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PubMed1999

[Selection of BVDV genotype II isolates using a monoclonal antibody and FACS analysis].

The infection of cattle with the bovine viral diarrhea virus (BVDV) in Germany is gaining attention and guidelines for the "protection of cattle farms against BVDV infections" were passed in 1997. New investigations about the damages induced by BVDV infections as well as the new occurrence of so-called BVDV genotypes (BVDV I and II) made the problems to become aware. The newly described BVDV genotype considerably differs both genetically and antigenetically from the up to now known BVD-viruses (BVDV I). The subdivision in BVDV genotypes I and II is based on genomic differences, which are determined by sequence analyses of different parts of the viral genome. Here, we describe the classification of BVDV in genotypes using a monoclonal antibody and indirect immunofluorescence with flow cytometry (FACS) based analysis. The suitability of the mab WB160 (Central Veterinary Laboratory, Weybridge; UK) for the classification of both BVDV-genotypes was first checked using genetically defined BVDV isolates. While all BVDV I isolates (n = 20) reacted with high fluorescence signals, the mab WB160 could not detect any of the defined BVDV II isolates (n = 20). Subsequently, 505 BVDV field strains isolated between 1993-1997 were screened for both genotypes using the mab WB160 and FACS analysis. 33 (6.5%) of the BVDV isolates were classified as BVDV II.

Animals↗
PubMed1992

Detection of varicella-zoster virus DNA by polymerase chain reaction in cerebrospinal fluid of patients with herpes zoster meningitis.

In three of five patients with herpes zoster meningitis, varicella-zoster virus (VZV) DNA was detected by the polymerase chain reaction (PCR) in the initial samples of cerebrospinal fluid. DNA fragments of group A or B, following classification of VZV strains by the size of the variable region IV of VZV genome, were found at the 7th, 10th and 24th illness day in the three positive cases: one of these cases did not have skin lesions. These results suggest that the detection of VZV DNA by PCR is useful for the diagnosis of herpes zoster meningitis, as well as for its molecular epidemiology.

Adult↗
PubMed1996

Predictors of response to interferon therapy.

An optimal treatment schedule is the first factor that influences sustained responses to interferon (IFN) therapy. There is growing evidence that prolonged IFN therapy (at least 12 months or longer) increases the sustained response rate. A low viremia at baseline favorably affects the long-term response to IFN. High viral replication does not preclude response, but highly viremic patients tend not to sustain their response. Patients with genotypes 2 and 3 (Simmonds classification) have an improved likelihood of responding compared to patients with genotype 1; unfortunately, genotype 1 predominates in Western countries. The "quasispecies" diversity of hepatitis C virus (HCV) may play a role in determining response to IFN, which is more likely in patients with lesser degrees of HCV diversity. However, studying the nucleotide diversity of the hypervariable region 1 of HCV is a very complex and expensive process that cannot be applied to a large number of patients. The sustained response rate is higher in patients with mild disease than in cirrhotic patients. Cirrhotics should be treated with caution, since IFN therapy could induce serious side effects and decompensation. Baseline predictive factors of response are useful to improve the cost-benefit ratio of IFN therapy but cannot be considered inclusion/exclusion criteria. The decision on how to treat should be based upon the individual characteristics of each patient.

Chronic Disease↗
PubMed2003

Fibromyalgia syndrome in patients with hepatitis C infection.

Fibromyalgia syndrome (FS) is characterized by widespread pain and tenderness at specific anatomic sites. Different theories have been proposed in the etiopathogenesis of this syndrome, and besides genetic, neuroendocrine, psychologic, and traumatic causes, infections have also been reported. The aim of the present study was to evaluate the presence of FS in patients with hepatitis C virus (HCV) infection. Ninety-five patients with chronic HCV infection and 95 healthy controls were enrolled in the study. The 1990 American College of Rheumatology classification criteria were used for the diagnosis of FS. Tender point count, pain intensity, sleep disturbance, stiffness, headache, paresthesia, fatigue, irritable bowel syndrome (IBS), and sicca- and Raynaud-like symptoms were assessed. Fibromyalgia was found in 18.9% of patients and 5.3% of healthy controls. Mean tender point count, pain intensity scored on a visual analog scale (VAS), sleep disturbance, stiffness, paresthesia, and fatigue were higher in the HCV group. No significant relationship was observed between the two groups regarding headache, IBS, and sicca- and Raynaud-like symptoms. In addition, mean tender point count and pain intensity scores were also significantly higher in HCV patients with FS than in control subjects with FS. All of the symptoms except stiffness were not statistically significant between the HCV and control groups with FS. Our results demonstrate a tendency toward higher prevalence of FS in patients with HCV infection. Besides various extrahepatic features, musculoskeletal disorders including fibromyalgia might be expected in the progression of HCV infection. Detailed examination of the patients helps to differentiate FS from other musculoskeletal complications of HCV infection. This will provide appropriate management approaches and better quality of life for them.

Adolescent↗
PubMed1988

Oral candidal infection as a sign of HIV infection in homosexual men.

The oral mucosae of 66 homosexual men were examined clinically and by means of cultivation to determine the presence of Candida infection. In addition, clinically detected mucosal changes were recorded and a biopsy specimen was obtained for the histopathologic classification. A total of forty one subjects (62%) showed clinical evidence of candidiasis. Fourteen (21%) of the sixty-six men were seropositive for human immunodeficiency virus (HIV). A total of thirteen of fourteen (93%) of the seropositive men and twenty-six of fifty-two (50%) of the HIV seronegative men had culture-confirmed oral candidiasis. In the latter group, oral candidiasis was clearly correlated to cigarette smoking. Clinical mucosal changes other than candidiasis were found in forty-five of the sixty-six subjects studied. The most frequent finding was trauma resulting from biting, which was usually localized on the cheek. Leukoplakia was found in twelve of sixty-six subjects, while cauliflower-like condylomas were present in 4 persons. The results emphasize the frequent occurrence of different oral lesions in subjects seropositive for HIV and in those at high risk for HIV infection. Oral examination in search for potential early manifestations of HIV infection in homosexual men is advocated.

Alcohol Drinking↗
PubMed1993

Human immunodeficiency virus-associated systemic lymphomas may be subdivided into two main groups according to Epstein-Barr viral latent gene expression.

PURPOSE: We report a pathologic characterization of human immunodeficiency virus (HIV)-associated systemic lymphomas, including the association of Epstein-Barr virus (EBV) in different categories. PATIENTS AND METHODS: Eighty-seven HIV-associated non-Hodgkin's lymphoma (NHL) were classified according to classic NHL classification and a recent description of morphologic variants of high-grade B-cell NHL. Seventy-one cases were immunophenotypically-genotypically characterized, whereas, in 49 representative cases, the association of EBV was assessed by nonisotopic in situ hybridization (ISH) and the immunohistochemical demonstration of latent membrane protein-1 (LMP-1). In addition, 14 Hodgkin's disease (HD) cases, occurring in patients with HIV infection, were investigated for the frequency of LMP-1 expression. RESULTS: Most lymphomas were of B-cell derivation and showed a blastic cell morphology, with (1) small noncleaved cells (SNCCs; 36 cases), (2) large noncleaved cells (10 cases), and (3) immunoblasts, usually polymorphic (12 cases). Moreover, 12 cases were classified as anaplastic large-cell (ALC) Ki-1-positive (Ki-1+) lymphoma. Combined ISH studies (for viral DNA and EBV RNA [EBER]) and immunohistologic demonstration of LMP-1 suggested that there were differences in viral latent gene expression between ALC Ki-1+ or immunoblastic lymphomas (usually EBV+, LMP-1+), and EBV-infected cells of SNCC lymphomas, which did not show LMP-1 expression. A high proportion (10 of 14) of LMP-1+ HD cases was found. CONCLUSION: Differences in EBV association and LMP-1 expression were found between a major group of HIV-associated systemic NHL with blastic cell morphology, including SNCC lymphoma and its variants, and anaplastic cell lymphomas. A proportion of immunoblastic (polymorphic) lymphomas was different in viral latent gene expression from other blastic cell systemic lymphomas. It is concluded that only a group of these lymphomas (most ALC Ki-1+ and HD cases, along with a nonnegligible fraction of immunoblastic lymphomas) seems to be linked etiopathologically to EBV.

Gene Expression Regulation, Viral↗
PubMed2004

[Hepatitis c virus genotype research by ABC programs of 5'-NCR restriction endonuclease digestion].

OBJECTIVE: In order to fully understand hepatitis c virus (HCV) genotype 3b, 1a, 2b and 6a infection in China, We built HCV 5'-noncoding region (5'-NCR) of different genotypes and subtypes. METHODS: The classification HCV into variable genotypes (subtypes) was carried on by programs A, B and C A. Using a combination of three restriction endonuclease BHH' (BsrB I, Hae II, Hinf I) digestions at the same time. The distinct genotypes were classified into 5 groups: genotype 1 (1a, 1b), 6a, 2 (2a, 2b), genotype 3 (3a, 3b), genotype4 (4a). B. With regard to genotype 1, we could distinguish subtype 1a from 1b using BstU I digestion. C. Using restriction endonuclease Hae III, genotype 2a, 2b, 3b, 4a, 6a are differentiated respectively. RESULTS: (1) HCV genotype 1a, 1b, 2a, 2b, 3a, 3b, 4a, 6a are fully discriminated by comparison with the genotypes regular samples. (2) Of the 93 patients, HCV genotype distribution in China was 66.67% for 1b, 18.28% for 2a, 3.23% for 1b/2b, 3b, 2b respectively. 2.15% for 2a/2b, 1b/2a respectively. 1.08% for 1a. CONCLUSION: This research indicated that adoption of HCV 5'-NCR A B C restriction endonuclease digestions techniques, might be sensitive and efficient to detect HCV and discriminate HCV genotype (subtypes) 1a to 6a.

5' Untranslated Regions↗
PubMed1990

HIV disease: a review for the family physician. Part I. Evaluation and conventional therapy.

Family physicians will be challenged with caring for increasing numbers of patients infected with human immunodeficiency virus. After confirming the presence of the infection, the physician must follow a logical sequence of evaluation, counseling and treatment. The current Centers for Disease Control classification and a series of evaluation and treatment protocols form the basis for prescribing zidovudine to delay or mitigate involvement of T lymphocytes and neuronal cells.

HIV Infections↗
PubMed1991

Acute otitis media in human immunodeficiency virus-infected children.

To evaluate the occurrence and outcome of acute otitis media (AOM) in human immunodeficiency virus (HIV)-infected children, a prospective comparative cohort study was performed. Twenty-seven HIV-infected children were individually matched with paired control subjects and followed up for 543 months (mean 19.4 +/- 11). Data collected were evaluated considering HIV-infected children both as a whole and as P1 and P2 patients according to Centers for Disease Control classification. During the observation period, 46 episodes of AOM were diagnosed in 15 HIV patients and 22 in 16 control children: 11 P1 had 27 AOM episodes vs 17 in 13 control children; 6 P2 had 19 AOM episodes vs 5 in 4 control children. Human immunodeficiency virus infection does not seem to modify the occurrence of AOM. Recurrent AOM (3 or more episodes in 6 months) was, however, significantly more common in P2 children. Amoxicillin, to which the bacteria isolated in P2 children were sensitive in vitro, cured 33 of 46 episodes in HIV-infected children compared with 20 of 22 in control children. Cure rate was similar in P1 children compared with control children but was significantly lower in P2 versus control children (47.3% vs 100%). Reasons for higher occurrence of failures in P2 children remain to be investigated.

Acute Disease↗
PubMed2005

Revising the way we conceive and name viruses below the species level: a review of geminivirus taxonomy calls for new standardized isolate descriptors.

Geminivirus taxonomy and nomenclature is increasing in complexity with time, and the growing number of geminivirus sequences deposited in gene banks requires regular taxonomic updates and calls for new descriptors to identify virus isolates unambiguously. Fauquet et al. [1] proposed a system to standardize the names of the viruses, and corresponding guidelines have been followed since, rendering nomenclature much easier. Recently, due to difficulties inherent in species identification, the ICTV Geminiviridae Study Group proposed new species demarcation criteria, the most important of which being an 89% identity threshold between complete DNA-A component nucleotide sequences of begomoviruses. This threshold has been utilised since with general satisfaction. In this paper, we review the status of geminivirus species demarcation and nomenclature for a total of 389 isolates. A small number of corrections have been made to comply with the adopted demarcation criteria but otherwise the classification system has remained robust and therefore we propose to continue using it. However, the large numbers of geminivirus sequences that have become available have led us to recognize the need for a better description of virus isolates. The pairwise comparison distribution below the taxonomic level of species identified two peaks, one at 90-91% identity that may correspond to "strains" and one at 96-98% identity that may correspond to "variants". Guidelines for descriptors for each of these levels are proposed to standardize nomenclature. As a consequence, we have revisited the status of some virus isolates to elevate them to "strains". An updated list of all geminivirus isolates currently available is provided.

DNA, Viral↗
PubMed1993

The spectrum of vasculitis in human immunodeficiency virus-infected patients. A clinicopathologic evaluation.

OBJECTIVE: To delineate the different types of inflammatory vascular diseases (IVD) occurring in patients with human immunodeficiency virus (HIV) infection. METHODS: Muscle, nerve, or skin biopsy specimens from 148 symptomatic HIV-infected individuals were reviewed, and subgroups of vasculitis were identified using the American College of Rheumatology (ACR) 1990 clinicopathologic criteria for the classification of vasculitis. RESULTS: IVD was documented in 34 patients (23%) and included necrotizing arteritis (3 patients), non-necrotizing arteritis (1 patient), neutrophilic IVD (7 patients), mononuclear IVD (17 patients), and other small vessel inflammatory changes (6 patients). According to the ACR criteria, 11 patients could be classified as having a distinct category of vasculitis, including polyarteritis nodosa (4 patients), Henoch-Schönlein purpura (1 patient), and drug-induced hypersensitivity vasculitis (6 patients), and 23 were classified in the group "other vasculitis, type unspecified." One patient had hepatitis B virus surface antigenemia, 2 had cryoglobulinemia, and 2 were coinfected by human T lymphotropic virus type I. Cytomegalovirus inclusions and antigens were found in endothelial cells in 1 patient. HIV antigens and genome were detected in perivascular cells of 2 of the 3 patients with necrotizing arteritis; in 1, HIV-like particles were seen by electron microscopy. Immune deposits were found in small vessel walls in 5 skin biopsy samples showing small vessel vasculitis and in the muscle of the 3 patients with necrotizing arteritis. CONCLUSION: A wide range of inflammatory vascular diseases may occur in HIV-infected individuals. Vascular inflammation appears multifactorial and may result from HIV-induced immunologic abnormalities and exposure to a variety of xenoantigens, such as HIV itself, other infectious agents, and drugs.

Adult↗
PubMed1989

Identification and classification of potyviruses on the basis of coat protein sequence data and serology. Brief review.

The identification and classification of potyviruses has been in a very unsatisfactory state due to the large size of the group, the apparent vast variation among the members and the lack satisfactory taxonomic parameters that will distinguish distinct viruses from strains. In the past, use of classical methods, such as host range and symptomatology, cross-protection, morphology of cytoplasmic inclusions and conventional serology, revealed a "continuum" implying that the "species" and "strain" concepts cannot be applied to potyviruses. In contrast nucleic acid and amino acid sequence data of coat proteins has clearly demonstrated that potyviruses can be divided into distinct members and strains. This sequence data in combination with information of the structure of the potyvirus particle has been used to develop simple techniques such as HPLC peptide profiling, serology (using polyclonal antibody probes obtained by cross-adsorption with core protein from trypsin treated particles) and cDNA hybridization. These findings, along with immunochemical analyses of overlapping synthetic peptides have established the molecular basis for potyvirus serology; explained many of the problems associated with the application of conventional serology; and provided a sound basis for the identification and classification of potyviruses. As a result, the virus/strain status of some potyviruses has been redefined, requiring a change in the potyvirus nomenclature. These new developments necessitate a re-evaluation of the earlier literature on symptomatology, cross-protection, cytoplasmic inclusion body morphology and serology.

Amino Acid Sequence↗
PubMed1985

Specificity of antibodies to Newcastle disease virus.

Specificity of antibodies to Victoria strain of Newcastle disease virus (NDV) found in infectious mononucleosis (IM) and other pathologic sera was investigated by agglutination of NDV-modified human O red blood cells, as well as by immunodiffusion and enzyme immunoassay with various preparations of the virus. These studies clearly demonstrated that the NDV antibodies are distinct from P-B or H-D antibodies. The unexpected observation that guinea pig kidney (GPK) tissues absorbed NDV antibodies allowed their classification into a group of 'GPK-positive' heterophile antibodies. The simultaneous occurrence of the NDV antibodies and H-D antibodies in IM and other diseases suggests the possibility that multiple new antigenic determinants, especially those of carbohydrate nature, may appear due to the alteration of self-antigens as a result of various pathologic processes.

Antibodies, Viral↗
PubMedDate not supplied

Classification of some active compounds and their inactive analogues using two three-dimensional molecular descriptors derived from computation of three-dimensional convex hulls for structures theoretically generated for them.

Two three-dimensional (3D) molecular descriptors are used to classify 73 protease inhibitors against the human immunodeficiency virus type 1 (HIV-1). X-ray structures of these HIV-1 protease bound inhibitors are used as templates to generate the most probable bioactive conformations of the inhibitors. A convex hull computation algorithm is applied to each structure generated. The frequency of atoms lying on the vertexes of each hull is counted. Vertexes of the same atomic charge state are then gathered together as a set of commonly exposed groups for all the structures generated. The first 3D descriptor is computed as the maximum molecular path length among any three distinct commonly exposed groups, while the second 3D one is computed as the maximum molecular path length among any three atoms of nonconvex hull vertexes. We find that the 73 HIV-1 protease inhibitors can be classified by the first 3D descriptor into two groups, which agrees with the result of visual classification using the activity data as a criterion for these compounds. The classification scheme is then used to classify a database of 427 active trypsin inhibitors and their inactive analogues. The structures of these compounds are generated theoretically from steps of energy minimization and molecular dynamics. Classification for all these compounds is performed using the SYBYL hierarchical clustering method on the first 3D descriptor and then the second 3D one computed. It is found that some inactive analogues are completely separated from the active inhibitors at the first stage of classification using the first 3D descriptor. Most of the highly active inhibitors are classified into a cluster at the second stage of classification using the second 3D descriptor. Finally, most of these highly active inhibitors are separated from all the accompanying inactive analogues in the cluster through a structural alignment process using a set of commonly exposed groups determined for them.

Algorithms↗
PubMed2003

Multiple resistance phenotypes to Lettuce mosaic virus among Arabidopsis thaliana accessions.

With the aim to characterize plant and viral factors involved in the molecular interactions between plants and potyviruses, a Lettuce mosaic virus (LMV)-Arabidopsis thaliana pathosystem was developed. Screening of Arabidopsis accessions with LMV isolates indicated the existence of a large variability in the outcome of the interaction, allowing the classification of Arabidopsis accessions into seven susceptibility groups. Using a reverse genetic approach, the genome-linked protein of LMV, a multifunctional protein shown to be involved in viral genome amplification and movement of potyviruses, was established as the viral determinant responsible for the ability to overcome the resistance of the Niederzenz accession to LMV-0. Preliminary genetic analyses from F2 and recombinant inbred lines available between susceptible and resistant Arabidopsis accessions revealed the existence of at least three resistance phenotypes to LMV with different genetic bases. One dominant resistance gene, designated LLM1, involved in blocking the replication or cell-to-cell movement of the LMV-0 isolate in the Columbia accession, was mapped to chromosome I and shown to be linked to the marker nga280. At the same time, genetic analyses of segregating F2 populations were consistent with the restriction of the systemic movement of the LMV-AF199 isolate in Columbia being controlled by two dominant genes and with the complete resistance to all tested LMV isolates of the Cape Verde islands (Cvi) accession being conferred by a single recessive resistance gene. Sequencing of the eukaryotic translation initiation factor 4E genes from the different LMV-resistant Arabidopsis accessions showed that these factors are not directly involved in the characterized resistance phenotypes.

Amino Acid Sequence↗
PubMed2005

Identification of gastroenteric viruses by electron microscopy using higher order spectral features.

BACKGROUND: Many paediatric illnesses are caused by viral agents, for example, acute gastroenteritis. Electron microscopy can provide images of viral particles and can be used to identify the agents. OBJECTIVES: The use of electron microscopy as a diagnostic tool is limited by the need for high level of expertise in interpreting these images and the time required. A semi-automated method is proposed in this paper. STUDY DESIGN: The method is based on bispectal features that capture contour and texture information while providing robustness to shift, rotation, changes in size and noise. The magnification or true size of the viral particles need not be known precisely, but if available can be used additionally for improved classification. Viral particles from one or more images are segmented and analyzed to verify whether they belong to a particular class (such as Adenovirus, Rotavirus, etc.) or not. Two experiments were conducted-depending on the populations from which virus particle images were collected for training and testing, respectively. In the first, disjoint subsets from a pooled population of virus particles obtained from several images were used. In the second, separate populations from separate images were used. The performance of the method on viruses of similar size was separately evaluated using Astrovirus, HAV and Poliovirus. A Gaussian Mixture Model was used for the probability density of the features. A threshold on the log-likelihood is varied to study false alarm and false rejection trade-off. Features from many particles and/or likelihoods from independent tests are averaged to yield better performance. RESULTS: An equal error rate (EER) of 2% is obtained for verification of Rotavirus (tested against three other viruses) when features from 15 viral particle images are averaged. It drops further to less than 0.2% when scores from two tests are averaged to make a decision. For verification of Astrovirus (tested against two others of the same size) the EER was less than 2% when 20 particles and two tests were used. CONCLUSION: Bispectral features and Gaussian mixture modelling of their probability density are shown to be effective in identifying viruses from electron microscope images. With the use of digital imaging in electron microscopes, this method can be fully automated.

Adenoviruses, Human↗
PubMed1994

Aspartate aminotransferase-linked immunoglobulin complexes in serum of a patient with primary biliary cirrhosis.

A 51-year-old woman who had been treated for primary biliary cirrhosis (PBC) was admitted to our hospital for evaluation of unexplained, isolated, persistently increased aspartate aminotransferase (AST) activity. Results of laboratory tests on admission showed: AST 171 KU, alanine aminotransferase 28 KU, and anti-mitochondrial titer 1/1280. Results of hepatitis B surface antigen (HBs Ag) and hepatitis C virus antibody (HCV Ab; C100-3) assays were negative. Histology of a liver biopsy specimen was compatible with a diagnosis of PBC (stage III of Scheuer's classification). The molecular size of serum AST was estimated to be more than 500,000 by high-performance size-exclusion liquid chromatography. Electrophoretic analysis showed an abnormal band of AST between supernatant AST (sAST) and mitochondrial AST (mAST), which band was characteristic of AST-immunoglobulin complexes (AST-Ig). Ouchterlony double-diffusion and immunoprecipitation tests identified the immunoglobulin component as IgM. The presence of AST-Ig appeared to be responsible for the elevated serum AST.

Aspartate Aminotransferases↗