Combined DECS Analysis and Next-Generation Sequencing Enable Efficient Detection of Novel Plant RNA Viruses

Identification of a novel viral factor inducing tumorous symptoms by disturbing vascular development in planta

Plant viruses induce various disease symptoms that substantially impact agriculture, but the underlying mechanisms of viral disease in plants are poorly understood. Kobu-sho is a disease in gentian that shows gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Here, we show that a gene fragment of gentian Kobu-sho-associated virus, which is designated as Kobu-sho-inducing factor (KOBU), induces gall formation accompanied by ectopic development of lignified cells and xylem-like tissue in Nicotiana benthamiana. Transgenic gentian expressing KOBU exhibited tumorous symptoms, confirming the gall-forming activity of KOBU. Surprisingly, KOBU expression can also induce differentiation of an additional leaf-like tissue on the abaxial side of veins in normal N. benthamiana and gentian leaves. Transcriptome analysis with Arabidopsis thaliana expressing KOBU revealed that KOBU activates signaling pathways that regulate xylem development. KOBU protein forms granules and plate-like structures and co-localizes with mRNA splicing factors within the nucleus. Our findings suggest that KOBU is a novel pleiotropic virulence factor that stimulates vascular and leaf development. IMPORTANCE While various mechanisms determine disease symptoms in plants depending on virus-host combinations, the details of how plant viruses induce symptoms remain largely unknown in most plant species. Kobu-sho is a disease in gentian that shows gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Our findings demonstrate that a gene fragment of gentian Kobu-sho-associated virus (GKaV), which is designated as Kobu-sho-inducing factor, induces the gall formation accompanied by the ectopic development of lignified cells and xylem-like tissue in Nicotiana benthamiana. The molecular mechanism by which gentian Kobu-sho-associated virus induces the Kobu-sho symptoms will provide new insight into not only plant-virus interactions but also the regulatory mechanisms underlying vascular and leaf development.

How do emerging long-read sequencing technologies function in transforming the plant pathology research landscape?

Long-read sequencing technologies are revolutionizing the sequencing and analysis of plant and pathogen genomes and transcriptomes, as well as contributing to emerging areas of interest in plant-pathogen interactions, disease management techniques, and the introduction of new plant varieties or cultivars. Long-read sequencing (LRS) technologies are progressively being implemented to study plants and pathogens of agricultural importance, which have substantial economic effects. The variability and complexity of the genome and transcriptome affect plant growth, development and pathogen responses. Overcoming the limitations of second-generation sequencing, LRS technology has significantly increased the length of a single contiguous read from a few hundred to millions of base pairs. Because of the longer read lengths, new analysis methods and tools have been developed for plant and pathogen genomics and transcriptomics. LRS technologies enable faster, more efficient, and high-throughput ultralong reads, allowing direct sequencing of genomes that would be impossible or difficult to investigate using short-read sequencing approaches. These benefits include genome assembly in repetitive areas, creating more comprehensive and exact genome determinations, assembling full-length transcripts, and detecting DNA and RNA alterations. Furthermore, these technologies allow for the identification of transcriptome diversity, significant structural variation analysis, and direct epigenetic mark detection in plant and pathogen genomic regions. LRS in plant pathology is found efficient for identifying and characterization of effectors in plants as well as known and unknown plant pathogens. In this review, we investigate how these technologies are transforming the landscape of determination and characterization of plant and pathogen genomes and transcriptomes efficiently and accurately. Moreover, we highlight potential areas of interest offered by LRS technologies for future study into plant-pathogen interactions, disease control strategies, and the development of new plant varieties or cultivars.

Complete genome sequence of vallota mosaic virus detected in a narcissus bulb imported from the United States to Japan

Narcissus (Narcissus albidus) imported from the United States exhibited leaf chlorosis during post-entry quarantine. We employed next-generation sequencing (NGS) on symptomatic leaf samples and detected vallota mosaic virus (ValMV), belonging to the genus Potyvirus, family Potyviridae, as the viral agent. Sanger sequencing of PCR products and rapid amplification of cDNA ends based on NGS contigs revealed that ValMV is 9,451 nucleotides (nt) in length, excluding the poly(A) tail. Nucleotide and amino acid (aa) sequences of the coat protein region had over 98% identity to previously reported ValMV isolates. In each of the 10 regions encoding mature proteins, however, the sequence identity to other potyviruses was 49.5-71.9% nt and 18.3-78.9% aa, values that are below the species demarcation thresholds for the family Potyviridae. Phylogenetic analysis revealed that our ValMV isolate is most closely related to known ValMV isolates and is grouped with other potyviruses. Taken together, our results indicate that the newly isolated ValMV belongs to a distinct species in the genus Potyvirus. This study provides the first report of the complete ValMV genome sequence and the first record of this virus in narcissus.

Known and New Emerging Viruses Infecting Blueberry

Blueberry (Vaccinium spp.) plants are exposed to existing and emerging viruses as a result of expanding acreage of blueberry plantations across the world, primarily in North America. Since blueberry is cultivated in areas where there are wild Vaccinium spp., there is increasing risk of virus movement between wild and cultivated blueberries. This is theoretically possible because viruses can spread from commercial cultivars to native species and vice versa causing the spread of existing and new viruses. The occurrence of these viruses in blueberry can be devastating to the industry considering the cost for cultivation and production of this perennial crop. However, the advent of high-throughput sequencing and bioinformatic sequence analysis have allowed for rapid identification of known and novel viruses in any crop including blueberry, thus facilitating proper intervention in response to serious viral diseases. In this paper, we aim to focus on the current status of known and novel viruses emerging in blueberry worldwide, which may impact the blueberry industry.

DsRNA Sequencing for RNA Virus Surveillance Using Human Clinical Samples

Although viruses infect various organs and are associated with diseases, there may be many unidentified pathogenic viruses. The recent development of next-generation sequencing technologies has facilitated the establishment of an environmental viral metagenomic approach targeting the intracellular viral genome. However, an efficient method for the detection of a viral genome derived from an RNA virus in animal or human samples has not been established. Here, we established a method for the efficient detection of RNA viruses in human clinical samples. We then tested the efficiency of the method compared to other conventional methods by using tissue samples collected from 57 recipients of living donor liver transplantations performed between June 2017 and February 2019 at Kyushu University Hospital. The viral read ratio in human clinical samples was higher by the new method than by the other conventional methods. In addition, the new method correctly identified viral RNA from liver tissues infected with hepatitis C virus. This new technique will be an effective tool for intracellular RNA virus surveillance in human clinical samples and may be useful for the detection of new RNA viruses associated with diseases.

Complete genome sequences of anemone mosaic virus and ranunculus mild mosaic virus isolated from anemone imported from the Netherlands into Japan

Anemone mosaic virus (AnMV) and ranunculus mild mosaic virus (RanMMV) infect anemone plants, which exhibit characteristic mosaic patterns on their leaves. Employing next-generation sequencing of plant material imported from the Netherlands, the complete genome sequences of these two viruses were determined for the first time. AnMV and RanMMV have 9698 and 9537 nucleotides (nt), respectively, excluding the poly(A) tail. They share 80.0%/82.0% and 98.0%/97.0% nt/amino acid (aa) sequence identity, which is above the species demarcation value, in the previously reported AnMV and RanMMV coat protein sequences, but they share 69.0%/70.0% nt/aa sequence identity or less with other potyviruses in all 10 mature protein coding regions of the genome. Additionally, phylogenetic analysis confirmed the relationship of the AnMV and RanMMV genome sequences to previously reported partial sequences and placed them within the genus Potyvirus. These results show that these two viruses represent separate species within the genus Potyvirus.

Comparative study on three viral enrichment approaches based on RNA extraction for plant virus/viroid detection using high-throughput sequencing

High-throughput sequencing (HTS) has become increasingly popular as virus diagnostic tool. It has been used to detect and identify plant viruses and viroids in different types of matrices and tissues. A viral sequence enrichment method prior to HTS is required to increase the viral reads in the generated data to ease the bioinformatic analysis of generated sequences. In this study, we compared the sensitivity of three viral enrichment approaches, i.e. double stranded RNA (dsRNA), ribosomal RNA depleted total RNA (ribo-depleted totRNA) and small RNA (sRNA) for plant virus/viroid detection, followed by sequencing on MiSeq and NextSeq Illumina platforms. The three viral enrichment approaches used here enabled the detection of all viruses/viroid used in this study. When the data was normalised, the recovered viral/viroid nucleotides and depths were depending on the viral genome and the enrichment method used. Both dsRNA and ribo-depleted totRNA approaches detected a divergent strain of Wuhan aphid virus 2 that was not expected in this sample. Additionally, Vicia cryptic virus was detected in the data of dsRNA and sRNA approaches only. The results suggest that dsRNA enrichment has the highest potential to detect and identify plant viruses and viroids. The dsRNA approach used here detected all viruses/viroid, consumed less time, was lower in cost, and required less starting material. Therefore, this approach appears to be suitable for diagnostics laboratories.

dsRNA-Seq: Identification of Viral Infection by Purifying and Sequencing dsRNA

RNA viruses are a major source of emerging and re-emerging infectious diseases around the world. We developed a method to identify RNA viruses that is based on the fact that RNA viruses produce double-stranded RNA (dsRNA) while replicating. Purifying and sequencing dsRNA from the total RNA isolated from infected tissue allowed us to recover dsRNA virus sequences and replicated sequences from single-stranded RNA (ssRNA) viruses. We refer to this approach as dsRNA-Seq. By assembling dsRNA sequences into contigs we identified full length or partial RNA viral genomes of varying genome types infecting mammalian culture samples, identified a known viral disease agent in laboratory infected mice, and successfully detected naturally occurring RNA viral infections in reptiles. Here, we show that dsRNA-Seq is a preferable method for identifying viruses in organisms that don’t have sequenced genomes and/or commercially available rRNA depletion reagents. In addition, a significant advantage of this method is the ability to identify replicated viral sequences of ssRNA viruses, which is useful for distinguishing infectious viral agents from potential noninfectious viral particles or contaminants.

Complete genome sequence of a divergent strain of potato virus P isolated from Solanum tuberosum in Russia

Contigs with sequence similarity to potato virus P (PVP), which belongs to the genus Carlavirus, were identified by high-throughput sequencing analysis in potato tubers collected from a farmer's potato production field in Surazhevka, Artyom, Primorskiy Krai (Russia) in 2018. The complete genome sequence of this virus consisted of 8,394 nucleotides, excluding the poly(A) tail. This is the first report of PVP being detected outside South America. The isolate had high sequence similarity to PVP isolates from Argentina and Brazil, but low sequence similarity was observed in the genes encoding the RNA-dependent RNA polymerase (69% nucleotide sequence identity and 80% amino acid sequence identity) and coat protein (78% nucleotide sequence identity and 89% amino acid sequence identity). Phylogenetic analysis revealed that this PVP-like virus clustered with known PVP isolates but was distinct from them. Comparison of the sequences using the classification criteria of the ICTV indicated that this PVP-like virus is a strain of PVP.

Immunocapture of virions with virus-specific antibodies prior to high-throughput sequencing effectively enriches for virus-specific sequences

Virus discovery based on high-throughput sequencing relies on enrichment for virus sequences prior to library preparation to achieve a sufficient number of viral reads. In general, preparations of double-stranded RNA or total RNA preparations treated to remove rRNA are used for sequence enrichment. We used virus-specific antibodies to immunocapture virions from plant sap to conduct cDNA synthesis, followed by library preparation and HTS. For the four potato viruses PLRV, PVY, PVA and PYV, template preparation by virion immunocapture provided a simpler and less expensive method than the enrichment of total RNA by ribosomal depletion. Specific enrichment of viral sequences without an intermediate amplification step was achieved, and this high coverage of sequences across the viral genomes was important to identify rare sequence variations. Using this approach, the first complete genome sequence of a potato yellowing virus isolate (PYV, DSMZ PV-0706) was determined in this study. PYV can be confidently assigned as a distinct species in the genus Ilarvirus.

Virological and Immunological Outcomes of Coinfections

Coinfections involving viruses are being recognized to influence the disease pattern that occurs relative to that with single infection. Classically, we usually think of a clinical syndrome as the consequence of infection by a single virus that is isolated from clinical specimens. However, this biased laboratory approach omits detection of additional agents that could be contributing to the clinical outcome, including novel agents not usually considered pathogens. The presence of an additional agent may also interfere with the targeted isolation of a known virus. Viral interference, a phenomenon where one virus competitively suppresses replication of other coinfecting viruses, is the most common outcome of viral coinfections. In addition, coinfections can modulate virus virulence and cell death, thereby altering disease severity and epidemiology. Immunity to primary virus infection can also modulate immune responses to subsequent secondary infections. In this review, various virological mechanisms that determine viral persistence/exclusion during coinfections are discussed, and insights into the isolation/detection of multiple viruses are provided. We also discuss features of heterologous infections that impact the pattern of immune responsiveness that develops.

Comparative transcriptome analysis reveals induction of apoptosis in chicken kidney cells associated with the virulence of nephropathogenic infectious bronchitis virus

Avian infectious bronchitis virus (IBV) that causes respiratory and nephritic diseases in chicken is a major poultry pathogen leading to serious economic loss worldwide. The nephropathogenic IBV strains cause nephritis and kidney lesions intrinsically and the pathogenic mechanism is still unclear. In the present study, SPF chicks were infected with three nephropathogenic IBVs of different virulence and their gene expression profiles in chicken kidney were compared at transcriptome level. As a result, 1279 differentially expressed (DE) genes were found in very virulent SCDY2 inoculated group, 145 in virulent SCK2 group and 74 in non-virulent LDT3-A group when compared to mock infected group. Gene Ontology (GO) and KEGG pathway enrichment analysis on SCDY2 group displayed that the up-regulated DE genes were mainly involved in cell apoptosis, and the down-regulated genes were involved in metabolic processes and DNA replication. Protein-Protein Interaction (PPI) analysis showed that DE genes in SCDY2 group formed a network, and the core of the network was composed by cell apoptosis and immune response proteins. The clustering of gene expression profile among the three virus inoculated groups indicated that the majority of up-regulated DE genes on apoptosis in very virulent SCDY2 group were up-regulated more or less in virulent SCK2 group and those down-regulated on innate immune response in SCDY2 group were also down-regulated differently in SCK2 group. In addition, the number of apoptotic cells detected experimentally in kidney tissue were very different among the three virus inoculated groups and were positively accordant with the viral titer, kidney lesions and viral virulence of each group. Taken all together, the present study revealed that virulent nephropathogenic IBV infection modified a number of gene expression and induction of apoptosis in kidney cells may be a major pathogenic determinant for virulent nephropathogenic IBV.

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Genes expression in chicken kidney cells post inoculation of three nephro IBVs was studied by transcriptome analysis.

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DE genes post challenge mainly involved in the pathways of apoptosis, immune response, metabolic and DNA replication.

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Activation of apoptosis and suppression of innate immune response were accordant with the virulence of inoculated IBVs.

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Induction of apoptosis is triggered by suppression of immune response and productive replication of virus post infection.

De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data

Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by de novo transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.