Necrotic Ringspot Research Articles

Selection and Validation of Reference Genes for Gene Expression Studies Using Quantitative Real-Time PCR in Prunus Necrotic Ringspot Virus-Infected Cucumis sativus.

Several members of the genus Ilarvirus infect fruit trees and are distributed worldwide. Prunus necrotic ringspot virus (PNRSV) is one of the most prevalent viruses, causing significant losses. Cucumis sativus can be infected by several ilarviruses, leading to obvious symptoms, including PNRSV, which suggests that cucumbers could be good hosts for the study of the pathogenesis of ilarviruses. Real-time quantitative PCR is an optimal choice for studying gene expression because of its simplicity and its fast and high sensitivity, while its accuracy is highly dependent on the stability of the reference genes. In this study, we assessed the stability of eleven reference genes with geNorm, NormFinder, ΔCt method, BestKeeper, and the ranking software, RefFinder. The results indicated that the combined use of EF1α and F-BOX was the most accurate normalization method. In addition, the host genes AGO1, AGO4, and RDR6 were selected to test the reliability of the reference genes. This study provides useful information for gene expression analysis during PNRSV infection and will facilitate gene expression studies associated with ilarvirus infection.

Natural Infection of Cichorium intybus (Asteraceae) by Groundnut Ringspot Virus (Genus Orthotospovirus) Isolates in Brazil.

Leaf chicory (Cichorium intybus L.) is a nutritionally rich vegetable used in regional cuisine in Brazil. Plants of C. intybus displaying symptoms (viz. chlorotic and necrotic ringspots, mosaic, and leaf deformation) similar to that induced by orthotospoviruses (genus Orthotospovirus, family Tospoviridae) were observed in three fields (≈ 0.2 ha each) in Gama County, in the Federal District, Brazil, from September 2016 to January 2020 in plants of the cultivars 'Folha-Larga' and 'Spadona' (Fig. 1). Incidence of symptomatic plants was nearly 10% in each field. Transmission electron microscopic examination of thin sections from symptomatic leaf samples showed typical membrane-bounded orthotospovirus particles within cisternae of spongy parenchymal cells (Fig 2). Two individual leaf samples per field were collected and submitted to dot enzyme-linked immunosorbent assay with polyclonal antisera against N protein of tomato spotted wilt virus (TSWV), groundnut ringspot virus (GRSV) and tomato chlorotic spot virus (TCSV). Symptomatic samples strongly reacted only against GRSV antibodies. Total RNA was extracted (Trizol®, Sigma) from all six samples and used as template in RT-PCR assays. The primer J13 (5'-CCCGGATCCAGAGCAAT-3') was employed for cDNA synthesis using M-MLV reverse transcriptase. PCR assays were done with the primer pair BR60/BR65 (Eiras et al., 2001) to obtain ≈ 500 bp fragment of untranslated region and partial N gene in the S RNA segment from each sample. Purified RT-PCR products of two randomly selected individual samples were directly sequenced (GenBank MW467981 and MZ126602) and their BLASTn analyses displayed 99 to 100% nucleotide identity to GRSV isolates previously reported infecting C. endivia L. in Brazil (Jorge et al., 2021). Our analyses combining N protein serology and N-gene sequencing (both directed to the S RNA segment) allowed us to confirm the GRSV infection of C. intybus, but the potential reassortant nature of these isolates (Webster et al., 2015; Silva et al., 2019) are unknown since their M RNA segments were not characterized. Individual leaf extracts (in phosphate buffer, pH 7.0) of the sequenced isolates were mechanically inoculated onto ten seedlings of two C. intybus cultivars ('Folha Larga' and 'Pão-de-Açúcar') and three plants each of the indicator hosts Capsicum chinense PI 159236, Nicandra physalodes; Nicotiana rustica; Datura stramonium; and tomato cv. Santa Clara. Systemic chlorotic and necrotic ringspots, mosaic, and leaf deformation developed in the indicator hosts and infection by GRSV was confirmed via serological assays 20 days after inoculation. However, no symptoms and no serological reaction to GRSV antibodies were observed on the C. intybus cultivars even after two successive mechanical inoculations. This transmission failure might be due to factors such as the requirement of the thrips vector(s), physicochemical barriers in the foliage or the presence of non-mechanically transmissible helper agent(s) necessary to ensure GRSV infection of C. intybus. The natural infection of C. intybus by a not fully characterized orthotospovirus (mostly likely TSWV) has been observed since 1938 in Brazil (Kitajima, 2020). Our report of GRSV infecting C. intybus is thus confirming previous speculations that similar symptoms in this vegetable crop were induced by orthotospovirus infection in Brazil.

A New Ilarvirus Found in French Hydrangea.

In this study, a new virus was identified in French hydrangea plants, exhibiting chlorotic vein banding and necrotic ring spots on older leaves. The virus was mechanically transmitted to herbaceous hosts, in which it induced local and systemic or only local symptoms. The genome of the new virus was characterized and consisted of three RNA sequences that were 3422 (RNA 1), 2905 (RNA 2) and 2299 (RNA 3) nucleotides long, with five predicted open reading frames; RNA2 was bicistronic and contained conserved domains and motifs typical of ilarviruses. The phylogenetic analysis of the predicted proteins—p1, p2a, p3a and p3b—revealed its close relationship to recognized members of subgroup 2 within the genus Ilarvirus. Homologous antiserum was effective in the detection of the virus in plant extracts and no cross reactions with two other distinct members of subgroup 2 were observed. Overall, the biological features, phylogenetic relationships and serological data suggest that this virus is a new member of the genus, for which we propose the name hydrangea vein banding virus (HdVBV).

Prevalence of Recombinant Strains of Potato Virus Y in Seed Potato Planted in Idaho and Washington States Between 2011 and 2021.

Potato virus Y (PVY) has emerged as the main reason for potato seed lot rejections, seriously affecting seed potato production in the United States throughout the past 20 years. The dynamics of PVY strain abundance and composition in various potato growing areas of the United States has not been well documented or understood up to now. The objective of this study was to find out the prevalence of PVY strains in potato fields in the Pacific Northwest (PNW), including seed potato production systems in the State of Idaho and commercial potato fields in the Columbia Basin of Washington State between 2011 and 2021. Based on the testing of >10,000 foliar samples during Idaho seed certification winter grow-out evaluations of seed potato lots and seed lot trials in Washington State, a dramatic shift in the PVY strain composition was revealed in the PNW between 2011 and 2016. During this time period, the prevalence of the ordinary, PVYO strain in seed potato dropped 8- to 10-fold, concomitantly with the rise of recombinant strains PVYN-Wi and PVYNTNa, which together accounted for 98% of all PVY positives by 2021. In Idaho seed potato, PVYNTNa strain associated with the potato tuber necrotic ringspot disease (PTNRD) was found to increase threefold between 2011 and 2019, accounting for 24% of all PVY positives in 2019. Mild foliar symptoms induced by recombinant PVY strains may be partially responsible for the proliferation of PVYN-Wi and PVYNTNa in potato crops. A spike of another PTNRD-associated recombinant, PVY-NE11, was recorded in the PNW between 2012 and 2016, but after reaching a 7 to 10% level in 2012 to 2013 this recombinant disappeared from the PNW potato by 2019. Whole genome sequence analysis of the PVY-NE11 suggested this recombinant was introduced in the United States at least three times. The data on PVY strain abundance in the PNW potato crops suggest that virus management strategies must consider the current dominance of the two recombinant PVY strains, PVYN-Wi and PVYNTNa.

Prunus necrotic ringspot virus in Turkey: an immigrant population

An outbreak in northwestern Turkey of prunus necrotic ringspot virus (PNRSV, genus Ilarvirus, family Bromoviridae) was sampled in 2016-2018. Gene sequences from these isolates, together with all of the gene sequence data for this virus in the GenBank database (>300 non-recombinant coat protein (CP) genes and 20 complete genomic sequences) were analysed to determine the relationship of the Turkish PNRSV isolates to those from other parts of the world. Phylogenetic and population genetic methods independently showed that the most recent common ancestor of the world PNRSV population was probably American, not Eurasian. PNRSV has spread to Turkey on several occasions, as its CP sequences are among the terminal branches of three of the most sampled CP phylogroups. The complete PNRSV genome consists of three segments (RNA1, RNA2, and RNA3), with the larger two encoding replicases and the smallest encoding the movement protein and the CP. One quarter of the RNA1 and RNA2 genes were recombinants. The phylogenies of the CP and MP genes (i.e., different regions of RNA3) were closely correlated but did not correlate with those of RNA1 and RNA2, indicating that some of the isolates were reassortants. However, the non-reassortant ancestor could not be identified, probably because none of the complete genome sequences were from isolates from the basal CP phylogroups. Our results emphasize the importance of strict quarantine, both international and local, for the world's stone fruit crops.

A novel technology for the one-step detection of prune dwarf virus: Colorimetric reverse transcription loop-mediated isothermal amplification assay

A one-step colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to target the coat protein region of genomic RNA of prune dwarf virus (PDV). WarmStart 2X Master Mix from NEB (New England Biolabs) was used for naked eye observation of positive LAMP reactions, where the changing in color from pink to yellowish indicates a positive result. The detection sensitivity of the new technique was 10-fold higher than that of conventional PCR. The assay's specificity was evaluated against the nucleic acids of potential hosts of PDV, prunus necrotic ringspot virus (PNRSV), and apple mosaic virus (ApMV) from the Ilarvirus genus. The novel RT-LAMP test showed high sensitivity in distinguishing PDV and genome of potential hosts and other Ilarvirus genus members. The RT-LAMP test was proven to be reliable for diagnosis of PDV in infected sweet cherry samples from the field. The specific, sensitive, and quick RT-LAMP test described in this study can be used in laboratories and for PDV surveillance in the field. To best of our knowledge, this is the first report of RT-LAMP detection for PDV.

Harmful viruses on stone fruit crops and sanitation methods

Relevance. Viral diseases can significantly reduce the yield of stone fruit crops. More than 30 viruses have been characterized on stone fruits crops, among which the most harmful are Plum pox virus (PPV), Prunus dwarf virus (PDV), Prunus necrotic ringspot virus (PNRSV), Cherry leaf roll spot virus (CLRV), Apple chlorotic leaf spot virus (ACLSV). Viral diseases monitoring is essential for controlling the viruses prevalence and choosing a control strategy. In the absence of healthy plants of a certain variety, health improvement is carried out using laboratory methods, including thermotherapy. Sanitation methods need to be improved in relation to the culture characteristics and the virus type. Of considerable interest is the development of techniques that reduce the viruses concentration when growing stone fruit trees in the field.Methods. During 2016–2020 using the ELISA (“Loewe” diagnostic kits) diagnostics of viruses on varieties and clonal rootstocks of cherry, sweet cherry and plum (660 plants) was carried out in the conditions of the Moscow region. For plant health in 2019–2021 used thermotherapy for 3 months. To study the effect of Pharmayod (“Farmbiomed”) on viruses in open ground, 24 plum plants of 5 varieties were treated with this drug at a concentration of 0.3 ml/l.Results. The total prevalence of viruses on cherries varieties was 44%, sweet cherries — 40%, plums — 59%, on clonal rootstocks — 46, 55 and 56% respectively. The highest incidence of PNRSV and PDV viruses has been established. Cherry plants of 11 varieties, free from the main harmful viruses, 4 varieties of sweet cherries, 12 varieties of plums and 9 forms of clonal rootstocks were revealed. The use of the Pharmayod on plum trees in the open field contributed to a decrease in the infection index of the studied viruses. Plum plants in a heat chamber were characterized by a higher survival rate and growth parameters in comparison with cherry and sweet cherry. After the completion of thermotherapy, a significant decrease in the index of infection in plants was noted.

Ligustrum necrotic ringspot virus

This datasheet on Ligustrum necrotic ringspot virus covers Identity, Hosts/Species Affected, Further Information.

A Survey for Viruses and Viroids of Peach in Tennessee Orchards by RNA Sequencing

The prevalent viruses and viroids in a population of 100 peach trees grown in Tennessee (TN) orchards were investigated by RNA sequencing and analysis of a pool of ribosomal-depleted total RNA derived from these plants. The sequences of nine viruses (cherry green ring mottle virus; cherry necrotic rusty mottle virus; grapevine-associated ilarvirus, GaIV; nectarine virus M, NeVM; Prunus necrotic ringspot virus, PNRSV; tomato mosaic virus, ToMV; tomato ringspot virus, ToRSV; turnip vein-clearing virus, TVCV; and white clover mosaic virus, WClMV) and one viroid (peach latent mosaic viroid, PLMVd) were detected. The presence of ToMV, PNRSV, NeVM, ToRSV and PLMVd sequences were confirmed in the original samples by RT-PCR followed by Sanger sequencing. This study represents the first survey of viruses and viroids of peach trees in TN orchards. To the best of our knowledge, ToMV, NeVM, GaIV, TVCV, and WClMV have not been reported previously associated with peach trees elsewhere in the world.

Advances and outlook of horticultural bioengineering

A Branch of modern biotechnology for creating unique relevant genotypes is bioengineering that harnesses a spectrum of plant genome modification technologies. The study aimed to analyse the current state of the art in genome modification of fruit and berry crops for more significant (vs. premium pure breeding varieties) deviations of norm in the traits and properties of biotic and abiotic resistance, productivity, fruit quality, etc. First horticultural crop transformation studies aimed at developing protocols based on selectable enzyme marker genes of phosphorylationmediated aminoglycoside antibiotics detoxification. Neomycin phosphotransferase nptII constitutes the most common system of transgenic fruit and berry crop selection. In pome crops, the transgenic selection priorities were resistance to scab (Venturia inaequalis (Wint.) Cke), rust (Gymnosporangium juniper-virginianae Schwein.) and bacterial blight (Erwinia amylovora Burrill, Winslow et al.), higher fruit quality, including bright colouring, and reduced enzymatic browning. In stone crops, it was tolerance to plum pox (PPV), papaya ringspot (PRSV) and Prunus necrotic ringspot (PNRSV) viruses. In berry crops — resistance to Sphaerotheca humuli (DC.) Burrill fungus, grey mould (Botrytis cinerea Pers.), root rot (Phytophthora cactorum (Lebert & Cohn) J.Schrot.) and powdery mildew (Oidium tuckeri Berkeley), as well as higher fruit quality. In citruses — resistance to bacterial canker (Xanthomonas citri sub sp.), citrus ulcer (Xanthomonas axonopodis pv citri), greening disease (Huanglongbing (HLB)) and fungi (Trichoderma harzianum Rifai). In tropical crops — resistance to papaya ringspot (PRSV) and banana streak (eBSV) viruses. Unique FT-phenotype transgenic fruit lines are leveraged in the new FasTrack breeding strategy. Nine fruit and berry transgenic crop lines have now been registered worldwide. Transgenic Arctic apples (Golden, Granny, Fuji), plums (Honey Sweet) and papaya (Rainbow, SunUp, Laie Gold) are industry-approved in fresh and processed form. The transgenic list regulated in the Russian Federation does not include fruit or berry crops.

Compost topdressing to suppress necrotic ringspot and improve the overall health of Kentucky bluegrass lawns

AbstractA study was conducted in northern Colorado to evaluate the effectiveness of two compost products on the improvement of turfgrass color and quality, necrotic ringspot (NRS) disease suppression, and thatch reduction. Two Kentucky bluegrass (Poa pratensis L.) home lawns with a history of NRS were chosen for the study. Treatments were applied twice during the 2018 growing season after all plots were aerated and consisted of (a) inoculated compost topdressing at a rate of 66 m3 ha–1, (b) dairy manure compost topdressing at a rate of 66 m3 ha–1, (c) urea fertilizer at 49 kg N ha–1, and (d) a control (aeration only with no fertilizer or compost applied). Data were collected every 2 wk from May to October in 2018, and included the percentage of disease‐affected turf, and turfgrass color and quality. Thatch depth was measured monthly. The inoculated and conventional compost plots had less disease than the control, and the inoculated compost showed significant disease suppression earlier than conventional compost. Season‐long averages showed that the plots treated with either of the compost products had better color and turf quality than the control. When data were pooled over the course of the growing season, there were no significant differences between the two compost treatments with regard to NRS disease severity or quality. Thatch depth in plots that received inoculated compost was 17% less than in plots that received conventional compost and fertilizer. This study demonstrated that compost decreased NRS incidence and improved turf color and quality.

Evaluation of Eggplant Cultivars for Tomato Spotted Wilt Orthotospovirus (TSWV) Disease Tolerance in Greenhouse Conditions

Eggplant (Solanum melongena L.) is widely consumed vegetables like potato and tomato. Worldwide, the eggplant is cultivated in all regions and Turkey is the fourth largest eggplant-producer. It is a rich source of minerals and as a low-calorie fruit. Eggplant plays a vital role having high phenolic content which enhance the radical absorbing capacity. Objective of this study was to evaluate the effect of tomato spotted wilt orthotospovirus (TSWV) on five different eggplant cultivars (Kemer, Aydın Siyahı, Halep Karası, Topan and Silindirik) under greenhouse conditions. Eggplant cultivars were mechanically inoculated with TSWV isolates and tested by DAS-ELISA method. According to DAS-ELISA and visible virus-like symptoms, all tested cultivars were susceptible to TSWV infection and showed typical tospo-like symptoms including concentric ringspot, necrosis, chlorotic ringspot, and necrotic ringspot. The highest infection rate was observed in Kemer (58%) followed by Topan (52%) whereas, the lowest infection rate was noticed in Silindirik (38%). Infection of TSWV caused significant (p≤0.05) reduction in fruit number (32.99-59.34%), fruit length (17.12-49.76%), fruit diameter (12.44-38.30%), fruit weight (31.31-67.70%), flesh thickness (18.11-46.05%), total soluble solid (16.83-40.69%), fruit color, fruit firmness (4.88-29.25%) and yield (50.22-84.22%) in infected plants. According to the results obtained, the cultivar Silindirik performed better performance against TSWV among all the tested cultivars. Whereas the performance of the Kemer and Topan was poor making them more sensitive to TSWV. These results will help breeders for the development of TSWV resistant varieties by using these tolerant cultivars.

A novel high-throughput sequencing approach reveals the presence of a new virus infecting Rosa: rosa ilarvirus-1 (RIV-1)

Roses are one of the most valuable ornamental flowering shrubs grown worldwide. Despite the widespread of rose viruses and their impact on cultivation, they have not been studied in detail in the United Kingdom (UK) since the 1980′s. As part of a survey of rose viruses entering the UK, 35 samples were collected at Heathrow Airport (London, UK) and were tested by RT-qPCR for different common rose viruses. Of the 35 samples tested using RT-qPCR for prunus necrotic ringspot virus (PNRSV; genus Ilarvirus), 10 were positive. Confirmatory testing was performed using RT-PCR with both PNRSV-specific and ilarvirus-generic primers, and diverse results were obtained: One sample was exclusively positive when using the ilarvirus-generic primers, and subsequent sequencing of the RT-PCR product revealed homology to other ilarviruses but not PNRSV. Further work to characterise the virus was performed using high throughput sequencing, both the MinION Flongle and Illumina MiSeq. The sequencing confirmed the presence of a new virus within group 2 of the genus Ilarvirus and we propose the name “rosa ilarvirus-1″ (RIV-1). Here, we describe the identification of a novel virus using the low-cost Flongle flow cell and discuss its potential as a front-line diagnostic tool.

First Report of Little Cherry Virus 1 Infecting Sweet Cherry in Ontario, Canada.

The Niagara fruit belt is one of the richest fruit-producing areas in Canada, contributing to 90% of Ontario's tender fruits such as peach, plum and sweet cherry. Little cherry virus 1 (LCV1) of the genus Velarivirus is a causal agent of little cherry disease which has devastated cherry crops in many regions (Eastwell and Bernardy 1998, Jelkmann and Eastwell, 2011). From 2013 to 2018, foliar symptoms indicative of viral infection such as leaf deformation, ringspot, mottling, vein clearing, and reddening were found on sweet cherry trees grown in the Niagara region. To determine if these trees were infected by a virus, small RNAs (sRNAs) were isolated from separately pooled asymptomatic and symptomatic leaves using the mirPremier microRNA isolation kit (Sigma Aldrich Canada, Oakville, ON). The sRNAs were used to create two libraries (four leaves per library) with the TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA). The sRNA libraries were separately sequenced with the MiSeq Desktop Sequencer (Illumina, San Diego, CA). In total, 5,380,196 reads were obtained and Trimmomatic (Bolger et al. 2014) was used to remove adaptors. The remaining 4,733,804 clean reads were assembled into contigs using Velvet 0.7.31 (Zerbino and Birney, 2008) and Oases 0.2.09 (Schulz et al. 2012) with minimum length of 75 nt (Supplementary Table 1). A BLASTn search (Altschul et al. 1997) of the contigs identified the presence of Cherry virus A (genus: Capillovirus), two members of the Ilarvirus genus (Prunus necrotic ringspot virus and Prune dwarf virus) in both libraries. LCV1 was only found in contigs derived from the symptomatic library. Of the clean reads, 22,016 were assembled into six contigs (with lengths ranging from 86 to 116 nt, Supplementary Table 1) mapping to LCV1, covering 7.07% of the viral genome. To confirm LCV1 infection, primers were designed from the assembled contigs and used for reverse transcription polymerase chain reaction (RT-PCR). Amplicons were sequenced and the terminal sequences were determined using 5' and 3' RACE Systems (Invitrogen, Burlington, ON). Degenerate primers were designed from multiple sequence alignments of published LCV1 genomes for amplification and primer walking to obtain the sequence of LCV1 (Table S2). The complete genome sequence of LCV1 has a length of 16,934 nt and was deposited in GenBank (accession no. MN508820). A BLASTn search showed that this isolate is nearly identical (99.6% sequence identity) to an isolate from California (accession no. MN131067). To determine the incidence of infection, a field survey was performed at the same location during spring months of 2014 to 2018 using RT-PCR with primers specific to the viral coat protein gene (Supplementary Tale 2). Among 46 cherry trees sampled, two (4.3%) trees were infected with LCV1 and showed negative results with CVA, PNRSV and PDV. Both trees displayed mild suturing of primary and secondary veins (Supplementary Figure 1). LCV1 has been identified in Western stone fruit producing regions (British Columbia in Canada, and Washington, California, and Oregon in the United States of America). To the best of our knowledge, this is the first report of LCV1 in any eastern region of Canada. The low incidence of LCV1 suggests that this virus is not widespread in this region. Routine monitoring and detection of LCV1 is required to prevent this devastating cherry disease from spreading in this region.

Plum Pox Virus Strain C Isolates Can Reduce Sour Cherry Productivity.

The impact of plum pox virus (PPV) on sour cherry (Prunus cerasus L.) productivity has been studied by comparing the yield of PPV-infected and PPV-free fruit-bearing trees. A total of 152 16- to 17-year-old trees of nine cultivars and hybrids were surveyed in the production orchards (cultivar collection and hybrid testing plots) in the Republic of Tatarstan, Russia. Sixty trees tested positive for PPV using ELISA and RT-PCR. Among them, 58 PPV isolates belonged to the strain C and the other 2 isolates to the strain CV. For the cultivars Sevastyanovskaya, Shakirovskaya, hybrids 88-2 and 80-8, the average (2012 to 2019) productivity of infected trees was 38% to 45% lower than for PPV-free trees of the same cultivar or hybrid. No ilarviruses (prunus necrotic ringspot virus, prune dwarf virus, apple mosaic virus, American plum line pattern virus) were detected in PPV-infected trees, suggesting that reduced cherry productivity was attributed to the PPV infection. Thus, it was shown for the first time that PPV can reduce the productivity of at least some sour cherry cultivars and hybrids, and strain C isolates are responsible for crop losses.

Biological and Molecular Characterization of Two Closely Related Arepaviruses and Their Antagonistic Interaction in Nicotiana benthamiana.

Previously, our group characterized two closely related viruses from Areca catechu, areca palm necrotic ringspot virus (ANRSV) and areca palm necrotic spindle-spot virus (ANSSV). These two viruses share a distinct genomic organization of leader proteases and represent the only two species of the newly established genus Arepavirus of the family Potyviridae. The biological features of the two viruses are largely unknown. In this study, we investigated the pathological properties, functional compatibility of viral elements, and interspecies interactions in the model plant, Nicotiana benthamiana. Using a newly obtained infectious clone of ANRSV, we showed that this virus induces more severe symptoms compared with ANSSV and that this is related to a rapid virus multiplication in planta. A series of hybrid viruses were constructed via the substitution of multiple elements in the ANRSV infectious clone with the counterparts of ANSSV. The replacement of either 5′-UTR-HCPro1–HCPro2 or CI effectively supported replication and systemic infection of ANRSV, whereas individual substitution of P3-7K, 9K-NIa, and NIb-CP-3′-UTR abolished viral infectivity. Finally, we demonstrated that ANRSV confers effective exclusion of ANSSV both in coinfection and super-infection assays. These results advance our understanding of fundamental aspects of these two distinct but closely related arepaviruses.

First report of Rose leaf rosette-associated virus infecting rose (Rosa spp.) in California, USA.

Rose leaf rosette-associated virus (RLRaV) is a member of genus Closterovirus, family Closteroviridae. The virus was first discovered in China in 2015 from a mixed infected wild rose (Rosa multiflora Thunb.) showing small leaf rosettes on branches, dieback and severe decline symptoms (He et al. 2015). In 2013, a rose plant (cv. Roses Are Red) was introduced to Foundation Plant Services (FPS, UC-Davis) rose collection. The plant was originated from a private rose breeder collection located in California. In 2019, total nucleic acids (TNA) were isolated from leaf tissues of one asymptomatic plant (Roses Are Red plant) using MagMax Plant RNA Isolation Kit (Thermo Fisher Scientific, USA). Extracted TNA were screened by reverse-transcription quantitative PCR (RT-qPCR) for six common viruses infecting roses, including prunus necrotic ringspot virus (PNRSV), apple mosaic virus (ApMV), rose spring dwarf associated virus (RSDaV), rose yellow vein virus (RYVV), rose rosette virus (RRV), and blackberry chlorotic ringspot virus (BCRV); however, the results were negative. Therefore, the sample was subjected to high throughput sequencing (HTS). Briefly, TNA was depleted of rRNA and advanced for cDNA library preparation using TruSeq Stranded Total RNA kit (Illumina, USA). HTS was performed on Illumina NextSeq 500 platform. The raw reads were trimmed, de novo assembled, and subsequently were annotated using tBLASTx algorithm (Al Rwahnih et al. 2018). HTS generated 23.6 million 75 nucleotide (nt) single-end raw data reads. De novo assembly generated a contig (16,528 nts) resembling RLRaV reference sequence (KJ748003) with 74% identity at the nucleotide level. Putative coat protein and heat shock protein 70-like protein were identified based on >90% identity with RLRaV genes. To confirm HTS results, RT-PCR was performed using two primer sets, 1) Clo-F4916 (5'-GGTGTTCCAACGCTATCGTG-3') and Clo-R5215 (5'- TGTCCTCAAACCGCCTACAT-3') targeting nucleotide sequences of putative polyprotein 1a, and 2) Clo-F10006 (5'-GATTCCGCGGACGAATTAAT-3') and Clo-R10311 (5'-GGTAACCGAAAGGTAAAGTATTC-3') targeting nucleotide sequences of putative protein p25. The RLRaV amplicons with expected size of 300 nt were confirmed using bidirectional Sanger sequencing. The near-complete sequence of the new RLRaV isolate was deposited in GenBank under accession number MW056181. In addition, HTS analysis showed that RLRaV was in mixed infection with two mycoviruses (rose cryptic virus with 8,267 mapped reads and rose partitivirus with 7,283 mapped readss). To our knowledge, this is the first report of RLRaV affecting roses in California. Further research is needed to determine the prevalence of RLRaV in California as well as evaluation of RLRaV effect on rose performance.

Molecular and Biological Characterization of Recombinant Isolates of Potato virus Y Circulating in Potato Fields in Mexico.

Potato virus Y (PVY) is a significant threat to potato (Solanum tuberosum) production in Mexico. The presence of recombinant strains of PVY circulating in potato has been reported in the country, but no systematic study on the genetic diversity of PVY in potato and prevalence of PVY strains has been conducted yet. We report on a series of surveys in seed potato production areas in two states in Mexico, namely, Chihuahua and Jalisco, between 2011 and 2019. PVY was detected through the period of nine years in multiple potato cultivars in both states, often remaining asymptomatic in the most popular cultivars, such as 'Fianna' and 'Agata'. When typed to strain, all PVY samples studied were found to have N-serotype, and were all identified molecularly as isolates of the same recombinant strain, PVYNTN. Five of these PVY isolates were tested on tobacco (Nicotiana tabacum), where they induced vein necrosis supporting the molecular typing. This identification was also confirmed biologically on differential potato cultivars, where one PVYNTN isolate from the 2013 survey triggered the hypersensitive resistance conferred by the Nztbr gene in the cv. Maris Bard. Seven of these Mexican PVYNTN isolates, collected between 2013 and 2019, including two PVY isolates from potato tubers exhibiting potato tuber necrotic ringspot disease, were subjected to whole genome sequencing and found to show a typical PVYNTNa recombinant structure. When subjected to phylogenetic analysis, Mexican PVYNTN sequences clustered in more than three separate clades, suggesting multiple introductions of PVYNTN in the country. The wide circulation of the PVYNTN strain in Mexican potato should be considered by potato producers, to develop mitigation strategies for this PVY strain associated with tuber necrotic symptoms.

Development of a reverse transcription droplet digital PCR assay for sensitive detection of peach latent mosaic viroid

Peach latent mosaic viroid (PLMVd) represents a continuing threat to peach tree production worldwide. In this study, a sensitive and accurate quantification of PLMVd in peach leaves was established using a reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) assay. The quantitative linearity, accuracy, and sensitivity of RT-ddPCR for the detection of PLMVd were comparatively assessed to those of reverse-transcription real-time quantitative polymerase chain reaction (RT-qPCR) assay. The specificity assay shows no amplification in major peach viruses, apple chlorotic leaf spot virus and prunus necrotic ring spot virus and negative control. Furthermore, the levels of PLMVd transcripts determined using RT-ddPCR and RT-qPCR showed a high degree of linearity and quantitative correlation. Our results also indicated that the RT-ddPCR assay is at least two-fold more sensitive than qPCR and could therefore, be used to detect PLMVd in field samples. Moreover, optimization of RT-ddPCR was found to enhance the sensitivity of PLMVd detection in the peach leaf samples with low viral loads. In summary, the established RT-ddPCR assay represents a promising alternative method for the precise quantitative detection of PLMVd; it would be particularly applicable for diagnosing PLMVd infections in plant quarantine inspection and PLMVd-free certification program.

Molecular characterization of cherry virus a and prunus necrotic ringspot virus and their variability based on nucleotide polymorphism

A survey was conducted to know the incidence of viruses in apricot growing in the Srinagar and Shopian regions of Jammu and Kashmir during May 2015. A total of 52 leaf samples were obtained and virus infection was confirmed using nucleic acid spot hybridization (NASH) and reverse transcription-polymerase chain reaction (RT-PCR). The infectivity of cherry virus A (CVA) and prunus necrotic ringspot virus (PNRSV) was found to be 44% and 98% by NASH and 36% and 77% by RT-PCR, respectively. Based on the sequence variability of RdRp, CVA isolates found globally have been grouped into six phylogroups (Group 1–6), whereas PNRSV isolates from India have been divided into three phylogroups (Group 1, Group 2A and Group 2B) based on coat protein gene. Our findings prove that PNRSV and CVA are the two significant viruses of apricot, with PNRSV being the leading cause of apricot necrosis in old orchards.