Carnation Italian Ringspot Virus p36 Expression Induces Mitochondrial Fission and Respiratory Chain Complex Impairment in Yeast.

Positive-strand RNA virus replication invariably occurs in association with host cell membranes, which are induced to proliferate and rearrange to form vesicular structures where the virus replication complex is assembled. In particular, carnation Italian ringspot virus (CIRV) replication takes place on the mitochondrial outer membrane in plant and yeast cells. In this work, the model host Saccharomyces cerevisiae was used to investigate the effects of CIRV p36 expression on the mitochondrial structure and function through the determination of mitochondrial morphology, mitochondrial respiratory parameters, and respiratory chain complex activities in p36-expressing cells. CIRV p36 ectopic expression was shown to induce alterations in the mitochondrial network associated with a decrease in mitochondrial respiration and the activities of NADH-cyt c, succinate-cyt c (C II-III), and cytochrome c oxidase (C IV) complexes. Our results suggest that the decrease in respiratory complex activity could be due, at least in part, to alterations in mitochondrial dynamics. This yeast-based model will be a valuable tool for identifying molecular targets to develop new anti-viral strategies.

Exogenous and endogenous dsRNAs perceived by plant Dicer-like 4 protein in the RNAi-depleted cellular context.

BACKGROUND: In plants, RNase III Dicer-like proteins (DCLs) act as sensors of dsRNAs and process them into short 21- to 24-nucleotide (nt) (s)RNAs. Plant DCL4 is involved in the biogenesis of either functional endogenous or exogenous (i.e. viral) short interfering (si)RNAs, thus playing crucial antiviral roles. METHODS: In this study we expressed plant DCL4 in Saccharomyces cerevisiae, an RNAi-depleted organism, in which we could highlight the role of dicing as neither Argonautes nor RNA-dependent RNA polymerase is present. We have therefore tested the DCL4 functionality in processing exogenous dsRNA-like substrates, such as a replicase-assisted viral replicon defective-interfering RNA and RNA hairpin substrates, or endogenous antisense transcripts. RESULTS: DCL4 was shown to be functional in processing dsRNA-like molecules in vitro and in vivo into 21- and 22-nt sRNAs. Conversely, DCL4 did not efficiently process a replicase-assisted viral replicon in vivo, providing evidence that viral RNAs are not accessible to DCL4 in membranes associated in active replication. Worthy of note, in yeast cells expressing DCL4, 21- and 22-nt sRNAs are associated with endogenous loci. CONCLUSIONS: We provide new keys to interpret what was studied so far on antiviral DCL4 in the host system. The results all together confirm the role of sense/antisense RNA-based regulation of gene expression, expanding the sense/antisense atlas of S. cerevisiae. The results described herein show that S. cerevisiae can provide insights into the functionality of plant dicers and extend the S. cerevisiae tool to new biotechnological applications.

Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023).

This article reports changes to virus taxonomy and taxon nomenclature that were approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2023. The entire ICTV membership was invited to vote on 174 taxonomic proposals that had been approved by the ICTV Executive Committee in July 2022, as well as a proposed revision of the ICTV Statutes. All proposals and the revised ICTV Statutes were approved by a majority of the voting membership. Of note, the ICTV continued the process of renaming existing species in accordance with the recently mandated binomial format and included gene transfer agents (GTAs) in the classification framework by classifying them as viriforms. In total, one class, seven orders, 31 families, 214 genera, and 858 species were created.

Pest categorisation of coconut cadang-cadang viroid.

The EFSA Panel on Plant Health updated its 2017 pest categorisation of coconut cadang cadang viroid (CCCVd) for the EU territory due to new data on its host range. The identity of CCCVd, a member of the genus Cocadviroid (family Pospiviroidae), is established and detection and identification methods are available. It is included as a quarantine pest for the EU in the Commission Implementing Regulation (EU) 2019/2072. CCCVd has been reported from the Philippines and Malaysia. It is not known to be present in the EU. The host range of CCCVd is restricted to Arecaceae species (palms), in particular, coconut palm (Cocos nucifera) to which it causes a lethal disease. Oil palm (Elaeis guineensis) and buri palm (Corypha utan) are other natural hosts of CCCVd. Palm species of several genera, including Phoenix spp. and other species grown and/or cultivated in the EU, have been identified as potential hosts. The viroid is naturally transmitted at low rate by seeds and pollen and possibly by additional not yet identified natural transmission means. It can be transmitted through vegetative propagation applied to some palm species. Plants for planting including seeds of its hosts have been identified as the main entry pathway of CCCVd. Potential hosts of CCCVd are present in the EU, therefore establishment is possible. Should the pest establish in the EU, an impact is expected, with uncertainty on its magnitude. The Panel identified the susceptibility of palm species grown in the EU as a key uncertainty potentially affecting the conclusion of this pest categorisation. Nevertheless, the pest satisfies the criteria that are within the remit of EFSA to assess for this viroid to be regarded as potential Union quarantine pest.

Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV).

The taxonomy of viruses is developed and overseen by the International Committee on Taxonomy of Viruses (ICTV), which scrutinizes, approves and ratifies taxonomic proposals, and maintains a list of virus taxa with approved names (https://ictv.global). The ICTV has approximately 180 members who vote by simple majority. Taxon-specific Study Groups established by the ICTV have a combined membership of over 600 scientists from the wider virology community; they provide comprehensive expertise across the range of known viruses and are major contributors to the creation and evaluation of taxonomic proposals. Proposals can be submitted by anyone and will be considered by the ICTV irrespective of Study Group support. Thus, virus taxonomy is developed from within the virology community and realized by a democratic decision-making process. The ICTV upholds the distinction between a virus or replicating genetic element as a physical entity and the taxon category to which it is assigned. This is reflected by the nomenclature of the virus species taxon, which is now mandated by the ICTV to be in a binomial format (genus + species epithet) and is typographically distinct from the names of viruses. Classification of viruses below the rank of species (such as, genotypes or strains) is not within the remit of the ICTV. This article, authored by the ICTV Executive Committee, explains the principles of virus taxonomy and the organization, function, processes and resources of the ICTV, with the aim of encouraging greater understanding and interaction among the wider virology community.

Pest categorisation of cowpea mosaic virus.

The EFSA Panel on Plant Health conducted a pest categorisation of cowpea mosaic virus (CPMV) for the EU territory. The identity of CPMV, a member of the genus Comovirus (family Secoviridae), is established and detection and identification methods are available. The pathogen is not included in the Commission Implementing Regulation (EU) 2019/2072. It has been reported from the Americas, and several countries in Africa and Asia and it is not known to be present in the EU in natural conditions. CPMV is considered a major pathogen of cowpea on which it causes symptoms ranging from mild to severe mosaic, chlorosis and necrosis. The virus has been reported sporadically on some other cultivated species of the family Fabaceae, including soybean and some common bean varieties. CPMV is transmitted by cowpea seeds, with uncertainty on the transmission rate. There is uncertainty on seed transmission by other Fabaceae host species due to lack of information. CPMV is also transmitted by several beetle species, one of which, Diabrotica virgifera virgifera, is present in the EU. Seeds for sowing of cowpea are identified as the major entry pathway. The cultivated area and production of cowpea in the EU territory are mainly limited to local varieties cultivated at a small scale in Mediterranean EU Member States. Should the pest establish in the EU, an impact is expected on cowpea crops at local scale. There is high uncertainty on the potential impact that CPMV would cause on other natural hosts cultivated in the EU due to the lack of information from the areas of CPMV's current distribution. Despite the uncertainty concerning the potential impact on bean and soybean crops in the EU, CPMV satisfies the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

Four principles to establish a universal virus taxonomy.

A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.

The Fine Legacy of Giovanni P. Martelli (1935-2020), a Preeminent Plant Virologist and the Founder of Modern Grapevine Virology.

Giovanni Paolo Martelli passed away on 8 January 2020 [...].

Pest categorisation of chickpea chlorotic dwarf virus.

The EFSA Panel on Plant Health conducted a pest categorisation of chickpea chlorotic dwarf virus (CpCDV) for the EU territory. The identity of CpCDV, a member of the genus Mastrevirus (family Geminiviridae) is established. Reliable detection and identification methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. CpCDV has been reported in Africa, Asia and Oceania. It has not been reported in the EU. CpCDV infects plant species in the family Fabaceae and several species of other families (Amaranthaceae, Brassicaceae, Caricaceae, Cucurbitaceae, Malvaceae and Solanaceae), including weeds. It may induce symptoms on its hosts, causing severe yield reduction. The virus is transmitted in a persistent, circulative and non-propagative manner by the leafhopper species Orosius orientalis and O. albicinctus, which are not regulated. O. orientalis is known to be present in some EU member states. Plants for planting (other than seeds), parts of plants and cut flowers of CpCDV hosts and viruliferous leafhoppers were identified as the most relevant pathways for the entry of CpCDV into the EU. Cultivated and wild hosts of CpCDV are distributed across the EU. Would the pest enter and establish in the EU territory, impact on the production of cultivated hosts is expected. Phytosanitary measures are available to prevent entry and spread of the virus in the EU. CpCDV fulfils the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022).

This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2022. The entire ICTV was invited to vote on 174 taxonomic proposals approved by the ICTV Executive Committee at its annual meeting in July 2021. All proposals were ratified by an absolute majority of the ICTV members. Of note, the Study Groups have started to implement the new rule for uniform virus species naming that became effective in 2021 and mandates the binomial 'Genus_name species_epithet' format with or without Latinization. As a result of this ratification, the names of 6,481 virus species (more than 60 percent of all species names currently recognized by ICTV) now follow this format.

Pest categorisation of Capsicum chlorosis virus.

The EFSA Panel on Plant Health conducted a pest categorisation of Capsicum chlorosis virus (CaCV) for the EU territory. The identity of CaCV, a member of the genus Orthotospovirus (family Tospoviridae), is established and reliable detection and identification methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. CaCV has been reported in Australia, China, India, Iran, Taiwan, Thailand and USA (Hawaii). In the EU, it has been reported once in Greece (Crete Island). The NPPO of Greece reported that CaCV is no longer present in Greece. CaCV infects plant species in the family Solanaceae (i.e. pepper, tomato) and several species of other families, including ornamentals. It may induce severe symptoms on its hosts, mainly on leaves and fruits, which may become unmarketable. The virus is transmitted in a persistent propagative mode by the thrips Ceratothripoides claratris, Frankliniella schultzei, Microcephalothrips abdominalis and Thrips palmi. C. claratris and T. palmi are EU quarantine pests. M. abdominalis is known to be present in several EU member states and it is not regulated in the EU. Plants for planting, parts of plants, fruits and cut flowers of CaCV hosts, and viruliferous thrips were identified as the most relevant pathways for the entry of CaCV into the EU. Cultivated and wild hosts of CaCV are distributed across the EU. Should the pest enter and establish in the EU territory, impact on the production of cultivated hosts is expected. Phytosanitary measures are available to prevent entry and spread of the virus in the EU. CaCV fulfils the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

Pest categorisation of High Plains wheat mosaic virus.

The EFSA Panel on Plant Health conducted a pest categorisation of High Plains wheat mosaic virus (HPWMoV) for the EU territory. The identity of HPWMoV, a member of the genus Emaravirus (family Fimoviridae), is well established and reliable identification methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. HPWMoV has been reported from Argentina, Australia, Canada, Ukraine and USA, and it is not known to be present in the EU. HPWMoV infects plant species of the family Poaceae (i.e. wheat, maize and several other cultivated or wild Poaceae species). It is the causal agent of High Plains disease of wheat and maize, inducing symptoms ranging from mild to severe mosaic, chlorosis and necrosis in wheat, and chlorotic streaks in maize plants. The virus is transmitted by the wheat curl mite Aceria tosichella, which is present in the EU. HPWMoV transmission via seeds was reported to occur in sweet corn. Sweet corn seeds for sowing were identified as the most relevant pathway for entry of HPWMoV into the EU. Seeds from other hosts and viruliferous wheat curl mites were identified as entry pathways associated with uncertainties. Machinery not appropriately cleaned may move infected seeds and/or parts of cereals infested by viruliferous mites. Cultivated and wild hosts of HPWMoV are distributed across the EU. Would the pest enter and establish in the EU territory, economic impact on the production of cultivated hosts is expected. Phytosanitary measures are available to prevent entry and spread of the virus in the EU. HPWMoV fulfils the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

Pest categorisation of Apium virus Y.

Following a request from the EU Commission, the EFSA Panel on Plant Health conducted a pest categorisation of Apium virus Y (ApVY) for the EU territory. The identity of the ApVY, a member of the genus Potyvirus (family Potyviridae), is well established and reliable detection methods are available. The pathogen is not included in EU Commission Implementing Regulation 2019/2072. ApVY, considered endemic in Australia, was reported also in New Zealand and USA. In the EU, the virus was identified in Germany and Slovenia. No information on adoption of official control measures is available. In natural conditions, ApVY infects plant species of the family Apiaceae (i.e. celery, coriander, dill, parsley, bishop's weed) in which it generally induces leaf symptoms and/or stunting. In some hosts (i.e. parsley and poison hemlock), ApVY may be asymptomatic. The virus is transmitted in a non-persistent manner by the aphid Myzus persicae which is widespread in the EU. Although ApVY transmission through seeds has been experimentally excluded for some hosts (i.e. poison hemlock and celery), uncertainty exists for the other hosts because seed transmission is not uncommon for potyvirids. Plants for planting, including seeds for sowing, were identified as potential pathways for entry of ApVY into the EU. Cultivated and wild hosts of ApVY are distributed across the EU. Economic impact on the production of the cultivated hosts is expected if further entry and spread in the EU occur. Phytosanitary measures are available to prevent further entry and spread of the virus. Currently, ApVY does not fulfil the criterion of being absent or present with restricted distribution and under official control to be regarded as a potential Union quarantine, unless official control is implemented. This conclusion is associated with high uncertainty regarding the current virus distribution in the EU.

Differentiating between viruses and virus species by writing their names correctly.

Following the results of the International Committee on Taxonomy of Viruses (ICTV) Ratification Vote held in March 2021, a standard two-part "binomial nomenclature" is now the norm for naming virus species. Adoption of the new nomenclature is still in its infancy; thus, it is timely to reiterate the distinction between "virus" and "virus species" and to provide guidelines for naming and writing them correctly.

Guidance for creating individual and batch latinized binomial virus species names.

The International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains optional, a standardized nomenclature based on Latinized binomials has the advantage of comparability with all other biological taxonomies. As a language without living native speakers, Latin is more culturally neutral than many contemporary languages, and words built from Latin roots are already widely used in the language of science across the world. Conversion of established species names to Latinized binomials or creation of Latinized binomials de novo may seem daunting, but the rules for name creation are straightforward and can be implemented in a formulaic manner. Here, we describe approaches, strategies and steps for creating Latinized binomials for virus species without prior knowledge of Latin. We also discuss a novel approach to the automated generation of large batches of novel genus and species names. Importantly, conversion to a binomial format does not affect virus names, many of which are created from local languages.

Pest categorisation of carrot thin leaf virus.

Following a request from the EU Commission, the EFSA Panel on Plant Health conducted a pest categorisation of carrot thin leaf virus (CTLV) for the EU territory. The identity of CTLV, a member of the genus Potyvirus (family Potyviridae), is well established and reliable detection methods are available. The pathogen is not included in the EU Commission Implementing Regulation 2019/2072. CTLV has been reported from the USA and Colombia. In the EU, the virus was reported in Germany and Slovenia and the NPPO of both countries confirmed these reports. No official national measures have been taken so far. In 2018, CTLV was reported from Greece on Torilis arvensis subsp. arvensis. Since then, no other reports exist. According to the NPPO, the virus did not establish in Greece. In natural conditions, CTLV infects plant species of the family Apiaceae (i.e., carrot, coriander, parsley and several wild weed species). The virus is transmitted in a non-persistent manner by the aphids Myzus persicae and Cavariella aegopodii, which are widely distributed in the EU. CTLV has been reported not to be transmitted by carrot seeds, while no information is available for the other hosts. Since transmission through seeds is not uncommon for potyvirids, it cannot be excluded that CTLV can be seed transmitted for some hosts. Plants for planting, including seeds for sowing, were identified as potential pathways for entry of CTLV into the EU. Cultivated and wild hosts of CTLV are distributed across the EU. Economic impact on the production of cultivated hosts is expected if further entry and spread in the EU occur. Phytosanitary measures are available to prevent further entry and spread of the virus on its cultivated hosts. Currently, CTLV does not fulfil the criterion of being absent or present with restricted distribution and under official control to be regarded as a potential Union quarantine pest, unless official control is implemented. This conclusion is associated with high uncertainty regarding the current virus distribution in the EU.

Perspective on taxonomic classification of uncultivated viruses.

Historically, virus taxonomy has been limited to describing viruses that were readily cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single-particle sequencing, and database mining efforts have yielded new sequence data on an astounding number of previously unknown viruses. As metagenomes are relatively free of biases, these data provide an unprecedented insight into the vastness of the virosphere, but to properly value the extent of this diversity it is critical that the viruses are taxonomically classified. Inclusion of uncultivated viruses has already improved the process as well as the understanding of the taxa, viruses, and their evolutionary relationships. The continuous development and testing of computational tools will be required to maintain a dynamic virus taxonomy that can accommodate the new discoveries.