Viruses

Editorial

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4 pages, 172 KiB

Open AccessEditorial

State-of-the-Art Plant Virus Research in Australasia

by Steve Wylie and Nuredin Habili

Viruses 2023, 15(6), 1311; https://doi.org/10.3390/v15061311 - 1 Jun 2023

Viewed by 1394

Abstract

The Special Issue ‘State-of-the-Art Plant Virus Research in Australasia’ in Viruses provided a fascinating snapshot of plant and fungus virus research being undertaken in Australasia during the final year of the official COVID-19 pandemic [...] Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in Australasia)

Research

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14 pages, 2265 KiB

Open AccessArticle

A Chronological Study on Grapevine Leafroll-Associated Virus 2 in Australia

by Nuredin Habili, Qi Wu, Amy Rinaldo and Fiona Constable

Viruses 2023, 15(5), 1105; https://doi.org/10.3390/v15051105 - 30 Apr 2023

Cited by 3 | Viewed by 2341

Abstract

Grapevine leafroll disease affects the health status of grapevines worldwide. Most studies in Australia have focused on grapevine leafroll-associated viruses 1 and 3, while little attention has been given to other leafroll virus types, in particular, grapevine leafroll-associated virus 2 (GLRaV-2). A chronological [...] Read more.

Grapevine leafroll disease affects the health status of grapevines worldwide. Most studies in Australia have focused on grapevine leafroll-associated viruses 1 and 3, while little attention has been given to other leafroll virus types, in particular, grapevine leafroll-associated virus 2 (GLRaV-2). A chronological record of the temporal occurrence of GLRaV-2 in Australia since 2001 is reported. From a total of 11,257 samples, 313 tested positive, with an overall incidence of 2.7%. This virus has been detected in 18 grapevine varieties and Vitis rootstocks in different regions of Australia. Most varieties were symptomless on their own roots, while Chardonnay showed a decline in virus-sensitive rootstocks. An isolate of GLRaV-2, on own-rooted Vitis vinifera cv. Grenache, clone SA137, was associated with severe leafroll symptoms after veraison with abnormal leaf necrosis. The metagenomic sequencing results of the virus in two plants of this variety confirmed the presence of GLRaV-2, as well as two inert viruses, grapevine rupestris stem pitting-associated virus (GRSPaV) and grapevine rupestris vein feathering virus (GRVFV). No other leafroll-associated viruses were detected. Among the viroids, hop stunt viroid and grapevine yellow speckle viroid 1 were detected. Of the six phylogenetic groups identified in GLRaV-2, we report the presence of four groups in Australia. Three of these groups were detected in two plants of cv. Grenache, without finding any recombination event. The hypersensitive reaction of certain American hybrid rootstocks to GLRaV-2 is discussed. Due to the association of GLRaV-2 with graft incompatibility and vine decline, the risk from this virus in regions where hybrid Vitis rootstocks are used cannot be overlooked. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in Australasia)

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20 pages, 1461 KiB

Open AccessArticle

Small RNA Analyses of a Ceratobasidium Isolate Infected with Three Endornaviruses

by Chi T. H. Cao, Mark C. Derbyshire, Roshan Regmi, Hua Li, Michael G. K. Jones and Stephen J. Wylie

Viruses 2022, 14(10), 2276; https://doi.org/10.3390/v14102276 - 17 Oct 2022

Cited by 3 | Viewed by 1923

Abstract

Isolates of three endornavirus species were identified co-infecting an unidentified species of Ceratobasidium, itself identified as a symbiont from within the roots of a wild plant of the terrestrial orchid Pterostylis vittata in Western Australia. Isogenic lines of the fungal isolate lacking [...] Read more.

Isolates of three endornavirus species were identified co-infecting an unidentified species of Ceratobasidium, itself identified as a symbiont from within the roots of a wild plant of the terrestrial orchid Pterostylis vittata in Western Australia. Isogenic lines of the fungal isolate lacking all three mycoviruses were derived from the virus-infected isolate. To observe how presence of endornaviruses influenced gene expression in the fungal host, we sequenced fungus-derived small RNA species from the virus-infected and virus-free isogenic lines and compared them. The presence of mycoviruses influenced expression of small RNAs. Of the 3272 fungus-derived small RNA species identified, the expression of 9.1% (300 of 3272) of them were up-regulated, and 0.6% (18 of 3272) were down-regulated in the presence of the viruses. Fourteen novel micro-RNA-like RNAs (Cer-milRNAs) were predicted. Gene target prediction of the differentially expressed Cer-milRNAs was quite ambiguous; however, fungal genes involved in transcriptional regulation, catalysis, molecular binding, and metabolic activities such as gene expression, DNA metabolic processes and regulation activities were differentially expressed in the presence of the mycoviruses. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in Australasia)

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23 pages, 2649 KiB

Open AccessArticle

Development and Validation of a Bioinformatic Workflow for the Rapid Detection of Viruses in Biosecurity

by David W. Waite, Lia Liefting, Catia Delmiglio, Anastasia Chernyavtseva, Hye Jeong Ha and Jeremy R. Thompson

Viruses 2022, 14(10), 2163; https://doi.org/10.3390/v14102163 - 30 Sep 2022

Cited by 7 | Viewed by 2795

Abstract

The field of biosecurity has greatly benefited from the widespread adoption of high-throughput sequencing technologies, for its ability to deeply query plant and animal samples for pathogens for which no tests exist. However, the bioinformatics analysis tools designed for rapid analysis of these [...] Read more.

The field of biosecurity has greatly benefited from the widespread adoption of high-throughput sequencing technologies, for its ability to deeply query plant and animal samples for pathogens for which no tests exist. However, the bioinformatics analysis tools designed for rapid analysis of these sequencing datasets are not developed with this application in mind, limiting the ability of diagnosticians to standardise their workflows using published tool kits. We sought to assess previously published bioinformatic tools for their ability to identify plant- and animal-infecting viruses while distinguishing from the host genetic material. We discovered that many of the current generation of virus-detection pipelines are not adequate for this task, being outperformed by more generic classification tools. We created synthetic MinION and HiSeq libraries simulating plant and animal infections of economically important viruses and assessed a series of tools for their suitability for rapid and accurate detection of infection, and further tested the top performing tools against the VIROMOCK Challenge dataset to ensure that our findings were reproducible when compared with international standards. Our work demonstrated that several methods provide sensitive and specific detection of agriculturally important viruses in a timely manner and provides a key piece of ground truthing for method development in this space. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in Australasia)

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19 pages, 2747 KiB

Open AccessArticle

Abundance of Poleroviruses within Tasmanian Pea Crops and Surrounding Weeds, and the Genetic Diversity of TuYV Isolates Found

by Muhammad Umar, Robert S. Tegg, Tahir Farooq, Tamilarasan Thangavel and Calum R. Wilson

Viruses 2022, 14(8), 1690; https://doi.org/10.3390/v14081690 - 30 Jul 2022

Cited by 5 | Viewed by 2470

Abstract

The genus Polerovirus contains positive-sense, single-stranded RNA plant viruses that cause significant disease in many agricultural crops, including vegetable legumes. This study aimed to identify and determine the abundance of Polerovirus species present within Tasmanian pea crops and surrounding weeds that may act [...] Read more.

The genus Polerovirus contains positive-sense, single-stranded RNA plant viruses that cause significant disease in many agricultural crops, including vegetable legumes. This study aimed to identify and determine the abundance of Polerovirus species present within Tasmanian pea crops and surrounding weeds that may act as virus reservoirs. We further sought to examine the genetic diversity of TuYV, the most commonly occurring polerovirus identified. Pea and weed samples were collected during 2019–2020 between October and January from thirty-four sites across three different regions (far northwest, north, and midlands) of Tasmania and tested by RT-PCR assay, with selected samples subject to next-generation sequencing. Results revealed that the presence of polerovirus infection and the prevalence of TuYV in both weeds and pea crops varied across the three Tasmanian cropping regions, with TuYV infection levels in pea crops ranging between 0 and 27.5% of tested plants. Overall, two species members from each genus, Polerovirus and Potyvirus, one member from each of Luteovirus, Potexvirus, and Carlavirus, and an unclassified virus from the family Partitiviridae were also found as a result of NGS data analysis. Analysis of gene sequences of the P0 and P3 genes of Tasmanian TuYV isolates revealed substantial genetic diversity within the collection, with a few isolates appearing more closely aligned with BrYV isolates. Questions remain around the differentiation of TuYV and BrYV species. Phylogenetic inconsistency in the P0 and P3 ORFs supports the concept that recombination may have played a role in TuYV evolution in Tasmania. Results of the evolutionary analysis showed that the selection pressure was higher in the P0 gene than in the P3 gene, and the majority of the codons for each gene are evolving under purifying selection. Future full genome-based analyses of the genetic variations will expand our understanding of the evolutionary patterns existing among TuYV populations in Tasmania. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in Australasia)

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13 pages, 3770 KiB

Open AccessArticle

Is the Glycoprotein Responsible for the Differences in Dispersal Rates between Lettuce Necrotic Yellows Virus Subgroups?

by Eko Y. Prabowo, Gardette R. Valmonte-Cortes, Toni Louise Darling, Elizabeth Buckley, Mark Duxbury, Brent Seale and Colleen M. Higgins

Viruses 2022, 14(7), 1574; https://doi.org/10.3390/v14071574 - 20 Jul 2022

Cited by 1 | Viewed by 2274

Abstract

Lettuce necrotic yellows virus is a type of species in the Cytorhabdovirus genus and appears to be endemic to Australia and Aotearoa New Zealand (NZ). The population of lettuce necrotic yellows virus (LNYV) is made up of two subgroups, SI and SII. Previous [...] Read more.

Lettuce necrotic yellows virus is a type of species in the Cytorhabdovirus genus and appears to be endemic to Australia and Aotearoa New Zealand (NZ). The population of lettuce necrotic yellows virus (LNYV) is made up of two subgroups, SI and SII. Previous studies demonstrated that SII appears to be outcompeting SI and suggested that SII may have greater vector transmission efficiency and/or higher replication rate in its host plant or insect vector. Rhabdovirus glycoproteins are important for virus–insect interactions. Here, we present an analysis of LNYV glycoprotein sequences to identify key features and variations that may cause SII to interact with its aphid vector with greater efficiency than SI. Phylogenetic analysis of glycoprotein sequences from NZ isolates confirmed the existence of two subgroups within the NZ LNYV population, while predicted 3D structures revealed the LNYV glycoproteins have domain architectures similar to Vesicular Stomatitis Virus (VSV). Importantly, changing amino acids at positions 244 and 247 of the post-fusion form of the LNYV glycoprotein altered the predicted structure of Domain III, glycosylation at N248 and the overall stability of the protein. These data support the glycoprotein as having a role in the population differences of LNYV observed between Australia and New Zealand. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in Australasia)

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15 pages, 1536 KiB

Open AccessArticle

Historical and Scientific Evidence for the Origin and Cultural Importance to Australia’s First-Nations Peoples of the Laboratory Accession of Nicotiana benthamiana, a Model for Plant Virology

by Steve Wylie and Hua Li

Viruses 2022, 14(4), 771; https://doi.org/10.3390/v14040771 - 8 Apr 2022

Cited by 7 | Viewed by 3010

Abstract

Nicotiana benthamiana is an indigenous plant species distributed across northern Australia. The laboratory accession (LAB) of N. benthamiana has become widely adopted as a model host for plant viruses, and it is distinct from other accessions morphologically, physiologically, and by having an attenuation-of-function [...] Read more.

Nicotiana benthamiana is an indigenous plant species distributed across northern Australia. The laboratory accession (LAB) of N. benthamiana has become widely adopted as a model host for plant viruses, and it is distinct from other accessions morphologically, physiologically, and by having an attenuation-of-function mutation in the RNA-dependent RNA polymerase 1 (NbRdr1) gene, referred to as NbRdr1m. Recent historical evidence suggested LAB was derived from a 1936 collection by John Cleland at The Granites of the Northern Territory, although no scientific evidence was provided. We provide scientific evidence and further historical evidence supporting the origin of LAB as The Granites. Analysis of a herbarium specimen of N. benthamiana collected by Cleland in 1936 revealed that The Granites population contains plants heterozygous for the NbRdr1 locus, having both the functional NbRdr1 and the mutant NbRdr1m alleles. N. benthamiana was an important cultural asset actively utilised as the narcotic Pituri (chewing tobacco) by the Warlpiri Aboriginal people at the site, who prevented women of child-bearing age from consuming it. We propose that Aboriginal people selected some of the unique traits of LAB that have subsequently facilitated its adoption as a model plant, such as lack of seed dormancy, fast maturity, low nornicotine content, and gracility. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in Australasia)

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Review

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15 pages, 1110 KiB

Open AccessReview

New Virus Diagnostic Approaches to Ensuring the Ongoing Plant Biosecurity of Aotearoa New Zealand

by Catia Delmiglio, David W. Waite, Sonia T. Lilly, Juncong Yan, Candace E. Elliott, Julie Pattemore, Paul L. Guy and Jeremy R. Thompson

Viruses 2023, 15(2), 418; https://doi.org/10.3390/v15020418 - 1 Feb 2023

Cited by 3 | Viewed by 2894

Abstract

To protect New Zealand’s unique ecosystems and primary industries, imported plant materials must be constantly monitored at the border for high-threat pathogens. Techniques adopted for this purpose must be robust, accurate, rapid, and sufficiently agile to respond to new and emerging threats. Polymerase [...] Read more.

To protect New Zealand’s unique ecosystems and primary industries, imported plant materials must be constantly monitored at the border for high-threat pathogens. Techniques adopted for this purpose must be robust, accurate, rapid, and sufficiently agile to respond to new and emerging threats. Polymerase chain reaction (PCR), especially real-time PCR, remains an essential diagnostic tool but it is now being complemented by high-throughput sequencing using both Oxford Nanopore and Illumina technologies, allowing unbiased screening of whole populations. The demand for and value of Point-of-Use (PoU) technologies, which allow for in situ screening, are also increasing. Isothermal PoU molecular diagnostics based on recombinase polymerase amplification (RPA) and loop-mediated amplification (LAMP) do not require expensive equipment and can reach PCR-comparable levels of sensitivity. Recent advances in PoU technologies offer opportunities for increased specificity, accuracy, and sensitivities which makes them suitable for wider utilization by frontline or border staff. National and international activities and initiatives are adopted to improve both the plant virus biosecurity infrastructure and the integration, development, and harmonization of new virus diagnostic technologies. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in Australasia)

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Other

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8 pages, 965 KiB

Open AccessBrief Report

Spillover of a Tobamovirus from the Australian Indigenous Flora to Invasive Weeds

by Weinan Xu, Hua Li, Krishnapillai Sivasithamparam, Dieu Thi Tran, Michael G. K. Jones, Xin Chen and Stephen J. Wylie

Viruses 2022, 14(8), 1676; https://doi.org/10.3390/v14081676 - 29 Jul 2022

Cited by 4 | Viewed by 1925

Abstract

The tobamovirus yellow tailflower mild mottle virus (YTMMV) was previously reported in wild plants of Anthocercis species (family Solanaceae) and other solanaceous indigenous species growing in natural habitats in Western Australia. Here, we undertook a survey of two introduced solanaceous weeds, namely Solanum [...] Read more.

The tobamovirus yellow tailflower mild mottle virus (YTMMV) was previously reported in wild plants of Anthocercis species (family Solanaceae) and other solanaceous indigenous species growing in natural habitats in Western Australia. Here, we undertook a survey of two introduced solanaceous weeds, namely Solanum nigrum (black nightshade) and Physalis peruviana (cape gooseberry) in the Perth metropolitan area and surrounds to determine if YTMMV has spread naturally to these species. At a remnant natural bushland site where both solanaceous weeds and indigenous Anthocercis hosts grew adjacent to one another, a proportion of S. nigrum and P. peruviana plants were asymptomatically-infected with YTMMV, confirming spillover had occurred. Populations of S. nigrum also grow as weeds in parts of the city isolated from remnant bushland and indigenous sources of YTMMV, and some of these populations were also infected with YTMMV. Fruit was harvested from virus-infected wild S. nigrum plants and the seed germinated under controlled conditions. Up to 80% of resultant seedlings derived from infected parent plants were infected with YTMMV, confirming that the virus is vertically-transmitted in S. nigrum, and therefore infection appears to be self-sustaining in this species. This is the first report of spillover of YTMMV to exotic weeds, and of vertical transmission of this tobamovirus. We discuss the roles of vertical and horizontal transmission in this spillover event, and its implications for biosecurity. Full article

(This article belongs to the Special Issue State-of-the-Art Plant Virus Research in Australasia)

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