Showing papers on "Virus classification published in 1996"

Evolutionary analysis of variants of hepatitis C virus found in South-East Asia: comparison with classifications based upon sequence similarity

Abstract: Variants of hepatitis C virus (HCV) have been classified by nucleotide sequence comparisons in different regions of the genome. Many investigators have defined the ranges of sequence similarity values or evolutionary distances corresponding to divisions of HCV into types, subtypes and isolates. Using these criteria, novel variants of HCV from Vietnam, Thailand and Indonesia have been classified as types 7, 8, 9, 10 and 11, many of which can be further subdivided into between two to four subtypes. In this study, this distance-based method of virus classification was compared with phylogenetic analysis and statistical measures to establish the confidence of the groupings. Using bootstrap resampling of phylogenetic trees in several subgenomic regions (core, E1, NS5) and with complete genomic sequences, we found that one set of novel HCV variants ('types 7, 8, 9 and 11') consistently grouped together into a single clade that also contained type 6a, while 'type 10a' grouped with type 3. In contrast, no robust higher-order groupings were observed between any of the other five previously described HCV genotypes (types 1-5). In each subgenomic region, the distribution of pairwise distances between members of the type 6 clade were consistently bi-modal and therefore provided no justification for classification of these variants into the three proposed categories (type, subtype, isolate). Based on these results, we propose that a more useful classification would regard all these variants as subtypes of type 6 or type 3, even though the level of sequence diversity within the clade was greater than observed for other genotypes. Classification by phylogenetic relatedness rules out simple sequence similarity measurements as a method for assigning HCV genotypes, but provides a more appropriate description of the evolutionary and epidemiological history of a virus.

Structure and Classification of Viruses

Abstract: Viruses are small obligate intracellular parasites, which by definition contain either a RNA or DNA genome surrounded by a protective, virus-coded protein coat. Viruses may be viewed as mobile genetic elements, most probably of cellular origin and characterized by a long co-evolution of virus and host. For propagation viruses depend on specialized host cells supplying the complex metabolic and biosynthetic machinery of eukaryotic or prokaryotic cells. A complete virus particle is called a virion. The main function of the virion is to deliver its DNA or RNA genome into the host cell so that the genome can be expressed (transcribed and translated) by the host cell. The viral genome, often with associated basic proteins, is packaged inside a symmetric protein capsid. The nucleic acid-associated protein, called nucleoprotein, together with the genome, forms the nucleocapsid. In enveloped viruses, the nucleocapsid is surrounded by a lipid bilayer derived from the modified host cell membrane and studded with an outer layer of virus envelope glycoproteins.

Resistance specificities to viruses in potato: Standardization of nomenclature

Abstract: Potato viruses are prevalent worldwide and cause substantial economical losses in the potato crop (Solanum tuberosum L.). Therefore, various types of resistance to potato viruses identified in cultivated and wild potato species are used in potato breeding programs and are briefly reviewed in this paper. However, the current nomenclature of virus resistance specificities is confusing because it was adopted at an earlier time when several virus strain groups were believed to represent individual virus species and because it does not distinguish between strain-specific and comprehensive resistance specificities. A consistent nomenclature is desirable to distinguish both currently known virus resistances and any novel virus resistances detected in the future. A descriptive and systematic nomenclature for resistance specificities is proposed which denotes (1) type of resistance (2) identity of virus (3) the virus strain group(s) against which the resistance is effective (4) the virus strain group(s) against which the resistance is not effective, and (5) the potato species in which the resistance is described.

Biology and Molecular Biology of Bunyaviruses

Abstract: The Bunyavirus genus is the largest genus in the Bunyaviridae family with more than 172 recognized virus serotypes and subtypes (Karabatsos, 1985; Chapter 1). As discussed in Chapter 1, they are organized into 18 serogroups with a small number of ungrouped viruses. The viruses have been placed into these serogroups on the basis of the results of a number of serological tests (Bishop and Shope, 1979). The data suggest that there are more significant antigenic differences between members of the different serogroups than between members of the same serogroup. Generally, there is no detectable cross-neutralization, or hemagglutinin inhibition, between members of different groups, but some degree of cross-neutralization, or hemagglutinin inhibition, between members of the same group (depending on the virus, see Hunt and Calisher, 1979). Some serogroups are more closely related to others than they are to the rest of the genus (Klimas et al., 1981b). None of the viruses exhibit any antigenic relationship to members of other genera of the family (Bishop and Shope, 1979). Within a serogroup virus isolates may be considered as separate species, or relatives of such species. In antigenic terms, viruses are classified by serological tests into serotypes (the original virus of a grouping), subtypes (in which there are some antigenic differences to the founder virus as demonstrated using polyclonal sera), variants (where such differences are only demonstrated using particular antibodies, such as a monoclonal antibody), or varieties (where the antigenic difference may be minor, or where sequence analyses indicate a small number of differences between virus isolates). These terms will be used in this chapter. However, what constitutes a bunyavirus species has yet to be defined (Bishop, 1985). It could be argued that each bunyavirus serogroup may include only a few virus species, or even only one if viruses that produce reassortants in dual infections are considered to constitute one species. This issue is, however, complicated by the fact that although certain viruses are genetically similar they may be ecologically distinct, thus reducing the opportunity for reassortment.

Recent revisions of the rules of virus classification and nomenclature

Abstract: The classification and nomenclature of viruses is the responsibility of the International Committee for the Taxonomy of Viruses (ICTV). This body comprises National Members, appointed by the member virological societies of the International Union of Microbiological Societies (IUMS), Life Members, appointed by vote at Plenary Sessions, and members of the ICTV Executive Committee. ICTV is controlled by Statutes approved by the Virology Division of IUMS and its decisions are guided by a set of Rules. These were modified at the recent Xth International Congress of Virology in Jerusalem by the Plenary, Session of ICTV. The version in force until August 1996 was as in Murphy et al. [4] and was developed from the previous Rules (Francki et al. [1]) as described by Mayo and Murphy [3]. The new version of the Rules has been designated as a Code, in line with how the nomenclature of other biological organisms is controlled (Greuter et al. [2]). The Code is printed below with comments in parentheses to indicate how the new Rules are related to those in the previous version. A major change is the provision of a section of explanatory notes to assist users of the Rules. The Notes, and to some extent the Rules, are subject to refinement in the face of unexpected difficulties in their application. The author, or any other member of the Executive Committee of ICTV, would welcome comment from the virological community to assist with this refinement process.

Virus Life in Diagrams

Abstract: INTRODUCTION A SUMMARY OF VIRUS CLASSIFICATION THE REPLICATION CYCLE COMPARATIVE DIAGRAMS DNA VIRUSES ssDNA Viruses dsDNA Viruses with Cubic or Helical Symmetry dsDNA Viruses with Binary Symmetry VIRUSES USING REVERSE TRANSCRIPTION Retrovirdae Others RNA VIRUSES ssRNA Viruses with (+) Strands ssRNA Viruses with (-) Strands dsRNA Viruses MISCELLANY Virus-Like Particles Agents with Circular ssRNA Prions ABBREVIATIONS AND UNITS GLOSSARY REFERENCES INDEX

Human and Animal Viruses

Abstract: Publisher Summary This chapter provides an overview of the human and animal viruses. Viruses held to a low number of passages in animals or cell cultures represent a viral population that is similar to that found in nature, and freezing these pools guards against genetic mutations that occur during subsequent passage. Aliquots of viral stocks frozen at a designated passage level can then be used for multiple and repeatable experiments with the same viral population. Furthermore, it is important that consistency should be maintained during the production of viral vaccines; new lots of final product are prepared with frozen viral seed stocks that consistently reproduce the desired immunogenic and attenuation characteristics. To better appreciate the requirements for freezing and freeze drying of human and animal viruses, some consideration is given to understanding the structural and functional organization of this diverse group of microorganisms. The classification of viruses is based on morphological and physiochemical properties. Thus, viruses are divided into those with DNA or RNA genomes and subdivided into families based on size and structural properties. Several methods for preservation of viruses are included in the chapter.

Present status of classification of viruses of vertebrates

Abstract: The VIth Report of the International Committee on Taxonomy of Viruses (ICTV) was published in 1995. We have briefly characterized its contents and discussed the most important changes that have been made in the classification of viruses of vertebrates. The present line up of families and genera of viruses of vertebrates, and subviral agents and unassigned viruses is also provided. We propose an allocation of families of viruses of vertebrates according to a conjectural evolutional connection between the type and class of genomic nucleic acid. Finally the directions and intentions of the ICTV have been reviewed from the Virology Division News in Archives of Virology (1994/1995). These will be considered in the VIIth Report of the ICTV scheduled for publication after the XIth International Congress of Virology in Sydney in 1999.

The cytoskeleton and virus infection

Abstract: Publisher Summary This chapter discusses the cytoskeleton and virus infection. Viruses are traditionally classified according to the type of nucleic acid they contain and the morphology of the virion particle, if naked, or the nucleocapsid, if enveloped. With the advent of molecular biological techniques, such as polymerase chain reaction (PCR) and nucleic acid sequencing, new virus isolates are grouped into virus families primarily based on their nucleic acid sequence homology to existing viruses. Virus infection is initiated by binding of a virus particle to the surface of a susceptible host cell. This binding is usually mediated by specific proteins on the virus particle and specific receptors on the plasma membrane of the host cell. The virus particle enters the cell by endocytosis for non-enveloped viruses or by fusion of envelope and plasma membrane for enveloped viruses.