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Viruses
Special Issues
Evolution, Ecology and Diversity of Plant Virus
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Evolution, Ecology and Diversity of Plant Virus

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viruses of Plants, Fungi and Protozoa".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 10393

Special Issue Editor

Dr. Wenxing Xu

E-Mail Website
Guest Editor
College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
Interests: identification of the viruses and viroids infecting horticultural crops and fungi; the interaction between viruses and viroids and their hosts

Special Issue Information

The next-generation sequencing method was developed in the second half of the 2000s and marked the beginning of high-throughput sequencing (HTS) analyses of viral communities. With this approach, numerous novel virus communities have been discovered in recent years and are further characterized in the molecular and biological aspects, greatly advancing our understanding of the evolution, ecology, and diversity of plant viruses. This Special Issue invites articles on recent developments and major accomplishments in the characterization of novel viruses, evolution, virus ecology, virus diversity, and biodiversity of plant viruses (including viroids, satellites, and other subviral agents), or related studies in these aspects, including the development of novel bioinformatics tools or approaches to advance knowledge around virus ecology and diversity. Particularly welcome are submissions on the characterization of viral communities in economically important plants using HTS approaches with novel viruses discovered. Studies, reviews, perspectives, and opinions summarizing the current state and future directions of and challenges in the field are all welcome in this collection.

Dr. Wenxing Xu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant virus
  • viroid
  • virus evolution
  • virus ecology
  • virus diversity
  • virus biodiversity
  • high-throughput sequencing
  • novel virus
  • virus population
  • virus variability

Published Papers (5 papers)

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Editorial

Jump to: Research

2 pages, 192 KiB  
Editorial
Special Issue: “Evolution, Ecology and Diversity of Plant Virus”
by Mengxue Yin and Wenxing Xu
Viruses 2023, 15(2), 487; https://doi.org/10.3390/v15020487 - 9 Feb 2023
Cited by 1 | Viewed by 1245
Abstract
The next-generation sequencing method was developed in the second half of the 2000s and marked the beginning of high-throughput sequencing (HTS) analyses of viral communities [...] Full article
(This article belongs to the Special Issue Evolution, Ecology and Diversity of Plant Virus)

Research

Jump to: Editorial

7 pages, 990 KiB  
Communication
The Spatial Diffusion of Cherry Leaf Roll Virus Revealed by a Bayesian Phylodynamic Analysis
by Jianguo Shen, Jing Guo, Xihong Chen, Wei Cai, Zhenguo Du and Yongjiang Zhang
Viruses 2022, 14(10), 2179; https://doi.org/10.3390/v14102179 - 1 Oct 2022
Cited by 3 | Viewed by 1397
Abstract
Cherry leaf roll virus (CLRV) is an important plant pathogen that causes severe and detrimental effects on cherry and other fruit plants. Despite recent progress in plant pathology, molecular biology, and population genetics of CLRV, the spatiotemporal spread of this virus remains poorly [...] Read more.
Cherry leaf roll virus (CLRV) is an important plant pathogen that causes severe and detrimental effects on cherry and other fruit plants. Despite recent progress in plant pathology, molecular biology, and population genetics of CLRV, the spatiotemporal spread of this virus remains poorly studied. In this study, we employed a Bayesian phylodynamics framework to investigate the spatial diffusion patterns of CLRV by analyzing the coat protein gene sequences of 81 viral isolates collected from five different countries. Consistent with the trade of cherry, our Bayesian phylodynamic analyses pointed to viral origins in New Zealand and identified multiple migration pathways between Germany and other countries, suggesting that Germany has played an important role in CLRV transmission. The results of our study will be useful in developing sustainable management strategies to control this pathogen. Full article
(This article belongs to the Special Issue Evolution, Ecology and Diversity of Plant Virus)
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16 pages, 4707 KiB  
Article
Interspecies Recombination-Led Speciation of a Novel Geminivirus in Pakistan
by Aamir Lal, Eui-Joon Kil, Thuy T. B. Vo, I Gusti Ngurah Prabu Wira Sanjaya, Muhammad Amir Qureshi, Bupi Nattanong, Muhammad Ali, Malik Nawaz Shuja and Sukchan Lee
Viruses 2022, 14(10), 2166; https://doi.org/10.3390/v14102166 - 30 Sep 2022
Cited by 3 | Viewed by 2013
Abstract
Recombination between isolates of different virus species has been known to be one of the sources of speciation. Weeds serve as mixing vessels for begomoviruses, infecting a wide range of economically important plants, thereby facilitating recombination. Chenopodium album is an economically important weed [...] Read more.
Recombination between isolates of different virus species has been known to be one of the sources of speciation. Weeds serve as mixing vessels for begomoviruses, infecting a wide range of economically important plants, thereby facilitating recombination. Chenopodium album is an economically important weed spread worldwide. Here, we present the molecular characterization of a novel recombinant begomovirus identified from C. album in Lahore, Pakistan. The complete DNA- A genome of the virus associated with the leaf distortion occurred in the infected C. album plants was cloned and sequenced. DNA sequence analysis showed that the nucleotide sequence of the virus shared 93% identity with those of the rose leaf curl virus and the duranta leaf curl virus. Interestingly, this newly identified virus is composed of open reading frames (ORFs) from different origins. Phylogenetic networks and complementary recombination detection methods revealed extensive recombination among the sequences. The infectious clone of the newly detected virus was found to be fully infectious in C. album and Nicotiana benthamiana as the viral DNA was successfully reconstituted from systemically infected tissues of inoculated plants, thus fulfilling Koch’s postulates. Our study reveals a new speciation of an emergent ssDNA plant virus associated with C. album through recombination and therefore, proposed the tentative name ‘Chenopodium leaf distortion virus’ (CLDV). Full article
(This article belongs to the Special Issue Evolution, Ecology and Diversity of Plant Virus)
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16 pages, 2397 KiB  
Article
Molecular Characteristics and Incidence of Apple Rubbery Wood Virus 2 and Citrus Virus A Infecting Pear Trees in China
by Yanxiang Wang, Ying Wang, Guoping Wang, Qingyu Li, Zhe Zhang, Liu Li, Yuzhuo Lv, Zuokun Yang, Jiashu Guo and Ni Hong
Viruses 2022, 14(3), 576; https://doi.org/10.3390/v14030576 - 11 Mar 2022
Cited by 5 | Viewed by 2611
Abstract
Apple rubbery wood virus 2 (ARWV-2) and citrus virus A (CiVA) belong to a recently approved family Phenuiviridae in the order Bunyavirales and possess negative-sense single-stranded RNA genomes. In this study, the genome sequence of three ARWV-2 isolates (S17E2, LYC2, and LYXS) and [...] Read more.
Apple rubbery wood virus 2 (ARWV-2) and citrus virus A (CiVA) belong to a recently approved family Phenuiviridae in the order Bunyavirales and possess negative-sense single-stranded RNA genomes. In this study, the genome sequence of three ARWV-2 isolates (S17E2, LYC2, and LYXS) and a CiVA isolate (CiVA-P) infecting pear trees grown in China were characterized using high-throughput sequencing combined with conventional reverse-transcription PCR (RT-PCR) assays. The genome-wide nt sequence identities were above 93.6% among the ARWV-2 isolates and above 93% among CiVA isolates. Sequence comparisons showed that sequence diversity occurred in the 5′ untranslated region of the ARWV-2 genome and the intergenic region of the CiVA genome. For the first time, this study revealed that ARWV-2 proteins Ma and Mb displayed a plasmodesma subcellular localization, and the MP of CiVA locates in cell periphery and can interact with the viral NP in bimolecular fluorescence complementation assays. RT-PCR tests disclosed that ARWV-2 widely occurs, while CiVA has a low incidence in pear trees grown in China. This study presents the first complete genome sequences and incidences of ARWV-2 and CiVA from pear trees and the obtained results extend our knowledge of the viral pathogens of pear grown in China. Full article
(This article belongs to the Special Issue Evolution, Ecology and Diversity of Plant Virus)
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11 pages, 3073 KiB  
Article
Identification of a New Badnavirus in the Chinaberry (Melia azedarach) Tree and Establishment of a LAMP-LFD Assay for Its Rapid and Visual Detection
by Huixin Lu, Jintian Tang, Kai Sun and Xiaoping Yu
Viruses 2021, 13(12), 2408; https://doi.org/10.3390/v13122408 - 1 Dec 2021
Cited by 4 | Viewed by 2024
Abstract
The Chinaberry tree, a member of the Meliaceae family, is cultivated in China for use in traditional medicines. In 2020, Chinaberry trees with leaf deformation symptoms were found in Hangzhou, Zhejiang province, China. In order to identify possible pathogenic viruses, a symptomatic sample [...] Read more.
The Chinaberry tree, a member of the Meliaceae family, is cultivated in China for use in traditional medicines. In 2020, Chinaberry trees with leaf deformation symptoms were found in Hangzhou, Zhejiang province, China. In order to identify possible pathogenic viruses, a symptomatic sample was subjected to deep sequencing of small interfering RNAs. Assembly of the resulting sequences led to the identification of a novel badnavirus, provisionally designated Chinaberry tree badnavirus 1 (ChTBV1). With the recent development of China’s seedling industry and increasing online shopping platforms, the risk of tree virus transmission has increased substantially. Therefore, it is important to detect the occurrence of ChTBV1 to ensure the safety of the Chinaberry tree seedling industry. Here, we describe the development and validation of a sensitive and robust method relying on a loop-mediated isothermal amplification (LAMP) assay, targeting a 197 nt region, to detect ChTBV1 from Chinaberry tree leaves. The LAMP assay was also adapted for rapid visualization of results by a lateral flow dipstick chromatographic detection method. Full article
(This article belongs to the Special Issue Evolution, Ecology and Diversity of Plant Virus)
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