Search Results (139)

Chilli veinal mottle virus (ChiVMV, Potyvirus capsivenamaculae) can infect various Solanaceae crops, causing a decrease in yield and quality. In recent years, ChiVMV has become one of the most prevalent viruses affecting tobacco production, but its diversity and genetic structure are still elusive. In this study, 202 ChiVMV isolates were obtained from 13 tobacco-producing areas in Yunnan Province between 2021 and 2025. Analysis of the coat protein (CP) genes of the 202 isolates showed that there exist 193 haplotypes and abundant genetic diversity. The highest variation was observed at the N-terminus of ChiVMV CP. Further analysis displayed three high-confidence recombination events in the CP gene of ChiVMV Yunnan isolates, with isolate 25DLYP-7 from the Dali region playing a putative parental isolate for these recombinations. The results of neutral and selection pressure analyses indicated that the CP gene of ChiVMV Yunnan isolates exhibits purifying selection. Distribution analysis of these ChiVMV Yunnan isolates showed that geographical isolation is closely related to the genetic diversity of ChiVMV, and field weeds may serve as important initial sources of infection. Phylogenetic analysis demonstrated that ChiVMV Yunnan populations display close association with isolates from southwestern China, as well as isolates from South Asia and Europe. Full article

Potyvirus rapae (turnip mosaic virus, TuMV) is widely used as a model system in plant–virus interaction studies. The TuMV RNA genome encodes 11 proteins, some of which remain poorly characterized, while the functions of others are well defined. Studying individual proteins in isolation may not recapitulate native expression levels, subcellular localization, and interaction with host factors during virus replication and movement. An alternative approach is to tag individual viral proteins in the context of an infectious clone. Epitope tags may alter protein functions and affect viral replication, movement, or a combination of essential steps, thus leading to changes in pathogenicity. Because they have central roles in viral infection, here we measured the effect of individually tagging the helper component proteinase (HC-Pro) and nuclear inclusion protein b (NIb) with a 6His-3xFLAG tag. Epitope tags were placed at the N-terminus of HC-Pro and the N- and C-termini of NIb within a TuMV infectious clone carrying coding sequences for the green fluorescent protein (TuMV-GFP). Constructs carrying a tagged HC-Pro displayed pathogenicity similar to that observed for TuMV-GFP in Nicotiana benthamiana and Arabidopsis thaliana plants. In contrast, infectivity of NIb-tagged clones became temperature sensitive and, even at the permissive temperature, showed reduced pathogenicity compared to TuMV-GFP. Providing a silencing suppressor in trans did not restore infection efficiency, suggesting reduced viral fitness due to structural or functional disruption caused by the epitope tags. Structural models generated using AlphaFold2 showed no effect of the tag on HC-Pro. In contrast, structural models illustrated tag interference with the NIb catalytic site. AlphaFold2 was further used to predict the structural impact of several tags on NIb and to predict the effect of a 6HIS-3xFlag tag on all other TuMV proteins. This study provides a broadly applicable framework for selecting suitable epitope tags to mark viral proteins and maintain function in the context of virus infection. Full article

Saffron (Crocus sativus L.) is a high-value crop vulnerable to potyvirus infections threatening its yield and quality. In this study, we combined Oxford Nanopore long-read sequencing with exploratory transcriptomic profiling to characterize the saffron virome and to describe expression profiles associated with two distinct infection histories: (i) saffron plants experimentally inoculated with cucumber mosaic virus (CMV; Cucumovirus CMV) and turnip mosaic virus (TuMV; Potyvirus rapae) under controlled greenhouse conditions, and (ii) saffron plants naturally infected by diverse viruses. We identified six plant-infecting viral families in both conditions, including Potyviridae, Geminiviridae, Caulimoviridae, Tymoviridae, Aspiviridae, and Partitiviridae. Transcriptomic profiling revealed distinct expression profiles associated with each infection background. Given the limitations of the experimental design, gene expression differences are interpreted descriptively. We describe pathway enrichments associated with antiviral responses. Naturally infected plants exhibited a broad-spectrum, tolerance-based response characterized by the upregulation of photosynthesis-related genes, calcium-mediated signaling components, and stress-responsive transcription factors. In contrast, virus-inoculated plants activated a targeted antiviral program involving RNA silencing, autophagy, ubiquitin-mediated proteolysis, and hormonal regulation. Both GO and KEGG enrichment analyses supported these findings, highlighting photosynthesis and metabolic flexibility in naturally infected plants versus hypersensitive response, RNA surveillance, and lignin biosynthesis in virus-inoculated plants. This work provides a comprehensive view of the saffron virome and offers a hypothesis-generating overview of transcriptional responses associated with natural versus experimental virus infections. These findings advance the understanding of the saffron virome and provide a valuable resource for breeding virus-resistant cultivars. Full article

Zucchini tigre mosaic virus (ZTMV; Potyvirus pepotigris), which infects wax gourd (Benincasa hispida), was first identified in Taiwan in 2017 and designated ZTMV-TW. In this study, mild strains of ZTMV-TW were generated by modifying the pathogenicity factor HC-Pro to develop cross-protection strategies for cucurbit crops. A full-length infectious cDNA clone of ZTMV-TW was cloned in pCAMBIA1304 under the control of the CaMV 35S promoter (ZTMV-TWic). ZTMV-TWic induced typical potyvirus particles, cytoplasmic inclusion bodies, and severe symptoms in wax gourd, pumpkin, and zucchini plants. Conserved motifs of HC-Pro were mutated to generate four single mutants (F7I, R181I, F206L, and D397N) and three double mutants (F7I+F206L, R181I+D397N, and F206L+D397N). Mutants R181I and R181I+D397N caused mild or no symptoms in zucchini, while D397N and F206L+D397N were mild in wax gourd. Cross-protection assays showed that R181I and R181I+D397N provided complete protection against ZTMV-GFP in zucchini, whereas D397N and F206L+D397N conferred high protection in wax gourd. These results demonstrate the feasibility of host-specific mild strain selection for effective ZTMV cross-protection. Full article

Passion fruit (Passiflora edulis Sims) is an important economic fruit crop in Rwanda grown for both domestic consumption and export markets. However, viral diseases pose a significant threat to passion fruit production. Among these, passion fruit woodiness disease (PWD) is the most destructive, causing yield losses of up to 100%. A survey was carried out to assess the distribution of Ugandan passiflora virus (UPV; Potyvirus passiflorafricanse) in major passion fruit growing areas. UPV is one of the major viruses known to cause PWD. The incidence of viral symptoms observed in the field did not differ significantly among districts, ranging from 81% in Rusizi to 100% in Rwamagana. However, mean symptom severity scores varied significantly between districts, with the highest severity recorded in Kayonza (3.1) and the lowest in Rulindo (1.9). Serological analysis detected potyviruses in 44% of the total samples (n = 216), including 43% of symptomatic (n = 144) and 47% of asymptomatic (n = 72) leaf samples collected from passion fruit fields. Further analysis using Reverse-Transcription Polymerase Chain Reaction (RT-PCR) detected UPV in 56% of symptomatic (n = 126) and 53% of asymptomatic (n = 60) samples, corresponding to 55% of the total samples tested (n = 186). The virus was present in all surveyed districts, with UPV infection prevalence of 89% in Rusizi, 75% in Rwamagana, 74% in Karongi, 59% in Nyamagabe, 44% in Nyaruguru, 38% in Kayonza, and 30% in both Gakenke and Rulindo. Fifteen partial coat-protein gene sequences for the Rwandan isolates were obtained. The newly described Rwandan isolates shared 97–99% nucleotide (nt) identity with one another, 89–94% with previously reported Rwandan isolates, 81–97% with Ugandan isolates, and 80–82% with Kenyan UPV isolates, suggesting that the Rwandan virus population is relatively homogenous. Genetic distances among the 15 new UPV isolates and previously reported Rwandan, Ugandan, and Kenyan isolates were very short (0.01–0.03), indicating high sequence similarity. All Rwandan isolates clustered into a single major clade, together with some Ugandan and Kenyan isolates. This close genetic relationship suggests a common ancestry and the regional spread of a single dominant UPV lineage. These findings highlight the need to reinforce seed and planting-material certification systems, as well as the need to enhance farmer capacity through targeted training on viral disease identification and management practices. This is vital to limiting the spread of viral diseases that threaten income security among smallholder passion fruit farmers. Full article

Cultivated species of the Prunus genus are of great economic importance worldwide and can be severely affected by viral diseases that compromise both yield and fruit quality. Among the most significant is Potyvirus plumpoxi (PPV), the causal agent of sharka disease, which has a direct and severe impact on stone fruit production. In this study, high-throughput RNA sequencing was employed to detect and characterize viruses present in commercial peach and apricot orchards located in different regions of Spain. After processing five samples, a total of ten viruses were identified, with PPV being the predominant virus in all analyzed samples, specifically the Marcus strain (PPV-M), which is described as one of the most aggressive PPV strains. In addition, other viruses were detected with high sequencing depth, including Luteovirus nucipersicae (nectarine stem pitting associated virus, NSPaV) and Peach-associated luteovirus (PaLV). Single-nucleotide variation (SNV) analysis of PPV-M populations revealed specific mutations distributed across the viral genome. Furthermore, phylogenetic analyses indicated the presence of multiple infection sources of European origin. These results highlight the presence of PPV-M in Spain, providing evidence of different routes of exchange of infected plant material. These findings underscore the need to strengthen monitoring programs, certification of planting material, and phytosanitary control measures to limit the dissemination of viruses and minimize their impact on stone fruit production. Full article

Here, we adopt an historical approach towards reviewing research since the 1970s on the seed-borne virus diseases of cool-season pulses caused by pea seed-borne mosaic virus (PSbMV) in Australia’s grain cropping regions. All relevant investigations concerning the principal cool-season pulse crops infected; field pea, lentil, faba bean, chickpea, and the minor ones, Lathyrus species, vetches and narbon bean, are covered. However, as the PSbMV field pea pathosystem is the most studied, this receives greatest emphasis. The review starts with brief background information, and by describing the disease symptoms caused and the advances in sample testing procedures. Next, findings from past PSbMV studies are covered in greater detail including transmission by aphids, contact and seeds; occurrence in crops and seed stocks; pathotypes and genetic diversity; host resistance; and phytosanitary, cultural and chemical control measures. What these studies found about PSbMV biology, epidemiology and control is emphasized by describing past glasshouse and field experimentation. Then, practical research outcomes identifying PSbMV’s epidemic drivers, forecasting its epidemics and devising an integrated disease management strategy are emphasized. Examples of images that illustrate past investigations and research outputs are provided. Finally, principal research achievements and priorities for future Australian PSbMV cool-season pulse research are highlighted. Full article

Climate warming has facilitated the expansion of insect vectors and plant viral pathogens, leading to increased incidence of viral diseases in crops. Cucurbit crops, including cucumber (Cucumis sativus), melon (Cucumis melo), squash (Cucurbita pepo), and watermelon (Citrullus lanatus), are of major economic importance worldwide, but their production is severely threatened by viral infections. Among the most damaging viruses are zucchini yellow mosaic virus (ZYMV; genus Potyvirus), transmitted by aphids, and melon yellow spot virus (MYSV; genus Orthotospovirus), transmitted by thrips, both of which cause significant yield losses in Asia, including Taiwan. Previously, an attenuated ZYMV mutant, ZAC, was shown to confer effective cross-protection against ZYMV in several cucurbit species. In the present study, we engineered a recombinant virus, ZAC-MYnp, by inserting the nucleocapsid protein (NP) open reading frame of MYSV into the ZAC genome. ZAC-MYnp retained the attenuated phenotype of ZAC and remained effective in protecting against ZYMV infection, with protection rates of 70.4% and 87.0% in zucchini and muskmelon plants, respectively. In addition, under both mechanical and thrips-mediated challenge conditions, ZAC-MYnp significantly reduced MYSV symptom severity in muskmelon, with a protection rate of 66.7% and a protective efficacy of 79.0%, respectively. These results demonstrate that ZAC-derived recombinant viruses can function as a bivalent viral vaccine, offering dual protection against an aphid-borne potyvirus and a thrips-borne orthotospovirus. Our study highlights the feasibility of using a bivalent recombinant vaccine to manage two distinct insect-borne viruses in cucurbit crops. Full article

Potyvirus genomes are expressed as a single large open reading frame, which is translated into a polyprotein that is post-translationally cleaved by three virus-encoded proteases into 10 functional proteins. Several of these potyviral proteins, including nuclear inclusion protein b (NIb), are multifunctional. Here, using the classic GFP silencing in Nicotiana benthamiana gfp-transgenic plants, we show that potato virus Y (PVY) NIb, in addition to its canonical role as the viral RNA-dependent RNA polymerase (RdRP), functions as a suppressor of RNA silencing. Mutational analyses reveal a previously unreported NIb nuclear localization signal (NLS) consisting of a triple-lysine motif. NIb suppression of RNA silencing activity was lost when the NLS was mutated, suggesting that nuclear localization is required for NIb suppression of RNA silencing activity. Analysis of sequenced GFP siRNAs revealed three reproducible hotspot regions at ≈175 nt, ≈320–330 nt, and a broader 3′-proximal region spanning ≈560–700 nt that contains multiple local maxima. These data show differences in the positional distribution of siRNAs between samples expressing NIb and those expressing NIb^Del3×2, the NIb null mutant that does not suppress RNA silencing. However, the positional distribution of GFP-derived small RNAs across the transgene differed modestly between NIb and NIb^Del3×2, while both treatments showed the same three reproducible hotspot regions. Furthermore, NIb was found to interact with four key RNA silencing pathway proteins—AGO4, HSP70, HSP90, and SGS3. Except for HSP90, each of these proteins showed degradation products that were absent in NIb mutants that did not suppress RNA silencing. These findings support a role for NIb in countering host defense during virus infection. Full article

Chilli veinal mottle virus (ChiVMV) is an important potyvirus that poses a serious threat to crop production. In this study, small RNA sequencing and molecular cloning were used to obtain the complete genome sequence of a ChiVMV isolate identified in pepper plants in Sichuan (SC1 isolate). Molecular evolutionary and phylogenetic analysis of SC1 and 35 ChiVMV isolates revealed four clades of ChiVMV isolates. Recombination analysis found 23 recombinant events and 28 recombinants, with the SC1 isolate arising from the recombination of the PK isolate from Pakistan and the YNpe isolate from Yunnan, China. A full-length infectious cDNA clone of ChiVMV was constructed and demonstrated to be infectious in both Nicotiana benthamiana and pepper plants. Moreover, a Myc-tag was inserted after NIb, and the derived infectious clone of ChiVMV remained infectious, and NIb-Myc was readily expressed in infected host plants. These reverse genetic tools will promote the study of the function of ChiVMV-encoded proteins, especially the NIb protein, and facilitate basic and translational studies of ChiVMV. Full article

N⁶-methyladenosine (m⁶A), the most prevalent internal mRNA modification in eukaryotes, is also present in plants and is known to influence plant–virus interactions. However, its specific role in regulating Potato virus Y (PVY; Potyvirus yituberosi) infection, a major pathogen of potatoes, remains unclear. This study identified 16 potential m⁶A regulator genes in Nicotiana benthamiana through homology screening of Arabidopsis thaliana AlkB family members. Based on expression profiles in leaves at various developmental stages and following PVY infection, NbALKBH1L was selected for further analysis. Enzyme assays confirmed its m⁶A demethylase activity. Experiments with NbALKBH1L mutants, using RT-qPCR and m⁶A-IP-qPCR, demonstrated that it regulates PVY infection via the m⁶A pathway. Further investigation revealed that NbALKBH1L interacts with the PVY-encoded cylindrical inclusion (CI) protein. An interaction network constructed through immunoprecipitation–mass spectrometry (IP-MS) and RNA sequencing (RNA-seq) suggested that NbALKBH1L may serve as a central node in plant antiviral immunity, potentially linking metabolic processes with the regulation of viral infection. In summary, this study advances our understanding of plant m⁶A modifications in antiviral defense and provides valuable insights for future antiviral breeding strategies. Full article

Yam (Dioscorea spp.) is a major staple food, contributing significantly to food security and income generation for millions of people worldwide. In 2019, surveys were conducted across the seven agro-ecological zones (AEZs) of Côte d’Ivoire, the third highest producer of yam globally, to ascertain the current status of viral diseases. In the 324 fields surveyed, a total of 1242 yam leaf samples were collected and tested for the presence of Potyvirus yamtesselati (yam mosaic virus, YMV), Potyvirus yamplacidum (yam mild mosaic virus, YMMV), Cucumovirus CMV (cucumber mosaic virus, CMV), and the badnaviruses using PCR, RT-PCR, and RCA followed by Sanger or MinION sequencing. The incidence of yam viral disease varied across the AEZs, with the lowest mean incidence observed in yam farms within the AEZ VII (71.95%) and the highest in AEZ V (88.15%). Viral disease symptom severity was moderate across the country, with more severe symptoms identified in AEZs II and VI. The virus screening revealed a potyvirus detection rate of 35.83% in all the AEZs. YMMV infection (25.12%) is the most prevalent in the samples, followed by YMV infection (15.61%). RCA-MinION sequencing revealed the presence of badnaviruses belonging to the T15 episomal groups K8, K9, and K5. Also, the use of this technique enabled the amplification and sequencing of four full-length episomal badnaviruses, namely Dioscorea bacilliform AL virus in group K8 and Dioscorea bacilliform RT virus in group K5. CMV was not detected in all the samples. It is noteworthy that 22.13% of mixed infections were detected in asymptomatic samples. This study revealed the first occurrence of YMMV in all the AEZs of Côte d’Ivoire. Of the yam species, Dioscorea alata was more widespread (78.03%) than Dioscorea cayenensis-rotundata (21.92%) in the visited fields. Also, D. alata had a highest incidence of YMMV (23.67%) infection than Dioscorea cayenensis-rotundata, while D. cayenensis-rotundata registered the highest incidence of YMV (15.84%) infection compared to D. alata. Phylogenetic analysis of representative of the various viruses detected in the country revealed that the sequences have high diversity for each virus species. This study revealed that viruses infecting yam are widespread and occur in mixed infection, which poses a real threat to yam production in Côte d’Ivoire. Full article

The potyvirus helper component proteinase (HcPro) is a multifunctional protein, with one of its most documented functions being host antiviral RNA silencing suppression. This study shows that the HcPro of potato virus Y (PVY), an important member of the potyvirus group, prevents the replication of a related competing secondary virus. This phenomenon, referred to as superinfection exclusion (SIE), is common in bacterial, human, and plant virus infections. We also report that HcPro’s induction of SIE is strain-specific and that this specificity is provided by the first four amino acid residues of the protein. Consistent with the mechanism of SIE, the study found that HcPro does not exclude a resident virus. Additionally, HcPro’s induction of SIE was observed to function independently of its ability to suppress antiviral RNA silencing. HcPro’s induction of SIE is relevant given the prevalence of multiple PVY strains that routinely co-infect the same cell and that may lead to recombination and emergence of new and more virulent strains. Furthermore, cross-protection or systemic acquired resistance (SAR) that is employed in plant virus disease management occurs when SIE moves from the cellular level and spreads systemically, emphasizing the importance of studying SIE. Full article

Taro (Colocasia esculenta) is a socioeconomically and nutritionally important crop that is predominantly cultivated in the derived savanna and humid forest agroecosystems of Nigeria. Taro production in the country has declined since the taro leaf blight (TLB) outbreak caused by Phytophthora colocasiae Raciborski. This study conducted field surveys during the 2021–2022 production season to assess the status of taro diseases, as well as a structured questionnaire to capture farmers’ management practices and the socio-economic determinants of taro cultivation across seven major taro-producing states in Nigeria. Data was collected from 63 randomly selected farmers across 53 farms, and 449 corms were sampled from farms and markets to assess corm-borne diseases. Sixty-three percent of farmers identified biotic constraints as the major production challenge, with TLB recognized as the most significant threat. Virus-symptomatic plants were not observed in the farmers’ fields, but the occurrence of Dasheen mosaic virus (or Potyvirus dasheenis) (DsMV, genus Potyvirus) was detected among the plants regenerated from corms collected from farms and markets. The widespread occurrence of TLB and DsMV suggests that these two pathogens pose a serious threat to taro production and that there is a risk of further spread through the continuous recycling of self-sourced planting materials across seasons. Full article

Bean common mosaic virus (BCMV; Potyvirus phaseovulgaris) is one of the primary viruses that severely impacts the yield and quality of common beans (Phaseolus vulgaris L.) and has a worldwide distribution. Utilizing small RNA sequencing and RT-PCR validation, this study identified widespread co-infection by multiple viruses in field-collected common bean samples, with BCMV being the dominant viral species. A novel isolate, designated DY9, was obtained from these field samples. Pathotype characterization confirmed DY9 as pathotype PG-III, while previous studies reported all other PG-III members as Bean common mosaic necrosis virus (BCMNV). Whole-genome sequencing and phylogenetic analysis revealed that DY9 was genetically closer to BCMV and diverged significantly from known PG-III isolates. Based on these findings, we constructed an infectious clone of DY9. To address the genetic instability of Potyvirus in the Escherichia coli (E. coli) expression system, we discovered that inserting Intron 2 (derived from the NiR gene of P. vulgaris, GenBank: U10419.1) at position 2431 of the HC-Pro gene and targeting Intron 1 (derived from the ST LS1 gene of Solanum tuberosum, GenBank: X04753.1) at position 4240 of the CI gene significantly improved the stability of the cloning vector. The clone was verified to systemically infect common bean plants and induce typical mosaic symptoms. Infectivity was validated through RT-PCR, RT-qPCR, Western blotting, and transmission electron microscopy. This study represents the first successful construction of an infectious clone for pathotype PG-III BCMV, providing a critical reverse genetics tool for dissecting viral pathogenesis and identifying resistance genes. These findings not only expand the genetic diversity of BCMV but also offer a methodological reference for constructing infectious clones of Potyvirus species. Full article