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Ben Mansour K, Komínek P, Komínková M, Brožová J. Characterization of Prunus Necrotic Ringspot Virus and Cherry Virus A Infecting Myrobalan Rootstock. Viruses 2023; 15:1723. [PMID: 37632065 PMCID: PMC10459944 DOI: 10.3390/v15081723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Prunus necrotic ringspot virus (PNRSV) and cherry virus A (CVA) are two viruses that mainly infect plants of the genus Prunus. Full-length sequences of these two viruses, collected in the Czech Republic from Prunus cerasifera plants, were obtained via HTS sequencing. Phylogenetic analyses based on the NJ method and Splitstree tools showed that the Czech PNRSV isolate (ON088600-ON088602) is a divergent isolate from other molecular groups, sharing less than 97% pairwise nucleotide identity with members of other groups. The Czech CVA isolate (ON088603) belonged to molecular subgroup III-2, clustered with isolates from non-cherry hosts, and shared the highest pairwise nucleotide identity (99.7%) with an isolate of Australian origin.
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Affiliation(s)
- Karima Ben Mansour
- Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic; (K.B.M.); (M.K.); (J.B.)
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Petr Komínek
- Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic; (K.B.M.); (M.K.); (J.B.)
| | - Marcela Komínková
- Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic; (K.B.M.); (M.K.); (J.B.)
| | - Jana Brožová
- Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic; (K.B.M.); (M.K.); (J.B.)
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Morán F, Canales C, Olmos A, Ruiz-García AB. Loquat ( Eriobotrya japonica) is a New Natural Host of Apple Stem Pitting Virus. PLANTS 2020; 9:plants9111560. [PMID: 33202713 PMCID: PMC7696262 DOI: 10.3390/plants9111560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 01/09/2023]
Abstract
Loquat (Eriobotrya japonica) is a minor but important woody crop cultivated in Asia and Europe. High-throughput sequencing (HTS) analysis of an asymptomatic loquat plant using RNAseq Illumina technology has allowed the detection for the first time of apple stem pitting virus (ASPV), the type species of the genus Foveavirus in the family Betaflexiviridae, infecting this crop. A nearly complete genome of 9303 nts (ASPV-SL61) reconstructed bioinformatically shows the typical genomic structure of this viral species and a highest nucleotide identity (85.9%) with the Chinese ASPV isolate YLX from pear. A close phylogenetic relationship between ASPV-SL61 and ASPV-YLX has been confirmed by the sequence analysis of full-length ASPV genomic sequences available in the databases. In fact, a phylogenetic study based on a partial CP N-terminal sequence previously proposed to be involved in host adaptation has shown that ASPV-SL61 loquat isolate is more closely related to ASPV pear isolates. The presence of ASPV in loquat has been further confirmed by RT-PCR and Sanger sequencing and DAS-ELISA. An incidence of 15% was determined in one of the loquat Spanish growing areas. The sequence analysis of the partial CP sequences amplified by RT-PCR has shown a high level of variability between loquat isolates. To our knowledge, this is the first record of loquat as a natural host of ASPV.
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Ma X, Hong N, Moffett P, Zhou Y, Wang G. Functional analysis of apple stem pitting virus coat protein variants. Virol J 2019; 16:20. [PMID: 30736799 PMCID: PMC6368714 DOI: 10.1186/s12985-019-1126-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/28/2019] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Although the canonical function of viral coat protein (CP) is to encapsidate the viral genome, they have come to be recognized as multifunctional proteins, involved in almost every stage of the viral infection cycle. However, CP functions of Apple stem pitting virus (ASPV) has not been comprehensively documented. This study aimed to characterize the functions of ASPV CP and any functional diversification caused by sequence diversity of six ASPV CP variants and studied their biological, serological, pathogenic and viral suppressor of RNA silencing (VSR) functions. METHODS Six ASPV CP variants that have previously been shown to belong to different subgroups were selected here to study their diversity functions. Agrobacterium mediated infiltration (Agroinfiltration) was used to express YFP-ASPV-CPs in Nicotiana. benthamiana and infect Nicotiana. occidental with PVX-ASPV-CPs in. Confocal microscopy was used to detect YFP-ASPV-CPs florescence. CPs expressed in Escherichia coli BL21 (DE3) were induced by IPTG. RESULTS In this study, we showed that recombinant CPs expressed in Escherichia coli BL21 (DE3) had different levels of serological reactivity to three anti-ASPV antibodies used to detect ASPV. Furthermore, fusion CPs with YFP (YFP-CPs) expressed in N. benthamiana cells differed in their ability to form aggregates. We also showed that ASPV isolates that harbour these CPs induced different biological symptoms on its herbaceous host N. occidentalis. At the same time, we found that all six CPs when expressed in PVX vector showed similar VSR activity and produced similar symptoms in N. occidentalis, despite their differences in amino acids. CONCLUSIONS Different ASPV isolates induced different symptoms in N. occidentalis, however, ASPV CP variants expressed in PVX vector showed the same symptoms in N. occidentalis plants. Also, we showed that ASPV CP variants has the same level of VSR activity, but they have different abilities to aggregate in N. benthamiana.
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Affiliation(s)
- Xiaofang Ma
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, 2500 Blvd. de l’Université, Sherbrooke, QC J1K 2R1 Canada
- Jiangsu Academy of Agricultural Sciences, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Nanjing, 210014 China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
| | - Peter Moffett
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, 2500 Blvd. de l’Université, Sherbrooke, QC J1K 2R1 Canada
| | - Yijun Zhou
- Jiangsu Academy of Agricultural Sciences, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Nanjing, 210014 China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 People’s Republic of China
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Malandraki I, Beris D, Isaioglou I, Olmos A, Varveri C, Vassilakos N. Simultaneous detection of three pome fruit tree viruses by one-step multiplex quantitative RT-PCR. PLoS One 2017; 12:e0180877. [PMID: 28749955 PMCID: PMC5547701 DOI: 10.1371/journal.pone.0180877] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 06/22/2017] [Indexed: 12/26/2022] Open
Abstract
A one-step multiplex real-time reverse transcription polymerase chain reaction (RT-qPCR) based on TaqMan probes was developed for the simultaneous detection of Apple mosaic virus (ApMV), Apple stem pitting virus (ASPV) and Apple stem grooving virus (ASGV) in total RNA of pome trees extracted with a CTAB method. The sensitivity of the method was established using in vitro synthesized viral transcripts serially diluted in RNA from healthy, virus-tested (negative) pome trees. The three viruses were simultaneously detected up to a 10-4 dilution of total RNA from a naturally triple-infected apple tree prepared in total RNA of healthy apple tissue. The newly developed RT-qPCR assay was at least one hundred times more sensitive than conventional single RT-PCRs. The assay was validated with 36 field samples for which nine triple and 11 double infections were detected. All viruses were detected simultaneously in composite samples at least up to the ratio of 1:150 triple-infected to healthy pear tissue, suggesting the assay has the capacity to examine rapidly a large number of samples in pome tree certification programs and surveys for virus presence.
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Affiliation(s)
- Ioanna Malandraki
- Benaki Phytopathological Institute, Department of Phytopathology, Laboratory of Virology, Athens, Greece
| | - Despoina Beris
- Benaki Phytopathological Institute, Department of Phytopathology, Laboratory of Virology, Athens, Greece
| | - Ioannis Isaioglou
- Benaki Phytopathological Institute, Department of Phytopathology, Laboratory of Virology, Athens, Greece
| | - Antonio Olmos
- Plant Protection and Biotechnology Centre, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Christina Varveri
- Benaki Phytopathological Institute, Department of Phytopathology, Laboratory of Virology, Athens, Greece
| | - Nikon Vassilakos
- Benaki Phytopathological Institute, Department of Phytopathology, Laboratory of Virology, Athens, Greece
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Molecular adaptation within the coat protein-encoding gene of Tunisian almond isolates of Prunus necrotic ringspot virus. J Genet 2013; 92:11-24. [PMID: 23640404 DOI: 10.1007/s12041-013-0211-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The sequence alignments of five Tunisian isolates of Prunus necrotic ringspot virus (PNRSV) were searched for evidence of recombination and diversifying selection. Since failing to account for recombination can elevate the false positive error rate in positive selection inference, a genetic algorithm (GARD) was used first and led to the detection of potential recombination events in the coat protein-encoding gene of that virus. The Recco algorithm confirmed these results by identifying, additionally, the potential recombinants. For neutrality testing and evaluation of nucleotide polymorphism in PNRSV CP gene, Tajima's D, and Fu and Li's D and F statistical tests were used. About selection inference, eight algorithms (SLAC, FEL, IFEL, REL, FUBAR, MEME, PARRIS, and GA branch) incorporated in HyPhy package were utilized to assess the selection pressure exerted on the expression of PNRSV capsid. Inferred phylogenies pointed out, in addition to the three classical groups (PE-5, PV-32, and PV-96), the delineation of a fourth cluster having the new proposed designation SW6, and a fifth clade comprising four Tunisian PNRSV isolates which underwent recombination and selective pressure and to which the name Tunisian outgroup was allocated.
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Boulila M. Positive selection, molecular recombination structure and phylogenetic reconstruction of members of the family Tombusviridae: Implication in virus taxonomy. Genet Mol Biol 2011; 34:647-60. [PMID: 22215970 PMCID: PMC3229121 DOI: 10.1590/s1415-47572011005000046] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 05/13/2011] [Indexed: 11/22/2022] Open
Abstract
A detailed study of putative recombination events and their evolution frequency in the whole genome of the currently known members of the family Tombusviridae, comprising 79 accessions retrieved from the international databases, was carried out by using the RECCO and RDP version 3.31β algorithms. The first program allowed the detection of potential recombination sites in seven out of eight virus genera (Aureusvirus, Avenavirus, Carmovirus, Dianthovirus, Necrovirus, Panicovirus, and Tombusvirus), the second program provided the same results except for genus Dianthovirus. On the other hand, both methods failed to detect recombination breakpoints in the genome of members of genus Machlomovirus. Furthermore, based on Fisher's Exact Test of Neutrality, positive selection exerted on protein-coding genes was detected in 17 accession pairs involving 15 different lineages. Except genera Machlomovirus, and Panicovirus along with unclassified Tombusviridae, all the other taxonomical genera and the unassigned Tombusviridae encompassed representatives under positive selection. The evolutionary history of all members of the Tombusviridae family showed that they segregated into eight distinct groups corresponding to the eight genera which constitute this family. The inferred phylogeny reshuffled the classification currently adopted by the International Committee on Taxonomy of Viruses. A reclassification was proposed.
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Thompson JR, Fuchs M, Perry KL. Genomic analysis of grapevine leafroll associated virus-5 and related viruses. Virus Res 2011; 163:19-27. [PMID: 21893115 DOI: 10.1016/j.virusres.2011.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Revised: 08/10/2011] [Accepted: 08/12/2011] [Indexed: 10/17/2022]
Abstract
The grapevine leafroll-associated viruses (GLRaVs) (Closteroviridae) represent an emerging threat to world grape production. One group of GLRaVs within the genus Ampelovirus, the GLRaV-4-like viruses (GLRaV-4LVs), contains a fragmented collection of seven viruses only two of which (GLRaV-Pr and GLRaCV) are fully sequenced. Here in reporting the sequence of GLRaV-5, a member of GLRaV-4LVs, we identify genomic elements common to the GLRaV-4LV group. Exclusive properties include a highly conserved p5 gene product and phylogenies for complete genes that, except for the p23 gene, are reliably monophyletic. In comparison with other members of the genus Ampelovirus, GLRaV-4LVs form a tight cluster for all genes analyzed. In addition, they all possess a conserved AlkB domain which is most similar to the more distantly related GLRaV-3, suggesting recombination. In silico RNA structural analyses revealed a conserved five stem-loop structure at the 3' untranslated region that extends to all GLRaV-4LVs, and the ampeloviruses Pineapple mealybug wilt-associated virus 1 and Pineapple mealybug wilt-associated virus 3. A conserved G-U rich stem loop was also found upstream of the ORF1a stop and 1b start codons. Taken together, this work allows for a more thorough contextualization of GLRaV-5 and the GLRaV-4LVs as a group within the genus Ampelovirus.
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Affiliation(s)
- Jeremy R Thompson
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, 334 Plant Science, Ithaca, NY 14853, USA.
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Boulila M. Selective pressure, putative recombination events and evolutionary relationships among members of the family Closteroviridae: A proposal for a new classification. BIOCHEM SYST ECOL 2010. [DOI: 10.1016/j.bse.2010.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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