Single berry reconstitution prior to RNA-sequencing reveals novel insights into transcriptomic remodeling by leafroll virus infections in grapevines

Abstract: Virus infections of olive (Olea europaea), to which littte attention has been paid up to a relatively recent past, are surprisingly widespread, as shown by: (i) the very high presence (above 50% in average) of double-stranded ribonucleic acids (dsRNAs) in the plants analysed in the course of field surveys carried out especially in the Mediterranean and Middle Eastern countries; (ii) the identification in these plants of 15 different viruses with diverse taxonomic allocation. Infections are generally symptomless. When shown, symptoms consist of deformations of fruits and leaves and of foliar discolourations ranging from chlorosis to bright yellowing. “Bumpy fruits” and the “Leaf yellowing complex” are the only two diseases whose viral aetiology seems to be convincingly ascertained. Virus identification is not based on biotests (mechanical transmission to herbaceous hosts is unreliable and there are no differential woody indicators available) nor on immunoenzymatic assays (ELISA), which are also unreliable, but on nucleic acid-based techniques (various RT-PCR protocols). The economic impact of infections has not been determined although recent reports indicate that some viruses seem to affect the yield and the quality of the oil. For an ultimate answer, a comparison needs to be done between selected and sanitazied accessions and their infected counterparts. Equally scanty is the information on the epidemiology of olive-infecting viruses, except for three necroviruses (OLV-1, TNV-D and OMMV), whose transmission through soil, direct or mediated by Olpidium brassicae, has been experimentally ascertained. Olive latent virus 1 (OLV-1) and Cherry leafroll virus (CLRV) are transmitted through seeds and seedlings and, like all the other viruses, with propagating material (nursery productions), which is the major responsible for their worldwide distribution. Viral infections have been detected in 22 countries in the five continents. Preventive control through certification schemes is desirable. One of such schemes designed and implemented in Italy, is based on the pomological and sanitary selection and sanitation of mother stocks.

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A Subgenomic RNA Associated with Cherry Leafroll Virus Infections

Virology ◽

10.1006/viro.1995.1376 ◽

1995 ◽

Vol 211 (1) ◽

pp. 33-41 ◽

Cited By ~ 10

Author(s):

Mindy Brooks ◽

George Bruening

Keyword(s):

Virus Infections ◽

Subgenomic Rna ◽

Leafroll Virus

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Comparative analysis of public RNA-sequencing data from human intestinal enteroid (HIEs) infected with enteric RNA viruses identifies universal and virus-specific epithelial responses

10.1101/2021.03.30.437726 ◽

2021 ◽

Author(s):

Roberto J Cieza ◽

Jonathan Louis Golob ◽

Justin A Colacino ◽

Christiane E Wobus

Keyword(s):

Rna Sequencing ◽

Transcriptional Response ◽

Enteric Virus ◽

Intestinal Biopsy ◽

Virus Infections ◽

Sequencing Data ◽

Virus Family ◽

Host Microbe Interactions ◽

Host Virus Interactions ◽

Human Intestinal Epithelium

Acute gastroenteritis (AGE) has a significant disease burden on society. Noroviruses, rotaviruses and astroviruses are important viral causes of AGE but are relatively understudied enteric pathogens. Recent developments in novel biomimetic human models of enteric disease are opening new possibilities for studying human-specific host-microbe interactions. Human intestinal enteroids (HIE), which are epithelium-only intestinal organoids derived from stem cells isolated from human intestinal biopsy tissues, have been successfully used to culture representative norovirus, rotavirus and astrovirus strains. Previous studies investigated host-virus interactions at the intestinal epithelial interface by individually profiling the epithelial transcriptional response to a member of each virus family by RNA sequencing (RNA-seq). We used these publicly available datasets to uniformly analyze these data and identify shared and unique transcriptional changes in the human intestinal epithelium upon human enteric virus infections.

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The Detection of viruses in olive cultivars in Greece, using a rapid and effective RNA extraction method, for certification of virus-tested propagation material

Phytopathologia Mediterranea ◽

10.36253/phyto-11033 ◽

2020 ◽

Vol 59 (1) ◽

pp. 203-211

Author(s):

Matthaios M. MATHIOUDAKIS ◽

Maria SAPONARI ◽

Beata HASIÓW-JAROSZEWSKA ◽

Toufic ELBEAINO ◽

Georgios KOUBOURIS

Keyword(s):

Rna Extraction ◽

Germplasm Collection ◽

Virus Infections ◽

Arabis Mosaic Virus ◽

Leaf Yellowing ◽

Production And Distribution ◽

Olive Cultivars ◽

Certification Programme ◽

Leafroll Virus ◽

Propagation Material

Although Greece is the world’s third largest olive production country, information about the presence of olive viruses is limited. A survey for the presence of virus infections in the ten most important Greek cultivars was conducted in a germplasm collection olive grove located in Chania, Crete. Samples were RT-PCR assayed for the presence of Arabis mosaic virus (ArMV), Cherry leafroll virus (CLRV), Strawberry latent ring spot virus (SLRSV), and Olive leaf yellowing-associated virus (OLYaV), amplifying part of the capsid protein (ArMV), the 3΄UTR (CLSRV, SLRSV) or the HSP70h (OLYaV) gene. Total RNAs were purified using the Trizol method, yielding good quality and purity, thereby confirming application of the method as a rapid economic extraction protocol for detection of olive viruses. SLRSV was the most predominant virus, with an infection rate of 55%, followed by CLRV and OLYaV in 5% of the tested samples. ArMV was detected only in one sample. Mixed virus infections were also commonly detected. The DNA amplicons of the obtained viruses from the infected samples were sequenced. The partial sequences of ArMV, CLRV and SLRSV from olives, which are reported for the first time, showed 74-100% nucleotide similarity with available homologous sequences from other crops, whereas OLYaV isolates showed high sequence variability of 25%. The phylogenetic analysis based on olive-OLYaV HSP70h partial-nucleotide sequences grouped the olive isolate sequences according to the geographical origins of the host germplasm collection. This is the first official report of the occurrence of olive viruses in Greece, emphasizing the need to implement a certification programme for production and distribution of high-quality (virus-free) olive propagation material, in Greece and more generally in the Mediterranean basin.

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A Brief Outline of Infectious Diseases of Olive

مجلة جامعة فلسطين التقنية للأبحاث ◽

10.53671/ptukrj.v1i1.6 ◽

2013 ◽

Vol 1 (1) ◽

pp. 1-9

Author(s):

Giovanni P. Martelli

Keyword(s):

Viral Infections ◽

Middle Eastern ◽

Mechanical Transmission ◽

Virus Infections ◽

Preventive Control ◽

Ribonucleic Acids ◽

Virus Identification ◽

Worldwide Distribution ◽

Viral Aetiology ◽

Leafroll Virus

Abstract: Virus infections of olive (Olea europaea), to which littte attention has been paid up to a relatively recent past, are surprisingly widespread, as shown by: (i) the very high presence (above 50% in average) of double-stranded ribonucleic acids (dsRNAs) in the plants analysed in the course of field surveys carried out especially in the Mediterranean and Middle Eastern countries; (ii) the identification in these plants of 15 different viruses with diverse taxonomic allocation. Infections are generally symptomless. When shown, symptoms consist of deformations of fruits and leaves and of foliar discolourations ranging from chlorosis to bright yellowing. “Bumpy fruits” and the “Leaf yellowing complex” are the only two diseases whose viral aetiology seems to be convincingly ascertained. Virus identification is not based on biotests (mechanical transmission to herbaceous hosts is unreliable and there are no differential woody indicators available) nor on immunoenzymatic assays (ELISA), which are also unreliable, but on nucleic acid-based techniques (various RT-PCR protocols). The economic impact of infections has not been determined although recent reports indicate that some viruses seem to affect the yield and the quality of the oil. For an ultimate answer, a comparison needs to be done between selected and sanitazied accessions and their infected counterparts. Equally scanty is the information on the epidemiology of olive-infecting viruses, except for three necroviruses (OLV-1, TNV-D and OMMV), whose transmission through soil, direct or mediated by Olpidium brassicae, has been experimentally ascertained. Olive latent virus 1 (OLV-1) and Cherry leafroll virus (CLRV) are transmitted through seeds and seedlings and, like all the other viruses, with propagating material (nursery productions), which is the major responsible for their worldwide distribution. Viral infections have been detected in 22 countries in the five continents. Preventive control through certification schemes is desirable. One of such schemes designed and implemented in Italy, is based on the pomological and sanitary selection and sanitation of mother stocks.

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Incidence and Distribution of Important Viral Pathogens in Some Iranian Potato Fields

Plant Disease ◽

10.1094/pdis-91-5-0609 ◽

2007 ◽

Vol 91 (5) ◽

pp. 609-615 ◽

Cited By ~ 15

Author(s):

R. Pourrahim ◽

Sh. Farzadfar ◽

A. R. Golnaraghi ◽

A. Ahoonmanesh

Keyword(s):

Potato Virus ◽

Alfalfa Mosaic Virus ◽

Potato Virus X ◽

Enzyme Linked Immunosorbent Assay ◽

Mixed Infections ◽

Virus Infections ◽

Potato Virus S ◽

Leafroll Virus ◽

Almost All ◽

Biological Methods

From a total of 8,135 potato leaves collected from 132 fields in 11 provinces of Iran, the incidence and distribution of Alfalfa mosaic virus (AlMV), Eggplant mottled dwarf virus (EMDV), Potato leafroll virus (PLRV), Potato virus A (PVA), Potato virus M (PVM), Potato virus S(PVS), Potato virus X (PVX), Potato virus Y (PVY), and Tomato yellow fruit ring virus (TYFRV) were assessed using serological and biological methods. Based on enzyme-linked immunosorbent assay (ELISA) results, viruses in decreasing order of incidence in potato were PVS (35.9%), PVY (34.4%), PVA (27.0%), PVX (20.8%), PLRV (13.9%), PVM (9.0%), AlMV (7.0%), TYFRV (5.9%), and EMDV (5.1%). All 132 fields surveyed had some degree of virus infection, ranging from 28.8 to 98.6%, with an overall incidence of 75.2%. The highest and lowest incidence of virus infections among the surveyed provinces occurred in Kerman (93.2%) and Ardabil (56.7%), respectively. Overall, 25.0 and 50.2% of the collected potato samples had single or mixed infections, respectively. High levels of mixed infections were found between PVX and PVS (8.6%), and PVX and PVY (7.6%). Moreover, co-infection of samples with PVS and PVY, PVA and PVS, and PVA and PVY, the aphid-vectored virus/virus combinations, occurred at the highest incidence in almost all provinces surveyed, 15.3, 13.8, and 12.8%, respectively. In this study, Beet curly top virus was detected in symptomatic potato samples collected from some fields in the Kermanshah province.

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