Satsuma Dwarf Virus Research Articles

Distribution and infection rate of satsuma dwarf virus in Mie Prefecture, Japan

Distribution and infection rate of satsuma dwarf virus in Mie Prefecture, Japan

Viral Metatranscriptomic Analysis to Reveal the Diversity of Viruses Infecting Satsuma Mandarin (Citrus unshiu) in Korea.

Citrus cultivation plays a pivotal role, making a significant contribution to global fruit production and dietary consumption. Accurate identification of viral pathogens is imperative for the effective management of plant viral disease in citrus crops. High-throughput sequencing serves as an alternative approach, enabling comprehensive pathogen identification on a large scale without requiring pre-existing information. In this study, we employed HTS to investigate viral pathogens infecting citrus in three different regions of South Korea: Jejudo (Jeju), Wando-gun (Wando), and Dangjin-si (Dangjin). The results unveiled diverse viruses and viroids that exhibited regional variations. Notably, alongside the identification of well-known citrus viruses such as satsuma dwarf virus, citrus tatter leaf virus, and citrus leaf blotch virus (CLBV), this study also uncovered several viruses and viroids previously unreported in Korean citrus. Phylogenetic analysis revealed that majority of identified viruses exhibited the closest affilations with isolates from China or Japan. However, CLBV and citrus viroid-I-LSS displayed diverse phylogenetic positions, reflecting their regional origins. This study advances our understanding of citrus virome diversity and regional dynamics through HTS, emphasizing its potential in unraveling intricate viral pathogens in agriculture. Consequently, it significantly contributes to disease management strategies, ensuring the resilience of the citrus industry.

Major Citrus Viruses in Japan

Citrus species grown in Japan are affected by three major viruses: satsuma dwarf virus (SDV), citrus tatter leaf virus (CTLV, apple stem grooving virus), and citrus tristeza virus (CTV). SDV has spread to other countries, such as China, Korea, and Turkey, apparently through unchecked budwoods and nursery trees; it is natural to assume that some of these contaminated plants harbored CTLV and CTV as well. Thus, citrus viruses in Japan are not only a domestic problem, they are also transboundary threats to agricultural production. This article reviews the occurrence and history of SDV, CTLV, and CTV in Japan as well as recent research developments in Japan and other countries.

Satsuma dwarf virus (dwarf disease of satsuma)

Satsuma dwarf virus (dwarf disease of satsuma)

Pest survey card on Satsuma dwarf virus

This document provides the conclusions of the pest survey card that was prepared in the context of the EFSA mandate on plant pest surveillance (M-2020-0114) at the request of the European Commission. The full pest survey card for the Satsuma dwarf virus is published and available online in the EFSA Plant Pest Survey Cards Gallery at the following link and will be updated whenever new information becomes available: https://arcg.is/1GCW4C0

제주도 온주밀감에 발생하는 주요 감귤 바이러스병 감염 현황

A survey was carried out to determine the distribution of 4 kinds of citrus viruses, Citrus tristeza virus (CTV), Citrus tatter leaf virus (CTLV), Citrus mosaic sadwavirus (CiMV), Satsuma dwarf virus (SDV) in the Citrus unshiu. The samples were harvested from 20 leaves each groove in the Jeju island and analyzed by multiplex PCR. The result showed that 95.5% and 1.5% of 400 trees in 20 grooves were infected with CTV and CTLV, respectively, and SDV or CiMV was not detected in any of the trees tested. The infection rate of CTV was greatly induced and the infection rates of CTLV, SDV, and CiMV were reduced compared to previous survey report in 1999.

First comprehensive sanitary report of citrus-infecting viruses and viroids in Uruguay

Citrus is the highest-value fruit crop in terms of international trade. However, citrus species are susceptible to several diseases caused by different pathogens which directly cause a decrease in production leading to economic losses. In the last half-century, the citrus industry in Uruguay has had a strong socio-economic impact and is also constantly evolving to stay competitive in world markets, by introduction of new varieties and improvement of production practices to obtain high yielding orchards. Nevertheless, despite the existence since 2014 of the Uruguayan National Citrus Sanitary and Certification Program, scarce information is available regarding the virus and viroid status of commercial citrus in Uruguay. The incidence of citrus tristeza virus (CTV), citrus psorosis virus (CPsV), satsuma dwarf virus (SDV), citrus exocortis viroid (CEVd), hop stunt viroid (HSVd), citrus dwarfing viroid (CDVd), citrus bark cracking viroid (CBCVd) and citrus bent leaf viroid (CBLVd) was investigated in this study, as well as CTV genotypes prevalent in the country. Molecular diagnostic assays were used to test 1175 samples including Valencia and Navel sweet oranges, Mandarin hybrids, Clementines and lemons, which were randomly collected from seven citrus-producing provinces. Only 6% of the samples were negative for the pathogens screened, while 93% of them were CTV positive. SDV, CBLVd and CBCVd were not detected. Co-infections were frequently detected, finding plants with up to four simultaneous pathogens, including CTV in all co-infected plants. This is the first comprehensive survey of several citrus-infecting viruses and viroids in Uruguay, as well as a determination of the CTV genotypes prevalent in the country.

Comparison of an Immunochromatographic Assay Kit with DAS-ELISA for Large-Scale Diagnosis and Molecular Discrimination of Satsuma Dwarf Virus Collected from Citrus Orchards

Satsuma dwarf virus (SDV) seriously damages citrus production by reducing the quality and yield of fruit. To avoid contamination with SDV, mother trees are checked to be SDV-free in advance of nursery tree distribution. In this study, we compared an immunochromatographic assay (ICA) kit with double-antibody sandwich enzyme-linked immunosorbent assay (DASELISA) for large-scale diagnosis of SDV in orchardgrown trees in Shizuoka Prefecture, Japan. The two methods gave conflicting results for 11 of 1,705 samples, all of which were negative by DAS-ELISA but positive by ICA. The samples scored as positive by either DASELISA or ICA were analyzed by reverse transcription polymerase chain reaction and all were confirmed to be positive. These results validate the use of ICA as a screening method for large-scale diagnosis. Strain discrimination revealed that 16 of 22 isolates belonged to SDV, while citrus mosaic virus (CiMV) infection only and co-infection (SDV and CiMV) were in a minority.

Complete genome sequences and recombination analysis of three divergent Satsuma dwarf virus isolates

Citrus mosaic virus (CiMV) and navel orange infectious mottling virus (NIMV) are considered strains of satsuma dwarf virus (SDV). To understand the distribution of different isolates of SDV in China, a field survey was conducted, which allowed for the detection of CiMV and NIMV in citrus plants in Zhejiang and Sichuan provinces, respectively. In the present work, two CiMV isolates, including one named CiMV-GTC1 from Goutoucheng sour orange and one named CiMV-SE1 from Setoka tangor, as well as one NIMV isolate named NIMV-EH1 from Ehime-ken No. 38 tangor were, for the first time, fully sequenced. Among the isolates, CiMV-SE1 and CiMV-GTC1 were closely associated with the partial genomes of known CiMV isolates, while NIMV-EH1 was markedly different from known NIMV isolate. Sequence analysis demonstrated that CiMV, NIMV, and SDV shared similar genome organization and high nucleotide identities at the genome level. In addition, phylogenetic reconstruction of the three viruses also suggested a close relationship. Furthermore, recombination analysis provided evidence for their common co-occurrence in nature. These findings contribute significantly to our understanding of the natural evolution of SDV populations and can provide a basis for preventing the spread of different SDV isolates in the main citrus production regions.

First Report of Citrus Chlorotic Dwarf-Associated Virus on Pomelo in Nakhon, Thailand

Citrus chlorotic dwarf disease (CCDD) was first reported in Turkey in the mid-1990s (Korkmaz et al. 1995) and subsequently in China (Guo et al. 2015). Symptoms included various chlorotic patterns, leaf crinkling, and other types of leaf distortion. Currently, CCDD is the most serious citrus disease in Turkey, where severe losses on different species are reported (Loconsole et al. 2012). Citrus chlorotic dwarf-associated virus (CCDaV; family Geminiviridae) is the causal agent of CCDD (Loconsole et al. 2012). In spring 2019, a new disease was observed at some Ruby Green pomelo orchards in Nakhon, Thailand, with symptoms of severe leaf curling, distortion, and chlorosis on young flushes. Approximately 20% of Ruby Green pomelo trees in this area were symptomatic. The budwoods from four symptomatic Ruby Green pomelo plants were grafted onto 15 plants each of healthy Ruby Green pomelo and Sanhongmiyou pomelo (Citrus grandis) plants and covered by insect-proof net. Three months later, the young flushes of these graft-inoculated plants displayed typical symptoms of CCDD. Total DNA extracts (Plant Genomic DNA Extraction Kit; Bioer, Hangzhou, China) were obtained from these symptomatic plants and 45 additional Ruby Green pomelo plants (symptomatic = 16, asymptomatic = 29), which were collected from four orchards in Nakhon. PCR tests were performed with CCDaV-specific primers (sense, 5′-ACAAGACTATCATAGCACGAGACG-3′; and antisense, 5′- TTTGAACTGTTTAAGTCCATCCC-3′) designed based on the conserved region of movement protein (accession no. JQ920490). The expected amplicon (789 bp) was obtained from the symptomatic Ruby Green pomelo samples and identified by BLASTn analysis as specific to CCDaV. All CCDaV-infected plants showed severe leaf curling, distortion, and chlorosis. Furthermore, all the samples tested negative for citrus yellow vein clearing virus, citrus tristeza virus, citrus tatter leaf virus, satsuma dwarf virus, and citrus exocortis viroid by reverse transcription PCR. The complete CCDaV genome was amplified from three randomly collected field samples (Tha1-17, Tha1-19, and Tha30) using two pairs of previously described primers, 1409fw/341rev and 221fw/1542rev (Loconsole et al. 2012). The obtained sequences were deposited in GenBank under accession numbers MN509440 to MN509442. In pairwise comparisons, the three CCDaV isolates from Thailand shared 99.5 to 99.6% complete genome identities with each other and 99.1 to 99.7% identities with corresponding sequences of 12 CCDaV isolates (JQ920490, KF561253, KX840467 to KX840470, and MG566050 to MG566055) previously reported from Turkey and China. Phylogenetic analysis of these 15 genomic sequences showed that the CCDaV isolates from Thailand clustered into the same clade as isolates from Turkey and apart from isolates from China. To our knowledge, this is the first report of CCDaV in Thailand. Our finding emphasizes the need for CCDaV indexing in production and distribution of pathogen-free citrus plants in Thailand.

Symptomatology of Citrus mosaic sadwavirus (CiMV) in Some Citrus Cultivars and Effect of CiMV Infection on Citrus Fruit Quality.

Citrus mosaic sadwavirus (CiMV) is a closely related virus with the Satsuma dwarf virus (SDV) along with Navel orange infectious mottling virus (NIMV), Natsudaidai dwarf virus (NDV), and Hyugagatsu virus (HV). The present study found that the typical symptoms of CiMV-infected citrus fruits include the appearance of dark blue speckles or ringspots on fruit rinds and the browning of oil glands in the spots as rind coloring began. As rind coloring progressed, the spots gradually faded, whereas the browning of the oil glands worsened to the point that the tissues surrounding the oil glands became necrotic. In very early satsuma mandarins (Citrus unshiu ‘Miyamoto Wase’) and ‘Setoka’ cultivar (C. hybrid ‘Setoka’) of late-maturity citrus, the symptomatic fruits were eventually dropped. And in early satsuma mandarin (C. unshiu ‘Miyakawa Wase’), the peel hardness of the virus-infected fruit (1,618.3 ± 305.5, g-force) was more than twice as hard as that of the healthy fruit (636.5 ± 39.1, g-force). The ratio of flesh weight to total fruit weight was higher for the healthy fruit (77.3 ± 1.7%) than for the infected fruit (70.7 ± 0.6) and peel puffing was more severe in the infected fruit (2.9 ± 0.4 mm) than in the healthy fruit (0.9 ± 0.2 mm). The soluble solids content in infected citrus fruits was less values than the healthy fruit by 0.5–1.5 °Brix. These findings reveal that CiMV infection on citrus trees reduces the fruit quality of citrus.

Effects of satsuma dwarf virus infection on medium-late-maturing citrus ‘Setoka’, ‘Tamami’ and ‘Harumi’

Satsuma dwarf virus (SDV) causes serious damage to citrus production, reducing fruit quality and yield. In this study of the effect of SDV infection on growth of 2-year-old pot-grown trees of Satsuma mandarin (Citrus unshiu) and citrus hybrids ‘Setoka’, ‘Tamami’, and ‘Harumi’, SDV-infected trees of Satsuma mandarin, ‘Tamami’, and ‘Setoka’ had altered leaf shapes, shorter leaves and tree forms than did virus-free trees, but these traits did not differ significantly between SDV-infected and SDV-free trees of ‘Harumi’.

Graft-transmissible citrus diseases in P. R. China-research developments

In the P.R. China, ten graft-transmissible pathogens have been identified towards citrus, including Candidatus Liberibacter asiaticus, Citrus tristeza virus (CTV), Citrus tatter-leaf virus (CTLV), Citrus exocortis viroid (CEVd), Citrus yellow vein clearing virus (CYVCV),Satsuma dwarf virus (SDV), Citrus vein enation virus (CVED), Citrus psorosis virus (CPsV), Citrus cachexia viroid (CCaVd) and Citrus chlorotic dwarf virus (CCDV). Of these pathogens, the first five cause damage in field citrus trees, whereas the latter five were occasionally detected from the imported citrus materials or field trees. The research progresses about HLB, CTV, CYVCV etc. within recent three years have briefly been reviewed.

Pest categorisation of Satsuma dwarf virus.

The EFSA Panel on Plant Health performed a pest categorisation of Satsuma dwarf virus (SDV) for the EU territory. SDV is a well‐known pathogen and the type species of the genus Sadwavirus in the family Secoviridae. SDV is now considered to include several other formerly distinct viruses which are therefore also covered in the present opinion. Citrus species and their relatives represent the main hosts of SDV and efficient diagnostic techniques are available. SDV is listed on some of its known hosts in Annex IIAI of Directive 2000/29/EC. It is transmitted by vegetative propagation of infected hosts and presumably through the soil, but the precise mechanism or vector(s) are still unknown. SDV is present in Asia and is not known to occur in the EU. Therefore, it does not meet this criterion to qualify as a Union regulated non‐quarantine pest (RNPQ). Plants for planting represent the main pathway for the entry, but this pathway is closed by existing legislation for the main hosts (Citrus, Fortunella and Poncirus). SDV is, however, able to enter the EU on plants for plants of its unregulated rutaceous or non‐rutaceous hosts. Should it be introduced, SDV has the potential to establish and subsequently spread with plants for planting and, possibly, through its poorly characterised natural spread mechanism(s). SDV is able to cause severe symptoms, quality and yield losses on a range of citrus crops. Overall, SDV meets all the criteria evaluated by EFSA to qualify as a Union quarantine pest. The main knowledge gaps and uncertainties concern (1) the potential significance of the unregulated rutaceous and non‐rutaceous hosts for virus dissemination and epidemiology, (2) the origin and trade volume of the plants for planting of these host imported in the EU and (3) the efficiency of natural spread of SDV under EU conditions.

Development of Multiplex PCR for Simultaneous Detection of Citrus Viruses and the Incidence of Citrus Viral Diseases in Late-Maturity Citrus Trees in Jeju Island.

Satsuma dwarf virus (SDV) or Citrus mosaic sadwavirus (CiMV) were not consistently detected in RT-PCR assay with the primer sets based on gene of Japan isolates. SDV and CiMV isolates were distinctively divided into two groups based on phylogenetic analysis of PP2 gene cloned from 22 Korean isolates, and the Korean CiMV and SDV isolates shared 95.5–96.2% and 97.1–97.7% sequence identity with Japanese isolate, respectively. We developed PP2-1 primer set based on the PP2 gene sequence of Korean isolates to simultaneously and effectively detect SDV and CiMV. And CTLV-2013 and CTV-po primer sets were newly designed for detection of Citrus tatter leaf virus (CTLV) and Citrus tristeza virus (CTV), respectively. Using these primer sets, a new multiplex PCR assay was developed as a means to simultaneously detect 4 citrus viruses, CTV, CTLV, SDV, and CiMV. The degree of detection by the multiplex PCR were consistent with those of uniplex RT-PCR for detection of each of the viruses. Therefore, the new multiplex PCR provides an efficient method for detecting 4 citrus viruses, which will help diagnose many citrus plants at the same time. We verified that 35.2% and 72.1% of 775 trees in 155 orchards were infected with SDV or CiMV (SDV/CiMV) and CTV by the multiplex-PCR assay, respectively, and CTLV was not detected in any of the trees tested.

和歌山県のカンキツ樹から検出された温州萎縮ウイルスの系統

和歌山県のカンキツ樹から検出された温州萎縮ウイルスの系統

Natural Satsuma Dwarf Virus Infection of Two Woody Plants, Daphniphyllum teijsmannii Zoll. ex Kurz. and Viburnum odoratissimum Ker-Gaul. var. awabuki (K. Koch) Zabel near Citrus Fields

In Japan, the production of Satsuma mandarin (Citrus unshiu Marc.) is seriously affected by Satsuma dwarf virus (SDV). This study provides evidence of the natural SDV infection of two woody plants, Daphniphyllum teijsmannii and Viburnum odoratissimum var. awabuki, which are common in the warm temperate forests of Japan. Forty-four species of wild woody plants that grew near several SDV-infested fields were surveyed for the presence of SDV using immunochromatography assay (ICA). Five D. teijsmannii trees and four trees of V. odoratissimum var. awabuki tested positive for SDV. Trees of D. teijsmannii and V. odoratissimum var. awabuki that grew far from the citrus fields tested negative for SDV, suggesting that these species are hosts but not the main natural reservoirs of SDV. Comparisons of the partial nucleotide sequences of the larger coat protein gene showed that SDV isolates from closely-grown trees of citrus, D. teijsmannii, and V. odoratissimum var. awabuki were genetically very homogeneous. The results suggested that the natural transmission of SDV occurred among trees of citrus, D. teijsmannii, and V. odoratissimum var. awabuki.

A broad spectrum, one-step RT-PCR to detect Satsuma dwarf virus variants using universal primers targeting both segmented RNAs 1 and 2

Universal primers to detect Satsuma dwarf virus (SDV), including distantly related strains Citrus mosaic virus (CiMV), Navel orange infectious mottling virus (NIMV), and Hyuganatsu virus (HV), were tested in a convenient one-step RT-PCR assay. SDV was the most broadly detected using uSDVup/uSDVdo primers that specifically targeted a nucleotide sequence in the 3′-noncoding region that is conserved in both segmented RNAs 1 and 2 of SDV among the tested primers. Nucleotide sequence analysis confirmed that the amplified RT-PCR products could be derived from RNAs 1 or 2 of SDV variants, some of which had interesting genetic diversity.

Evaluation of Novel Antiviral Agents in the Elimination of Satsuma dwarf virus (SDV) by Semi-micrografting in Citrus

In fruit trees and vegetative reproductive plants, viral elimination from mother plants is conducted to produce virus- and viroid-free nursery plants. In citrus, shoot tip culture and semi-micrografting combined with thermotherapy were adopted for viral elimination; however, these methods should be modified for ease or higher efficiency. One solution might be the application of effective antiviral agents. In this study, we tested the efficacy of 4 antiviral agents, ribavirin, foscarnet, zidovudine, and enfuvirtide, against Satsuma dwarf virus (SDV) in Citrus unshiu Marc. ‘Ueno-wase’ to screen effective agents. The results showed that foscarnet had the highest efficacy against SDV at semi-micrografting combined with thermotherapy, and that the efficacy was significantly different from that of the untreated control. On the other hand, ribavirin, which was thought to be efficient against some citrus viruses, has no significant effect against SDV. There were no harmful effects of foscarnet or ribavirin on re-generation. It was considered that the optimization of treatment method and concentration is required before applying ribavirin as an antiviral agent against SDV. Foscarnet was thought to be highly effective against SDV and was also expected to have high efficacy against other plant viruses. Moreover, our results suggested the possibility that other human antiviral agents that have not been investigated in plants could be effective against plant viruses.

Molecular Characterization of Satsuma Dwarf Virus Strains Collected in Japan

Satsuma dwarf virus (SDV), Citrus mosaic virus (CiMV), Natsudaidai dwarf virus (NDV), Navel orange infectious mottling virus (NIMV), and Hyuganatsu virus (HV) are strains of Satsuma dwarf virus in the genus Sadwavirus that are widely spread in citrus orchards in Japan. The aim of this study was to investigate the population structure of these strains and the geographical distribution in Japan. The nucleotide sequences of two coat protein genes (CPL and CPS) and the 3’ non-coding region in RNA2 were determined. Of six isolates sequenced in this study, four isolates (N3, T4, MIE09-3-1 and TZ31) were SDV, and the other two isolates (SIYO and JATA) were CiMV. The phylogenetic analysis based on amino acid sequences of CPL and CPS showed that SDV isolates clustered one tight-knit group and CiMV isolates divided in two definite groups, which was supported a high bootstrap values. These results suggested that the genetic diversity of CiMV was larger than that of SDV. The inter-strain relationships between SDV, CiMV, NDV, NIMV, and HV were discussed.