International Committee On The Taxonomy Of Viruses Research Articles

Fungal Viruses Unveiled: A Comprehensive Review of Mycoviruses.

Mycoviruses (viruses of fungi) are ubiquitous throughout the fungal kingdom and are currently classified into 23 viral families and the genus botybirnavirus by the International Committee on the Taxonomy of Viruses (ICTV). The primary focus of mycoviral research has been on mycoviruses that infect plant pathogenic fungi, due to the ability of some to reduce the virulence of their host and thus act as potential biocontrol against these fungi. However, mycoviruses lack extracellular transmission mechanisms and rely on intercellular transmission through the hyphal anastomosis, which impedes successful transmission between different fungal strains. This review provides a comprehensive overview of mycoviruses, including their origins, host range, taxonomic classification into families, effects on their fungal counterparts, and the techniques employed in their discovery. The application of mycoviruses as biocontrol agents of plant pathogenic fungi is also discussed.

КЛИНИЧЕСКИЙ СЛУЧАЙ ТЯЖЕЛОЙ ФОРМЫ COVID-19-ИНФЕКЦИИ У ПАЦИЕНТА С ЕДИНСТВЕННЫМ ЛЕГКИМ

In December 2019, in the People’s Republic of China (PRC) in Hubei province, cases of pneumonia caused by a coronavirus were registered, which the International Committee on the Taxonomy of Viruses (ICTV) later designated as SARS-CoV-2. The World Health Organization (WHO) has named the new disease COVID-19 [1]. Clinical symptoms in COVID-19 can vary from an asymptomatic course of the disease to a pronounced clinical picture [2,3]. Persons with concomitant pathology deserve special attention. In patients with COVID-19, arterial hypertension (13–17%), diabetes mellitus (5–35%), cardiovascular diseases (3–4%) are most often found, less often – chronic lung diseases (2%) and oncological pathology (0, 5–3%) [4]. For a number of reasons, patients with COVID-19 admitted to the ICU are at high risk of developing infectious complications during their ICU stay [5]. First, they frequently develop multiple organ failure with need for vasopressors, renal replacement therapy (RRT) and, in some cases, extracorporeal membrane oxygenation support. The duration of mechanical ventilation and the ICU lengths of stay of these patients are therefore usually prolonged [6, 7]. Second, COVID-19 per se is associated with significant dysfunction of the patient’s immune system. Multiple studies have shown the involvement of both innate and acquired immunity as a response to SARS-CoV-2 infection. Third, after the publication of the results of the RECOVERY trial [8], treatment with systemic corticosteroids has become standard of care in all patients requiring supplemental oxygen. Finally, secondary bacterial and fungal infections as a complication of viral respiratory diseases have been described previously, and some studies highlight their role in increasing the severity of viral pneumonia [9]. Our experience of treatment of critically ill patient with laboratory-confirmed Covid-19 and ARDS with severe comorbidities is presented in this article. Features of anamnesis, approaches to respiratory support, treatment are considered. The dynamics of clinical, laboratoric and radiologic parameters is also presented. Results: In this clinical case, despite severe concomitant pathology and a significant degree of lung tissue damage, early transfer to invasive mechanical ventilation, addition of nosocomial flora, we managed to achieve positive clinical and laboratory dynamics, weaned the patient from mechanical respiratory support on the 9th day, and on the 18th day to write out for outpatient treatment in a satisfactory condition.

Nature of viruses and the radical change in viral taxonomy

A short report is devoted to the radical changes in the taxonomy of viruses. The metagenomic sequencing has revealed the presence of a vast variety of viruses in diverse environmental samples without any connections with banal parasitism, infectivity, or pathogenicity. The understanding of viruses has expanded beyond the original parasitic–pathogen model, and now virologists recognize the role of viruses in host regulation and the maintenance of natural ecosystems. Co-evolution of the viral and cellular genomes includes mutual horizontal gene transfer and joint development of new biological functions, such as the mechanism of phylogenesis and phylodynamics of coactants. The concepts of the origin of viruses and their relation to the Universal Tree of Life are formulated. In this regard, the International Committee on the Taxonomy of Viruses (ICTV) changed the previous Code of their classification hierarchy from five ranks to a fifteen-rank one, that emulates a Linnaean framework and accommodates the entire spectrum of genetic divergence in the virosphere. Changes in the rank hierarchy are based on the evolution of the recognition of virus taxa over time, from a traditional phenotype-based characterization process to a multistage process that includes comparative sequence analyses of conserved genes and proteins, including gene phylogeny, gene synteny and shared gene content. The ICTV, that oversees the official classification of viruses and nomenclature of taxa, accepts possible non-hierarchical classifications of viruses beyond taxonomic attribution. The above provisions are illustrated with schemes of chimeric polyphyletic origin of viruses and a new rank structure; the table gives examples of the modern classification of viruses that cause some socially significant infections.

Molecular characterization of a novel bat-associated circovirus with a poly-T tract in the 3′ intergenic region

The family Circoviridae comprises a large group of small circular single-stranded DNA viruses with several members causing severe pig and poultry diseases. In recent years the number of new viruses within the family has had an explosive increase showing a high level of genetic diversity and a broad host range. In this report we describe two more circoviruses identified from bats in Yunnan and Heilongjiang provinces in China. Full genome sequencing has revealed that these bat associated circoviruses (bat ACV) should be classified as new species within the genus Circovirus based on the demarcation criteria of the International Committee on the Taxonomy of Viruses (ICTV). The most striking result is the novel finding of a 21–28 nt polythymidine (poly-T) tract in the 3′ terminal intergenic region of bat ACV isolates from Heilongjiang province. To understand its role in viral replication, a wild type bat ACV and a mutated version with the entire poly-T deleted were rescued through construction of infectious clones. Replication comparison in vitro showed that the poly-T is not essential for viral replication. Identification of additional bat ACV isolates and study of their biological characteristics will be the main task in future to understand the potential roles of bats in transmission of circoviruses to terrestrial mammals and humans.

How to Name and Classify Your Phage: An Informal Guide.

With this informal guide, we try to assist both new and experienced phage researchers through two important stages that follow phage discovery; that is, naming and classification. Providing an appropriate name for a bacteriophage is not as trivial as it sounds, and the effects might be long-lasting in databases and in official taxon names. Phage classification is the responsibility of the Bacterial and Archaeal Viruses Subcommittee (BAVS) of the International Committee on the Taxonomy of Viruses (ICTV). While the BAVS aims at providing a holistic approach to phage taxonomy, for individual researchers who have isolated and sequenced a new phage, this can be a little overwhelming. We are now providing these researchers with an informal guide to phage naming and classification, taking a “bottom-up” approach from the phage isolate level.

What is a virus species? Radical pluralism in viral taxonomy

Early attempts in the 1960s at constructing a classification scheme for viruses were phenetic and focused on structural properties of the virion. Over time, the International Committee on the Taxonomy of Viruses (ICTV) has refined its definition of a virus species to include an appeal to evolutionary history. The current ICTV definition defines a viral species in terms of monophyly. The existence of prolific horizontal genetic transfer (HGT) among various groups of viruses presents a challenge to this definition. I argue that the proper response to this mode of evolution is to allow for radical pluralism. Some viruses can be members of more than one species; others don't form species at all and should be classified using new reticulate categories.

First Evidence of Bovine Viral Diarrhea Virus Infection in Wild Boars

Background: The farming of wild boars has growing due to the interest of the human consumption of this exotic meat. Such a development may pose an increased risk of disease transmission between boars and domestic animals. The wild boar population has increased in South America in the last years due the absence of predator causing economic losses due to direct damage to crops and risk of disease transmission. The genus Pestivirus within the family Flaviviridae are composed by four recognized species by the International Committee on the Taxonomy of Viruses (ICTV): classical swine fever virus (CSFV), border disease virus (BDV), bovine viral diarrhea virus type 1 (BVDV-1) and 2 (BVDV-2). Other putative species denoted as atypical pesitiviruses have been reported as ‘HoBi’-like virus, giraffe pestivirus, Bungowannah pestivirus, Pronghorn antelope virus, atypical porcine pestivirus (APPV), Norwegian rat pestivirus (NrPV) and Rhinolophus affinis bat pestivirus (RaPestV-1). CSFV is commonly detected in wild boars, but despite positive serology, bovine viral diarrhea virus (BVDV) was never detected in this animal species. Thereby, the present communication describes the first detection of BVDV in the lungs of captive boars using RT-PCR and DNA sequencing.Materials, Methods & Results: Forty lung samples from farmed wild boars were collected after slaughter in a commercial abattoir. The organs were crushed separately, centrifuged, and the supernatant was stored for further analysis. The total RNA was isolated using a phenol-based protocol and RT-PCR protocol that amplified 118 bp of 5’ untranslated region (5’UTR) was carried out. One out 40 samples resulted positive. The positive sample had partial fragments of 5’UTR and N terminal autoprotease (Npro) sequenced and analyzed. The strain LV Java/2012 presented 99% of identity in 5’UTR and 98% in Npro region with a BVDV-2 previously reported in bovines in Southern Brazil. In both 5’UTR and Npro phylogenetic analysis, the strain LV Java/2015 clustered with BVDV-2 strains and was most closely related to subtype 2b identified in bovines in Southern Brazil grouping in the same terminal node.Discussion: Wild boars are commonly associated to pathogen transmission to domestic animals. This animal species is considered a reservoir of the pestivirus CSFV and important keys in CSFV control and eradication programs in Europe. Despite indirect presence of BVDV was reported in wild boars by serology tests, the direct detection of the viral agent was never reported. The present study showed the presence of BVDV-2 genomic segments obtained by RT-PCR followed by DNA sequencing in captive wild boars. The reported data suggests a possible importance of this animal species in the epidemiology of ruminant pestiviruses which could interfere in control and eradication programs of these important pathogens for cattle worldwide. The strain LV Java/2012 was closely related to BVDV-2b and presented highest identity with a strain detected in cattle from Southern Brazil. This data suggests that wild boars and bovines could be sharing this pathogen due the similarity of the strains and that both were reported in the same region. It can lead to need of inclusion of wild swines in BVDV control programs since boars can circulate between different regions and carry this pathogen to different cattle herds. The present study reported the first molecular evidence of BVDV in wild boars in the literature. The data generated herein suggests a possible importance of boars in the epidemiology of ruminant pestiviruses.

Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world

Sireviruses are an ancient and plant-specific LTR retrotransposon genus. They possess a unique genome structure that is characterized by a plethora of highly conserved sequence motifs in key domains of the non-coding genome, and often, by the presence of an envelope-like gene. Recently, their crucial role in the organization of the maize genome, where Sireviruses occupy approximately 21% of its nuclear content, was revealed, followed by an analysis of their distribution across the plant kingdom. It is now suggested that Sireviruses have been a major mediator of the evolution of many plant genomes. However, the name ‘Sirevirus’ has caused confusion in the scientific community in regards to their classification within the LTR retrotransposon order and their relationship with viruses - a situation that is not unique to Sireviruses, but also affects other LTR retrotransposon genera. Here, we clarify the phylogenetic position of Sireviruses as typical LTR retrotransposons of the Copia superfamily and explain that the confusion stems from the discrepancy in the categorization of LTR retrotransposons by the two main classification systems: the International Committee on the Taxonomy of Viruses (ICTV) system and the unified classification system for eukaryotic transposable elements. While the name ‘Sirevirus’ has been given by ICTV, we show that the transposable element system, which is more suitable for eukaryotic genome studies, lacks an appropriate taxonomic level for describing them. We urge for this inconsistency to be addressed. Finally, we provide data suggesting that of the three ICTV-proposed genera of the Pseudoviridae (that is, Copia) family, only Sireviruses form a monophyletic group, while the phylogenetic distinction between Pseudoviruses and Hemiviruses is unclear. We conclude that because of their ongoing important contribution to the classification of transposable elements, these schemes need to be frequently revisited and revised - as shown by the example of the Sirevirus LTR retrotransposon genus.

ORION-VIRCAT: a tool for mapping ICTV and NCBI taxonomies

Viruses, viroids and prions are the smallest infectious biological entities that depend on their host for replication. The number of pathogenic viruses is considerably large and their impact in human global health is well documented. Currently, the International Committee on the Taxonomy of Viruses (ICTV) has classified ∼4379 virus species while the National Center for Biotechnology Information Viral Genomes Resource (NCBI-VGR) database has mapped 617 705 proteins to eight large taxonomic groups. Despite these efforts, an automated approach for mapping the ICTV master list and its officially accepted virus naming to the NCBI-VGR’s taxonomical classification is not available. Due to metagenomic sequencing, it is likely that the discovery and naming of new viral species will increase by at least ten fold. Unfortunately, existing viral databases are not adequately prepared to scale, maintain and annotate automatically ultra-high throughput sequences and place this information into specific taxonomic categories. ORION-VIRCAT is a scalable and interoperable object-relational database designed to serve as a resource for the integration and verification of taxonomical classifications generated by the ICTV and NCBI-VGR. The current release (v1.0) of ORION-VIRCAT is implemented in PostgreSQL and it has been extended to ORACLE, MySQL and SyBase. ORION-VIRCAT automatically mapped and joined 617 705 entries from the NCBI-VGR to the viral naming of the ICTV. This detailed analysis revealed that 399 095 entries from the NCBI-VGR can be mapped to the ICTV classification and that one Order, 10 families, 35 genera and 503 species listed in the ICTV disagree with the the NCBI-VGR classification schema. Nevertheless, we were eable to correct several discrepancies mapping 234 000 additional entries.Database URL: http://www.orionbiosciences.com/research/orion-vircat.html

The taxonomy of vertebrate viruses

Viruses that infect vertebrates (i.e. humans and higher animals) exhibit great diversity. They also create a variety of diseases that arise from interaction with their vertebrate hosts. This review presents the diversity of the biological and molecular properties of vertebrate viruses that aid their transmission and survival using the currently accepted taxonomic system. The Universal System of Virus Taxonomy has been developed to its present state through a series of 8 Reports, the most recent of which was published in 2005. The system of taxonomy adopted by the International Committee on the Taxonomy of Viruses (ICTV) is flexible enough to embrace the continual discovery of new viruses from an ever-increasing diversity of host organisms. New vertebrate viruses continue to be discovered, such as the human pathogens herpes virus 6, 7 and 8 and the SARS coronavirus. All these viruses have been fitted into the lower levels of the existing taxonomy as new species or new genera

Classification of papillomaviruses

One hundred eighteen papillomavirus (PV) types have been completely described, and a yet higher number of presumed new types have been detected by preliminary data such as subgenomic amplicons. The classification of this diverse group of viruses, which include important human pathogens, has been debated for three decades. This article describes the higher-order PV taxonomy following the general criteria established by the International Committee on the Taxonomy of Viruses (ICTV), reviews the literature of the lower order taxa, lists all known “PV types”, and interprets their phylogenetic relationship. PVs are a taxonomic family of their own, Papillomaviridae, unrelated to the polyomaviruses. Higher-order phylogenetic assemblages of PV types, such as the “genital human PVs”, are considered a genus, the latter group, for example, the genus “Alpha-Papillomavirus”. Lower-order assemblages of PV types within each genus are treated as species because they are phylogenetically closely related, but while they have distinct genomic sequences, they have identical or very similar biological or pathological properties. The taxonomic status of PV types, subtypes, and variants remains unchanged and is based on the traditional criteria that the sequence of their L1 genes should be at least 10%, 2–10%, and maximally 2% dissimilar from one another.

The classification and nomenclature of viruses. Summary of results of meetings of the International Committee on Taxonomy of Viruses in Madrid, September 1975.

Introduction. The International Committee on the Taxonomy of Viruses (ICTV), which is a committee of the Section on Virology of the International Association of Microbiological Societies (IAMS), completed a round of meetings during the Third International Congress for Virology that was held in Madrid from 10 to 17 September 1975. Since ICTV only meets during these conferences, which are held every four years, the meetings are important occasions for reviewing the classification and nomenclature of viruses. Decisions on new names, which encapsulate the recognition of natural ‘groups’ of viruses, evolve slowly. Official approval for new names depends upon a series of sequential steps; recommendations by one or more of the subcommittees of the Executive Committee of ICTV (subcommittees on Bacterial, Invertebrate, Plant and Vertebrate Viruses respectively, and for some of the larger viral groups which span several kinds of hosts — the Coordination Subcommittee), which are considered by the Executive Committee of ICTV and may finally be submitted for approval by ICTV itself.

The classification and nomenclature of viruses summary of results of meetings of the International Committee on Taxonomy of Viruses in Madrid, September 1975

The International Committee on the Taxonomy of Viruses (ICTV), which is a committee of the Section on Virology of the International Association of Microbiological Societies (IAMS), completed a round of meetings during the Third International Congress for Virology that was held in Madrid from September 10-17, 1975. Since ICTV only meets during these conferences, which are held every four years, the meetings are important occasions for reviewing the classification and nomenclature of viruses. Decisions on new names, which encapsulate the recognition of natural “groups” of viruses, evolve slowly. Official approval for new names depends upon a series of sequential steps; recommendations by one or more of the subcommittees of the Executive Committee of ICTV (subcommittees on Bacterial, Invertebrate, Plant, and Vertebrate Viruses, respectively, and for some of the larger viral groups which span several kinds of hosts, the Coordination Subcommittee), which are considered by the Executive Committee of ICTV, and may finally be submitted for approval by ICTV itself. Only after this