Virus taxonomy and megataxonomy (Vira domain) - current status.

This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2016.Changes to virus taxonomy (the Universal Scheme of Virus Classification of the International Committee on Taxonomy of Viruses [ICTV]) now take place annually and are the result of a multi-stage process. In accordance with the ICTV Statutes (http://www.ictvonline.org/statutes.asp), proposals submitted to the ICTV Executive Committee (EC) undergo a review process that involves input from the ICTV Study Groups (SGs) and Subcommittees (SCs), other interested virologists, and the EC. After final approval by the EC, proposals are then presented for ratification to the full ICTV membership by publication on an ICTV web site (http://www.ictvonline.org/) followed by an electronic vote. The latest set of proposals approved by the EC was made available on the ICTV website by January 2016 (https://talk.ictvonline.org/files/proposals/). A list of these proposals was then emailed on 28 March 2016 to the 148 members of ICTV, namely the EC Members, Life Members, ICTV Subcommittee Members (including the SG chairs) and ICTV National Representatives. Members were then requested to vote on whether to ratify the taxonomic proposals (voting closed on 29 April 2016).

Microorganisms that cannot be grown in the laboratory can now be tentatively identified, by cloning and sequencing particular nucleic acid segments and then carrying out a comparative sequence analysis with an appropriate database. For bacteria, a few universally distributed genes and gene products have enabled comparative sequence analysis to be used for tentative identification and classification of uncultured bacteria. For viruses, there is no universally distributed viral gene or gene product. However, in a few cases, viruses that could not be propagated in the laboratory have been identified and classified. In these cases, either the entire viral genome sequence was determined or partial sequence information was supplemented with additional data. The Executive Committee of the International Committee on Taxonomy of Viruses (ICTV) has reviewed the issue of identification and classification of viruses that have not been propagated. Under the ICTV system, formal review of any taxonomic proposal is carried out by the relevant ICTV Subcommittee or Study Group. The few examples of unpropagated viruses that have arisen thus far have been readily accommodated within existing viral taxonomy, with the international group of experts comprising each Subcommittee and Study Group determining the necessary and sufficient amount of information needed for classification of an unpropagated virus on a case-by-case basis.

High Plains virus (HPV), a tentative member of the genus Emaravirus, causes a potentially serious economic disease in cereals. Recently, in this journal, Tatineni et al. (1) mistakenly reported HPV as being present in New Zealand, citing the paper by Lebas et al. from 2005 (2). The 2005 report clearly states that New Zealand is HPV free in both the abstract and the introduction (2). To date, HPV is not known to occur in New Zealand. The Ministry for Primary Industries of New Zealand has very strict regulations in place to prevent the importation of unwanted organisms such as HPV. For example, the importation of Zea mays seeds must follow the requirements stated in Import Health Standard 155.02.05 (for seed for sowing) (3), which includes testing of HPV by enzyme-linked immunosorbent assay (ELISA) or PCR. The Tatineni et al. statement (1) will mislead regulatory officials of New Zealand’s trading partners who regularly monitor world microbe dynamics in the scientific literature. In fact, there are plant biosecurity actions in place (4) that directly affect New Zealand’s international trade when a regulated plant virus like HPV is reported as present. The situation above is aggravated by the lack of a definitive virus name yet to be ruled on by the Emaravirus Study Group, Plant Viruses Subcommittee, International Committee on Taxonomy of Viruses (ICTV). Historically, many names have been used to refer to this virus. The name Wheat spot mosaic virus (WSpM virus) was given to a virus associated with High Plains disease studied in the 1950s (5). WSpM virus-diseased samples were not preserved, and therefore it is not possible to do comparative studies (6, 7). The name High Plains virus, which causes red striping symptoms on maize, was first coined by Jensen et al. in 1996 (8). Subsequently, a virus associated with High Plains disease also eliciting red striping symptoms was partially characterized and sequenced and the name maize red stripe virus (MRStV) was introduced as a replacement for HPV (9). A note added in proof for this paper suggested the name of Wheat mosaic virus (WMoV) based on the fact that the virus is more prevalent in wheat than in maize (9). WMoV was subsequently referred to into recent publications (10, 11). All proposed names reflect diverse symptoms observed among infected wheat and sweet corn varieties and the fact that the virus is commonly detected in mixed infections. HPV is reported to coinfect with Wheat streak mosaic virus (WSMV), Triticum mosaic virus (TriMV), Barley yellow dwarf virus PAV (BYDVPAV), and Cereal yellow dwarf virus RPV (CYDV-RPV) in the Great Plains region of the United States (10, 12). In general, all proposed names do not conflict with ICTV definitions of species, construction of names, and/or rules for orthography. The fact that the HPV name does not refer to a specific host name, but to a geographical location, and its elusiveness for years may have sparked this populated name list. However, other plant viruses have been named based only on geographical origin; examples are the tombusviruses Havel River virus, Lato River virus, and Neckar River virus, which are all ICTV-approved names (13). MacDiarmid et al. in 2013 (4) had proposed and justified new recommendations for plant virus characterization and classification in the context of new virus discovery. Both the ICTV and MacDiarmid et al. (4) are seeking (i) fluent communication among scientists, (ii) stability, (iii) to not use names that might cause error or confusion, and (iv) to avoid the unnecessary creation of names as stated by the ICTV principles of nomenclature. Certainly, HPV is not known to be present in New Zealand, and acknowledgment of the HPV-free status of New Zealand is urgently required. This also implies the requirement of a more meticulous review of manuscripts by referees and editors of the journal. Regarding HPV naming, less confusion in the long term will be expected if HPV is kept as a name, which is justified by the existence of precedent plant virus naming using geographical location markers and HPV’s broader usage in literature and sequence repositories.

The International Committee on Taxonomy of Viruses (ICTV) has implemented numerous changes to the taxonomic classification of bunyaviruses over the years. Whereas most changes have been justified and necessary because of the need to accommodate newly discovered and unclassified viruses, other changes are a cause of concern, especially the decision to demote scores of formerly recognized species to essentially strains of newly designated species. This practice was first described in the seventh taxonomy report of the ICTV and has continued in all subsequent reports. In some instances, viruses that share less than 75% nucleotide sequence identity across their genomes, produce vastly different clinical presentations, possess distinct vector and host associations, have different biosafety recommendations, and occur in nonoverlapping geographic regions are classified as strains of the same species. Complicating the matter is the fact that virus strains have been completely eliminated from ICTV reports; thus, critically important information on virus identities and their associated biological and epidemiological features cannot be readily related to the ICTV classification. Here, we summarize the current status of bunyavirus taxonomy and discuss the adverse consequences associated with the reclassification and resulting omission of numerous viruses of public health importance from ICTV reports. As members of the American Committee on Arthropod-borne Viruses, we encourage the ICTV Bunyavirus Study Group to reconsider their stance on bunyavirus taxonomy, to revise the criteria currently used for species demarcation, and to list additional strains of public and veterinary importance.

In 1966, the International Classification of Viruses (ICNV) was established to standardize the naming of viruses. In 1975, the organization was renamed “International Committee on Taxonomy of Viruses (ICTV),” by which it is still known today. The primary virus classification provided by ICTV in 1971 was for viruses infecting vertebrates, which includes 19 genera, 2 families, and 24 unclassified groups. Presently, the 10th virus taxonomy has been published. However, the early classification of viruses was based on clinical results “in vivo” and “in vitro,” as well as on the shape of the Phenotype virus. Due to the development of next-generation sequencing and the accompanying bioinformatics analysis pipelines, a reconstruction of the classification system has been proposed. At a meeting held in Boston, USA between June 9–11, 2016, there was even an in-depth discussion regarding the classification of viruses using metagenomic data. One suggested activity that arose from the meeting was that viral taxonomy should be reconstructed, based on genotype and bioinformatics analysis “in silico.” This article describes our efforts to achieve this goal by construction of a web-based system and the extension of an associated database, based on ICTV taxonomy. This virus taxonomy web system was designed specifically to extend the virus taxonomy up to strain and isolation, which was then connected with the NCBI database to facilitate searches for specific viral genes; there are also links to journals provided by the EMBL RESTful API that improves accessibility for academic groups.

As any classification is essentially an arbitrary human invention, it is imperative to have a unique source of classification also for viruses. The International Committee on Taxonomy of Viruses (ICTV), a committee of the Virology Division of the International Union of Microbiological Societies, has been in charge of this task since 1966 and has already published nine Reports updating the status of viral taxonomy. Contrary to other biological entities (vertebrates, invertebrates, plants, fungi and bacteria), viruses are not classified according to a Linnean latinised binomial system but, like these, they are arranged into species, genera, subfamilies, families and orders, whose names are written in italics with an initial capital letter. The last ICTV report (2011) lists 6 orders, 94 families, 22 subfamilies, 395 genera and 2480 recognised species. Species are the building blocks of the taxonomic construction. Although species identification is based on discriminating traits, their allocation into higher taxa takes into account common characters of increasingly hierarchical significance. Key Concepts: Taxonomy is an arbitrary organisation of biological entities to facilitate scientific studies and to identify common traits within similar taxonomic levels. Classification and nomenclature are the two facets of taxonomy. Classification is the arrangement of biological entities into taxonomic categories (taxa) on the basis of similarities and/or relationships (phylogeny). Nomenclature is the assignment of names to taxa, according to international rules. Virus classification is a rapidly evolving science particularly with the input of viral genome sequencing. Viruses are not named according to a Linnean latinised binomial system and instead are named with international English‐based names and de novo international taxonomic names. The ICTV is entrusted with the task of classifying and naming virus taxa.

This paper aims to construct two relationship trees of all viruses using two types of genomic sequences, DNA(deoxyribonucleic acid) and CDS (coding sequence), respectively, via a previously developed approach BBRD (BLAST-Based Relative Distance). The BBRD approach is capable to construct the relationship trees of different genomic sequences without identifying common conserved regions among these sequences for comparison in advance. The experimental resources of viruses, with complete genome sequences, were downloaded from NCBI(National Center for Biotechnology Information) at 2018/3/1, and there are 7,535 viruses with whole DNA sequences and 7,434 viruses with at least one CDS sequences. Experimental results show that the relationship tree constructed via DNA sequences seems to be more consistent with the taxonomy of viruses in ICTV (International Committee on Taxonomy of Viruses) than that constructed via CDS sequences. Furthermore, observing the neighbors of one unknown virus within the relationship trees can provide hints to determine or guess its taxonomic information for the biologist or virologist. This study may inspect the fitness of the structures (skeletons) of one existing taxonomy, e.g. ICTV, by observing the relationship tree and providing the parts of subtree without consistence.

While taxonomy is an often-unappreciated branch of science it serves very important roles. Bacteriophage taxonomy has evolved from a mainly morphology-based discipline, characterized by the work of David Bradley and Hans-Wolfgang Ackermann, to the holistic approach that is taken today. The Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) takes a comprehensive approach to classifying prokaryote viruses measuring overall DNA and protein identity and phylogeny before making decisions about the taxonomic position of a new virus. The huge number of complete genomes being deposited with NCBI and other public databases has resulted in a reassessment of the taxonomy of many viruses, and the future will see the introduction of new viral families and higher orders.

Escherichia phage N4 was isolated in 1966 in Italy and has remained a genomic orphan for a long time. It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that became characteristic for this group. In recent years, due to new and relatively inexpensive sequencing techniques the number of publicly available phage genome sequences expanded rapidly. This revealed new members of the N4-like phage group, from 33 members in 2015 to 115 N4-like viruses in 2020. Using new technologies and methods for classification, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) has moved the classification and taxonomy of bacterial viruses from mere morphological approaches to genomic and proteomic methods. The analysis of 115 N4-like genomes resulted in a huge reassessment of this group and the proposal of a new family “Schitoviridae”, including eight subfamilies and numerous new genera.

It is perhaps human nature to seek order in everything that surrounds us. With the number of individual viral particles in the biosphere considerably exceeding that of their hosts (33), the virosphere—or the viral universe, if you wish—shares this quest. In fact, the number of viruses is so high that the entire tree of cellular life, from its roots to the tips of its branches, seems to be immersed in the sea of viruses (5). The attempt to bring order to the virosphere is manifested in the work carried out by the International Committee on Taxonomy of Viruses (ICTV) (9), an official body consisting of numerous experts in the field of virology. The ICTV currently recognizes the hierarchical levels of order, family, subfamily, genus, and species. The dominant (but not exclusive) demarcation criterion employed to delineate viruses into different taxonomic levels is sequence comparison, the main advantage of which is the quantitative reflection of the divergence between taxa. Virus origin and evolution are issues that have never ceased to fascinate biologists and are currently highly debated (see recent studies, e.g., references 11-13, 16, 18-19, 21, 23, 27, and 34). Unfortunately, sequence comparisons do not reach far enough to recognize the relationships between viruses that diversified further back in time while leaving no detectable signal at the sequence level. However, new information, coming mainly from structural studies, might help us (i) to reveal deeper evolutionary connections between viruses that were not previously considered to be related and (ii) to establish biologically relevant higher levels of virus classification, thereby bringing additional biology to taxonomy.

The Retroviridae are a family of viruses that reverse transcribe their RNA genome and integrate the resulting double-stranded DNA copy into the genome of the host cell. Retroviruses are well-documented pathogens that have been associated with a variety of diseases. The International Committee on Taxonomy of Viruses (ICTV) currently lists 65 species of retroviruses. As required by the ICTV, we have converted the species nomenclature to a binomial format comprised of the genus and a freeform epithet. Assigning binomial species names to classify new retroviruses will be facilitated when following the epithet rules described herein.

RNA viruses have a higher mutation rate than DNA viruses; however, RNA viruses are insufficiently studied outside disease settings. The International Committee on Taxonomy of Viruses (ICTV) is an organization set up by virologists to standardize virus classification. To better understand ICTV taxonomy and the characteristics and rules of different RNA virus families, we analyzed the 3,529 RNA viruses included in the 2020 ICTV report using five widely used metrics: length, host, GC content, number of predicted ORFs, and sequence similarity. The results show that host type has a significant influence on viral genome length and GC content. The genome lengths of virus members within the same genus are quite similar: 98.28% of the genome length differences within any particular genus are less than 20%. The species within those genera containing segmented viruses also have a similar length and number of segments. The number of predicted ORFs in the RNA viral genomes also shows a strong, statistically significant correlation with genome length. We suggest that due to the high mutation rate of RNA virus genomes, current RNA virus classification should mainly rely on protein similarities rather than nucleic acid similarities.

Viroids are the smallest autonomous infectious nucleic acids known so far. With a small circular RNA genome of about 250-400 nt, which apparently does not code for any protein, viroids replicate and move systemically in host plants. Since the discovery of the first viroid almost forty-five years ago, many different viroids have been isolated, characterized and, frequently, identified as the causal agents of plant diseases. The first viroid classification scheme was proposed in the early 1990s and adopted by the International Committee on Taxonomy of Viruses (ICTV) a few years later. Here, the current viroid taxonomy scheme and the criteria for viroid species demarcation are discussed, highlighting the main taxonomic questions currently under consideration by the ICTV Viroid Study Group. The impact of correct taxonomic annotation of viroid sequence variants is also addressed, taking into consideration the increasing application of next-generation sequencing and bioinformatics for known and previously unrecognized viroids.

Nowadays, coronavirus disease 2019 (COVID-19) poses a major threat to humanity which is caused by a novel coronavirus in Wuhan, China, at the end of December 2019. This novel coronavirus named the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) according to the International Committee on Taxonomy of Viruses (ICTV). It spreads directly through close contact with an asymptomatic (carrier) or symptomatic person who is coughing, sneezing, talking, singing and kissing. It also spreads indirectly through contact with an environment contaminated by viral particles of SARS-COV-2. In the absence of effective treatment against COVID-19, awareness can play an important role in reducing cases of COVID-19. In this study, we develop a mathematical model to better describe the dynamics of COVID-19 by taking into account the above modes of transmission and the prosocial awareness. The existence, uniqueness, positivity and boundedness of solutions of the model are discussed. All possible equilibrium points are determined. The local asymptotic stability of these equilibrium points is studied. Suitable Lyapunov functionals are constructed to investigate the global dynamics of the model.

Hantavirus causes two important rodent-borne viral zoonoses, hemorrhagic fever with renal syndrome (HFRS) in Eurasia and hantavirus pulmonary syndrome (HPS) in North and South America. Twenty-four species that represent sero- and genotypes have been registered within the genus Hantavirus by the International Committee on Taxonomy of Viruses (ICTV). Among the viral proteins, nucleocapsid (N) protein possesses an immunodominant antigen. The antigenicitiy of N protein is conserved compared with that of envelope glycoproteins. Therefore, N protein has been used for serological diagnoses and seroepidemiological studies. An understanding of the antigenic properties of N protein is important for the interpretation of results from serological tests using N antigen. N protein consists of about 430 amino acids and possesses various epitopes. The N-terminal quarter of N protein bears linear and immunodominant epitopes. However, a serotype-specific and multimerization-dependent antigenic site was found in the C-terminal half of N protein. In this paper, the structure, function, and antigenicity of N protein are reviewed.