Showing papers on "Virus classification published in 2016"

Reorganization and expansion of the nidoviral family Arteriviridae

Abstract: The family Arteriviridae presently includes a single genus Arterivirus. This genus includes four species as the taxonomic homes for equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), porcine respiratory and reproductive syndrome virus (PRRSV), and simian hemorrhagic fever virus (SHFV), respectively. A revision of this classification is urgently needed to accommodate the recent description of eleven highly divergent simian arteriviruses in diverse African nonhuman primates, one novel arterivirus in an African forest giant pouched rat, and a novel arterivirus in common brushtails in New Zealand. In addition, the current arterivirus nomenclature is not in accordance with the most recent version of the International Code of Virus Classification and Nomenclature. Here we outline an updated, amended, and improved arterivirus taxonomy based on current data. Taxon-specific sequence cut-offs are established relying on a newly established open reading frame 1b phylogeny and pairwise sequence comparison (PASC) of coding-complete arterivirus genomes. As a result, the current genus Arterivirus is replaced by five genera: Equartevirus (for EAV), Rodartevirus (LDV + PRRSV), Simartevirus (SHFV + simian arteriviruses), Nesartevirus (for the arterivirus from forest giant pouched rats), and Dipartevirus (common brushtail arterivirus). The current species Porcine reproductive and respiratory syndrome virus is divided into two species to accommodate the clear divergence of the European and American “types” of PRRSV, both of which now receive virus status. The current species Simian hemorrhagic fever virus is divided into nine species to accommodate the twelve known simian arteriviruses. Non-Latinized binomial species names are introduced to replace all current species names to clearly differentiate them from virus names, which remain largely unchanged.

Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

Abstract: This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.

Genomoviridae: a new family of widespread single-stranded DNA viruses.

Abstract: Here, we introduce a new family of eukaryote-infecting single-stranded (ss) DNA viruses that was created recently by the International Committee on Taxonomy of Viruses (ICTV). The family, named Genomoviridae, contains a single genus, Gemycircularvirus, which currently has one recognized virus species, Sclerotinia gemycircularvirus 1. Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) is currently the sole representative isolate of the family; however, a great number of SsHADV-1-like ssDNA virus genomes has been sequenced from various environmental, plant- and animal-associated samples, indicating that members of family Genomoviridae are widespread and abundant in the environment.

Time-Dependent Rate Phenomenon in Viruses

Abstract: Among the most fundamental questions in viral evolutionary biology are how fast viruses evolve and how evolutionary rates differ among viruses and fluctuate through time. Traditionally, viruses are loosely classed into two groups: slow-evolving DNA viruses and fast-evolving RNA viruses. As viral evolutionary rate estimates become more available, it appears that the rates are negatively correlated with the measurement timescales and that the boundary between the rates of DNA and RNA viruses might not be as clear as previously thought. In this study, we collected 396 viral evolutionary rate estimates across almost all viral genome types and replication strategies, and we examined their rate dynamics. We showed that the time-dependent rate phenomenon exists across multiple levels of viral taxonomy, from the Baltimore classification viral groups to genera. We also showed that, by taking the rate decay dynamics into account, a clear division between the rates of DNA and RNA viruses as well as reverse-transcribing viruses could be recovered. Surprisingly, despite large differences in their biology, our analyses suggested that the rate decay speed is independent of viral types and thus might be useful for better estimation of the evolutionary time scale of any virus. To illustrate this, we used our model to reestimate the evolutionary timescales of extant lentiviruses, which were previously suggested to be very young by standard phylogenetic analyses. Our analyses suggested that these viruses are millions of years old, in agreement with paleovirological evidence, and therefore, for the first time, reconciled molecular analyses of ancient and extant viruses. IMPORTANCE This work provides direct evidence that viral evolutionary rate estimates decay with their measurement timescales and that the rate decay speeds do not differ significantly among viruses despite the vast differences in their molecular features. After adjustment for the rate decay dynamics, the division between the rates of double-stranded DNA (dsDNA), single-stranded RNA (ssRNA), and ssDNA/reverse-transcribing viruses could be seen more clearly than before. Our results provide a guideline for further improvement of the molecular clock. As a demonstration of this, we used our model to reestimate the timescales of modern lentiviruses, which were previously thought to be very young, and concluded that they are millions of years old. This result matches the estimate from paleovirological analyses, thus bridging the gap between ancient and extant viral evolutionary studies.

Influenza A virus transmission via respiratory aerosols or droplets as it relates to pandemic potential

Abstract: Many respiratory viruses of humans originate from animals. For instance, there are now eight paramyxoviruses, four coronaviruses and four orthomxoviruses that cause recurrent epidemics in humans but were once confined to other hosts. In the last decade, several members of the same virus families have jumped the species barrier from animals to humans. Fortunately, these viruses have not become established in humans, because they lacked the ability of sustained transmission between humans. However, these outbreaks highlighted the lack of understanding of what makes a virus transmissible. In part triggered by the relatively high frequency of occurrence of influenza A virus zoonoses and pandemics, the influenza research community has started to investigate the viral genetic and biological traits that drive virus transmission via aerosols or respiratory droplets between mammals. Here we summarize recent discoveries on the genetic and phenotypic traits required for airborne transmission of zoonotic influenza viruses of subtypes H5, H7 and H9 and pandemic viruses of subtypes H1, H2 and H3. Increased understanding of the determinants and mechanisms of respiratory virus transmission is not only key from a basic scientific perspective, but may also aid in assessing the risks posed by zoonotic viruses to human health, and preparedness for such risks.

Opportunistic intruders: how viruses orchestrate ER functions to infect cells.

Abstract: Viruses subvert the functions of their host cells to replicate and form new viral progeny. The endoplasmic reticulum (ER) has been identified as a central organelle that governs the intracellular interplay between viruses and hosts. In this Review, we analyse how viruses from vastly different families converge on this unique intracellular organelle during infection, co-opting some of the endogenous functions of the ER to promote distinct steps of the viral life cycle from entry and replication to assembly and egress. The ER can act as the common denominator during infection for diverse virus families, thereby providing a shared principle that underlies the apparent complexity of relationships between viruses and host cells. As a plethora of information illuminating the molecular and cellular basis of virus-ER interactions has become available, these insights may lead to the development of crucial therapeutic agents.

viruSITE-integrated database for viral genomics.

Abstract: Viruses are the most abundant biological entities and the reservoir of most of the genetic diversity in the Earth's biosphere. Viral genomes are very diverse, generally short in length and compared to other organisms carry only few genes. viruSITE is a novel database which brings together high-value information compiled from various resources. viruSITE covers the whole universe of viruses and focuses on viral genomes, genes and proteins. The database contains information on virus taxonomy, host range, genome features, sequential relatedness as well as the properties and functions of viral genes and proteins. All entries in the database are linked to numerous information resources. The above-mentioned features make viruSITE a comprehensive knowledge hub in the field of viral genomics.The web interface of the database was designed so as to offer an easy-to-navigate, intuitive and user-friendly environment. It provides sophisticated text searching and a taxonomy-based browsing system. viruSITE also allows for an alternative approach based on sequence search. A proprietary genome browser generates a graphical representation of viral genomes. In addition to retrieving and visualising data, users can perform comparative genomics analyses using a variety of tools.Database URL: http://www.virusite.org/.

Genomic Characterization of the Genus Nairovirus (Family Bunyaviridae)

Abstract: Nairovirus, one of five bunyaviral genera, includes seven species. Genomic sequence information is limited for members of the Dera Ghazi Khan, Hughes, Qalyub, Sakhalin, and Thiafora nairovirus species. We used next-generation sequencing and historical virus-culture samples to determine 14 complete and nine coding-complete nairoviral genome sequences to further characterize these species. Previously unsequenced viruses include Abu Mina, Clo Mor, Great Saltee, Hughes, Raza, Sakhalin, Soldado, and Tillamook viruses. In addition, we present genomic sequence information on additional isolates of previously sequenced Avalon, Dugbe, Sapphire II, and Zirqa viruses. Finally, we identify Tunis virus, previously thought to be a phlebovirus, as an isolate of Abu Hammad virus. Phylogenetic analyses indicate the need for reassignment of Sapphire II virus to Dera Ghazi Khan nairovirus and reassignment of Hazara, Tofla, and Nairobi sheep disease viruses to novel species. We also propose new species for the Kasokero group (Kasokero, Leopards Hill, Yogue viruses), the Ketarah group (Gossas, Issyk-kul, Keterah/soft tick viruses) and the Burana group (Wēnzhōu tick virus, Huangpi tick virus 1, Tǎcheng tick virus 1). Our analyses emphasize the sister relationship of nairoviruses and arenaviruses, and indicate that several nairo-like viruses (Shāyang spider virus 1, Xīnzhōu spider virus, Sānxia water strider virus 1, South Bay virus, Wǔhan millipede virus 2) require establishment of novel genera in a larger nairovirus-arenavirus supergroup.

Virus Structure and Classification

Abstract: Viruses have several common characteristics: they are small, have DNA or RNA genomes, and are obligate intracellular parasites. The virus capsid functions to protect the nucleic acid from the environment, and some viruses surround their capsid with a membrane envelope. Most viruses have icosahedral or helical capsid structure, although a few have complex virion architecture. An icosahedron is a geometric shape with 20 sides, each composed of an equilateral triangle, and icosahedral viruses increase the number of structural units in each face to expand capsid size. The classification of viruses is very useful, and the International Committee on Taxonomy of Viruses is the official body that classifies viruses into order, family, genus, and species taxa. There are currently seven orders of viruses.

Developments in Plant Negative-Strand RNA Virus Reverse Genetics.

Abstract: Twenty years ago, breakthroughs for reverse genetics analyses of negative-strand RNA (NSR) viruses were achieved by devising conditions for generation of infectious viruses in susceptible cells. Recombinant strategies have subsequently been engineered for members of all vertebrate NSR virus families, and research arising from these advances has profoundly increased understanding of infection cycles, pathogenesis, and complexities of host interactions of animal NSR viruses. These strategies also permitted development of many applications, including attenuated vaccines and delivery vehicles for therapeutic and biotechnology proteins. However, for a variety of reasons, it was difficult to devise procedures for reverse genetics analyses of plant NSR viruses. In this review, we discuss advances that have circumvented these problems and resulted in construction of a recombinant system for Sonchus yellow net nucleorhabdovirus. We also discuss possible extensions to other plant NSR viruses as well as the applicat...

Ecogenomic survey of plant viruses infecting Tobacco by Next generation sequencing

Abstract: The invasion of plant by viruses cause major damage to plants and reduces crop yield and integrity. Devastating plant virus infection has been experienced at different times all over the world, which are attributed to different events of mutation, re-assortment and recombination occurring in the viruses. Strategies for proper virus management has been mostly limited to eradicating the vectors that spreads the plant viruses. However, development of prompt and effective diagnostic methods are required to monitor emerging and re-emerging diseases that may be symptomatic or asymptomatic in the plant as well as the genetic variation and evolution in the plant viruses. A survey of plant viruses infecting field-grown Tobacco crop was conducted in Anhui Province of China by the deep sequencing of sRNAs. Survey of plant viruses infecting Tobacco was carried based on 104 samples collected across the province. Nine different sRNA libraries was prepared and custom-made bioinformatics pipeline coupled with molecular techniques was developed to sequence, assemble and analyze the siRNAs for plant virus discovery. We also carried out phylogenetic and recombination analysis of the identified viruses. Twenty two isolates from eight different virus species including Cucumber mosaic virus, Potato virus Y, Tobacco mosaic virus, Tobacco vein banding Mosaic virus, Pepper mottle virus, Brassica yellow virus, Chilli venial mottle virus, Broad bean wilt virus 2 were identified in tobacco across the survey area. The near-complete genome sequence of the 22 new isolates were determined and analyzed. The isolates were grouped together with known strains in the phylogenetic tree. Molecular variation in the isolates indicated the conserved coding regions have majorly a nucleotide sequence identity of 80-94 % with previously identified isolates. Various events of recombination were discovered among some of the isolates indicating that two or more viruses or different isolates of one virus infect the same host cell. This study describes the discovery of a consortium of plant viruses infecting Tobacco that are broadly distributed in Anhui province of China. It also demonstrates the effectiveness of NGS in identifying plant viruses without a prior knowledge of the virus and the genetic diversity that enhanced mixed infection.

An updated evolutionary study of Flaviviridae NS3 helicase and NS5 RNA-dependent RNA polymerase reveals novel invariable motifs as potential pharmacological targets

Abstract: The rate of Flaviviridae family virus infections worldwide has increased dramatically in the last few years. In addition, infections caused by arthropod vector viruses including Hepatitis C, West Nile, Dengue fever, Yellow fever and Japanese encephalitis are emerging throughout the world. Based on a recent taxon update, the Flaviviridae family comprises four main genera; Flavivirus, Hepacivirus, Pestivirus and a recent genus Pegivirus. Although the new scientific classification plays a key role in providing useful information about the relationships between viruses, many new documented viruses remain unclassified. Furthermore, based on the different results of several studies the classification is unclear. In an effort to provide more insights into the classification of viruses, a holistic evolutionary study of the two viral enzymes NS3 helicase and NS5 RNA-dependent RNA polymerase (RdRp) has been conducted in this study. These two viral enzymes are very crucial for the inhibition of viruses due to the fact that they are involved in the survival, proliferation and transmission of viruses. The main goal of this study is the presentation of two novel updated phylogenetic trees of the enzymes NS3 helicase and NS5 RdRp as a reliable phylogeny "map" to correlate the information of the closely related viruses and identify new possible targets for the Flaviviridae family virus inhibition. Despite the earliest trials for drugs against Flaviviridae related viruses, no antiviral drug vaccine has been available to date. Therefore there is an urgent need for research towards the development of efficient antiviral agents.

Iridoviruses of Fish

Abstract: Iridoviruses are large, double-stranded DNA viruses with a host range restricted to insects and ectothermic vertebrates. Viruses of the family Iridoviridae are emerging pathogens that are widespread in a diverse range of environments and hosts. The family includes numerous virus species belonging to the genera Ranavirus, Lymphocystivirus and Megalocytivirus. These species are the cause of important diseases characterized by mortality with impacts on the production, conservation and welfare of fish. These pathogens are the focus of biosecurity and regulatory controls because the threat to naive fish populations with an expanded geographic distribution would have severe impacts on aquaculture production. The nomenclature of this family is confusing and the taxonomy is under review as knowledge of the epidemiology and techniques for diagnosis and control is rapidly developed.

Classes, taxa and categories in hierarchical virus classification: a review of current debates on definitions and names of virus species

Abstract: The species taxon was introduced in virus classification as late as 1991 when it was endorsed by the International Committee on Taxonomy of Viruses (ICTV). The official definition of virus species was as follows: “A virus species is a polythetic class of viruses that constitute a replicating lineage and occupy a particular ecological niche”. Its key feature was that it incorporated the notion of polythetic class also known as a cluster class. Whereas monothetic classes are defined by one or a few properties that are both necessary and sufficient for membership in the class, polythetic classes are defined by a variable set of statistically covariant properties, none of which is a defining property necessarily present in every member of the class. Since a virus species class is a conceptual construction, it cannot be described by its physical or material properties and can only be defined by listing certain properties of the viruses that are its members. Properties used for defining virus species are properties of viruses that can be altered by a few mutations, such as their natural host range, pathogenicity, mode of transmission and small differences in the viral genome. This means that these species-defining properties vary considerably in different members of the same virus species. Since higher taxa such as genera and families have more viruses as members than species taxa, they require fewer defining properties than species taxa which require more properties to meet the qualifications for membership. The logical principle that increasing the number of qualifications decreases membership invalidates the claim that a single property could be sufficient for defining a virus species. The bionominalist school of thought which claims that species are individuals instead of classes is examined and it is concluded that bionominalism does not provide a useful framework for classifying viruses. Since large numbers of sequences of viral genomes have become available, many attempts are currently made to establish species solely on the basis of genome data obtained from putative members of a viral species. Since the nucleic acid sequence present in a virus particle is part of the phenotype of the virus, a virus classification based on nucleotide sequences is a phenotypic classification that relies on molecular sequences rather than on the morphological and biological properties of viruses. Since it is not possible to infer the phenotypic properties of a virus from its genome sequence, a genome-based classification which privileges phylogeny is actually a classification of viral genomes rather than a classification of viruses. In recent years, it has been suggested that it should be possible to define a virus species monothetically by a single species-defining property such as a genome nucleotide motif and that the term ‘polythetic’ should therefore be removed from the official species definition. In 2013, the ICTV ratified the following new definition of virus species: “A virus species is a monophyletic group of viruses whose properties can be distinguished from those of other species by multiple criteria”. Since every virus species, genus or family could be considered to be a monophyletic group, this was actually a definition of ‘virus taxon’ instead of virus species. Many objections were raised against this new species definition and these are available on the ICTV website. A major concern was that ‘polythetic class’ in the earlier definition had been replaced by ‘group’ of viruses, because a group is a collection of viruses that are linked by a part-whole relation, whereas the term class implies the logical relations of class membership and class inclusion used in all hierarchical classifications. The authors of the new definition actually claimed that the term class should be used only to denote a category in the classification hierarchy, above the category order and below the category phylum. Examples were also given of the pernicious consequences that followed from the fact that new species could now be established on the basis of a single criterion of nucleotide sequence similarity in viral genomes. In 1998, the ICTV introduced species names that differed from virus names only by typography, with the result that measles virus became officially a member of the species Measles virus (italicized, with a capital initial). This led to considerable confusion and the ICTV subsequently agreed that its Study Groups in charge of the taxonomy and nomenclature of individual virus families could propose non-Latinized binomial names (NLBNs) for species in certain virus genera. Such NLBNs, which had been used unofficially for 50 years, are obtained by replacing the terminal word ‘virus’ that occurs in all common English virus names with the name of the genus to which the virus belongs, which also ends in -virus. Measles virus thus became a member of the species Measles morbillivirus which was more easily recognized as a species name since binomial names in biology are associated with taxonomic species names. In the last four years, numerous species NLBNs have been introduced in several virus families.

Peering below the diffraction limit: robust and specific sorting of viruses with flow cytometry

Abstract: Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population. Specific sorting opens new avenues in the study of uncultivable viruses, including recovering the full genomes of viruses based on genetic fragments in metagenomes, or identifying the hosts of viruses. PAVS enables specific sorting of viruses with flow cytometry. A sample containing a virus population is processed through a microfluidic device to encapsulate it into droplets, such that the droplets contain different viruses from the sample. TaqMan PCR reagents are also included targeting specific virus species such that, upon thermal cycling, droplets containing the species become fluorescent. The target viruses are then recovered via droplet sorting. The recovered virus genomes can then be analyzed with qPCR and next generation sequencing. We describe the PAVS workflow and demonstrate its specificity for identifying target viruses in a heterogeneous population. In addition, we demonstrate recovery of the target viruses via droplet sorting and analysis of their nucleic acids with qPCR.

The Molecular Virology of Enteric Viruses

Abstract: Foodborne and waterborne viruses cause a range of illnesses, from acute gastroenteritis (caliciviruses –noroviruses and sapoviruses-, rotaviruses, astroviruses, and enteric adenoviruses), to hepatitis (hepatitis A virus and hepatitis E virus), and other diseases. Recently, next-generation sequencing technologies have allowed the discovery of new enteric viruses (novel astroviruses, kobuviruses, saliviruses, etc.). Noroviruses are the leading cause of acute gastroenteritis outbreaks and sporadic cases in children and adults worldwide and they still remain refractory to routine cell culture propagation. Recent studies have shown that histo-blood group antigens (HBGAs) are cellular carbohydrates that serve as receptors and host susceptibility factors for human noroviruses. They evolve based on antigenic changes and differential glycan binding specificities. In the last years there have been significant advances in the knowledge of their replication mechanisms, pathogenicity and genetic evolution. The strain diversity and the evolution of rotaviruses are also a matter of concern, despite the introduction of rotavirus vaccines. Similarly, molecular analyses of orally transmitted viruses causing hepatitis are clarifying the phylogenetic relationships between these viruses and other viral genera, as well as their pathophysiological mechanisms.

Viral Contamination of Food

Abstract: A review of the relevant foodborne viruses is presented. Published data from scientific journals as well as the data presented in official reports and published on the Internet were used for this review. In the review, information is given for the main foodborne viruses, implicated virus species, and food matrices involved, some history data are given, as well as modes of transmission, and sources of the virus presence in food. Results of surveys on the presence of viruses in different kind of foods commodities (fresh produces and shellfish) and in some cases connections to caused outbreaks are presented. Also, possible zoonotic infection and implicated viruses that could be transmitted through food are given. Human Norovirus followed by hepatitis A virus are the most common foodborne viruses, which are transmitted by food consumed raw, such as shellfish, fresh vegetables, and berry fruit. In developed countries, hepatitis E virus is increasingly being recognized as an emerging viral foodborne pathogen that includes zoonotic transmission via pork products. The existing knowledge gaps and the major future expectations in the detection and surveillance of foodborne viruses are mentioned.

Review: Approaches to the Viral Extraction, Detection, and Identification of Hepatitis Viruses, HAV and HEV, in Foods.

Abstract: Although the incidence rate of hepatitis A virus (HAV) infection has been on the decline in developed countries, in part due to immunization availability, high profile outbreaks continue to be reported. Hepatitis E virus has been recognized as an emerging pathogen in industrialized countries. While associated with waterborne illnesses, particularly in undeveloped countries, several animal species have been identified as reservoirs for the virus. Consequently, the potential of zoonotic transmission exists as a function of the consumption of infected animals. In this review we provide a comparative overview of these two virus species with regard to their known virus properties, discuss extraction methodologies, and describe some basic principles and methodology applied toward the isolation of these viruses (as particles or their isolated genomes) from food commodities. We also discuss the challenges that remain as experimental hurdles to extraction of such viruses from food. As HAV has been the most extensively studied with regard to virus detection in foods, it often serves as a model virus for current and future development of sample preparation methodology for foodborne virus detection. Lastly, we discuss the application and role of current and developing technologies in the post-extraction detection and identification of these viruses from foods.

The taxonomy of viruses should include viruses

Abstract: Having lost sight of its goal, the International Committee on Taxonomy of Viruses has redoubled its efforts. That goal is to arrive at a consensus regarding virus classification, i.e., proper placement of viruses in a hierarchical taxonomic scheme; not an easy task given the wide variety of recognized viruses. Rather than suggesting a continuation of the bureaucratic machinations of the past, this opinion piece is a call for insertion of common sense in sorting out the avalanche of information already, and soon-to-be, accrued data. In this way information about viruses ideally would be taxonomically correct as well as useful to working virologists and journal editors, rather than being lost, minimized, or ignored.

Metagenomic characterization of viral communities in Goseong Bay, Korea

Abstract: In this study, seawater samples were collected from Goseong Bay, Korea in March 2014 and viral populations were examined by metagenomics assembly. Enrichment of marine viral particles using FeCl3 followed by next-generation sequencing produced numerous sequences. De novo assembly and BLAST search showed that most of the obtained contigs were unknown sequences and only 0.74% of sequences were associated with known viruses. As a result, 138 viruses, including bacteriophages (87%), viruses infecting algae and others (13%) were identified. The identified 138 viruses were divided into 11 orders, 14 families, 34 genera, and 133 species. The dominant viruses were Pelagibacter phage HTVC010P and Roseobacter phage SIO1. The viruses infecting algae, including the Ostreococcus species, accounted for 9.4% of total identified viruses. In addition, we identified pathogenic herpes viruses infecting fishes and giant viruses infecting parasitic acanthamoeba species. This is a comprehensive study to reveal the viral populations in the Goseong Bay using metagenomics. The information associated with the marine viral community in Goseong Bay, Korea will be useful for comparative analysis in other marine viral communities.

Classification and Identification of Aquatic Animal Viruses

Abstract: The classification of microorganisms is now considered mature. There are over 1000 individual viruses that cause infections of veterinary significance in the major animal species/groups; most are assigned to virus families. Despite considerable advances in animal virology in recent years, coupled with an economically important global aquaculture industry, knowledge of viruses of animal aquaculture is still sparse and in some cases outdated, although these viruses are closely related to well-known virus families. The purpose of this chapter is that viruses within groups share characteristics that help in our understanding of the epidemiology and pathogenesis of infections they produced. If you know the member viruses of a particular family and understand the group properties of each family, it is possible to know some vocabulary about the particular viral disease. Furthermore, this knowledge gives valuable information on laboratory methods used to properly identify new viruses.

The Taxonomy, Classification, and Characterization of Medically Important Viruses

Abstract: Viruses are a complex and diverse group of organisms that may have incredibly diverse and ancient origins. Their interaction with humans not only involves disease processes, but also evolutionary pressures that shape viral characteristics. Viral taxonomy, classification, and characterization is not a simple academic exercise but practically improves our ability to diagnose, track, and compare viruses of medical importance and develop a better understanding of pathophysiologic processes. Over the last 5 years, there have been significant changes in the proper names of some commonly identified viruses of medical importance, relationships between these medically relevant viruses, technologic tools, as well as websites and bioinformatics tools. Changes, including what constitutes the definition of a viral species, have already had an impact on how viruses are characterized and classified. The expanded utilization of whole genome sequence analysis and metagenomic approaches has increased the amount of biological information available to the scientific community for virus characterization and categorization. With these newer molecular approaches for virus identification and characterization, as well as enhanced bioinformatics approaches, viral classification is as dynamic and challenging as ever, requiring continuous monitoring, reassessment, and updating to achieve a rational taxonomic framework.

Towards a coherent nomenclature of plant viruses

Abstract: The International Committee on Taxonomy of Viruses(ICTV)has the decree to set the rules for the classification and naming of virusesThe species is the lowest level considered in the taxonomic hierarchyIn general,virus species are named according to the structure"and the word‘virus’"A typical example is Tobacco mosaic virus[Genus:To-

Classification of Viruses and Phylogenetic Relationships

Abstract: The taxonomy of viruses represents a unique classification system that recognizes boundaries among at first sight a continuum of properties. Genome sequencing has brought into sharp debate the origin of viruses, with RNA viruses perhaps having a separate evolutionary lineage. The criteria adopted for assessing the causal linkage between virus and disease deviates from those normally adopted for bacterial diseases and reflects those unique properties that underlie the principles of virus classification.