A bushel of viruses: Identification of seventeen novel putative viruses by RNA-seq in six apple trees

Wright, Alice A.; Cross, Alex R.; Harper, Scott J.

doi:10.1371/journal.pone.0227669

Cited by 39 publications

(36 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…o Penicillimonavirus alphapenicillii for Penicillium adametzioides negative-stranded RNA virus 1 (PaN-sRV-1), discovered by HTS in a fungus (Penicillium adametzioides S. Abe ex G. Smith 1963) sampled in Spresiano, Veneto Region, Italy [73]; o Penicillimonavirus alphaplasmoparae for Plasmopara viticola lesion associated mononegaambi virus 1 (PvaMV- [110].…”

Section: Family Mymonaviridaementioning

confidence: 99%

2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

et al. 2021

View full text Add to dashboard Cite

王林发) 186 • Guoping Wang (王国平) 85 • Yanxiang Wang (王雁翔) 85 • Yaqin Wang (王亚琴) 38 • Muhammad Waqas 187 • Tàiyún Wèi (魏太云) 188 • Shaohua Wen (温少华) 85 • Anna E. Whitfield 189 • John V. Williams 190 • Yuri I. Wolf 99 • Jiangxiang Wu (吴建祥) 38 • Lei Xu (徐雷) 138 • Hironobu Yanagisawa (栁澤広宣) 191 • Caixia Yang (杨彩霞) 69 • Zuokun Yang (杨作坤) 85 • F. Murilo Zerbini 192 • Lifeng Zhai (翟立峰) 193 • Yong-Zhen Zhang (张永振) 220,221 • Song Zhang (张松) 34 • Jinguo Zhang (张靖国) 194 • Zhe Zhang (张哲) 85 • Xueping Zhou (周雪平) 195

show abstract

Section: Family Mymonaviridaementioning

confidence: 99%

2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Journals have very different policies on this subject. For example, a recent publication presenting only the contigs generated without any biological confirmation has been recently accepted (Wright et al, 2020), while other journals require biological characterization experiments for accepting the publication of a new virus. Whatever the policy of the journal, our retrospective analysis suggests that in more than 90% of the cases, the confirmation of the detection of the new virus by an independent technique and the characterization of the full or nearly full genome have been presented for a peer-review publication of a new fruit tree virus.…”

Section: Resultsmentioning

confidence: 99%

“…The scientific information provided in the original publication describing a new virus is highly variable. The minimal information corresponded to a recent publication of HTS sequences gathered into contigs without any biology confirmation of the results (Wright et al, 2020). On the other hand, a comprehensive biological characterization of the newly identified viruses was provided for temperate fruit decay associated virus (TFDaV).…”

Section: Analysis Of the Scientific Information Added When A New Viramentioning

confidence: 99%

See 1 more Smart Citation

Is There a “Biological Desert” With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses

Hou

Massart

2020

Front. Microbiol.

View full text Add to dashboard Cite

High throughput sequencing technologies accelerated the pace of discovery and identification of new viral species. Nevertheless, biological characterization of a new virus is a complex and long process, which can hardly follow the current pace of virus discovery. This review has analyzed 78 publications of new viruses and viroids discovered from 32 fruit tree species since 2011. The scientific biological information useful for a pest risk assessment and published together with the discovery of a new fruit tree virus or viroid has been analyzed. In addition, the 933 publications citing at least one of these original publications were reviewed, focusing on the biology-related information provided. In the original publications, the scientific information provided was the development of a detection test (94%), whole-genome sequence including UTRs (92%), local and large-scale epidemiological surveys (68%), infectivity and indicators experiments (50%), association with symptoms (25%), host range infection (23%), and natural vector identification (8%). The publication of a new virus is cited 2.8 times per year on average. Only 18% of the citations reported information on the biology or geographical repartition of the new viruses. These citing publications improved the new virus characterization by identifying the virus in a new country or continent, determining a new host, developing a new diagnostic test, studying genome or gene diversity, or by studying the transmission. Based on the gathered scientific information on the virus biology, the fulfillment of a recently proposed framework has been evaluated. A baseline prioritization approach for publishing a new plant virus is proposed for proper assessment of the potential risks caused by a newly identified fruit tree virus.

show abstract

“…Recently, the RdRp-encoding segment was also identified for three ourmia-like viruses from apple trees with proposed names apple ourmia-like virus 1, 2 and 3. It was, however, not possible to decide whether the host of these viruses was apple or a fungus associated with the analyzed apple samples [27]. Due to the very limited information on these new ourmia-like viruses, it is not possible to conclude on a possible contribution of the detected ourmia-like viruses to the symptoms observed on pomegranate.…”

Section: Discussionmentioning

confidence: 97%

Identification of Pomegranate as a New Host of Passiflora Edulis Symptomless Virus (PeSV) and Analysis of PeSV Diversity

et al. 2020

View full text Add to dashboard Cite

Pomegranate is an important crop in the Mediterranean Basin that can be affected by a range of pathogens. With the aim to better understand the impact of viral diseases on pomegranate, two leaf samples from Turkey showing virus-like symptoms such as chlorotic spots and oak-leaf patterns were subjected to high throughput sequencing (HTS). Data analysis indicated the presence of passiflora edulis symptomless virus (PeSV: genus Roymovirus, Potyviridae family) in these two pomegranate samples, consistent with the observation by electron microscopy of flexuous filamentous viral particles 760 to 780 nm long. Further analysis of HTS reads revealed the presence of five PeSV variants in one of the samples and another single variant in the other. PeSV occurrence was also identified from publicly available SRA pomegranate RNA-Seq transcriptomic data from India and China. The genome of these PeSV-pomegranate variants share 78.0–86.8% nucleotide identity with that of the reference isolate from passionfruit (MH379332). The presence of PeSV in pomegranate was confirmed by specific RT-PCR assays targeting either the coat protein (CP) or Nla-Pro genes in 37 cultivated and one ornamental pomegranate out of 133 samples collected from the Eastern Mediterranean region of Turkey. To our knowledge, this is the first application of HTS to assess virus occurrence in pomegranate and the first recognition of pomegranate as a new host for PeSV.

show abstract

A bushel of viruses: Identification of seventeen novel putative viruses by RNA-seq in six apple trees

Abstract: Apple decline in Washington state has been increasing in incidence, particularly on Honeycrisp trees grown on G.935 rootstock. In this disease the trees exhibit dieback with necrosis at the graft union and in the rootstock.

Cited by 39 publications

References 49 publications

2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales

Is There a “Biological Desert” With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses

Identification of Pomegranate as a New Host of Passiflora Edulis Symptomless Virus (PeSV) and Analysis of PeSV Diversity

Contact Info

Product

Resources

About