Problems in diagnosis and classification of dengue virus infection.
Explore the source record for details and available documents.
Adolescent↗
SEARCH · Search PubMed
Results for “virus classification”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
[A classification of virus-related neurological disease].
Virus-related neurological diseases (VRNDS) are classified according to, (1) the site of main pathologic changes, (2) the type of cells infected with (parasitized by) pathogenic viruses, (3) the species of causative viruses. In the acutenesis of the development of clinical manifections and (5) the length of latency (period between infection and the onset of the illness). VRNDs were classified into meningitides, encephalitides, myelitides and neuritides. The VRNDs in which nerve cells (neurons, neuroglial cells or both) are parasitized by pathogenic viruses can be called neuroinfective viral neurological diseases. The VRDs in which nerve cells can be called non neuro-infective neurological viral disease. VRNDs were classified into those by Papova viruses, those by Herpes viruses, those by Picornaviruses, those by Toga viruses, those by Flaviviruses, those by Paramyxoviruses, those by Rhabdoviruses, those by Arenaviruses, those by Buniaviruses and those by Retroviruses. VRNDs may develop acutely, subacutely on chronically. There are VRNDs that can be called progressive because their course is progressive and their outcome is fatal. Some VRNDs develop soon after primary infection and other VRNDs develop long after primary infection on reactivation of the virus.
Humans↗
[Classification of influenza viruses and problems of new viruses].
Explore the source record for details and available documents.
Aged↗
A whole genome perspective on the phylogeny of the plant virus family Tombusviridae.
Most current classifications of viruses are based on single gene analysis of capsid protein or polymerase. The comparison of entire genomes is a more balanced approach that should provide a more complete picture of relatedness. We have used a singular value decomposition (SVD)-based analysis to generate phylogenetic trees using whole genome protein sequences from a family of single-stranded RNA plant viruses. Our dataset includes the 26 species of the family Tombusviridae, 25 of which have complete genome sequences cataloged in GenBank. The resulting phylogenetic tree agrees well with current taxonomic classifications, but with significant exceptions. One previously unassigned virus within this family, Maize necrotic streak virus, is definitively placed within the genus Tombusvirus by this analysis. In addition, the analysis defines two distinct subsets within the genus Necrovirus. Future datasets will be expanded to include other icosahedral positive strand RNA plant viruses, and then perhaps all positive strand RNA plant viruses.
Amino Acid Sequence↗
[Etiological diagnosis and classification of Herpes virus-associated disturbances of the central nervous system].
An etiological classification is submitted of Herpes virus-induced affections of the central nervous system (CNS), such as monoherpesviral, herpesvirus-bacterial, herpesvirus-spirochetal, herpesvirus-mycotic, herpesvirus-protozoan affections. Excerpts from case records of etiologically confirmed mixed infections are given. Consideration is given to such herpesviruses as HSV, CMV, EBV, VZV. Other possible combinations of etiological agents include herpesvirus + chlamidia, mycoplasms, prions.
Adolescent↗
[Sexually transmitted viruses. General principles and classification].
Explore the source record for details and available documents.
Hepatitis Viruses↗
[Current classification and nomenclature of plant viruses (by materials of the International Committee on Virus Taxonomy). Part I].
The rules of classification and nomenclature of plant viruses are reviewed in connection with the reports of the International Committee on Viruses Taxonomy. The characteristics of the families and genera of plant viruses approved by the Committee in 1995 are presented.
Animals↗
A novel transformer model of protein domains for viral taxonomy classification.
MOTIVATION: Viruses with carefully curated taxonomic assignments (such as those in the ICTV taxonomy) still represent only a small fraction of viruses identified through sequencing data from virome or microbiome projects. It is therefore critical to develop methods that can assign viruses at multiple taxonomic ranks, so that a virus deemed novel at a given rank may still be placed into a higher-level taxon. Sequence-similarity-based approaches can classify viruses that share substantial genomic similarity with known viruses (e.g. those belonging to the same species or genus); however, their performance drops significantly when applied to more divergent viruses. Recent deep learning models, such as ViTax, which utilize DNA language models, aim to address these limitations, but their performance also degrades when applied to novel viruses lacking genus-level similarity to known references. Proteins are more conserved than genomic sequences, and the multiple proteins encoded by a virus can be leveraged to reveal evolutionary relationships among viruses. RESULTS: We propose a new tool, D2T (Domain-to-Taxonomy), that leverages recent advances in protein language models to improve viral taxonomic assignment. D2T represents a virus as a sequence of protein domain tokens and learns a transformer-based model for taxonomic classification. Experiments on multiple closed-set and open-set datasets show that D2T excels at assigning higher-level taxonomic labels (family and above). Furthermore, by combining D2T with Kraken2, which performs well at the genus level, the hybrid method (K+D2T) achieves accurate viral taxonomic classification across multiple taxonomic ranks. AVAILABILITY AND IMPLEMENTATION: D2T is available as a GitHub repository at https://github.com/mgtools/D2T.
Viruses↗
A provisional classification of cytoplasmic polyhedrosis viruses based on the sizes of the RNA genome segments.
The RNA genome segments of thirty-three isolates of cytoplasmic polyhedrosis viruses (CPVs) were examined by polyacrylamide gel electrophoresis. Major differences were observed in the gel profiles of the RNA segments from many of the viruses; differences which were reinforced by polyacrylamide gel electrophoresis of the virus structural proteins. As a result of these studies, a provisional classification scheme for CPVs is proposed, where viruses with similar RNA gel profiles are included within the same 'type', while isolates differing in the molecular weights of most, or all of the RNA segments are assigned to different types. Using this system, eleven distinct CPV types were recognized. All eleven CPV types, like reoviruses, probably contain ten segments of RNA with a toatl mol. wt. of approx. 15 X 10(6).
Electrophoresis, Polyacrylamide Gel↗
Cowpox virus infection in an 11-year-old girl.
We describe an 11-year-old girl with a cowpox virus infection, who presented with a 14-day-old crusted, ulcerated nodule on the chin/neck and a 6-day-old eroded blister on the left leg. The girl lived in a rural environment, had close contact to several cats from the neighborhood, and had an atopic predisposition. The presence of orthopox virus in the lesion on the left leg was demonstrated by electron microscopy (negative staining, transmission electron microscopy) and virus isolation. Classification as a cowpox virus was determined by polymerase chain reaction (PCR), followed by restriction enzyme digestion of the PCR product.
Animals↗
Taxonomic classification of human hepatitis B virus.
Sufficient data have accumulated to permit the ICTV Study Group on the Nomenclature of Hepatitis Viruses to recognize human hepatitis B virus as a member of a unique group of viruses and to classify it, together with a number of related animal viruses, into a new family called the Hepadnaviridae. Over the past decade, the International Committee on Taxonomy of Viruses (ICTV) has been active in the development of a classification system for viruses. The majority of viruses infecting vertebrate hosts have been classified into families and genera on the recommendations of the Vertebrate Virus Subcommittee (VVSC). In June 1980, the VVSC authorized the formation of an ad hoc Study Group on the Nomenclature of Hepatitis Viruses under the Chairmanship of Dr. Ian D. Gust. This paper represents the first report of the Study Group on the Taxonomic Classification of Human Hepatitis B Virus.
Animals↗
Partial nucleotide sequence of poplar mosaic virus RNA confirms its classification as a carlavirus.
The nucleotide sequence of the 3'-proximal 1328 nucleotides of poplar mosaic virus (PMV) was determined and shown to contain two large open reading frames (ORFs). The ORF nearer to the 3' terminus of the RNA is capable of encoding a polypeptide of 14K with a 'zinc-finger' motif, and is homologous to sequences in corresponding positions in five other carlaviruses. The other ORF encodes a protein of 36K which includes two sequences of amino acids identified in tryptic digests as virion capsid protein, and has amino acid sequences in common with both carlaviruses and potexviruses.
Amino Acid Sequence↗
Characterization of the genes encoding UL24, TK and gH proteins from duck enteritis virus (DEV): a proof for the classification of DEV.
Duck enteritis virus (DEV) is classified to the family Herpesviridae, but has not been grouped into any genus so far. Four overlapped fragments were amplified from the DEV genome with polymerase chain reaction (PCR). The assembled length of the four fragments was 6,202 bp, which contained the genes encoding unique long (UL) 24, thymidine kinase (TK) and glycoprotein H (gH) proteins. The UL24 overlapped with TK by 64 nucleotides (nt), in a head-to-head transcription orientation, and the TK and gH had the same transcription orientation. The comparison of amino acid sequences of these 3 deduced DEV proteins with other 12 alphaherpesviruses displayed 5 highly conserved sites in the UL24, as well as another 5 consensus regions in the TK and 4 consensus regions in the gH. The RNA polymerase II transcriptional control elements were identified in all the UL24, TK and gH of DEV. These elements included core promoters, TATA motifs and polyadenylation sites. Phylogenetic analysis for the genetic classification of DEV in the Alphaherpesvirinae subfamily with other 12 alphaherpesviruses was computed. The result showed that DEV was more closely related to avian herpesviruses, except infectious laryngotracheitis virus (ILTV), than to other alphaherpesviruses. Conclusively, according to the phylogenesis-based analysis and the homology comparison of functional domains of UL24, TK and gH, DEV should be classified to a separate genus of the Alphaherpesvirinae subfamily in the family Herpesviridae.
Alphaherpesvirinae↗
Classification of hepatitis C viruses based on phylogenetic analysis of the envelope 1 and nonstructural 5B regions and identification of five additional subtypes.
Genotyping of hepatitis C virus-positive sera by means of a line probe assay indicated that < 3% of European samples, but up to 30% of Gabonese sera, could not be classified as either 1a, 1b, 2a, 2b, 3a, 3b, 4c, 5a, or 6a. Such samples were analyzed in the 5' untranslated region and in the nonstructural 5 (NS5) region. Classification based on phylogenetic analysis of the commonly used 222-bp-long NS5B region was possible for most but not all of the selected sera. Therefore, the core/envelope 1 region (579 bp) and a larger NS5B (340 bp) region were also analyzed. Only the phylogenetic analysis of the 340-bp NS5B region of these newly identified and published isolates provided unambiguous classification into types and subtypes. Furthermore, unequivocal evidence for four subtypes in type 2 and eight subtypes in type 4 was provided. A specific recognition sequence in the 5' untranslated region was observed for every newly identified subtype. Based on 1830 pair-wise comparisons in NS5B, isolates belonging to the same subtype showed evolutionary distances of < 0.127 and isolates of the same type exhibited evolutionary distances of < 0.328. These phylogenetic border distances can be conveniently used for classification of hepatitis C virus isolates into types and subtypes.
Amino Acid Sequence↗
Nonrandom development of immunologic abnormalities after infection with human immunodeficiency virus: implications for immunologic classification of the disease.
Blood specimens from 165 intravenous drug users who were seropositive for the human immunodeficiency virus (HIV), from 158 seropositive homosexual men with lymphadenopathy, and from 77 patients with acquired immunodeficiency syndrome (AIDS) were assessed immunologically. Immunologic parameters were analyzed by the Guttman scalogram technique to determine if immunologic abnormalities occurred in a nonrandom pattern. The following four patterns emerged: (i) seropositivity for HIV with no immunologic abnormalities; (ii) seropositivity for HIV with a depressed T4/T8 cell ratio; (iii) seropositivity with a depressed T4/T8 cell ratio and T4-cell depletion; and (iv) seropositivity with a depressed T4/T8 cell ratio, T4-cell depletion, and lymphopenia. Ninety-two to 100% of subjects in each of the three groups of patients were found "to scale" because the abnormalities occurred in the cumulative, ordered fashion described. This nonrandom occurrence of abnormalities indicates an ordered progression of immunologic abnormalities in individuals infected with HIV, a finding useful in the staging of both symptomatic and asymptomatic HIV-seropositive subjects.
AIDS-Related Complex↗
[Chronic hepatitis B virus and hepatitis C virus infections. Hidtology-classification--examination].
Clinicians disagree over the need to perform liver biopsy in chronic infections with hepatitis B and C viruses, with opinions ranging from "useless" to "conditionally advisable" to "absolutely necessary." The frequency of liver biopsies has generally been declining, which entails decreased practical knowledge in the morphological examination of liver biopsies. As a result certain basic considerations must occasionally reemphasized.
Biopsy↗
Molecular classification of hepatitis C virus.
Many sequences of hepatitis C virus (HCV) have been reported, but there has been no report about the evolutionary classification of HCV. The aim of this study is to classify the nucleotide sequences of HCV into appropriate genetical groups by molecular evolutionary methods. A number of nucleotide sequences of HCV were collected from all over the world. First, all HCV nucleotide sequences for each region were aligned to optimize homologies. Phylogenetic trees were then constructed for each region of HCV according to the number of the nucleotide substitutions. HCVs can be classified into two or three major groups in the trees of each regions. However, minor groups can be classified into two in that of 5' non-coding, four in that of Core, Env., E2/NS1, NS3 and NS4 region and six in that of NS5 region. However, the full sequences such as HCV-1, HCVH and HCV-J4, were always located in the same major and minor groups in that trees of all regions. These data indicated that HCVs can be classified into two or three major and six minor groups.
Base Sequence↗
Evolutionary analysis of variants of hepatitis C virus found in South-East Asia: comparison with classifications based upon sequence similarity.
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.
Asia, Southeastern↗