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At least 217 records · Page 12Linked to original sources
PubMed1982

The electron microscopical and physical characteristics of small round human fecal viruses: an interim scheme for classification.

Many of the small round human fecal viruses implicated in outbreaks of nonbacterial gastroenteritis have been collected together and examined under the electron microscope. Negatively stained preparations without the addition of antibody were used so that the surface morphology of the virus particles remained clearly visible. It was apparent that several viruses, previously thought to be simply antigenic variants within the Norwalk group of viruses, show distinct morphological differences and quite clearly belong to other virus groups. By comparing the features of all the viruses examined in this study, both with each other and with standard cell culture strains of enterovirus, parvovirus, and calicivirus, it has been possible to propose an interim classification scheme, based primarily on the morphological appearance of the particles and supported by estimations of size and buoyant density.

Caliciviridae↗
PubMed2001

Fluorogenic RT-PCR assay (TaqMan) for detection and classification of bovine viral diarrhea virus.

A single tube fluorogenic RT-PCR-based 'TaqMan' assay was developed for detection and classification of bovine viral diarrhea virus (BVDV). TaqMan-PCR was optimized to quantify BVD virus using the ABI PRISM 7700 sequence detection system and dual-labeled fluorogenic probes. Two different gene specific labeled fluorogenic probes for the 5' untranslated region (5' UTR) were used to differentiate between BVD types I and II. Sensitivity of the single tube TaqMan assay was compared with two-tube TaqMan assay and standard RT-PCR using 10-fold dilutions of RNA. Single tube TaqMan assay was 10-100-fold more sensitive than the two-tube TaqMan assay and the standardized single tube RT-PCR. Specificity of the assay was evaluated by testing different BVD virus strains and other bovine viruses. A total of 106 BVD positive and negative pooled or single serum samples, field isolates and reference strains were tested. Quantitation of cRNA from types I and II BVD virus was accomplished by a standard curve plotting cycle threshold values (C(T)) versus copy number. Single tube TaqMan-PCR assay was sensitive, specific and rapid for detection, quantitation and classification of BVD virus.

Animals↗
PubMed1995

Evaluation of complete genome sequences and sequences of individual gene products for the classification of hepatitis C viruses.

Comparisons of genome and polyprotein sequences of hepatitis C virus (HCV) isolates world-wide has led to the identification of nine major genotypes and many subtypes. This classification is based on either complete genome/polyprotein sequences or sequence data from the 5' noncoding region, core, E1, NS3 or NS5B genes. The relative merit of different gene segments as taxonomic markers and the validity of the resulting assignments is not clear at this stage. To resolve the taxonomy of HCV genotypes and subtypes, we have compared the complete genome and polyprotein sequences of 19 HCV isolates available in the databases as well as sequences of individual genes and gene products of these isolates. Based on the correlation between sequence relationships and taxonomic assignments of other RNA viruses, we show that the nine major genotypes of HCV represent nine distinct virus species and their subtypes subspecies. Our sequence comparison of the 5' noncoding regions and the individual gene products suggests that E2, NS2, NS5B, E1, NS4A, NS4B and NS5A (in that order) are the most appropriate regions for the discrimination between species, subspecies and strains of HCV. The 5' noncoding, core and NS3 regions are less effective in distinguishing between species, subspecies and strains. Based on a comparison of the polymerase sequence identities of HCVs, pestiviruses and flaviviruses as well as the recent information on the size and morphology of HCV virions, we propose that HCVs, pestiviruses and flaviviruses should be classified into three separate families, named Hepciviridae, Pestiviridae and Flaviviridae, respectively rather than three genera of the Flaviviridae as currently classified. We also propose "Hepcivirus" as the genus name for HCVs.

Base Sequence↗
PubMed1993

Molecular biology and evolution of filoviruses.

The family Filoviridae contains extremely pathogenic human viruses causing a fulminating, febrile hemorrhagic disease. Filoviruses are enveloped, filamentous particles with a nonsegmented negative-strand RNA genome showing the gene arrangement 3'-NP-VP35-VP40-GP-VP30-VP24-L-5'. Genes are flanked by highly conserved transcriptional signals and are generally separated by variable intergenic regions. They are transcribed into monocistronic polyadenylated messenger RNAs which contain relatively long 5' and 3' untranslated regions. Seven structural proteins are encoded by the genome of which four form the helical nucleocapsid (NP-VP35-VP30-L), two are membrane-associated (VP40-VP24), and one is a transmembrane glycoprotein (GP). Comparison of filovirus genomes with those of other nonsegmented negative-strand RNA viruses suggest comparable mechanisms of transcription and replication and a common evolutionary lineage for all these viruses. Sequence analyses of single genes, however, showed that filoviruses are more closely related to paramyxoviruses, particularly human respiratory syncytial virus. These data support the concept of the taxonomic order Mononegavirales for all nonsegmented negative-strand RNA viruses and the classification of Marburg virus, Ebola virus, and Reston virus in the family Filoviridae, separate from the families Paramyxoviridae and Rhabdoviridae.

Animals↗
PubMed1983

Comparison of biological properties of St. Louis encephalitis and Rio bravo viruses.

St. Louis encephalitis (SLE) virus, an arbovirus, and Rio Bravo (RB) virus, a non-arthropod-borne virus, are flaviviruses which cross-react in neutralization tests. Several of their biological properties were compared. Viral growth curves revealed that greater than 99% of infectious SLE (Parton) virus remained cell-associated in Vero cells but was released slowly into the medium of infected BHK-21 cells. In contrast, RB (M-64) virus was released upon maturation into the fluids of Vero and BHK-21 cell cultures. Fortyfold more SLE virus than RB virus adsorbed to monolayer cultures of Aedes dorsalis cells. SLE but not RB virus replicated and reached high titers (10(8) pfu/ml) in Ae. dorsalis cell cultures maintained in media which were expected to enhance recovery of RB virus. Further, SLE but not RB virus replicated in cultured bat epithelial cells and primary duck embryo cells incubated at 42 degrees C. Clearly, the prototype strains of RB and SLE viruses are distinct viruses. Both the classification of RB virus in the genus flavivirus and the antigenic relationship between RB and SLE viruses require further clarification.

Aedes↗
PubMedDate not supplied

Single-stranded genomic RNA from turkey enterovirus-like virus.

Previously, we described a disease syndrome in young turkeys caused by an enterovirus-like virus. The virus was designated an enterovirus-like virus based on size, morphology, and intracytoplasmic crystalline arrays of virus. In the present study, further characterization of the virus was performed to ascertain its classification. The virus has a buoyant density of 1.33 g/ml in CsCl and single-stranded RNA genome of approximately 7.5 kilobases. These combined characteristics indicate that this agent is an enterovirus.

Animals↗
PubMed1989

[Natural history and classification of HIV-virus infections].

Clinical concepts about the acquired immunodeficiency syndrome, are evolving constantly. Laboratory tests are used to prove the infection virologically and serologically, to quantify the importance of immunodeficiency and to give a tentative prognosis. We discuss three classification systems (CDC, Haverkos, Walter Reed). They are more or less precise and suitable. They may indicate the status of the disease, from seroconversion up to opportunistic infections and secondary cancers. Then we compare those different systems of classification, their advantages and disadvantages. These classification systems may change with evolving concepts about the syndrome.

AIDS-Related Complex↗
PubMed1999

GB virus C/hepatitis G virus groups and subgroups: classification by a restriction fragment length polymorphism method based on phylogenetic analysis of the 5' untranslated region.

A phylogenetic tree based on 150 5' untranslated region sequences deposited in GenBank database allowed segregation of the sequences into three major groups, including two subgroups, i.e., 1, 2a, 2b, and 3, supported by bootstrap analysis. Restriction site analysis of these sequences predicted that HinfI and either AatII or AciI could be used for genomic typing with 99.4% accuracy. cDNA sequencing and subsequent alignment of 21 Argentine GB virus C/hepatitis G virus strains confirmed restriction fragment length polymorphism patterns theoretically predicted. This method may be useful for a rapid screening of samples when either epidemiological or transmission studies of this agent are carried out.

5' Untranslated Regions↗
PubMed1971

A revised system of nomenclature for influenza viruses.

The present system of classification of influenza viruses was developed by WHO Expert Committees meeting in 1953 and 1959, and was based on the ribonucleoprotein and haemagglutinin antigens. Since then, another antigen, neuraminidase, has been identified and it has been found that the haemagglutinin and the neuraminidase undergo independent antigenic variation. It is therefore necessary that the system of classification should describe all three antigens. Furthermore, it is now known that both the haemagglutinin and neuraminidase antigens of influenza A viruses of human origin may be similar to, or identical with, those of strains from non-human hosts, and it is necessary that this antigenic relationship should be indicated. For influenza A viruses, therefore, a new system retaining as much as possible of the old system but also including the new information has been developed. It is the intention of WHO that the new system should be brought into use on 1 January 1972.

Antigens, Viral↗
PubMed1997

Classification of hepatitis C virus variants in six major types based on analysis of the envelope 1 and nonstructural 5B genome regions and complete polyprotein sequences.

The phylogenetic status of recently described isolates of hepatitis C virus (HCV) from Vietnam, Thailand and Indonesia (previously classified as types 7, 8, 9, 10 and 11) was re-analysed by the neighbour-joining method instead of the unweighted pair-group method with arithmetic mean (UPGMA) that was first used by the discoverers of these strains. The analysis of complete amino acid sequences and of nucleotide sequences of the envelope 1 (672 nt) and nonstructural 5B (1092 nt) genomic regions permitted the re-assignment of the type 7, 8, 9 and 1 1 isolates to type 6, and that of type 10 strains to type 3. Finally, this study made possible the classification of the previously described HCV strains (including these South-East Asian isolates) in six major types and at least 30 subtypes. It confirms that analysis of the E 1 and NS5B genomic regions using the neighbour-joining method is a reliable tool for the assignment of most new isolates.

Genome, Viral↗
PubMed2000

Genetic classification of "Norwalk-like viruses..

Reverse transcription-polymerase chain reaction has been used worldwide for the diagnosis of Norwalk-like virus (NLV) infection, yet a commonly accepted genetic classification scheme has not been established. Amino acid sequences from four regions of open-reading frame 2 (ORF2) were used to analyze 101 NLV strains, including 2 bovine strains. On the basis of this analysis, a genetic classification scheme is proposed that differentiates 99 human strains into 2 major genetic groups consisting of 5 and 10 genetic clusters, respectively. The 2 bovine strains constitute a newly defined third major genetic group composed of 2 putative clusters represented by each strain. This classification scheme is well supported by the analysis of the entire ORF2 sequences from 38 strains selected to represent the genetic diversity of the human strains used above. This scheme should provide a firm scientific basis for the unified classification of NLV strains detected around the world.

Amino Acid Sequence↗
PubMed1998

Comparative sequence analysis of American, European and Asian isolates of viruses in the genus Coltivirus.

In this study, the basis for the classification of virus isolates grouped within the genus Coltivirus, family Reoviridae, is discussed. Sequences of dsRNA segments from American (segments 9-12), European (segment 12) and Asian (segments 7-12) isolates were characterized and polythetic criteria were defined for their taxonomic classification. These criteria (including sequence analysis) permitted the different species to be distinguished and classified into two groups. In both groups, subgroups were defined according to the degree of homology between the genomic sequences. American and European isolates are classified within group A, which includes subgroups A1 (Colorado tick fever virus species) and A2 (Eyach virus species). Asian isolates are classified in group B, which includes subgroups B1 (JKT-7075 virus species) and B2 (JKT-6423 virus species). The proteins encoded by the sequenced genomic segments were analysed. This allowed the identification of dsRNA binding domains in the proteins encoded by segment 8 of subgroup B1 isolates and segment 12 of subgroup B2 isolates. A conserved pattern of amino acids in segment 7 of group B isolates matched sequences found in the catalytic domains of protein kinases.

Amino Acid Sequence↗
PubMed1993

Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region.

Hepatitis C virus (HCV) showed substantial nucleotide sequence diversity distributed throughout the viral genome, with many variants showing only 68 to 79% overall sequence similarity to one another. Phylogenetic analysis of nucleotide sequences derived from part of the gene encoding a non-structural protein (NS-5) has provided evidence for six major genotypes of HCV amongst a worldwide collection of 76 samples from HCV-infected blood donors and patients with chronic hepatitis. Many of these HCV types comprised a number of more closely related subtypes, leading to a current total of 11 genetically distinct viral populations. Phylogenetic analysis of other regions of the viral genome produced relationships between published sequences equivalent to those found in NS-5, apart from the more highly conserved 5' non-coding region in which only the six major HCV types, but not subtypes, could be differentiated. A new nomenclature for HCV variants is proposed in this communication that reflects the two-tiered nature of sequence differences between different viral isolates. The scheme classifies all known HCV variants to date, and describes criteria that would enable new variants to be assigned within the classification as they are discovered.

Base Sequence↗
PubMed2002

Molecular classification of coxsackie A viruses on the basis of the 5'-UTR: structural and evolutionary aspects.

The sequences from a large part of the 5'-UTR of 21 coxsackie A virus (CAV) reference strains for which such data did not exist in the past were obtained. Those sequences, along with the respective available sequences from the rest of the CAV reference strains and many other enteroviruses, were compared. According to the results of this comparison, enteroviruses are classified into two genetic clusters on the basis of 5'-UTR, and CAVs are divided into these two clusters. Specifically, it was found that CAV1, -11, -13, -15, -17 to -22, and -24 are classified together with polioviruses and enterovirus 70, whereas the rest of the CAVs are classified along with coxsackie B viruses, echoviruses, and the rest of the other enteroviruses. No correlation between overall 5'-UTR identity and the currently recognized human enterovirus species was found. The phenomenon of "covariance" in the 5'-UTR was followed for the prediction of the possible secondary structure of the 5'-UTR of the CAVs sequenced in the present study.

5' Untranslated Regions↗
PubMed2000

Molecular phylogenetics and the classification of honey bee viruses.

We present the phylogenetic relationships of several picorna-like RNA viruses found in honey bees, with respect to 13 additional plant and animal positive-strand RNA viruses. Most of the honey bee viruses fall into an unnamed family of insect RNA viruses typified by the Drosophila C virus. Different bee viruses are broadly distributed within this group, suggesting either that the ability to infect honey bees has evolved multiple times, or that these viruses are generalistic in their abilities to infect insect hosts. At least one major change in gene order has occurred among the bee viruses, based on their phylogenetic affiliations. At the amino-acid level, the bee viruses differed by 15-28% at three conserved loci. Most differed by greater than 50% at the RNA level, indicating that sequence-based methods for bee virus identification must be tailored to at least three different virus clades independently.

Amino Acid Sequence↗