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At least 559 records · Page 31Linked to original sources
PubMed2006

Isolation and characterization of a Sagiyama virus from domestic pigs.

In 2002, a strain of Sagiyama virus (SAGV) designated ML/Taiwan/02 was isolated from farmed pigs in Taiwan. The nsP1 and E1 gene sequences of the ML/Taiwan/02 strain shared 98.6 and 96.7% homology, respectively, with corresponding genes of a Japanese strain of SAGV. Nucleotide and amino acid sequence comparison revealed this strain of SAGV to be most closely related to Getah virus, as opposed to its current classification as a subtype of Ross River virus. To investigate the seroprevalence of SAGV infection in Taiwan, a total of 586 pig sera collected from 11 of 17 Taiwanese districts were tested for serum neutralizing antibodies (SNA) against SAGV. Results indicated that 51% of the samples had SNA titer > or = 4, and 40% had SNA titer > or = 48, indicative of repeated exposure to SAGV in the field. To study the pathogenicity of the ML/Taiwan/02 strain, this strain was experimentally inoculated into 4-week-old specific-pathogen-free pigs that were seronegative for SAGV. Viremia was detected during postinoculation days (PID) 2-4, when the SNA titer was < or = 16. By PID 7, viremia was no longer detectable, coinciding with the increase of SNA titer to > or = 48. Clinical illnesses or remarkable lesions were not observed. To the authors' knowledge, this is the first reported isolation of a strain of SAGV from pigs in the field. The virus is experimentally nonpathogenic to pigs but is moderately widespread, most likely via repeated exposure to virus-carrying mosquitoes.

Alphavirus Infections↗
PubMed2001

A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species.

Identification of previously unrecognized viral agents in serum or plasma samples is of great medical interest but remains a major challenge, primarily because of abundant host DNA. The current methods, library screening or representational difference analysis (RDA), are very laborious and require selected sample sets. We have developed a simple and reproducible method for discovering viruses in single serum samples that is based on DNase treatment of the serum followed by restriction enzyme digestion and sequence-independent single primer amplification (SISPA) of the fragments, and have evaluated its performance on known viruses. Both DNA viruses and RNA viruses at a concentration of approximately 10(6) genome equivalents per ml were reproducibly identified in 50 microl of serum. While evaluating the method, two previously unknown parvoviruses were discovered in the bovine sera used as diluent. The near complete genome sequence of each virus was determined; their classification as two species (provisionally named bovine parvoviruses 2 and 3) was confirmed by phylogenetic analysis. Both viruses were found to be frequent contaminants of commercial bovine serum. DNase treatment of serum samples may prove to be a very useful tool for virus discovery. The DNase-SISPA method is suitable for screening of a large number of samples and also enables rapid sequence determination of high-titer viruses.

Animals↗
PubMed1967

Rabbit macrophage interferons. II. Some physicochemical properties and estimations of molecular weights.

Antiviral factors present in cultures of rabbit peritoneal macrophages or rabbit kidney (RK) cells infected with Newcastle disease virus (NDV) and those in cultures of uninfected macrophages all fulfilled the biological and physicochemical criteria for classification as interferons. Virus-induced macrophage and RK interferons were slightly more stable to heat or acid than "spontaneously produced" or endotoxin-induced macrophage interferon. Interferon activity in serum of NDV-infected rabbits was decidedly more labile than NDV-induced macrophage interferon. However, these differences in lability were too slight to serve as a useful basis for distinguishing one rabbit interferon from another. Rabbit interferons from various sources could be differentiated by filtration through Sephadex G-100 and their molecular weights estimated by comparison with elution profiles of a series of marker proteins of known molecular weight. Each of four different preparations of rabbit interferons was found to contain more than one molecular component. Elution peaks for three NDV-induced interferons were equivalent to the following molecular weights: RK approximately 44,000-45,000 and > 134,000 (variable and < 1% when present); macrophage approximately 37,000, 44,000-45,000, and > 134,000 (variable and <1% when present); and serum approximately 50,000-52,000 and > 134,000 ( approximately 10% and heat labile). NDV-induced serum interferon may also contain another molecular component of mol wt approximately 45,000 represented by a trailing shoulder from the major 51,000 mol wt peak. Endotoxin-induced macrophage interferon proved to be polydisperse. Sephadex filtration of this interferon did not reveal clear and consistent elution patterns, partially owing to its low initial titer and lability. However, variable peaks of biological activity could be detected in Sephadex fractions equivalent to approximate molecular weight values of > 134,000, 72,000-78,000, 33,000-38,000, 28,000-30,000, and possibly a component of 42,000-45,000. A major component of mol wt approximately 37,000 was present in all samples of endotoxin-induced macrophage interferon. The other constituents may be biologically active subunits or polymers. These data indicate that rabbit macrophages produce two primary kinds of interferon: (a) an RK-like component of mol wt approximately 45,000 that is synthesized in greatest amount after viral induction, and (b) a different species of mol wt approximately 37,000 that can also be synthesized in the absence of viral induction. The presence of major interferon constituents of mol wt approximately 51,000 and > 134,000 in rabbit serum after viral induction suggests that macrophages are not the principal interferon-producing cells that respond to intravenous injection of NDV.

Animals↗
PubMed1976

[Classification of strains of foot-and-mouth disease virus according to the relationship-dominance model for a better understanding of the concept of serologic and immunologic subtype].

The homologous and heterologous serological titers of a specific serum can be integrated in a bidimensional system which characterizes the criteria of relationship and dominace. This bidimensional classification specifies more precisely the serological properties of each strain compared with the others (taxonomic purpose) and allows eventual guidance in the choice of vaccinal strains (epizootiologic and prophylactic purposes).

Aphthovirus↗
PubMed1980

Purification and characterization of Aleutian disease virus.

Virus was isolated from infected mink organs by a combination of tissue homogenization, fluorocarbon extraction and ultracentrifugation. The final preparation was analysed by crossed immunoelectrophoresis and electronmicroscopy. Virions had a capsid diameter of 22 nm. Preparative agarose electrophoresis separated virions from contaminating ferritin. Crossed immunoelectrophoresis of virus gave a single precipitate with sera from infected mink. Crossed immunoelectrophoretic analysis with intermediate gels showed that a part of the virus preparation was complexed with antibody. Serum from a certain mink was found to contain precipitating antibody to (poly)nucleotid. Virus and virus-antibody complexes were found to focus at pH 4.0-4.4 in isoelectric focusing. In SDS-polyacrylamide gel-electrophoresis the main virus protein was found to have a molecular weight of 69000. This study gives further support to the classification of aleutian disease virus as a parvovirus.

Aleutian Mink Disease Virus↗
PubMedDate not supplied

[Common oligopeptides of influenza virus A hemagglutinin].

Oligopeptide maps of the light chain of hemagglutinin of all 17 serotypes: H0-H3, Hsw1, Heq1-Heq2, Hav1-Hav10, were studied for classification of influenza A viruses isolated from man and animals. The comparisons revealed common oligopeptides in many viruses isolated from man and animals, so that in the final analysis all influenza A viruses of man and animals form a continuous series. It is concluded that human and animal influenza A viruses comprise a single but extremely heterogeneous population capable of continuous exchange of genes.

Animals↗
PubMed2005

Norovirus classification and proposed strain nomenclature.

Without a virus culture system, genetic analysis becomes the principal method to classify norovirus (NoV) strains. Currently, classification of NoV strains beneath the species level has been based on sequences from different regions of the viral genome. As a result, the phylogenetic insights of some virus were not appropriately interpreted, and no consensus has been reached to establish a uniform classification scheme. To provide a consistent and reliable scientific basis for classifying NoVs, we analyzed the amino acid sequences for the major capsid protein of 164 NoV strains by first using an alignment based on the predicted 3D structures. A Bayesian tree was generated, and the maximum likelihood pairwise distances of the aligned sequences were used to evaluate the results from the uncorrected pairwise distance method. Analyses of the pairwise distances demonstrated three clearly resolved peaks, suggesting that NoV strains beneath the species level can be classified at three levels: strain (S), cluster (C), and genogroup (G). The uncorrected pairwise distance ranges for S, C, and G were 0-14.1%, 14.3-43.8%, and 44.9-61.4%, respectively. A scheme with 29 genetic clusters [8 in genogroup 1 (G1), 17 in G2, 2 in G3, and 1 each in G4 and G5] was defined on the basis of the tree topology with the standards provided and was supported by the distance analysis. Of these, five clusters in G2 and one in G1 are newly described. This analysis can serve as the basis for a standardized nomenclature to genetically describe NoV strains.

Animals↗
PubMed2026

A unified benchmark of supervised and retrieval-based methods for viral genomic sequence classification.

The rapid growth of genomic sequencing demands fast, accurate, and scalable analysis methods. In viral genomic classification, expanding labeled reference collections can make supervised models costly to update and dependent on fixed label sets, motivating retrieval-based genomic classification as a simpler, more flexible alternative. We present a unified benchmark of supervised and retrieval-based methods for viral genomic sequence classification across three viral classification tasks: hepatitis C virus (HCV) genotyping, COVID-19 discrimination, and human papillomavirus (HPV) genotyping. We compare standard sequence encodings (one-hot, k-mers, FCGR) with dense embeddings (dna2vec, DNABERT). For each representation, we evaluate supervised classifiers (Random Forest, Decision Tree, XGBoost) and retrieval-based classification, where sequence vectors are indexed with FAISS and labels are assigned via similarity-weighted k-NN. Furthermore, we benchmark multiple FAISS index types (Flat, IVF, HNSW, IVFPQ, OPQ) to characterize accuracy-speed-memory trade-offs at scale. The results show that XGBoost and retrieval using Flat or IVF indexes achieve strong classification performance under different computational profiles. Compressed indexes such as IVFPQ and OPQ substantially reduce memory usage, although their accuracy loss depends on the dataset and representation. Overall, supervised XGBoost provides a favorable accuracy-size trade-off, while retrieval-based classification remains competitive and allows labeled reference sequences to be incorporated without retraining a global classifier. This benchmark provides practical guidance for selecting sequence representations, classifiers, and vector-search indexes under different accuracy, memory, and update requirements.

Genome, Viral↗
PubMed1975

The sub-type classification of strains of foot-and-mouth disease virus.

Sixteen foot-and-mouth disease virus (FMDV) strains of type SAT 1 were compared in complement-fixation tests. With the test used, the range of antigenic variation within a type appeared to be greater than previously described. The concept of a sub-type group within which all strains are more closely related to each other than to any strain outside the group was not supported. Considering the group of strains studied, it is suggested that the classification of strains is best achieved by moninating a reference strain for each sub-type. Others are classified as related strains in one or more sub-type groups according to their relationships with the reference strains.

Animals↗
PubMed2002

Evolution of viral structure.

Viruses vastly outnumber their host cells and must present a huge selective pressure. It is also becoming evident that only a small percent of the eukaryotic genome codes for molecules involved in cellular structures and functions, and that much of the remainder may have a viral origin. Viruses clearly play a central role in the biosphere, but how is this viral world organized? Classification was originally based on virus morphology and the particular host infected, but now there is an increasing trend to rely on sequence information. The type of genome (e.g., RNA or DNA, single- or double-stranded) provides fundamental classification criteria, while sequence comparisons can provide fine mapping for closely related viruses. However, it is currently very difficult to identify long-range evolutionary relationships. We present here a different approach, based on the idea that each virus has an innate "self." When the structures and functions characteristic of this "self" are identified, then they uncover relationships beyond those accessible from sequence information alone. The new approach is illustrated by sketching some possible viral lineages. We propose that urviruses were present before the division of cellular life into its current domains, and that the viral world has lineages that can be traced back to the root of the universal tree of life.

Biological Evolution↗
PubMed1985

A serological classification of bovine enteroviruses.

Cross virus neutralization (VN), complement fixation (CF) and immunoprecipitation (IP) tests were employed to compare the seven currently recognized bovine enterovirus (BEV) serotypes with seven serologically distinct strains previously isolated in Great Britain and two other BEV from the United Kingdom. Based on criteria used to differentiate other human and animal picornavirus serotypes, it was discovered that BEV types 1, 4, 5 and 6 were related to each other and could be included in a single serotype. Types 3 and 7 were found to be identical, and related to serotype 2. All of the other nine BEV were included in either serotype 1 or 2. Not all of the strains in each serotype were identical and antigenic variants were designated as subtypes. Antigenic relationships not revealed by VN were demonstrated in CF and IP tests. Bovine enterovirus strains whose antisera had the broadest intratypic reactivity were suggested as prototypes. The two proposed BEV serotypes could also be distinguished by their ability to agglutinate erythrocytes. Guinea pig erythrocytes were agglutinates by both serotypes while sheep red cells only reacted with serotype 1.

Animals↗