Probable mechanical transmission of a virus-like agent from rose rosette disease-infected multiflora rose to Nicotiana species

As part of efforts to identify the causal agent of the rose rosette disease (RRD) of multiflora rose (Rosa multiflora Thunb.), root tip extracts from both symptomatic and nonsymptomatic roses were used to mechanically inoculate leaves of Nicotiana glutinosa. Pale green spots were observed along the margins of the major leaf veins only on leaves inoculated with extracts prepared from symptomatic rose plants. Light microscopy revealed abnormal development of the palisade and spongy mesophyll cells in the symptomatic tissue, although no virus‐like particles (VLPs) were observed by electron microscopy. However, VLPs were observed in cells from tissue adjacent to the leaf veins and bordered by the pale green spots. Inoculation of N. benthamiana with extracts from symptomatic N. glutinosa initially did not result in visible symptoms on N. benthamiana inoculated leaves. However, approximately 4 wk post inoculation, splitting of leaf tissue across and along major leaf veins in expanding leaves occurred. In later stages of leaf expansion some leaves split in regions not associated with veins. Light microscopy of thick sections revealed separation between palisade cells and groups of small dead cells in the mesophyll tissue of expanding systemically infected leaf blades. Electron microscopy revealed crystalline arrays in the cytoplasm of mesophyll cells. No abnormal cellular changes were observed in plants inoculated with extracts prepared from nonsymptomatic rose plants.     

Purification and properties of closterovirus-like particles associated with a whitefly-transmitted disease of sweet potato

A virus causing sunken veins on ‘Georgia Jet’ sweet potato, and yellow brittle leaves and stunting on Ipomoea setosa, was purified and a specific antiserum was prepared. Flexuous particles with a normal length of 850 nm and a diameter of 12 nm with an open helical structure typical of closteroviruses were observed. The virus particle protein has an apparent mol. wt of c. 34 kD. Double-stranded RNA isolated from SPSVV-infected I. setosa and subjected to electrophoresis in agarose consisted of one major band with an estimated M_r of 10.5 kbp and two minor bands with M_r of 9.0 and 5.0 kbp. Fibril-containing vesicles in phloem cells were observed in ultrathin sections of infected leaf tissues. The virus was transmitted by the whitefly Bemisia tabaci in a semi-persistent manner and by grafting, but not mechanically. The virus could be transmitted to various Ipomoea species, to Nicotiana clevelandii, N. benthamiana and Amaranthus palmeri. The virus did not react with an antiserum to lettuce infectious yellows virus. Based on particle morphology, serology and symptom expression, the virus appears unique and different from all other reported whitefly-transmitted closteroviruses. We propose it be named “sweet potato sunken vein virus” (SPSVV).     

Differentiation of phytoplasmas associated with sugarcane and gramineous weed white leaf disease and sugarcane grassy shoot disease by RFLP and sequencing

 Restriction fragment length polymorphism (RFLP) and sequencing were used to elucidate the genetic relationship between phytoplasmas that cause white lead disease and grassy shoot disease in sugarcane and white leaf disease in gramineous weeds found in the cane-growing areas (Crowfoot grass, Bermuda grass and Brachiaria grass). A 1.35-kb DNA fragment encoding for the 16s rRNA was amplified by PCR using universal primers and analysed by digestion with nine restriction endonucleases. A DNA fragment containing the 3′ end of the 16s rRNA and the spacer region between the 16s rRNA and the tRNA(Ile) was amplified by PCR and sequenced. Analysis of the RFLP patterns and of the sequence showed that grassy shoot and white leaf diseases in sugarcane are caused by two different phytoplasmas. Sequence analysis of phytoplasma DNA obtained from three species of weeds showing symptoms of white leaf disease failed to detect any organism that is identical to those infecting the sugarcane. Moreover the phytoplasma species that infect the three types of gramineous weeds, although closely related, are nevertheless different Received: 15 April 1997 / Accepted: 18 April 1997     

A new phytoplasma associated with little leaf disease in azalea: multilocus sequence characterization reveals a distinct lineage within the aster yellows phytoplasma group

An azalea little leaf (AzLL) disease characterised by abnormally small leaves, yellowing and witches'‐broom growth symptoms was observed in suburban Kunming, southwest China. Transmission electron microscopic observations of single‐membrane‐bound, ovoid to spherical bodies in phloem sieve elements of diseased plants and detection of phytoplasma‐characteristic 16S rRNA gene sequence in DNA samples from diseased plants provided evidence linking the disease to infection by a phytoplasma. Results from restriction fragment length polymorphism, phylogenetic and comparative structural analyses of multiple genetic loci containing 16S rRNA, rpsS, rplV, rpsC and secY genes indicated that the AzLL phytoplasma represented a distinct, new 16Sr subgroup lineage, designated as 16SrI‐T, in the aster yellows phytoplasma group. The genotyping also revealed that the AzLL phytoplasma represented new rp and secY gene lineages [rp(I)‐P and secY(I)‐O, respectively]. Phylogenetic analyses of secY and rp gene sequences allowed clearer distinctions between AzLL and closely related strains than did analysis of 16S rDNA.     

Whole‐exome sequencing identifies a novel mutation of GPD1L (R189X) associated with familial conduction disease and sudden death

Cardiac conduction disease (CCD) is a serious disorder and the leading cause of mortality worldwide. It is characterized by arrhythmia, syncope or even sudden cardiac death caused by the dysfunction of cardiac voltage‐gated channel. Previous study has demonstrated that mutations in genes encoding voltage‐gated channel and related proteins were the crucial genetic lesion of CCD. In this study, we employed whole‐exome sequencing to explore the potential causative genes in a Chinese family with ventricular tachycardia and syncope. A novel nonsense mutation (c.565C>T/p.R189X) of glycerol‐3‐phosphate dehydrogenase‐like (GPD1L) was identified and co‐segregated with the affected family members. GPD1L is a crucial interacting protein of SCN5A, a gene encoded sodium channel α‐subunit Na_v1.5 and mainly associated with Brugada syndrome (BrS). The novel mutation (c.565C>T/p.R189X) may result in a premature stop codon at position 189 in exon 4 of the GPD1L gene and lead to functional haploinsufficiency of GPD1L due to mRNA carrying this mutation will be degraded by nonsense‐mediated mRNA decay, which has been confirmed by Western blot in HEK293 cells transfected HIS‐GPD1L plasmid. The levels of GPD1L decreasing may disturb the function of Na_v1.5 and induce arrhythmia and syncope in the end. In conclusion, our study not only further supported the important role of GPD1L in CCD, but also expanded the spectrum of GPD1L mutations and will contribute to the genetic diagnosis and counselling of families with CCD.     

Detection of multiple sequence variants of Grapevine rupestris stem pitting‐associated virus using primers targeting the polymerase domain and partial genome sequencing of a novel variant

Grapevine rupestris stem pitting‐associated virus (GRSPaV) is a member of the genus Foveavirus within the new family Betaflexiviridae. GRSPaV is distributed among grapevines worldwide and is implicated in the disease rupestris stem pitting (RSP) of the rugose wood complex and two other disorders. GRSPaV is composed of a wide range of sequence variants, and so far, the complete genomes of five sequence variants have been sequenced. Quick and reliable detection of different GRSPaV variants is a critical step in the elimination and control of GRSPaV. Previously, primers designed from various genomic regions have been used in RT‐PCR for the detection of GRSPaV variants. The efficiency of RT‐PCR varied widely depending on the spectrum of the primers that were used. In this study, we designed a pair of degenerate primers based on the consensus sequence of the genomic region encoding the highly conserved RNA‐dependent RNA polymerase domain from five reference isolates of GRSPaV for which the genome sequence are available. We demonstrate that this set of primers is comparable, if not superior, to the broad‐spectrum primers RSP13&14 in detecting multiple GRSPaV variants. Using these degenerate primers, we identified two new and distinct sequence variants. The 3′ terminal genomic region of one of the new variants, GRSPaV‐ML, spanning the 3′ part of ORF1, through the entire open reading frames 2–4, and the 5′ region of ORF5 were sequenced. Sequence comparison demonstrates that GRSPaV‐ML is distinct from each of the five reference isolates.     

High-throughput sequencing exclusively identified a novel Torque teno virus genotype in serum of a patient with fatal fever

Torque teno virus (TTV) has been found to be prevalent world-wide in healthy populations and in patients with various diseases, but its etiological role has not yet been determined. Using high-throughput unbiased sequencing to screen for viruses in the serum of a patient with persistent high fever who died of suspected viral infection and prolonged weakness, we identified the complete genome sequence of a TTV (isolate Hebei-1). The genome of TTV-Hebei-1 is 3649 bp in length, encoding four putative open reading frames, and it has a G+C content of 49%. Genomic comparison and a BLASTN search revealed that the assembled genome of TTV-Hebei-1 represented a novel isolate, with a genome sequence that was highly heterologous to the sequences of other reported TTV strains. A phylogenetic tree constructed using the complete genome sequence showed that TTV-Hebei-1 and an uncharacterized Taiwanese strain, TW53A37, constitute a new TTV genotype. The patient was strongly suspected of carrying a viral infection and died eventually without any other possible causes being apparent. No virus other than the novel TTV was identified in his serum sample. Although a direct causal link between the novel TTV genotype infection and the patient’s disease could not be confirmed, the findings suggest that surveillance of this novel TTV genotype is necessary and that its role in disease deserves to be explored.     

Serous fluid cytology of multicentric Castleman’s disease and other lymphoproliferative disorders associated with Kaposi sarcoma‐associated herpes virus: a review with case reports

C. Lobo, S. Amin, A. Ramsay, T. Diss and G. Kocjan Serous fluid cytology of multicentric Castleman’s disease and other lymphoproliferative disorders associated with Kaposi sarcoma‐associated herpes virus: a review with case reports Objective: The aim of this study is to describe and review the cytological features of Kaposi sarcoma‐associated herpes virus (KSHV) related entities, such as multicentric Castleman’s disease (MCD), plasmablastic‐lymphoma (PBL) and primary effusion lymphoma (PEL), which all may present as body cavity effusions. Serous fluid cytology of MCD and PBL has not, to our knowledge, thus far been described. Although different in nature, MCD, PBL and PEL are characterized by similar morphological features. Materials and methods: Body cavity effusions from four different patients with previously known or unknown KSHV‐related lymphoproliferations have been examined by routine cytology, immunocytochemistry (IC) and polymerase chain reaction (PCR). Results: MCD, PBL and PEL are all characterized by increased cellularity, comprising mainly lymphoid and plasmacytoid cells with variable proportions of immunoblasts. Immunocytochemistry and PCR results show the MCD to be CD138 and KSHV positive, CD30 negative, IgM, IgH and lambda restricted but IgH polyclonal. PBL was CD138 positive, kappa restricted, weakly positive with VS38 and over 80% positive with MIB 1. PEL was CD45, EMA, CD138, KSHV, p53 and CD3 positive, CD20, EBV, CD30, CD2, CD4, ALK1, epithelial and mesothelial markers negative, and PCR monoclonal B‐cell expanded (Ig‐kappa bands). Conclusion: Cytological examination of effusions in KSHV‐related lymphoproliferative disorders may show similar morphological features but clonality studies and immunocytochemistry are very helpful in distinguishing between these rare benign and malignant lymphoproliferative diseases.     

Association of tomato leaf curl Palampur virus with yellow mosaic disease of Armenian cucumber (Cucumis melo var. flexuoses) and wild melon (C. callosus var. agrestis) in India

Natural occurrence of yellow mosaic disease was observed on Armenian cucumber (Cucumis melo var. flexuoses) and wild melon (C. callosus var. agrestis) with disease incidences of ~36 and ~27%, respectively. Association of tomato leaf curl Palampur virus (ToLCPV) with the disease was investigated by Polymersae chain reaction (PCR) using begomovirus-specific primers. Full-length genome was amplified by rolling circle amplification (RCA) method from representative samples of C. melo and C. callosus. RCA products obtained were cloned and sequenced. Analyses of sequence data revealed the presence of full-length begomoviral genome of 2756 nucleotides with the gene arrangement of a typical begomovirus: HQ848383 (C. melo) and GU253914 (C. callosus). Both the isolates shared 99% sequence identity together and high 97–99% identities and the closest phylogenetic relationships with ToLCPV strains reported worldwide, hence identified as two new members of ToLCPV. Natural occurrence of ToLCPV on C. melo and C. callosus is the first report.     

Morphological and molecular identification of Colletotrichum siamense,a novel leaf pathogen associated with Sterculia lanceolata recorded in China

Sterculia lanceolata, an important tropical woody plant, has high ornamental and medicinal value. To our knowledge, only brown root disease in this plant has been reported. In Nanning, Guangxi, China, an outbreak of leaf blight disease was observed on S. lanceolata in June 2019, with the leaf infection rate ranging from 80% to 100%. The disease seriously affected the leaves of trees and caused economic loss. Eight isolates were recovered from the infected leaves of different trees, and the pathogenicity was then determined by the methods of mycelial disc and conidial suspension, fulfilling Koch's postulates. According to the morphological and molecular biological characteristics of isolates, the pathogen causing leaf blight on S. lanceolata was identified as Colletotrichum siamense. Accurate identification of the pathogen provides a reliable basis for the control of the disease.     

Extreme‐phenotype genome‐wide association study (XP‐GWAS): a method for identifying trait‐associated variants by sequencing pools of individuals selected from a diversity panel

Although approaches for performing genome‐wide association studies (GWAS) are well developed, conventional GWAS requires high‐density genotyping of large numbers of individuals from a diversity panel. Here we report a method for performing GWAS that does not require genotyping of large numbers of individuals. Instead XP‐GWAS (extreme‐phenotype GWAS) relies on genotyping pools of individuals from a diversity panel that have extreme phenotypes. This analysis measures allele frequencies in the extreme pools, enabling discovery of associations between genetic variants and traits of interest. This method was evaluated in maize (Zea mays) using the well‐characterized kernel row number trait, which was selected to enable comparisons between the results of XP‐GWAS and conventional GWAS. An exome‐sequencing strategy was used to focus sequencing resources on genes and their flanking regions. A total of 0.94 million variants were identified and served as evaluation markers; comparisons among pools showed that 145 of these variants were statistically associated with the kernel row number phenotype. These trait‐associated variants were significantly enriched in regions identified by conventional GWAS. XP‐GWAS was able to resolve several linked QTL and detect trait‐associated variants within a single gene under a QTL peak. XP‐GWAS is expected to be particularly valuable for detecting genes or alleles responsible for quantitative variation in species for which extensive genotyping resources are not available, such as wild progenitors of crops, orphan crops, and other poorly characterized species such as those of ecological interest.     

Gene therapy with novel adeno-associated virus vectors substantially diminishes atherosclerosis in a murine model of familial hypercholesterolemia

BACKGROUND: Familial hypercholesterolemia is an inherited disease caused by mutations in the LDL receptor gene leading to severe hypercholesterolemia and atherosclerosis. The LDL receptor is predominantly expressed in the liver, making it a preferred target organ for somatic gene therapy. We recently isolated a new family of vectors based on adeno-associated viruses (AAVs) isolated from nonhuman primates, which enable efficient and stable transgene expression following in vivo gene delivery to liver. METHODS: Traditional vectors based on AAV serotype 2 and two novel AAVs from nonhuman primates, serotypes AAV7 and AAV8, were produced encoding for the human LDL receptor. Vectors were injected into the portal veins of LDL receptor deficient mice that were fed a high-fat diet to achieve severe pretreatment hypercholesterolemia. RESULTS: Animals receiving the novel AAV vectors realized nearly complete normalization of serum lipids and failed to develop the severe atherosclerosis that characterized the untreated animals; the AAV2 vector constructs demonstrated partial lipid correction and only a modest improvement in atherosclerosis. CONCLUSIONS: Using vectors based on novel nonhuman primate AAVs, which provide advantages in terms of efficiency, we were able to achieve a long-term correction of the metabolic defect in LDL receptor deficient mice.     

A genome‐wide SNP scan reveals two loci associated with the chicken resistance to Marek's disease

Marek's disease (MD) is a neoplastic disease in chickens, caused by the Marek's disease virus (MDV). To investigate host genetic resistance to MD, we conducted a genome‐wide association study (GWAS) on 67 MDV‐infected chickens based on a case and control design, including 57 susceptible chickens in the case group and 10 resistant chickens as controls. After searching 38 655 valid genomic markers, two SNPs were found to be associated with host resistance to MD. One SNP, rs14527240, reaching chromosome‐wide significance level (P < 0.01) was located in the SPARC‐related modular calcium‐binding 1 (SMOC1) gene on GGA5. The other one, GGaluGA156129, reaching genome‐wide significance (P < 0.05), was located in the protein tyrosine phosphatase, non‐receptor type 3 (PTPN3) gene on GGA2. In addition, expression patterns of these two genes in spleens were detected by qPCR. The expression of SMOC1 was significantly up‐regulated (P < 0.05), whereas the expression of PTNP3 did not show significance when the case group was compared with the control group. Up‐regulation of SMOC1 in susceptible spleens suggests its important roles in MD tumorigenesis. This is the first study to investigate MD‐resistant loci, and it demonstrates the power of GWASs for mapping genes associated with MD resistance.     

Disease distribution and characterisation of a new macluravirus associated with chirke disease of large cardamom

Large cardamom (Amomum subulatum), an important spice crop grown in eastern sub‐Himalayan mountains of India, is affected by a viral disease commonly known as ‘chirke’, which is characterised by light and dark green streaks on the leaf lamina. Although chirke has been known to affect large cardamom for over 50 years, its distribution in large cardamom growing regions and aetiology have remained unaddressed. In this study for the first time, distribution of chirke in the major large cardamom growing regions in India has been determined. North Sikkim and eastern region of Darjeeling hills were endemic region with average disease incidence of 19.2–35%, whereas, Mirik region of Darjeeling hills were free from the disease. Suckers, the commonly used planting material, were the major source for spread of the disease. The virus was sap transmissible to the popular large cardamom cultivars Golsey, Ramsey, Swaney and Varlangey and vectored by Rhopalosiphum maidis and Myzus persicae in a non‐persistent manner. Flexuous virus particles measuring 625–650 × 12.5 nm were observed consistently associated with the diseased samples. Polyclonal antiserum to the purified virus showed serological affinity with a macluravirus, cardamom mosaic virus (CdMV) associated with a similar disease known as katte disease of small cardamom (Elettaria cardamomum) occurring in southern India. The 3^′ terminal genome sequence (1776 nucleotides) of the virus was determined, which revealed a close sequence identity and phylogenetic relationships with the members of the genus Macluravirus. The deduced amino acid sequence of putative coat protein (CP) gene showed maximum similarity of 65.7% with the CdMV. Phylogenetic analysis based on CP and 3^′ UTR showed that the virus was closer to Alpinia mosaic virus, CdMV and Chinese yam necrotic mosaic virus subclade. The results suggest that the virus associated with the chirke disease of large cardamom is a new species under the genus Macluravirus in the family Potyviridae for which the name large cardamom chirke virus (LCCV) is proposed.     

Mapping quantitative trait loci associated with southern leaf blight resistance in maize (Zea mays L.)

Southern leaf blight (SLB) caused by the fungus Cochliobolus heterostrophus (Drechs.) Drechs. is a major foliar disease of maize worldwide. Our objectives were to identify quantitative trait loci (QTL) for resistance to SLB and flowering traits in recombinant inbred line (RIL) population derived from the cross of inbred lines LM5 (resistant) and CM140 (susceptible). A set of 207 RILs were phenotyped for resistance to SLB at three time intervals for two consecutive years. Four putative QTL for SLB resistance were detected on chromosomes 3, 8 and 9 that accounted for 54% of the total phenotypic variation. Days to silking and anthesis–silking interval (ASI) QTL were located on chromosomes 6, 7 and 9. A comparison of the obtained results with the published SLB resistance QTL studies suggested that the detected bins 9.03/02 and 8.03/8.02 are the hot spots for SLB resistance whereas novel QTL were identified in bins 3.08 and 8.01/8.04. The linked markers are being utilized for marker‐assisted mobilization of QTL conferring resistance to SLB in elite maize backgrounds. Fine mapping of identified QTL will facilitate identification of candidate genes underlying SLB resistance.