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14 pages, 1857 KiB

Open AccessArticle

Two Novel Geminiviruses Identified in Bees (Apis mellifera and Nomia sp.)

by Rohan Antonio Bandoo, Simona Kraberger and Arvind Varsani

Viruses 2024, 16(4), 602; https://doi.org/10.3390/v16040602 - 13 Apr 2024

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Members of the Geminviridae family are circular single-stranded DNA plant-infecting viruses, some of which impact global food production. Geminiviruses are vectored by sap-feeding insects such as leafhoppers, treehoppers, aphids, and whiteflies. Additionally, geminivirus sequences have also been identified in other insects such as [...] Read more.

Members of the Geminviridae family are circular single-stranded DNA plant-infecting viruses, some of which impact global food production. Geminiviruses are vectored by sap-feeding insects such as leafhoppers, treehoppers, aphids, and whiteflies. Additionally, geminivirus sequences have also been identified in other insects such as dragonflies, mosquitoes, and stingless bees. As part of a viral metagenomics study on honeybees and solitary bees (Nomia sp.), two geminivirus genomes were identified. These represent a novel citlodavirus (from honeybees collected from Westmoreland, Jamaica) and a mastrevirus-like genome (from a solitary bee collected from Tempe, Arizona, USA). The novel honeybee-derived citlodavirus genome shares ~61 to 69% genome-wide nucleotide pairwise identity with other citlodavirus genome sequences and is most closely related to the passion fruit chlorotic mottle virus identified in Brazil. Whereas the novel solitary bee-derived mastrevirus-like genome shares ~55 to 61% genome-wide nucleotide identity with other mastreviruses and is most closely related to tobacco yellow dwarf virus identified in Australia, based on pairwise identity scores of the full genome, replication-associated protein, and capsid protein sequences. Previously, two geminiviruses in the Begomovirus genus were identified in samples of stingless bee (Trigona spp.) samples. Here, we identify viruses that represent two new species of geminiviruses from a honeybee and a solitary bee, which continues to demonstrate that plant pollinators can be utilized for the identification of plant-infecting DNA viruses in ecosystems. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology 2.0)

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15 pages, 4053 KiB

Open AccessArticle

Molecular Characterization of a Novel Enamovirus Infecting Raspberry

by Igor Koloniuk, Jana Fránová, Jaroslava Přibylová, Tatiana Sarkisova, Josef Špak, Jiunn Luh Tan, Rostislav Zemek, Radek Čmejla, Martina Rejlová, Lucie Valentová, Jiří Sedlák, Jan Holub, Jan Skalík, Dag-Ragnar Blystad, Bijaya Sapkota and Zhibo Hamborg

Viruses 2023, 15(12), 2281; https://doi.org/10.3390/v15122281 - 21 Nov 2023

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Abstract

Raspberry plants, valued for their fruits, are vulnerable to a range of viruses that adversely affect their yield and quality. Utilizing high-throughput sequencing (HTS), we identified a novel virus, tentatively named raspberry enamovirus 1 (RaEV1), in three distinct raspberry plants. This study provides [...] Read more.

Raspberry plants, valued for their fruits, are vulnerable to a range of viruses that adversely affect their yield and quality. Utilizing high-throughput sequencing (HTS), we identified a novel virus, tentatively named raspberry enamovirus 1 (RaEV1), in three distinct raspberry plants. This study provides a comprehensive characterization of RaEV1, focusing on its genomic structure, phylogeny, and possible transmission routes. Analysis of nearly complete genomes from 14 RaEV1 isolates highlighted regions of variance, particularly marked by indel events. The evidence from phylogenetic and sequence analyses supports the classification of RaEV1 as a distinct species within the Enamovirus genus. Among the 289 plant and 168 invertebrate samples analyzed, RaEV1 was detected in 10.4% and 0.4%, respectively. Most detections occurred in plants that were also infected with other common raspberry viruses. The virus was present in both commercial and wild raspberries, indicating the potential of wild plants to act as viral reservoirs. Experiments involving aphids as potential vectors demonstrated their ability to acquire RaEV1 but not to successfully transmit it to plants. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology 2.0)

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10 pages, 1149 KiB

Open AccessArticle

Elimination of Solanum nigrum ilarvirus 1 and Apple Hammerhead Viroid from Apple Cultivars Using Antivirals Ribavirin, Rimantadine, and Zidovudine

by Jiří Sedlák, Jaroslava Přibylová, Igor Koloňuk, Josef Špak, Ondřej Lenz and Matěj Semerák

Viruses 2023, 15(8), 1684; https://doi.org/10.3390/v15081684 - 02 Aug 2023

Cited by 1 | Viewed by 944

Abstract

Apple hammerhead viroid (AHVd) was detected in the apple cultivar ‘Šampion’ and in mixed infection with Solanum nigrum ilarvirus 1 (SnIV-1) in the cultivars ‘Selena’ and ‘Jonagored Supra’, using a high-throughput sequencing method. Experiments were conducted to eliminate both pathogens in apples using [...] Read more.

Apple hammerhead viroid (AHVd) was detected in the apple cultivar ‘Šampion’ and in mixed infection with Solanum nigrum ilarvirus 1 (SnIV-1) in the cultivars ‘Selena’ and ‘Jonagored Supra’, using a high-throughput sequencing method. Experiments were conducted to eliminate both pathogens in apples using meristem tip cultures in combination with the antivirotics ribavirin, rimantadine, and zidovudine. Elimination of both pathogens was verified by repeated RT-PCR and qRT-PCR assays after 7–11 months. Elimination of SnIV-1 from all cultivars was successful with each of the three antivirotics at concentrations of 20, 40, and 80 mg L⁻¹. Elimination of AHVd was also achieved, although less effectively and only with ribavirin in the concentration range of 20–160 mg L⁻¹. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology 2.0)

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12 pages, 5652 KiB

Open AccessArticle

The Additional 15 nt of 5′ UTR in a Novel Recombinant Isolate of Chilli Veinal Mottle Virus in Solanum nigrum L. Is Crucial for Infection

by Qionglian Wan, Kaiyue Zheng, Jian Wu, Shan Bu, Mengting Jiao, Huijie Zhou, Yuwen Lu, Hongying Zheng, Guanwei Wu, Shaofei Rao, Hairu Chen, Fei Yan and Jiejun Peng

Viruses 2023, 15(7), 1428; https://doi.org/10.3390/v15071428 - 23 Jun 2023

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Abstract

An isolate of chilli veinal mottle virus (ChiVMV; genus Potyvirus) of Solanum nigrum L. from southwest China (ChiVMV-YunN/Yuxi) was identified and sequenced (GenBank: OP404087). Comparison with other ChiVMV isolates and recombination analyses suggested a recombinant origin. The most significant recombination event among [...] Read more.

An isolate of chilli veinal mottle virus (ChiVMV; genus Potyvirus) of Solanum nigrum L. from southwest China (ChiVMV-YunN/Yuxi) was identified and sequenced (GenBank: OP404087). Comparison with other ChiVMV isolates and recombination analyses suggested a recombinant origin. The most significant recombination event among all 21 complete ChiVMV isolates was an ending breakpoint at 1408–1488 for ChiVMV-YunN/Yuxi with ChiVMV-TaiW and ChiVMV-YunN/Ca operating as the respective major and minor parents. Interestingly, the 5′ UTR of ChiVMV-YunN/Yuxi is 15 nucleotides (‘AAAAATAAAACAACC’) longer than other reported isolates. A full-length clone of ChiVMV-YunN/Yuxi was constructed and was shown to be infectious in Nicotiana benthamiana. The additional 15 nt of 5′ UTR in ChiVMV-YunN/Yuxi was stable when transmitted through three generations. Experiments with modified clones showed that the additional 15 nt are essential for infection by this isolate. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology 2.0)

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14 pages, 3497 KiB

Open AccessArticle

Virome Profiling, New Virus Identification and the Prevalence and Distribution of Viruses Infecting Chieh-Qua (Benincasa hispida Cogn. var. chieh-qua How) in China

by Haiyan Che, Yuxin Ma, Yating Lin, Tuizi Feng, Daquan Luo and Haibo Long

Viruses 2023, 15(6), 1396; https://doi.org/10.3390/v15061396 - 19 Jun 2023

Cited by 1 | Viewed by 1407

Abstract

The cucurbit vegetable chieh-qua (Benincasa hispida var. chieh-qua How) is an important crop in South China and southeast Asian countries. Viral diseases cause substantial loss of chieh-qua yield. To identify the viruses that affect chieh-qua in China, ribosomal RNA-depleted total RNA sequencing [...] Read more.

The cucurbit vegetable chieh-qua (Benincasa hispida var. chieh-qua How) is an important crop in South China and southeast Asian countries. Viral diseases cause substantial loss of chieh-qua yield. To identify the viruses that affect chieh-qua in China, ribosomal RNA-depleted total RNA sequencing was performed using chieh-qua leaf samples with typical viral symptoms. The virome of chieh-qua comprises four known viruses (melon yellow spot virus (MYSV), cucurbit chlorotic yellows virus (CCYV), papaya ringspot virus (PRSV) and watermelon silver mottle virus (WSMoV) and two novel viruses: cucurbit chlorotic virus (CuCV) in the genus Crinivirus and chieh-qua endornavirus (CqEV) in the genus Alphaendornavirus. The complete genomes of the two novel viruses in chieh-qua and three other isolates of CuCV in pumpkin, watermelon and cucumber were determined and the recombination signals of pumpkin and watermelon isolates of CuCV were detected. A reverse transcriptase PCR indicated that the dominant viruses of chieh-qua in Hainan are MYSV (66.67%) and CCYV (55.56%), followed by CuCV (27.41%), WSMoV (7.41%), cucumber mosaic virus (8.15%), zucchini yellow mosaic virus (6.67%), PRSV (6.67%) and CqEV (35.56%). Our findings support diagnostic and prevalence studies of viruses infecting chieh-qua in China, enabling sustainable control strategies for cucurbit viruses worldwide. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology 2.0)

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14 pages, 3916 KiB

Open AccessArticle

The Virome of Babaco (Vasconcellea × heilbornii) Expands to Include New Members of the Rhabdoviridae and Bromoviridae

by Edison G. Reyes-Proaño, Maria G. Cañada-Bautista, Juan F. Cornejo-Franco, Robert A. Alvarez-Quinto, Dimitre Mollov, Eduardo Sanchez-Timm and Diego F. Quito-Avila

Viruses 2023, 15(6), 1380; https://doi.org/10.3390/v15061380 - 16 Jun 2023

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Abstract

Babaco (Vasconcellea × heilbornii) is a subtropical species in the Caricaceae family. The plant is native to Ecuador and represents an important crop for hundreds of families. The objective of this study was to characterize, at the genomic level, two new [...] Read more.

Babaco (Vasconcellea × heilbornii) is a subtropical species in the Caricaceae family. The plant is native to Ecuador and represents an important crop for hundreds of families. The objective of this study was to characterize, at the genomic level, two new babaco viruses identified by high-throughput sequencing. The viruses, an ilarvirus and a nucleorhabdovirus, were found in a symptomatic babaco plant from a commercial nursery in the Azuay province of Ecuador. The tripartite genome of the new ilarvirus, provisionally named babaco ilarvirus 1 (BabIV-1), is related to subgroup 3 ilarviruses, including apple mosaic virus, apple necrotic mosaic virus, and prunus necrotic ringspot virus as the closest relatives. The genome of the nucleorhabdovirus, provisionally named babaco nucleorhabdovirus 1 (BabRV-1), showed the closest relation with joa yellow blotch-associated virus and potato yellow dwarf nucleorhabdovirus. Molecular-based detection methods found BabIV-1 and BabRV-1 in 21% and 36%, respectively, of plants surveyed in a commercial babaco nursery, highlighting the importance of enforcing virus testing and nursery certification programs for babaco. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology 2.0)

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15 pages, 4275 KiB

Open AccessArticle

Identification and Molecular Characterization of a Novel Carlavirus Infecting Chrysanthemum morifolium in China

by Jiapeng Li, Xiaoyin Wu, Hui Liu, Xiaomei Wang, Shaokui Yi, Xueting Zhong, Yaqin Wang and Zhanqi Wang

Viruses 2023, 15(4), 1029; https://doi.org/10.3390/v15041029 - 21 Apr 2023

Cited by 3 | Viewed by 1787

Abstract

Chrysanthemum (Chrysanthemum morifolium) is an important ornamental and medicinal plant suffering from many viruses and viroids worldwide. In this study, a new carlavirus, tentatively named Chinese isolate of Carya illinoinensis carlavirus 1 (CiCV1-CN), was identified from chrysanthemum plants in Zhejiang Province, [...] Read more.

Chrysanthemum (Chrysanthemum morifolium) is an important ornamental and medicinal plant suffering from many viruses and viroids worldwide. In this study, a new carlavirus, tentatively named Chinese isolate of Carya illinoinensis carlavirus 1 (CiCV1-CN), was identified from chrysanthemum plants in Zhejiang Province, China. The genome sequence of CiCV1-CN was 8795 nucleotides (nt) in length, with a 68-nt 5′-untranslated region (UTR) and a 76-nt 3′-UTR, which contained six predicted open reading frames (ORFs) that encode six corresponding proteins of various sizes. Phylogenetic analyses based on full-length genome and coat protein sequences revealed that CiCV1-CN is in an evolutionary branch with chrysanthemum virus R (CVR) in the Carlavirus genus. Pairwise sequence identity analysis showed that, except for CiCV1, CiCV1-CN has the highest whole-genome sequence identity of 71.3% to CVR-X6. At the amino acid level, the highest identities of predicted proteins encoded by the ORF1, ORF2, ORF3, ORF4, ORF5, and ORF6 of CiCV1-CN were 77.1% in the CVR-X21 ORF1, 80.3% in the CVR-X13 ORF2, 74.8% in the CVR-X21 ORF3, 60.9% in the CVR-BJ ORF4, 90.2% in the CVR-X6 and CVR-TX ORF5s, and 79.4% in the CVR-X21 ORF6. Furthermore, we also found a transient expression of the cysteine-rich protein (CRP) encoded by the ORF6 of CiCV1-CN in Nicotiana benthamiana plants using a potato virus X-based vector, which can result in a downward leaf curl and hypersensitive cell death over the time course. These results demonstrated that CiCV1-CN is a pathogenic virus and C. morifolium is a natural host of CiCV1. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology 2.0)

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14 pages, 3454 KiB

Open AccessArticle

A Rice Receptor-like Protein Negatively Regulates Rice Resistance to Southern Rice Black-Streaked Dwarf Virus Infection

by Fengmin Wang, Weiqi Song, Chaorui Huang, Zhongyan Wei, Yanjun Li, Jianping Chen, Hehong Zhang and Zongtao Sun

Viruses 2023, 15(4), 973; https://doi.org/10.3390/v15040973 - 15 Apr 2023

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Abstract

Plants rely on various receptor-like proteins and receptor-like kinases to recognize and defend against invading pathogens. However, research on the role of receptor-like proteins in plant antiviral defense, particularly in rice–virus interactions, is limited. In this study, we identified a receptor-like gene, OsBAP1 [...] Read more.

Plants rely on various receptor-like proteins and receptor-like kinases to recognize and defend against invading pathogens. However, research on the role of receptor-like proteins in plant antiviral defense, particularly in rice–virus interactions, is limited. In this study, we identified a receptor-like gene, OsBAP1, which was significantly induced upon infection with southern rice black-streaked dwarf virus (SRBSDV) infection. A viral inoculation assay showed that the OsBAP1 knockout mutant exhibited enhanced resistance to SRBSDV infection, indicating that OsBAP1 plays a negatively regulated role in rice resistance to viral infection. Transcriptome analysis revealed that the genes involved in plant–pathogen interactions, plant hormone signal transduction, oxidation–reduction reactions, and protein phosphorylation pathways were significantly enriched in OsBAP1 mutant plants (osbap1-cas). Quantitative real-time PCR (RT-qPCR) analysis further demonstrated that some defense-related genes were significantly induced during SRBSDV infection in osbap1-cas mutants. Our findings provide new insights into the role of receptor-like proteins in plant immune signaling pathways, and demonstrate that OsBAP1 negatively regulates rice resistance to SRBSDV infection. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology 2.0)

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8 pages, 2299 KiB

Open AccessBrief Report

Identification and Genome Characterization of a Novel Virus within the Genus Totivirus from Chinese Bayberry (Myrica rubra)

by Zhongtian Xu, Yi’nan Gao, Kun Teng, Huoyang Ge, Xiaoqi Zhang, Mengjing Wu, Ruhui Li, Zujian Wu and Luping Zheng

Viruses 2024, 16(2), 283; https://doi.org/10.3390/v16020283 - 12 Feb 2024

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Abstract

Chinese bayberry (Myrica rubra) is an economically significant fruit tree native to eastern Asia and widely planted in south-central China. However, studies about the viruses infecting M. rubra remain largely lacking. In the present study, we employed the metatranscriptomic method to [...] Read more.

Chinese bayberry (Myrica rubra) is an economically significant fruit tree native to eastern Asia and widely planted in south-central China. However, studies about the viruses infecting M. rubra remain largely lacking. In the present study, we employed the metatranscriptomic method to identify viruses in M. rubra leaves exhibiting yellowing and irregular margin symptoms collected in Fuzhou, a city located in China’s Fujian province in the year 2022. As a consequence, a novel member of the genus Totivirus was identified and tentatively named “Myrica rubra associated totivirus 1” (MRaTV1). The genome sequencing of MRaTV1 was determined by overlapping reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The two deduced proteins encoded by MRaTV1 have the highest amino acid (aa) sequence identity to the coat protein (CP) and RNA-dependent RNA polymerase (RdRP) of Panax notoginseng virus A (PNVA), a member of the genus Totivirus within the family Totiviridae, at 49.7% and 61.7%, respectively. According to the results of the phylogenetic tree and the species demarcation criteria of the International Committee on Taxonomy of Viruses (ICTV) for the genus Totivirus, MRaTV1 is considered a new member of the genus Totivirus. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Plant Virology 2.0)

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