Showing papers on "Virus classification published in 2000"

Virus taxonomy: classification and nomenclature of viruses. Seventh report of the International Committee on Taxonomy of Viruses.

Abstract: The practical need to partition the world of viruses into distinguishable, universally agreed upon entities is the ultimate justification for developing a virus classification system. Since 1971, the International Committee on Taxonomy of Viruses (ICTV) operating on behalf of the world community of virologists has taken on the task of developing a single, universal taxonomic scheme for all viruses infecting animals (vertebrate, invertebrates, and protozoa), plants (higher plants and algae), fungi, bacteria, and archaea. The current report builds on the accumulated taxonomic construction of the eight previous reports dating back to 1971 and records the proceedings of the Committee since publication of the last report in 2005. Representing the work of more than 500 virologists worldwide, this report is the authoritative reference for virus organization, distinction, and structure.

Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs

Abstract: Viruses are cellular parasites. The linkage between viral and host functions makes the study of a viral life cycle an important key to cellular functions. A deeper understanding of many aspects of viral life cycles has emerged from coordinated molecular and structural studies carried out with a wide range of viral pathogens. Structural studies of viruses by means of cryo-electron microscopy and three-dimensional image reconstruction methods have grown explosively in the last decade. Here we review the use of cryo-electron microscopy for the determination of the structures of a number of icosahedral viruses. These studies span more than 20 virus families. Representative examples illustrate the use of moderate- to low-resolution (7- to 35-A) structural analyses to illuminate functional aspects of viral life cycles including host recognition, viral attachment, entry, genome release, viral transcription, translation, proassembly, maturation, release, and transmission, as well as mechanisms of host defense. The success of cryo-electron microscopy in combination with three-dimensional image reconstruction for icosahedral viruses provides a firm foundation for future explorations of more-complex viral pathogens, including the vast number that are nonspherical or nonsymmetrical.

Virus nomenclature: consensus versus chaos.

Abstract: A recent, highly polemical contribution to these columns [10] criticized the workings of the International Committee on Taxonomy of Viruses (ICTV) and suggested that the new Rules about the orthography of virus species names approved by ICTV were leading virus nomenclature into chaos. References to receding or impending chaos are frequently made by those who approve [6, 7] or disapprove [10] of the work done by the ICTV on behalf of the world community of virologists. In his one-sided and unbalanced diatribe against the work of the ICTV, Gibbs [10] raises several issues that need to be answered. We have gauged the opinions of the ICTV Executive Committee and of the ICTV Life Members regarding the various criticisms levelled by Gibbs and summarize the responses below. Several of the respondents deplored the derogatory tone used by Gibbs to refer to the activities of the ICTV, an organization of which he is a Life Member, and stated that they regard the ICTV as a valuable international body which, in spite of certain organizational concerns, has served virologists well.

Phylogenetic analysis of some large double-stranded RNA replicons from plants suggests they evolved from a defective single-stranded RNA virus.

Abstract: Sequences were recently obtained from four double-stranded (ds) RNAs from different plant species. These dsRNAs are not associated with particles and as they appeared not to be horizontally transmitted, they were thought to be a kind of RNA plasmid. Here we report that the RNA-dependent RNA polymerase (RdRp) and helicase domains encoded by these dsRNAs are related to those of viruses of the alpha-like virus supergroup. Recent work on the RdRp sequences of alpha-like viruses raised doubts about their relatedness, but our analyses confirm that almost all the viruses previously assigned to the supergroup are related. Alpha-like viruses have single-stranded (ss) RNA genomes and produce particles, and they are much more diverse than the dsRNAs. This difference in diversity suggests the ssRNA alpha-like virus form is older, and we speculate that the transformation to a dsRNA form began when an ancestral ssRNA virus lost its virion protein gene. The phylogeny of the dsRNAs indicates this transformation was not recent and features of the dsRNA genome structure and translation strategy suggest it is now irreversible. Our analyses also show some dsRNAs from distantly related plants are closely related, indicating they have not strictly co-speciated with their hosts. In view of the affinities of the dsRNAs, we believe they should be classified as viruses and we suggest they be recognized as members of a new virus genus (Endornavirus) and family (Endoviridae).

Phylogenetic position of the Diadromus pulchellus ascovirus DNA polymerase among viruses with large double-stranded DNA genomes

Abstract: The Ascoviridae is a family of large double-stranded (ds) DNA insect viruses that contains four species, the Spodoptera frugiperda (SfAV1), Trichoplusia ni (TnAV2), Heliothis virescens (HvAV3) and Diadromus pulchellus (DpAV4) ascoviruses. These are unique among insect viruses in that the primary means of transmission among their lepidopteran hosts is generally by being vectored mechanically by hymenopteran parasitoids. Ascoviruses are similar in virion structure, but their relationships with their parasitoid vectors vary from being opportunistic to obligate. Little is known, however, about the relatedness of these viruses to one another or to other large dsDNA viruses. We therefore cloned and sequenced the δ DNA polymerase gene of DpAV4, characterized it and compared it to 59 eukaryotic and viral δ and ϵ DNA polymerases. Phylogenetic analyses based on these genes revealed that the ascoviruses DpAV4 and SfAV1 formed a group of virus species distinct from, but closely related to, species of the family Iridoviridae. Detailed analyses of the relatedness of ascovirus species based on conserved δ DNA polymerase motifs showed two groups within the family Ascoviridae, one containing DpAV4 and the other containing SfAV1, TnAV2 and HvAV3, which was consistent with their host–vector relationships. Despite significant differences in capsid symmetry between ascoviruses and iridoviruses, these results suggest that these viruses may have originated from a common ancestral virus.

On the relative merits of italics, Latin and binomial nomenclature in virus taxonomy

Abstract: classes like species or families cannot be seen or centrifuged. It certainly is not possible to centrifuge the species Tobacco mosaic virus, the genus Enterovirus or the family Picornaviridae. Some virologists may incorrectly write that they have inoculated the species Nicotiana tabacum with one or other viral species, instead of saying that they inoculated a tobacco plant (a member of the species Nicotiana tabacum) with a member of a viral species. Precision in a scientific publication is, indeed, desirable and can be achieved by referring once, for instance in the Materials and methods section, to the taxonomic placement of the virus under study (species X, genus Y, family Z). Thereafter, vernacular names can be used throughout the publication. However, no conceptual precision would remain if one followed Bos [4] and called the virus that infects a plant an abstraction. An infecting virus is no more an abstraction than an infected plant. Bos is confusing a class Table 3. Examples of current names of vertebrate viruses and their binomial counterparts

Virus nomenclature descending into chaos.

Abstract: Taxonomy with its two faces, systematics and nomenclature, is the mother of sciences; we must know what we are talking about, and that is the function of names. Hence rules of nomenclature in biology at large, including virology, aim to promote the meaningfulness, reliability and stability of names. That is why it is surprising that the International Committee on Taxonomy of Viruses (ICTV) breaks two of the basic rules it promulgates in the recently published Revisions of the Code of Virus Classification and Nomenclature [6]. It is stated in the Foreword to this revision states that the Code “is revised occasionally to conform with accepted virological practice”, and in Rule 3.9 that “Existing names of taxa and viruses shall be retained whenever feasible”. Nonetheless the ICTV then issues edicts (new Rule 3.40) telling all virologists to italicize all ICTV-approved virus names, and to capitalize the first letter of all names of virus species (e.g. Frangipani mosaic virus). It thus insists that virologists should stop using the informative taxonomy-based non-Latinized binomial system of naming viruses (e.g. frangipani mosaic tobamovirus and Iris fulva mosaic potyvirus), that has been increasingly widely used since first proposed informally in the second ICTV report [4]. The new orthographic ‘rules’ thus change, in essence, all existing virus names, conflict with other Codes of biological nomenclature, hinder proper notation of scientific names of host species included in virus names (such as Iris fulva) and distinction between such names and geographic names [1, 3], and are contrary to currently “accepted virological practice”. Thus the ICTV breaks the rules it advocates, but nonetheless has given no cogent reasons for doing so. Van Regenmortel [9] states that non-Latinized binomials have been widely accepted by plant virologists, but opposed by animal virologists, but he gives no details of how this opinion has been gauged nor, if true, why the views of the former are less important than those of the latter. It seems strange that he can give no more compelling reason for virology to become unique among the biological disciplines by returning to preLinnaean mononomials, even though they are to be superficially dignified by italicization to draw attention to the ICTV [10]. Plant virologists, who have a greater call on nomenclature than most working animal virologists, and widely use the vernacular binomials, are to be ignored. Furthermore a quick glance at Bos’s latest textbook [2] shows the great value of the

Human virology: a text for students of medicine, dentistry, and microbiology.

Abstract: PART 1 General properties and classification of viruses Viral replication and genetics How viruses cause disease Resistance to infection Viruses and cancer Viruses and the community PART 2 Upper respiratory tract and eye infections Childhood infections caused by paramyxoviruses Orthomyxoviruses and influenza Gastroenteritis viruses Rubella: postnatal infections Parvoviruses Poxviruses Papovaviruses Poliomyelitis and other picornavirus infections The herpesviruses: general properties Alphaherpesviruses Betaviruses Gammaviruses Introduction to the hepatitis viruses The blood-borne hepatitis viruses B and Delta The enteric hepatitis viruses A and E The bloodborne hepatits flaviviruses Retroviruses and AIDS Lyssavirus and rabies Arthropod-borne viruses Some exotic and dangerous infections: filoviruses and arenaviruses Prion diseases: the spongiform encephalopathies PART 3 Viral diseases of the central nervous system Intrauterine and perinatal infections Viral infections in patients with defective immunity Summary of respiratory infections Summary of sexually transmitted viral infections Emerging infections PART 4 The laboratory diagnosis of viral infections Control of viral diseases by immunization Antiviral chemotherapy Appendices Safety precautions: codes of practice, disinfection and sterilization Notifiable infections Infections possibly or definitely caused by viruses Further reading

2 – An Introduction to Viral Taxonomy and the Proposal of Akamara, a Potential Domain for the Genomic Acellular Agents

Abstract: This chapter introduces viral taxonomy and the proposal of akamara, which is a potential domain for the genomic acellular agents. This chapter also introduces the idea that the taxonomy of the viruses and their biological relatives could be extended to the domain level. There currently exist three biological domains, archaea, bacteria, and eukarya, that consist only of cellular organisms. The establishment of these three existing domains and the taxonomic placement of biological entities within them are based largely on the ribosomal RNA nucleotide sequence of those constituent organisms. This chapter proposes the creation of an additional biological domain that would represent the acellular infectious agents that possess nucleic acid genomes. The proposed constituents of this domain are the agents commonly termed to be either viruses, satellite viruses, virusoids, or viroids. The proposed domain title is Akamara. A possible organizational structure within this proposed new domain is also suggested, with its occupants being divided into two kingdoms: plus phyla and classes premised on the basic characteristics of the genomic biochemistry of the organisms.

Taxonomy of phytopathogenic viruses identified in the Russian far east

Abstract: The work is devoted to a problem of study of the taxonomy phytopathogenic viruses of Far East. The performance to genera, species and strain of viruses identified in Far East region is briefly given. A genus Potyvirus in more detail is described, as the greatest number identified on Far East phytoviruses is included into structure of this genus. In the given article the classification phythopathogenic of Russian Far East is represented, for which basis the classification of viruses of the message of International Committee on the taxonomy of viruses (1995) is taken.

Online identification of viruses.

Abstract: A computerized animal virus information system is developed in the Sequence Retrieval System (SRS) format. This database is available on the Word Wide Web (WWW) at the site http://bioinfo.ernet.in/www/avis/avis++ +.html. The database has been used to generate large number of identification matrices for each family. The software is developed in C. Unix shell scripts and Hypertext Marked-up Language (HTML) to assign the family to an unknown virus deterministically and to identify the virus probabilistically. It has been shown that such web based virus identification approach provides results with high confidence in those cases where identification matrix uses large number of independent characters. Protein sequence data for animal viruses have been analyzed and oligopeptides specific to each virus family and also specific to each virus species are identified for several viruses. These peptides thus could be used to identify the virus and to assign the virus family with high confidence showing the usefulness of sequence data in virus identification.

Viral Pathogenesis in Diagrams

Abstract: INTRODUCTION A SUMMARY OF VIRUS CLASSIFICATION VIRAL PATHOGENESIS IN VERTEBRATES: PRINCIPLES VERTEBRATE VIRUSES: INFECTION Types of disease Virus spread Cytopathology VERTEBRATE VIRUSES: HOST DEFENSE Organismic Defense Cellular Defense VERTEBRATE VIRUSES BY FAMILY Adenoviridae Arenaviridae Bunyaviridae Caliciviridae Coronaviridae Filoviridae Flaviviridae Hepadnaviridae Herpesvirida Orthomyxoviridae Papillomaviridae Paramyxoviridae Parvoviridae Picornaviridae Poxviridae Reoviridae Retroviridae Rhabdoviridae Togaviridae INSECT VIRUSES Baculoviridae Polydnaviridae PLANT VIRUSES Infection and Virus Spread Histo- and Cytopathology ABBREVIATIONS AND UNITS GLOSSARY REFERENCES INDEX