Occurrence and Molecular Variability of Kiwifruit Viruses in Actinidia deliciosa 'Xuxiang' in the Shaanxi Province of China

Rapid and Visual Detection of Actinidia Chlorotic Ringspot-Associated Virus Using One-Step Reverse-Transcription Recombinase Polymerase Amplification Combined with Lateral Flow Dipstick Assay

Actinidia chlorotic ringspot-associated virus (AcCRaV) occurs widely in major kiwifruit producing areas of China and is often accompanied by coinfecting viruses, affecting the growth, yield, and quality of kiwifruit. Therefore, a rapid and sensitive detection method is crucial for diagnosing and developing effective AcCRaV management strategies. In this study, a one-step reverse-transcription recombinase polymerase amplification combined with a lateral flow dipstick (RT-RPA-LFD) assay was developed for rapid detection of AcCRaV. Specific primers and a probe were designed based on the conserved region of the coat protein gene sequence of AcCRaV. The one-step RT-RPA reaction can be performed at 35 and 40°C within 10 to 30 min, and the amplification results can be read directly on the LFD within 5 min. The detection limit of the one-step RT-RPA-LFD assay was 10-8 ng (about 20 viral copies), which was equal with one-step RT-qPCR and 100 times more sensitive than one-step RT-PCR. Moreover, the one-step RT-RPA-LFD assay was successfully applied to detect AcCRaV from crude extracts, and the entire detection process can be completed within 40 min. These results indicate that the RT-RPA-LFD assay is a simple, rapid, and sensitive strategy that can be used for accurate diagnosis of AcCRaV-infected kiwifruit plants in the field. To our knowledge, this is the first study applying the one-step RT-RPA-LFD assay to detect a kiwifruit virus.

Discovery of a Closterovirus Infecting Jujube Plants Grown at Aksu Area in Xinjiang of China

Chinese jujube (Ziziphus jujuba Mill.) is a widely grown fruit crop at Aksu in Xinjiang Uygur Autonomous Region of China. Viral disease-like symptoms are common on jujube plants. Here, for the first time, we report a virus tentatively named persimmon ampelovirus jujube isolate (PAmpV-Ju) infecting jujube plants. The virus was identified using high-throughput sequencing from a jujube plant (ID: AKS15) and molecularly related to viruses in the family Closteroviridae. The genomic sequences of two PAmpV-Ju variants named AKS15-20 and AKS15-17 were determined by RT-PCR amplifications. The genome structure of PAmpV-Ju was identical to that of a recently reported persimmon ampelovirus (PAmpV) and consisted of seven open reading frames. The genomes of AKS15-20 and AKS15-17 shared 83.7% nt identity with each other, and the highest nt sequence identity of 79% with two variants of PAmpV. The incidence of PAmpV-Ju on Aksu jujube plants was evaluated by RT-PCR assays. The phylogenetic analysis of amplified partial sequences coding for polymerase, HSP70h, and CP revealed two phylogenetic clades represented by AKS15-20 and AKS15-17. Our study provides important evidence for understanding viruses infecting jujube plants and establishing efficient measures to prevent virus spread.

Efficient Elimination of Actinidia Chlorotic Ringspot-Associated Virus from Infected Kiwifruit Shoots Cultured In Vitro

In this study, methods of Actinidia chlorotic ringspot-associated virus (AcCRaV) elimination by shoot tip culture, thermotherapy followed by shoot tip culture, and chemotherapy followed by shoot tip culture were explored. The results showed that the AcCRaV elimination rate was 23.3% when the secondary shoot tip culture method was used and when the shoot tip length was less than 0.5 mm. The AcCRaV elimination rate was 100% when thermotherapy (36°C [day] and 32°C [night]) was applied for 20 days followed by shoot tip culture (shoot tip length less than 1.0 mm). When shoot segments were treated with ribavirin at 15 µg/ml for 2 months followed by shoot tip culture, the elimination rate of AcCRaV was 100% (shoot tip length less than 1.0 mm). When shoot segments were treated with ribavirin at 25 µg/ml for 2 months followed by shoot tip culture, the elimination rate of AcCRaV was 100% (shoot tip length less than 1.5 mm). This is the first report on kiwifruit virus elimination methods.

Viromics Reveals the Viral Diversity in Cultivated and Wild Kiwifruit

China, the center of origin of kiwifruit, has the largest kiwifruit cultivation and production area worldwide, and Shaanxi Province is the major kiwifruit-growing region in China. However, our knowledge of kiwifruit viruses is largely skewed toward their pathology in cultivated orchards, and little is known about viral diversity in wild kiwifruit. To determine the viral diversity in cultivated and wild kiwifruit, 32 cultivated kiwifruit samples from Shaanxi Province and 30 wild kiwifruit samples from the Qinling Mountains were collected and subjected to high-throughput sequencing in this study. Eleven known viruses were found among the 32 cultivated kiwifruit samples, and 8 known viruses and 2 new viruses were found among the 30 wild kiwifruit samples. One of the two new viruses, Actinidia yellowing virus 3 (AcYV3), a member of the genus Idaeovirus, may be associated with severe yellowing of kiwifruit leaves. In addition, more than 50 nearly full-length genome sequences of known viruses were obtained. The detection rates, recombination, and molecular variation of these viruses were further analyzed. The results obtained in this study provide valuable information for understanding the virome of cultivated and wild kiwifruit.

Occurrence and Molecular Variability of the Main Kiwifruit Viruses in the Sichuan Province of China

Viruses cause important yield losses in kiwifruit. Here, we studied the occurrence and population structure of the major kiwifruit viruses in the Sichuan province of China. RT-PCR results showed the presence of Actinidia virus A (AcVA), Actinidia virus B (AcVB), Actinidia chlorotic ringspot-associated virus (AcCRaV), and the cucumber mosaic virus (CMV). AcCRaV was widely distributed, followed by CMV. These two viruses were often detected in co-infection with AcVA and AcVB. The virus detection rate was positively correlated with vine age. Four phylogenetic groups of AcVA and AcVB were identified, with AcVA isolates clustering mainly in subgroup I, and AcVB isolates clustering mainly in subgroups II, III, and IV. All CMV isolates clustered in subgroup II, and AcCRaV isolates clustered in subgroup IA. The genome of AcVA and AcCRaV was under negative selection pressure, while the genome of AcVB and CMV was under positive selection pressure. All the viruses, except AcVB, were in a state of expansion. The full-length genome of the most widely distributed AcCRaV isolate in kiwifruits in the Sichuan province was characterized by sequencing. Unique eight-nucleotide (TTTTTGAT) repeats were found in the 5'-terminal non-coding region of the AcCRaV RNA3 in a possible association with reduced disease symptoms. This is the first study of kiwifruit viruses in Sichuan.

Advances in and Prospects for Actinidia Viruses

Kiwifruit (Actinidia spp.) is an economically important fruit crop worldwide. Before 2010, kiwifruit viruses had not received much attention; since then, more than 20 viruses infecting kiwifruit have been discovered. Some of these viruses cause severe yellowing, mosaic, necrosis, ringspots, and other symptoms on leaves, seriously impacting yield and quality. Many of these viruses are widely distributed. This review summarizes recent research advances in the identification, genomic variation, distribution, transmission, detection, incidence, prevention, and control of kiwifruit viruses and proposes directions for future research. Using virus-tested propagation material is the most economical and effective method for controlling kiwifruit viruses.

Effects of Actinidia Yellowing Ringspot Virus on the Yield and Quality of Kiwifruit

China is the origin and distribution center of kiwifruit, as well as the country with the largest cultivated area and output of kiwifruit. A previous study found that a new kiwifruit virus, Actinidia yellowing ringspot virus (AYRSpV), has been detected in kiwifruit samples with yellowed leaves. The incidence of this virus was high in kiwifruit plantings in Shaanxi Province. To determine the symptoms of this viral infection and the effects of this virus on the yield and quality of kiwifruit, we measured leaf chlorophyll levels and the fruit yield, total sugar, total acid, and dry matter contents of 'Hayward' kiwifruit grafted with AYRSpV-infected scions. The results showed that, after AYRSpV infection, symptoms including chlorotic ringspots were mainly observed in the spring and gradually recovered with high summer temperatures. A few of the leaves that did not recover showed symptoms of albinism, which lasted until the leaves fell. We found that AYRSpV infection could reduce the chlorophyll content of Hayward kiwifruit by 74.61 to 76.64%, fruit yield by 14.50 to 24.10%, sugar-to-acid ratio by 50.09 to 50.57%, and fruit dry matter content by 1.67 to 1.78%. Our results showed that AYRSpV infection could significantly affect the yield and quality of Hayward kiwifruit.

A Comparative Analysis of the Microbiome of Kiwifruit at Harvest Under Open-Field and Rain-Shelter Cultivation Systems

The composition of microbial communities can directly affect fruit quality, health status, and storability. The present study characterized the epiphytes and endophytes of “Hongyang” and “Cuiyu” kiwifruit at harvest under grown under open-field (OF) and rain-shelter (RS) cultivation systems. Disease incidence in kiwifruit was significantly lower (p < 0.05) under the RS system than it was under the OF system. High-throughput sequencing [16S V3-V4 ribosomal region and the fungal internal transcribed spacer (ITS2)] was conducted to compare the composition of the epiphytic and endophytic microbial community of kiwifruit under the two cultivation systems. Results indicated that the abundance of Actinobacteria, Bacteroidetes, Enterobacteriales, Acetobacterales, Sphingomonas, Pseudomonas, and Sphingobacterium was higher under the RS system, relative to the OF system, while the abundance of Capnodiales, Hypocreales, Vishniacozyma, and Plectosphaerella was also higher under the RS system. Some of these bacterial and fungal taxa have been reported to as act as biocontrol agents and reduce disease incidence. Notably, the α-diversity of the epiphytic bacterial and fungal communities on kiwifruit was higher under RS cultivation. In summary, RS cultivation reduced natural disease incidence in kiwifruit, which may be partially attributed to differences in the structure and composition of the microbial community present in and on kiwifruit.

A novel Actinidia cytorhabdovirus characterized using genomic and viral protein interaction features

A novel cytorhabdovirus, tentatively named Actinidia virus D (AcVD), was identified from kiwifruit (Actinidia chinensis) in China using high-throughput sequencing technology. The genome of AcVD consists of 13,589 nucleotides and is organized into seven open reading frames (ORFs) in its antisense strand, coding for proteins in the order N-P-P3-M-G-P6-L. The ORFs were flanked by a 3' leader sequence and a 5' trailer sequence and are separated by conserved intergenic junctions. The genome sequence of AcVD was 44.6%-51.5% identical to those of reported cytorhabdoviruses. The proteins encoded by AcVD shared the highest sequence identities, ranging from 27.3% (P6) to 44.5% (L), with the respective proteins encoded by reported cytorhabdoviruses. Phylogenetic analysis revealed that AcVD clustered together with the cytorhabdovirus Wuhan insect virus 4. The subcellular locations of the viral proteins N, P, P3, M, G, and P6 in epidermal cells of Nicotiana benthamiana leaves were determined. The M protein of AcVD uniquely formed filament structures and was associated with microtubules. Bimolecular fluorescence complementation assays showed that three proteins, N, P, and M, self-interact, protein N plays a role in the formation of cytoplasm viroplasm, and protein M recruits N, P, P3, and G to microtubules. In addition, numerous paired proteins interact in the nucleus. This study presents the first evidence of a cytorhabdovirus infecting kiwifruit plants and full location and interaction maps to gain insight into viral protein functions.

Occurrence and Distribution of Actinidia Viruses in Shaanxi Province of China

Kiwifruit (Actinidia spp.) is an economically important fruit crop globally. China is the largest kiwifruit-growing country in the world, and Shaanxi Province is the major kiwifruit-growing region in China. A systematic survey detected various symptoms in kiwifruit plants grown in a commercial kiwifruit field in Shaanxi Province. Samples were collected from kiwifruit plants showing symptoms and used for virus detection by high-throughput sequencing. In addition to 10 known kiwifruit viruses, three new viruses were detected and tentatively named Actinidia yellowing ringspot virus (AYRSpV), Actinidia yellowing virus 1 (AcYV1), and Actinidia yellowing virus 2 (AcYV2). The genome sequences of the three new viruses and four known viruses were determined. Based on the demarcation criteria of the International Committee on Taxonomy of Viruses, AYRSpV might be a new member of the genus Ilarvirus in the family Bromoviridae, AcYV1 might be a new virus of the genus Waikavirus in the family Secoviridae, and AcYV2 might be a novel virus in the family Tombusviridae. Spherical viral particles were found in the samples infected with AYRSpV, AcYV1, and AcYV2 by transmission electron microscopy. Further analysis showed that all 13 viruses can infect both Actinidia deliciosa and A. chinensis but the incidences of these infections vary among different kiwifruit cultivars in different regions. These results provide valuable information for understanding the virome of kiwifruit in China.

Next-Generation Sequencing Combined With Conventional Sanger Sequencing Reveals High Molecular Diversity in Actinidia Virus 1 Populations From Kiwifruit Grown in China

Kiwifruit (Actinidia spp.) is native to China. Viral disease–like symptoms are common on kiwifruit plants. In this study, six libraries prepared from total RNA of leaf samples from 69 kiwifruit plants were subjected to next-generation sequencing (NGS). Actinidia virus 1 (AcV-1), a tentative species in the family Closteroviridae, was discovered in the six libraries. Two full-length and two near-full genome sequences of AcV-1 variants were determined by Sanger sequencing. The genome structure of these Chinese AcV-1 variants was identical to that of isolate K75 and consisted of 12 open reading frames (ORFs). Analyses of these sequences together with the NGS-derived contig sequences revealed high molecular diversity in AcV-1 populations, with the highest sequence variation occurring at ORF1a, ORF2, and ORF3, and the available variants clustered into three phylogenetic clades. For the first time, our study revealed different domain compositions in the viral ORF1a and molecular recombination events among AcV-1 variants. Specific reverse transcriptase–polymerase chain reaction assays disclosed the presence of AcV-1 in plants of four kiwifruit species and unknown Actinidia spp. in seven provinces and one city.

Is There a "Biological Desert" With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses

High throughput sequencing technologies accelerated the pace of discovery and identification of new viral species. Nevertheless, biological characterization of a new virus is a complex and long process, which can hardly follow the current pace of virus discovery. This review has analyzed 78 publications of new viruses and viroids discovered from 32 fruit tree species since 2011. The scientific biological information useful for a pest risk assessment and published together with the discovery of a new fruit tree virus or viroid has been analyzed. In addition, the 933 publications citing at least one of these original publications were reviewed, focusing on the biology-related information provided. In the original publications, the scientific information provided was the development of a detection test (94%), whole-genome sequence including UTRs (92%), local and large-scale epidemiological surveys (68%), infectivity and indicators experiments (50%), association with symptoms (25%), host range infection (23%), and natural vector identification (8%). The publication of a new virus is cited 2.8 times per year on average. Only 18% of the citations reported information on the biology or geographical repartition of the new viruses. These citing publications improved the new virus characterization by identifying the virus in a new country or continent, determining a new host, developing a new diagnostic test, studying genome or gene diversity, or by studying the transmission. Based on the gathered scientific information on the virus biology, the fulfillment of a recently proposed framework has been evaluated. A baseline prioritization approach for publishing a new plant virus is proposed for proper assessment of the potential risks caused by a newly identified fruit tree virus.

Molecular characterization of a novel emaravrius infecting Actinidia spp. in China

Viruses in the genus Emaravirus contain 5-8 negative genomic RNAs and cause severe diseases of plants. In this study, a novel emaravirus, provisionally named Actinidia emaravirus 2 (AcEV-2), was identified from a kiwifruit tree showing leaf mottle and chlorosis symptoms. The genome of AcEV-2 consisted of at least six RNAs (RNAs 1-6) with sizes of 7079, 2252, 1387, 1514, 1744 and 1233 nucleotides (nts), respectively. Proteins encoded by RNAs1-4 of AcEV-2 shared the highest amino acid (aa) sequence identities of 62.2%-77.3% with the corresponding proteins of fig mosaic emaravirues (FMV) and pigeonpea sterility mosaic emaravirus 2 (PPSMV-2). Whilst, the P5 and P6 encoded by AcEV-2 exhibited the highest identities of 44.2% and 39.2% with the corresponding proteins of PPSMV-2. It was the second emaravirus infecting Actinidia trees in China. Preliminary virus detection disclosed the presence of AcEV-2 in three Actinidia species grown in three provinces in the central and southern China.