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At least 721 records · Page 40Linked to original sources
PubMed1993

Proposed classification of the bipartite-genomed raspberry bushy dwarf idaeovirus, with tripartite-genomed viruses in the family Bromoviridae.

Raspberry bushy dwarf virus (RBDV) has an unusual combination of properties and has been classified as the sole member of a new plant virus genus, for which the name idaeovirus has been proposed. Particles of RBDV resemble those of ilarviruses (family Bromoviridae) in appearance and in being transmitted in association with pollen. RBDV has two genomic RNA species, RNA-1 (5,449 nt) and RNA-2 (2,231 nt). The particles also contain RNA-3 (946 nt), a subgenomic monocistronic coat protein mRNA which is derived from the 3' end of the bicistronic RNA-2. The single 190 K protein encoded by RNA-1 contains methyltransferase, helicase and polymerase domains. Evolutionary distance data obtained from multiple alignments of the amino acid sequence of the RBDV 190 K protein and corresponding proteins with replicative function from other plant viruses suggest that the closest affinities of RBDV are with the tripartite genomed viruses in the family Bromoviridae. We propose that the genus idaeovirus be included in the family Bromoviridae.

Cluster Analysis↗
PubMed2004

Genotype classification and molecular evidence for the presence of mixed infections in Indian Citrus tristeza virus isolates.

Citrus tristeza virus (CTV) is usually present in field trees as a mixture or complex of isolates. Different biological types of CTV exist in India and this affects disease incidence and yield in the various citrus growing areas. Genotypic profiles were determined for 21 Indian CTV isolates. Of the 21 isolates, 15 contained only the VT genotype. The other isolates contained mixtures of either T30 or T3 with VT or T30, T3 and VT genotypes. One exception was isolate BAN-1, which contained a mixture of T36, T30 and T3 genotypes. Sequence diversity of Indian CTV isolates was determined by characterization in the k17 region of ORF 1a and the overlapping region of RdRp, gene p33, and sequence differences were utilized to identify group-specific genome features. A phylogenetic analysis of these regions divided the isolates into five distinct groups. There was a general trend for severe isolates to cluster into one of four groups and mild isolates into the fifth group. All the sequences from the two different regions of the CTV genome showed nucleotide identity to either VT, T30 or T36 isolates and confirmed the mixed infection of mild isolates with severe CTV isolates from three distinct geographical citrus growing regions in India.

Amino Acid Sequence↗
PubMed2004

Conserved RNA secondary structures in Flaviviridae genomes.

Presented here is a comprehensive computational survey of evolutionarily conserved secondary structure motifs in the genomic RNAs of the family Flaviviridae: This virus family consists of the three genera Flavivirus, Pestivirus and Hepacivirus and the group of GB virus C/hepatitis G virus with a currently uncertain taxonomic classification. Based on the control of replication and translation, two subgroups were considered separately: the genus Flavivirus, with its type I cap structure at the 5' untranslated region (UTR) and a highly structured 3' UTR, and the remaining three groups, which exhibit translation control by means of an internal ribosomal entry site (IRES) in the 5' UTR and a much shorter less-structured 3' UTR. The main findings of this survey are strong hints for the possibility of genome cyclization in hepatitis C virus and GB virus C/hepatitis G virus in addition to the flaviviruses; a surprisingly large number of conserved RNA motifs in the coding regions; and a lower level of detailed structural conservation in the IRES and 3' UTR motifs than reported in the literature. An electronic atlas organizes the information on the more than 150 conserved, and therefore putatively functional, RNA secondary structure elements.

3' Untranslated Regions↗
PubMed2003

Real-time PCR for simultaneous detection and genotyping of bovine viral diarrhea virus.

Since two genotypes of bovine viral diarrhea viruses (BVDV) occur in Belgian herds, their differentiation is important for disease surveillance. A quantitative real-time PCR assay was developed to detect and classify bovine viral diarrhea viruses in genotype I and II. A pair of primers specific for highly conserved regions of the 5'UTR and two TaqMan probes were designed. The FAM and VIC-labeled probe sequences differed by three nucleotides, allowing the differentiation between genotype I and II. The assay detectability of genotype I and II real-time PCR assay was 1000 and 100 copies, respectively. Highly reproducible data were obtained as the coefficients of variation of threshold cycle values in inter-runs were less than 2.2%. The correct classification of genotype I and II viruses was assessed by using reference strains and characterized field isolates of both genotypes. The application to clinical diagnosis was evaluated on pooled blood samples by post run measurement of the FAM- and VIC-associated fluorescence. The 100% agreement with the conventional RT-PCR method confirmed that this new technique could be used for routine detection of persistently infected immunotolerant animals.

Animals↗
PubMed1998

A short history of plant virology. II. The twenties.

Plant virology, born at the end of the last century, consolidated during the Twenties. Important new viral diseases were described and their causal agents partially purified and characterized not least because of the development of methods and techniques. An interesting debate concerned the so called "intracellular bodies", which were finally demonstrated to be aggregates of virus particles. Discoveries mainly arrived from experimental investigations on tobacco mosaic virus, and concerned the identification of strains, the demonstration of antigenic property, and the protein nature of viruses. A new concept of virus drew great advantage from the first attempts of classification and nomenclature, and a debate on the living or non-living nature of viruses, universally accepted as a new class of pathogens, was opened. The idea of viruses as self-reproducing particles was first advanced, although on a controversial basis. On the contrary, there was only erratic investigations on the physiological alterations produced by viral diseases in plants and on the relationships between viruses and vectors. In spite of this gaps, the Twenties must be mentioned as the years of the turning-point towards a biochemical concept of viruses, which will be achieved in the next decade.

Antigens, Viral↗
PubMed1983

Comparative study and grouping of nonstructural (NS1) proteins of influenza A viruses by the method of oligopeptide mapping.

Oligopeptide mapping of 35S-methionine labeled non-structural (NS1) proteins of 23 influenza. A virus strains showed the presence of both common and variable oligopeptides. Analysis of the oligopeptide maps revealed at least four groups of NS1 proteins. The first group includes NS1 proteins of several human H1N1 influenza viruses (that were designated as H0N1 according to the old classification). The second group is composed of NS1 proteins of H1N1 and H2N2 viruses. The third group includes NS1 proteins of H3N2 human influenza viruses. The fourth group is composed of NS1 proteins of five avian influenza viruses and an equine (H3N8) influenza virus. Two animal influenza viruses A/equi/Prague/56 (H7N7) and A/duck/England/56 (H11N6) contain NS1 proteins that belong to the second group.

Influenza A virus↗
PubMed2001

[Relationship between TT virus infection and hepatocellular carcinoma].

OBJECTIVE: To clarify the relationship between TT virus (TTV) infection and the development of hepatocellular carcinoma (HCC). METHODS: TTV was examined in sera of 112 patients with HCC and 95 patients with chronic liver disease (CLD) without HCC. 30 patients without liver disease were examined as control. TTV DNA was detected by the second generation of TTV PCR primers (NG059, NG061 and NG063) after extraction of DNA from 50 microliters serum. The relationship between TTV infection and clinical features of each group patients was analyzed. RESULTS: TTV DNA was detected in 17.86% (20/112) of HCC patients, and this prevalence in HCC patients was not significantly higher than that of TTV DNA in CLD patients (15.78%, 15/95). There were no significant differences in age, gender, tumor factors (size, TNM classification and markers) and other hepatitis virus markers between TTV-positive and TTV-negative in HCC and CLD patients, except history of blood transfusion [(80.00% vs 35.87% (P < 0.05) in HCC patients and 73.33% vs 27.50% (P < 0.05) in CLD patients)] and ALT [(93 +/- 27) IU/L vs (68 +/- 31) IU/L (P < 0.05) in HCC patients]. It seemed that TTV did not do any harm to the liver function of patients who infected with HBV or HCV, except for elevating ALT level in such a kind of HCC patients. CONCLUSION: Although TTV could do harm to the liver function of HCC patients, it does not contribute to the development of HCC from CLD.

Carcinoma, Hepatocellular↗
PubMedDate not supplied

[The use of Aedes albopictus C6/36 cells in the propagation and classification of arbovirus of the Togaviridae, Flaviviridae, Bunyaviridae and Rhabdoviridae families].

C6/36 Aedes albopictus cells were infected with Brazilian arbovirus from the families Togaviridae, Flaviviridae, Bunyaviridae and Rhabdoviridae. Replication was obtained with all the studied viruses and cytopathic effect was observed with some. Viral antigen was assayed in C6/36 cell cultures for antigen was assayed in C6/36 cells by an indirect immunofluorescence test using specific mouse immune ascitic fluid. Antigen production was detected in C6/36 cells infected with all the studied viruses. The author recommends the inoculation of C6/36 cell cultures for isolation of virus from the four studied families. The immunofluorescence technique is an important tool for classification and identification of virus growing in C6/36 cells.

Aedes↗
PubMed2000

Genomic and molecular evolutionary analysis of a newly identified infectious agent (SEN virus) and its relationship to the TT virus family.

A new group of transmissible single-stranded (ss) DNA viruses (SENV) distantly related to the large TT virus (TTV) family was recently identified. Eight different SENV isolates have been found, some with an association with posttransfusion hepatitis. A phylogenetic analysis of near-complete open-reading frame 1, including conserved motifs and excluding recombinant regions, was performed. The analysis used TTV-like minivirus as an outgroup, to determine a root of the phylogenetic tree, and compared 8 SENV isolates, 6 prototype TTV isolates, and 7 TTV variants (including SANBAN, TUS01, PMV, and YONBAN). Four distinct clusters separated by a bootstrap value of 100% were observed. YONBAN isolates formed a distinct outer group, representing the earliest recognized phylogenetic divergence (group 1). Prototype TTV formed group 2, PMV formed group 3, and SENV, SANBAN, and TUS01 isolates formed group 4, the most recently evolved group. This taxonomic classification suggests that these circular ssDNA viruses probably evolved from a common ancestor virus.

Amino Acid Sequence↗
PubMed1988

Prognostic usefulness of the Walter Reed staging classification for HIV infection.

We evaluated the usefulness of both the Walter Reed (WR) staging classification and the component criteria used in the system in predicting progression to AIDS. The WR classification was applied to a cohort of 431 men who were seropositive for the human immunodeficiency virus on entry into a prospective study. The WR classification was of limited usefulness, as only 133 men (31%) could be assigned to a WR stage. Among men who could be WR classified, only individuals in WR stage 5 were found to have a significantly more rapid progression to AIDS. The seropositive cohort was also classified based on initial CD4 cell number. Low CD4 counts (less than 400 cells/mm3) were significantly associated with progression to AIDS, and grouping seropositive men by CD4 number alone provided as much prognostic information as the WR classification. Skin test anergy was also a significant predictor for progression to AIDS, but only in individuals with low CD4 counts.

Acquired Immunodeficiency Syndrome↗
PubMed2005

Protein sequence-based risk classification for human papillomaviruses.

Human papillomaviruses (HPVs) are small DNA tumor viruses which infect epithelial tissues and induce hyperproliferative lesions. Infection by high-risk genital HPVs is associated with the development of anogenital cancers. Classification of risk types is important in understanding the mechanisms in infection and in developing novel instruments for medical examination such as DNA microarrays. The sequence-based classification methods are useful in classifying risk types by considering residues in conserved positions. In this paper, we present a machine learning approach to the classification of HPV risk types by using the protein sequences. Our approach is based on the hidden Markov model and the kernel method. The former searches informative subsequence positions and the latter computes efficiently to classify protein sequences. In the experiments, the classifier predicted four unknown HPV types exactly. An additional result shows that the kernel-based classifiers learned with more informative subsequences outperform the classifiers learned with the whole sequence or random subsequences.

Amino Acid Sequence↗
PubMed1998

Angiocentric cutaneous T-cell lymphoma of childhood (hydroa-like lymphoma): a distinctive type of cutaneous T-cell lymphoma.

BACKGROUND: Angiocentric cutaneous T-cell lymphomas of childhood (ACTCLC) are an unusual type of T-cell lymphomas that present with a vesiculopapular eruption mimicking hydroa vacciniforme. Most patients have been children from Asia and Latin America. OBJECTIVE: The purpose of this study was to describe four cases of ACTCLC; to discuss its clinical, histopathologic, and immunohistochemical features; to consider its possible relationship to the Epstein-Barr virus (EBV); and to clarify its classification within the spectrum of angiocentric lymphomas. METHODS: The clinical, histopathologic, and immunohistochemical features of four cases of ACTCLC were identified and analyzed. In addition in situ hybridization for EBV was performed in all cases. RESULTS: The clinical features were similar to previous cases reported under different names, such as hydroa-like lymphomas, edematous, scarring vasculitic panniculitis. Histologically, all showed angiocentric infiltrates composed mainly of T cells. In all cases there were variable numbers of CD30+ cells. The EBV was present in three of the cases. CONCLUSION: ACTCLC is a distinct type of T-cell lymphoma. It affects mainly children, and the EBV appears to play a role in the pathogenesis of this disease.

Child↗
PubMed2006

Design of microarray probes for virus identification and detection of emerging viruses at the genus level.

BACKGROUND: Most virus detection methods are geared towards the detection of specific single viruses or just a few known targets, and lack the capability to uncover the novel viruses that cause emerging viral infections. To address this issue, we developed a computational method that identifies the conserved viral sequences at the genus level for all viral genomes available in GenBank, and established a virus probe library. The virus probes are used not only to identify known viruses but also for discerning the genera of emerging or uncharacterized ones. RESULTS: Using the microarray approach, the identity of the virus in a test sample is determined by the signals of both genus and species-specific probes. The genera of emerging and uncharacterized viruses are determined based on hybridization of the viral sequences to the conserved probes for the existing viral genera. A detection and classification procedure to determine the identity of a virus directly from detection signals results in the rapid identification of the virus. CONCLUSION: We have demonstrated the validity and feasibility of the above strategy with a small number of viral samples. The probe design algorithm can be applied to any publicly available viral sequence database. The strategy of using separate genus and species probe sets enables the use of a straightforward virus identity calculation directly based on the hybridization signals. Our virus identification strategy has great potential in the diagnosis of viral infections. The virus genus and specific probe database and the associated summary tables are available at http://genestamp.sinica.edu.tw/virus/index.htm.

Animals↗
PubMed1985

Molecular biology of human T-lymphotropic retroviruses.

The generic name for a family of human T-lymphotropic retroviruses is HTLV. Two of the three members in this family have been linked etiologically to human diseases: HTLV-I with adult T-cell leukemia and HTLV-III with the acquired immunodeficiency syndrome. In addition to their T-cell tropism and a number of other common biological and biochemical properties, the most unique common features of these viruses from a molecular biological point of view are the presence of the x-lor gene towards the 3' end of the genome and the phenomenon of a virus-induced trans-acting factor in activation of transcription initiated in the viral long terminal repeat. These features may not only be key in understanding the mechanism of transformation or cell killing by these viruses, but they also provide a basis for new classification of retroviruses. In spite of these similarities among HTLV-I, -II, -III, and bovine leukemia virus, the genome of HTLV-III is only distantly related to these other viruses. Instead, it shows greater homology to members of the Lentivirus family. Therefore, all these viruses may have a common progenitor. Two other salient features arose from the analyses of HTLV-III and acquired immunodeficiency syndrome. (a) HTLV-III frequently infects the brain of acquired immunodeficiency syndrome patients who suffer from central nervous system disorders. This not only identifies HTLV-III as the direct candidate in these central nervous system disorders but also poses the problem of crossing the blood-brain barrier in therapy strategies to eradicate the virus. (b) Different HTLV-III isolates comprise a spectrum of related viruses, with the degree of divergence varying from virtual identity to 10-15% difference. The most divergent region resides in the envelope gene. Whether this finding has implications in the development of an effective vaccine for acquired immunodeficiency syndrome remains to be determined.

Acquired Immunodeficiency Syndrome↗
PubMed2003

Mixed infection of a child care provider with hepatitis A virus isolates from subgenotypes IA and IB revealed by heteroduplex mobility assay.

Phylogenetic analysis based on a 168 base segment encompassing the putative VP1/2A junction of the hepatitis A virus (HAV) genome has enabled the classification of HAV isolates into seven genotypes (I-VII). Genotype I, which includes the vast majority of the human HAV isolates, has been divided further into subgenotypes IA and IB. An heteroduplex mobility assay was designed with amplification products from the VP1/2A junction region, and used as a genotyping method able to discriminate HAV isolates belonging to IA, IB and non-I genotypes. The method was used to successfully genotype 48 samples (16 IA and 32 IB). However, one HAV RNA positive serum sample (AUX-23), collected from a 15 year old female employed at a child care center located in Rio de Janeiro, Brazil, showed an unusual pattern. PCR products from sample AUX-23 gave rise to heteroduplex bands when mixed with IA products as well as with IB products, suggesting the presence of HAV isolates from both subgenotypes in the serum. PCR products from sample AUX-23 were then cloned and 20 clones were analyzed by heteroduplex mobility assay. Eleven were subgenotype IA and 9 were IB. Three clones of each subgenotype were then sequenced to confirm the results. These data constitute the first report of mixed infection of a single individual with different HAV isolates.

Adolescent↗
PubMed2004

Evaluation of various species demarcation criteria in attempts to classify ten new tombusvirus isolates.

The usefulness of various suggested species demarcation criteria was compared in attempts to determine the taxonomic status of ten new tombusvirus isolates. Five of them (Lim 1, 2, 3, 5 and 6) were obtained from different sources of commercially grown statice (Limonium sinuatum), two (Gyp 1 and 2) from different sources of commercially grown Gypsophila paniculata and three from water samples, i.e. from a small river (Schunter) in Northern Germany, from a brook (near Dossenheim) in Southern Germany and from the groundwater in a Limonium production glasshouse in the Netherlands (Lim 4). The immunoelectron microscopical decoration test allowed a quick preliminary assignment of various isolates to several known tombusviruses. A more precise analysis of the relationships was achieved by comparing the deduced amino acid sequences of the coat proteins. Sequence as well as serological data suggested that eight of the isolates should be classified as strains or variants of either Carnation Italian ringspot virus, Grapevine Algerian latent virus, Petunia asteroid mosaic virus or Sikte waterborne virus, respectively, whereas the 9th isolate (Lim 2) appears to represent a distinct new tombusvirus species. The case of the 10th isolate (Lim 5) illustrates the classification problems experienced when the properties of a virus place it close to the more or less arbitrary man-made borderline between virus species and virus strains. The coat protein gene sequences were also determined for some viruses for which these data had not yet been available, i.e. Neckar river virus, Sikte waterborne virus and Eggplant mottled crinkle virus. The sequences of the coat protein gene and also of ORF 1 of the latter virus proved to be almost identical to the corresponding genome regions of the recently described Pear latent virus, which for priority reasons should be renamed. Criteria which have been suggested in addition to serology and sequence comparisons for tombusvirus species demarcation, i.e. differences in natural and in experimental host ranges, in cytopathological features and in coat protein size, appear to be of little value for the classification of new tombusviruses.

Base Sequence↗