of WSMoV NSs protein. The WSMoV sero-group-specific NSs MAbs provide a means for reliable identification of tospoviruses in this large serogroup.

The complete nucleotide sequence of a capsicum chlorosis virus isolate from Lycopersicum esculentum in Thailand

The complete nucleotide sequence of a tospovirus isolated from Lycopersicum esculentum in Thailand was determined. The L RNA comprises of 8912 nt and codes for the RNA-dependent RNA-polymerase (RdRp) (2877 aa). Two ORFs are located on the M RNA (4823 nt) encoding the non-structural (NSm) protein (308 aa) and the viral glycoprotein precursors (Gn/Gc) (1121 aa) separated by an intergenic region of 433 nt. ORFs coding for the non-structural (NSs) and nucleocapsid (N) protein, 439 aa and 275 aa, respectively, were identified on the S RNA (3477 nt) separated by an intergenic region of 1202 nt. The N protein of the Thailand isolate was most closely related to that of capsicum chlorosis virus (CaCV), sharing an amino acid sequence identity of 92.7%. Additionally, multiple sequence analyses revealed significant similarities to tospoviruses of the species Watermelon silver mottle virus and to several putative tospovirus entries in GenBank. Based on these alignments it is proposed to refer to all these different viruses as isolates of CaCV.

Serological Comparison and Molecular Characterization for Verification of Calla lily chlorotic spot virus as a New Tospovirus Species Belonging to Watermelon silver mottle virus Serogroup

ABSTRACT Calla lily chlorotic spot virus (CCSV) isolated from central Taiwan was recently identified as a tospovirus serologically but distantly related to Watermelon silver mottle virus (WSMoV). To clarify the serological relationship between the two viruses, rabbit polyclonal antibody (PAb) to CCSV and mouse monoclonal antibodies (MAbs) to WSMoV NP or CCSV NP were produced in this investigation, using purified nucleocapsid protein (NP) as immunogens. The PAb to CCSV NP reacted stronger with the homologous antigen than with the heterologous antigen, with much lower A(405) readings in indirect enzyme-linked immunosorbent assay (ELISA) and low-intensity banding in immunoblotting. MAbs produced to CCSV NP or WSMoV NP reacted specifically with the homologous antigens but not with the heterologous antigens in both ELISA and immunoblot analyses. The CCSV S RNA was determined to be 3,172 nucleotides in length, with an inverted repeat at the 5' and 3' ends and two open reading frames encoding the NP and a nonstructural (NSs) protein in an ambisense arrangement. A typical 3'-terminal sequence (5'-AUUGCUCU-3') that is shared by all members of the genus Tospovirus also is present in the CCSV S RNA. The CCSV NP and NSs protein share low amino acid identities of 20.1 to 65.1% and 19.9 to 66.1%, respectively, with those of reported tospoviruses. Phylogenetic dendrogram analysis indicates that CCSV is a distinct member in the genus Tospovirus. The results provide evidence that CCSV is a new species in the genus Tospovirus and belongs to WSMoV serogroup.

Serological and Molecular Characterization of Peanut chlorotic fan-spot virus, a New Species of the Genus Tospovirus

ABSTRACT To clarify the serological relationship of Peanut chlorotic fan-spot virus (PCFV) with other tospoviruses, antisera were produced against the nucleocapsid (N) proteins of this virus and tospoviruses from four serogroups including Tomato spotted wilt virus (TSWV), Impatiens necrotic spot virus (INSV), Groundnut ringspot virus (GRSV), and Watermelon silver mottle virus (WSMoV). In immunodiffusion tests, the antisera only reacted with their homologous antigens. Similar results were noticed in indirect enzyme-linked immunosorbent assay and immunoblot tests, with the exception that strong cross-reactions were observed in heterologous combinations between TSWV and GRSV. The results indicated that the N protein of PCFV is not serologically related to those of the tospoviruses from the four serogroups. To further characterize the virus, viral S double-stranded RNA was extracted from PCFV-infected Chenopodium quinoa and used for cDNA cloning and sequencing. The full-length viral strand of the S RNA was determined to be 2,833 nucleotides, with an inverted repeat at the 5' and 3' ends and two open reading frames in an ambisense arrangement. The 3'-terminal sequence (5'-AUUGCUCU-3') of the viral S RNA is identical to those of other tospoviruses, indicating that PCFV belongs to the genus Tospovirus. The N and the NSs proteins of PCFV share low amino acid identities (22.3 to 67.5% and 19.3 to 54.2%) with those of reported tospoviruses, respectively. The phylogenetic dendrogram of the N gene of PCFV compared with those of other tospoviruses indicates that PCFV is distinct from other tospoviruses. In hybridization analyses, an N gene cDNA probe of PCFV did not react with viral RNAs of TSWV, GRSV, INSV, and WSMoV, and vice versa. Thus, based on these results, we conclude that PCFV is a new tospovirus species.

RT-PCR for detecting five distinct Tospovirus species using degenerate primers and dsRNA template

RT-PCR procedures for detection of multiple species of tospovirus from plant tissues were investigated. Downstream primers were designated from the 3' untranslated sequences of the S RNA. An upstream primer was designated from the degenerated sequences of the nucleocapsid protein. Approximately 450 bp DNA fragments were detected when Tomato spotted wilt virus (TSWV)- or Impatiens necrotic spot virus (INSV)- infected tissues were examined. Approximately 350 bp DNA fragments were detected when Watermelon silver mottle virus (WSMoV)- or Melon yellow spot virus (MYSV)-infected tissues were examined. Template RNA was extracted using CF 11 cellulose powder, and nonspecific amplification became unnoticeable when double-stranded RNA was used. The amplified fragments of WSMoV were differentiated from those of MYSV by AluI or TaqI digestion. The amplified fragments of TSWV were differentiated from those of INSV by DraI or HindIII digestion. An alstroemeria plant that was infected with an unidentified tospovirus was also examined, and a 350 bp fragment that was 97% identical to Iris yellow spot virus was detected. This method, therefore, detected at least five distinct Tospovirus species.

Completion of the Genome Sequence of Watermelon silver mottle virus and Utilization of Degenerate Primers for Detecting Tospoviruses in Five Serogroups

ABSTRACT The nucleotide sequence of the L RNA of Watermelon silver mottle virus (WSMoV) was determined. Combined with the previous work on M and S RNAs, the whole genomic sequence of this member of the genus Tospovirus was completed. The L RNA is 8,917 nucleotides in length, with one large open reading frame encoding a translation product of 2,878 amino acids (331.8 kDa) on the viral complementary strand. The L protein shares amino acid identities of only 44.3 and 46.5% with Tomato spotted wilt virus (TSWV) and Impatiens necrotic spot virus, respectively; but an amino acid identity of 91.3% with Peanut bud necrosis virus. Among the sequenced tospoviruses, L protein was the most conserved gene product, whereas the nonstructural S protein was generally the most variable. Comparison of the deduced L protein of WSMoV with those of other members of the family Bunyaviridae revealed that its amino acid sequence includes the reported conserved motifs of RNA-dependent RNA polymerases. To develop a method for detecting tospo-viruses by reverse transcription-polymerase chain reaction (RT-PCR), two pairs of degenerate primers were designed from conserved regions of the L genes and used to amplify the corresponding regions of the L genes from total RNAs extracted from plant tissues infected with five serologically distinct tospoviruses. The DNA fragments obtained were identified as those of tospoviruses by restriction enzyme digestion and DNA sequencing. For field samples, watermelon and wax gourd infected with WSMoV, and lisianthus infected with TSWV were also successfully detected by these two pairs of degenerate primers, with a sensitivity similar to N-gene-specific primers. The results indicated that the RT-PCR with the degenerate primers is a fast and reliable method for detecting tospoviruses in different serogroups.

Melon yellow spot virus: A Distinct Species of the Genus Tospovirus Isolated from Melon

ABSTRACT A tospovirus-like virus recovered from netted melon was transmitted by Thrips palmi in a persistent manner but had different cytopathological features from tospoviruses previously reported. Viral nucleocapsid (N) was purified with two protective reagents, 2-mercaptoethanol and L-ascorbic acid, and RNA extracted from the viral nucleocapsid was used for genomic analysis. The virus had a genome consisting of three single-stranded RNA molecules. The open reading frame on the viral complementary strand, located at the 3' end of the viral S RNA, encoded the N protein. The 3' terminus of this RNA also contained an eight-nucleotide sequence similar to the conserved sequence at the 3' end of genomic RNA molecules of tospoviruses. These features of the viral genome are identical to those of tospoviruses; therefore, this virus is considered to belong to the genus Tospovirus. Its N protein comprised 279 amino acids and had a molecular mass of 31.0 kDa. Comparisons of its amino acid sequence with those of known tospoviruses revealed less than 60% identity. This melon virus is concluded to be a distinct species in the genus Tospovirus, and the name Melon yellow spot virus is proposed.

Increase of tospoviral diversity in Brazil with the identification of two new tospovirus species, one from chrysanthemum and one from zucchini

ABSTRACT During a survey conducted in several different regions of Brazil, two unique tospoviruses were isolated and characterized, one from chrysanthemum and the other from zucchini. The chrysanthemum virus displayed a broad host range, whereas the virus from zucchini was restricted mainly to the family Cucurbitaceae. Double-antibody sandwich-enzyme-linked immunosorbent assay and western immunoblot analyses demonstrated that both viruses were serologically distinct from all reported tospovirus species including the recently proposed peanut yellow spot virus and iris yellow spot virus (IYSV) species. The nucleotide sequences of the nucleocapsid (N) genes of both viruses contain 780 nucleotides encoding for deduced proteins of 260 amino acids. The N proteins of these two viruses displayed amino acid sequence similarities with the previously described tospovirus species ranging from 20 to 75%, but they were more closely related to each other (80%). Based on the biological and molecular features, these viruses are proposed as two new tospovirus species, designated chrysanthemum stem necrosis virus (CSNV) and zucchini lethal chlorosis virus (ZLCV). With the identification of CSNV and ZLCV, in addition to tomato spotted wilt virus, groundnut ring spot virus, tomato chlorotic spot virus, and IYSV, Brazil harbors the broadest spectrum of tospovirus species reported.

Characterization of a Tospovirus Isolate of Iris Yellow Spot Virus Associated with a Disease in Onion Fields in Brazil

A tospovirus from onion causing a disease known as "sapeca" by growers in Brazil was characterized. Symptoms on onion consisted of numerous eyelike spots on the leaves and flower stalks resulting in flower abortion. Nicotiana benthamiana and N. rustica were the only systemic hosts experimentally found. Double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) experiments demonstrated that this virus was serologically related to iris yellow spot virus (IYSV), a tospovirus recently described in the Netherlands. This virus, from onion, based on an amino acid sequence identity of 90.5% for the N gene protein, is regarded as a strain of IYSV and is designated IYSV_BR This 10% divergence in the nucleocapsid protein may represent an adaptation of the virus to distinct ecological niches.

Molecular and serological characterization of iris yellow spot virus, a new and distinct tospovirus species

ABSTRACT A new tospovirus was identified in iris cultivations in the Netherlands. Both serological comparisons and sequence determination of the S RNA demonstrate that this virus represents a new and distinct species, belonging to a separate serogroup, and for which the name iris yellow spot virus (IYSV) is proposed. The disease symptoms on iris are characterized by yellow spots on the leaves. Its experimental host range is very narrow and, in addition to iris, only includes Nicotiana benthamiana and Datura stramonium. The nucleoprotein of IYSV shows only 30 to 44% sequence identity with those of other tospoviruses identified so far; the highest homology being found with the tospovirus species of serogroup IV.

Comparison of ambisense m RNA of watermelon silver mottle virus with other tospoviruses

ABSTRACT Double-stranded genomic RNAs (dsRNAs) extracted from Chenopodium quinoa infected with watermelon silver mottle virus (WSMV) were similar to those of tomato spotted wilt virus (TSWV, serogroup I) and impatiens necrotic spot virus (INSV, serogroup III), except that the S dsRNA of WSMV is 0.75 and 0.6 kbp longer than those of TSWV and INSV, respectively. The complete nucleotide sequence of the genomic M RNA of WSMV was determined from cDNA clones generated from separated M dsRNA. The M RNA is 4,880 nucleotides in length with two open reading frames (ORFs) in an ambisense organization. The M RNA-encoded nonstructural (NSm) ORF located on the viral strand encodes a protein of 312 amino acids (35 kDa), and the G1/G2 ORF located on the viral complementary strand encodes a protein of 1,121 amino acids (127.6 kDa). The RNA probe corresponding to the NSm or G1/G2 ORF of WSMV failed to hybridize with the M dsRNAs of TSWV and INSV. Comparison of M and S RNAs of WSMV, TSWV, INSV, and peanut bud necrosis virus (PBNV, serogroup IV) revealed a consensus sequence of eight nucleotides of 5'-AGAGCAAU...-3' at their 5' ends and 5'-...AUUGCUCU-3' at their 3' ends. The low overall nucleotide identities (56.4 to 56.9%) of the M RNA and the low amino acid identities of the NSm and G1/G2 proteins (30.5 to 40.9%) with those of TSWV and INSV indicate that WSMV belongs to the Tospovirus genus but is phylogenetically distinct from viruses in serogroups I and III. The M RNA of WSMV shares a nucleotide identity of 79.6% with that of PBNV, and the two viruses share 83.4 and 88.7% amino acid identities for their NSm and G1/G2 proteins, respectively. It is concluded that they are two related but distinct species of serogroup IV. In addition to the viral or viral complementary full-length M RNA, two putative RNA messages for the NSm gene and the G1/G2 gene, 1.0 and 3.4 kb, respectively, were detected from the total RNA extracted from WSMV-infected tissue of Nicotiana benthamiana. The 1.0- and 3.4-kb RNAs were also detected in the viral RNAs extracted from purified nucleocapsids, suggesting that the putative messages of the M RNA of WSMV can also be encapsidated by the nucleocapsid protein.

The emerging problem of tospovirus infection and nonconventional methods of control

The emergence of tospoviruses as a significant problem in the cultivation of many crops around the world makes it vital to develop strategies to restrain these viruses. So far, only a few natural resistance genes suitable for introduction into plant breeding programs have been identified, prompting the exploitation of alternative ways of introducing virus resistance into crop plants, such as genetic modifications.