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Analysis of the triple gene block and coat protein sequences of two strains of Kalanchoë latent carlavirus.

A region of the Kalanchoë latent carlavirus (KLV) genome, containing the coding capacity for the triple gene block and the coat protein, was cloned and sequenced for two isolates, the one infecting Chenopodium quinoa systemically whereas the other infects C. quinoa locally. The sequence confirmed the classification of KLV as a carlavirus. There was the highest identity in the amino acid sequences to the carlaviruses potato rough dwarf virus, lily latent virus, lily symptomless virus, blueberry scorch virus and potato virus S. The aminoacid sequences of proteins of the two KLV isolates had an identity between 86% and 91%.

Amino Acid Sequence↗

Pediatric human immunodeficiency virus and acquired immunodeficiency syndrome: an overview.

This article covers the epidemiological manifestations of human immunodeficiency virus and acquired immunodeficiency syndrome (HIV/AIDS) in children, demographic statistics, and information on the three modes of virus transmission. The various opportunistic diseases and neurological dysfunction that characterize pediatric HIV are described. The Center for Disease Control pediatric HIV classification system is presented, and the developmental disorders often found in children with HIV are discussed. The Universal Disease Precautions of the American Speech and Hearing Association (ASHA) for clinicians is also presented.

AIDS-Related Opportunistic Infections↗

Identification of genotypes of hepatitis C virus by sequence comparisons in the core, E1 and NS-5 regions.

Isolates of hepatitis C virus (HCV) show considerable nucleotide sequence variability throughout the genome. Comparisons of complete genome sequences have been used as the basis of classification of HCV into a number of genotypes that show 67 to 77% sequence similarity. In order to investigate whether sequence relationships between genotypes are equivalent in different regions of the genome, we have carried out formal sequence analysis of variants in the 5' non-coding region (5'NCR) and in the genes encoding the core protein, an envelope protein (E1) and a non-structural protein (NS-5). In the E1 region, variants grouped into a series of six major genotypes and a series of subtypes that could be matched to the phylogenetic groupings previously observed for the NS-5 region. Furthermore, core and E1 sequences showed three non-overlapping ranges of sequence similarity corresponding to those between different genotypes, subtypes and isolates previously described in NS-5. Each major genotype could also be reliably identified by sequence comparisons in the well conserved 5'NCR, although many subtypes, such as 1a/1b, 2a/2c and some of those of type 4, could not be reliably distinguished from each other in this region. These data indicate that subgenomic regions such as E1 and NS-5 contain sufficient phylogenetic information for the identification of each of the 11 or 12 known types and subtypes of HCV. No evidence was found for variants of HCV that had sequences of one genotype in the 5'NCR but of a different one in the E1 or NS-5 region. This suggests that recombination between different HCV types is rare or non-existent and does not currently pose a problem in the use of subgenomic regions in classification.

Base Sequence↗

Oral viral infections and the therapeutic use of antiviral agents in dentistry.

This paper reviews the current concepts of viral classification, infection and replication. The clinical presentation of common oral viral infections encountered in the dental practice are discussed, including: herpes simplex virus types 1 and 2; Epstein-Barr virus; varicella-zoster virus; Coxsackie virus; human papilloma virus; and human immunodeficiency virus. The diagnosis, principles of management and pharmacological agents available for the treatment of oral viral infections are also discussed.

Antiviral Agents↗

Epstein-Barr virus-induced precursor B cell lines from patients with congenital agammaglobulinemia.

We have established lymphoid cell lines with diversity of immunoglobulin expression by infection of bone marrow cells of four patients with congenital agammaglobulinemia with Epstein-Barr virus. Immunofluorescent study revealed that the cells of many of these lymphoid cell lines had characteristics of possible precursor B cells, permitting classification as follows: 1) cell lines without any surface or cytoplasmic immunoglobulins (17/28 lines), 2) cell lines which had only cytoplasmic mu heavy chains (line K4 and O2), 3) cell lines with both mu and delta heavy chains in the cytoplasm (line O6 and M5), 4) cell lines which bore surface mu chains and possessed cytoplasmic mu chains but lacked light chain expression (line S5), 5) cell lines which had surface and cytoplasmic delta and lambda chains, and secreted the immunoglobulins (line K5), and 6) cell lines which had surface IgM and cytoplasmic mu and light chains, and secreted the immunoglobulins (5/28 lines). Biosynthetic studies with 14C-leucine confirmed the patterns of immunoglobulin expression found by immunofluorescent analysis. These cell lines may represent some stages of B cell development and provide useful information on the pathophysiology of congenital agammaglobulinemia.

Agammaglobulinemia↗

Nitazoxanide in the treatment of cryptosporidial diarrhea and other intestinal parasitic infections associated with acquired immunodeficiency syndrome in tropical Africa.

Eighteen patients hospitalized with intestinal parasitic infections associated with diarrhea and dehydration completed a study of nitazoxanide in the treatment of Cryptosporidium parvum and other intestinal parasitic infections. Seventeen of the 18 patients were positive for human immunodeficiency virus. Twelve patients were diagnosed with clinical Stage 4 acquired immunodeficiency syndrome (AIDS) according to the 1990 World Health Organization proposed clinical classification system and cryptosporidiosis. Nitazoxanide (500 mg tablets) were administered orally, one tablet twice a day for seven consecutive days. Cryptosporidium parvum oocysts were eradicated or reduced by more than 95% in seven of the 12 Stage 4 AIDS patients who completed the study based upon two post-treatment fecal examinations conducted on days 7 and 14 following the initiation of treatment. The elimination or reduction of C. parvum oocysts was associated with a complete resolution of diarrhea in four of the seven patients. The test drug was also effective against cases of Isospora belli, Entamoeba histolytica, Giardia lamblia, Ascaris lumbricoides, Enterobius vermicularis, Hymenolepis nana, and Dicrocoelium dentriticum. Treatment with nitazoxanide was well tolerated by the patients. There were no abnormalities in blood chemistry or hematology data that were considered to be attributable to nitazoxanide therapy. Transient episodes of vomiting were observed in four patients, all with Stage 4 AIDS and cryptosporidiosis, which resolved spontaneously without discontinuation of treatment and were not considered to be related to administration of nitazoxanide.

AIDS-Related Opportunistic Infections↗

The pattern of lymphoma in east Malaysian patients as experienced in the University Hospital, Kuala Lumpur.

Lymphoma is a highly heterogeneous group of malignant disease. This study aimed to elucidate the pattern of lymphoma in the East Malaysian patient population. 107 cases of confirmed lymphomas from East Malaysian biopsy material were retrieved from the files of the Department of Pathology, University of Malaya, in the 3-year period between 1981 to 1983. With the use of a panel of lymphoid antibodies, the disease was sub-classified using the Rye classification for Hodgkin's lymphoma (HL) and the REAL classification for non-Hodgkin's lymphoma (NHL). All of the cases were tested for the presence of the Epstein-Barr virus by EBER-ISH. There were 11 (10.3%) HL, 80 (74.7%) B-NHL and 16 (15%) T-NHL. The HL:NHL ratio was 1:9. The most common tumour in children was Burkitt's lymphoma 7/13 (53.8%). In the adult group, there were 72/94 (76.6%) B-NHL ¿diffuse large cell type 51 (of which 2 were CD30+), Burkitt's lymphoma 8, follicular lymphoma 5, low grade MALT 2, mantle cell type 1 and not otherwise specified due to poor morphology 5¿, 13/94 (13.8%) T-NHL and 9/94 (9.6%) HL. Of the 9 adult HL, the most common subtype was nodular sclerosis (6, 66.7%). The EBER positive rate in classical HL, T-NHL, BL and B-NHL were 33.3%, 56.3%, 60.0% and 3.1% respectively. In conclusion, the spectrum of lymphoma seen in East Malaysia was rather similar to West Malaysia except for the very low prevalence of peripheral T-cell lymphoma (PTCL) in Sarawak (3.3%).

Adolescent↗

Chronic anaemia and adhesion molecules in patients with liver cirrhosis. A preliminary report.

AIM: The aim of our study was to investigate circulating levels of intercellular adhesion molecule-1 (sICAM-1) and vascular cellular adhesion molecule-1 (sVCAM-1) in cirrhotic patients, with and without chronic anaemia, to establish whether there was a relationship between inflammatory activity and anaemia. METHODS: We investigated 14 anaemic (mean hemoglobin value 10.65+/-1.06 g/dL) and 14 non anaemic (mean hemoglobin value 13.8+/-0.89 g/dL) subjects affected by virus C-related liver cirrhosis comparable for sex, age and degree of liver dysfunction such as expressed by Child-Pugh classification. Circulating sICAM-1 and sVCAM-1 were measured by EIA commercial kit (R&D System Co, Abington, UK) and mean+/- standard deviation values in two groups were compared by t-test and Kruskall-Wallis test. RESULTS: Mean+/-standard deviation sICAM-1 was 35.06+/-4.06 ng/mL in anaemic and 23.39+/- 6.1 ng/mL in non anaemic cirrhotic patients. Mean+/-standard deviation sVCAM-1 was 47.66+/-8.18 ng/mL in anaemic 31.77+/-6.08 ng/mL in non anaemic patients, respectively. Statistical analysis showed a significant difference between the two groups both in sICAM-1 (p=0.01) and sVCAM-1 (p=0.03) values. CONCLUSIONS: Our study show that chronic anaemia, in liver cirrhosis, is associated to a greater increase of circulating adhesion molecules and suggests that inflammation may contribute to persistence of anaemic state, worsening the outcome of cirrhotic patients.

Aged↗

[Primary extralymphatic non-Hodgkin's lymphomas: the response to treatment and prognostic factors in 73 patients].

BACKGROUND: The aim of the present study was to determine the prognostic factors for treatment response, relapse-free survival (RFS) and overall survival (OS) in a series of 73 patients with primary extranodal lymphomas (PEL). METHODS: All the patients diagnosed with PEL in one center from January 1984 to December 1993 were studied. The Working Formulation was used for histologic classification and the stage was determined according to the Ann Arbor classification modified by Mushoff. Age, sex, localization of the lymphoma, the presence of B symptoms, the existence of bulky disease, human immunodeficiency virus (HIV) infection, the main hematological and biochemical parameters, the histologic grade of malignancy, the immunologic phenotype and stage were reported. Univariate and multivariate analyses of prognostic factors for complete response (CR), RFS and OS were carried out. RESULTS: The most frequent localization of PEL was the gastrointestinal tract (43 cases). Fourteen cases had HIV infection. CR was obtained in 37 out of the 55 patients (67%) of whom 8 (21%) had relapsed. Serum LDH level was the main prognostic factor for CR attainment (p = 0.01). The variables which negatively affected RFS were the presence of HIV infection (p = 0.02), advanced age (p = 0.018) and the existence of B symptoms (p = 0.02). OS was shorter in patients with high LDH levels (p = 0.004) and more aggressive histologic subtype (p = 0.0002). CONCLUSIONS: The prognostic factors observed in the patients with primary extranodal lymphomas are the same as those found in nodal non Hodgkin's lymphomas. The stage is not a factor of bad prognosis if chemotherapy is included in the treatment.

Adult↗

Transfusion-transmitted retrovirus infection.

This article reviews the history, classification, and disease associations of the known human retroviruses and outlines their profound effects on the practice of transfusion medicine. The immunodeficiency viruses, HIV-1 and HIV-2, produce a cytolytic effect on infected lymphocytes, and are the causative agents of AIDS. In contrast are the oncoviruses, including HTLV-I and HTLV-II, which are typically lymphoproliferative and able to induce cellular transformation. Human foamy viruses, more recently recognized as a potential human neuropathogen, resemble the other retroviruses with their complex genome organization and structure.

AIDS Serodiagnosis↗

Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

BACKGROUND: MicroRNAs (miRNAs) are a group of short (approximately 22 nt) non-coding RNAs that play important regulatory roles. MiRNA precursors (pre-miRNAs) are characterized by their hairpin structures. However, a large amount of similar hairpins can be folded in many genomes. Almost all current methods for computational prediction of miRNAs use comparative genomic approaches to identify putative pre-miRNAs from candidate hairpins. Ab initio method for distinguishing pre-miRNAs from sequence segments with pre-miRNA-like hairpin structures is lacking. Being able to classify real vs. pseudo pre-miRNAs is important both for understanding of the nature of miRNAs and for developing ab initio prediction methods that can discovery new miRNAs without known homology. RESULTS: A set of novel features of local contiguous structure-sequence information is proposed for distinguishing the hairpins of real pre-miRNAs and pseudo pre-miRNAs. Support vector machine (SVM) is applied on these features to classify real vs. pseudo pre-miRNAs, achieving about 90% accuracy on human data. Remarkably, the SVM classifier built on human data can correctly identify up to 90% of the pre-miRNAs from other species, including plants and virus, without utilizing any comparative genomics information. CONCLUSION: The local structure-sequence features reflect discriminative and conserved characteristics of miRNAs, and the successful ab initio classification of real and pseudo pre-miRNAs opens a new approach for discovering new miRNAs.

Animals↗

Hepatitis B: the disease.

Hepatitis B virus (HBV) is carried by approximately 300 million people in the world. The natural history of the disease in an individual patient depends on the method by which the infection was acquired, whether perinatal, in childhood, as a result of drug abuse, or in the course of health care work. Other important factors determining the course of the disease include an individual's sex and immunological status. Geographic factors also contribute. Changing lifestyles and the use of prophylactic hepatitis B vaccination affect the prevalence in various groups in the community. The clinical course of the disease, possible complications, and a recent classification system for chronic HBsAg carriers are discussed.

Chronic Disease↗

Semi-quantitative in situ hybridization and immunohistology for antigen expression of human herpesvirus-6 in various lymphoproliferative diseases.

Fifty patients with various hyperplastic and malignant lymphoproliferative diseases were investigated for evidence of human herpesvirus-6 infection. Virus DNA and antigen expression was investigated in lymph node biopsies by in situ hybridization and immunohistology and was correlated with data of immunophenotyping. Supplemental immunoglobulin- and T cell receptor gene rearrangement studies were used to support the classification of the proliferative lymphoid lesion. Elevated numbers of cells carrying HHV-6 DNA and/or antigens were found in cases of Hodgkin's lymphoma and follicular center cell non-Hodgkin's lymphoma as well as atypical polyclonal lymphoproliferation (APL), yet not in reactive lymphoid hyperplasia and in most other lymphomas. Immunophenotyping showed that virus -infected cells were primarily lympho-histiocytic elements, less frequently Hodgkin's- and Reed-Sternberg cells, and not malignant B lymphocytes as in follicular center cell lymphomas. This suggests that the virus is rather not the causative oncogen in these cases, yet does not exclude a cocarcinogenic effect of it during the development and ths course of uncontrolled lymphoproliferation.

Antigens, Viral↗

Intratype HPV16 sequence variation within LCR of isolates from asymptomatic carriers and cervical cancers.

BACKGROUND: HPV16 is a predominant type of virus identified in genital lesions and strongly associated with the development of genital cancers. Infection with the virus is considered to be the main risk factor in the development of cervical cancer. Based on HPV16 DNA isolated from invasive cancers, a classification of intratype genetic variants was established and the strains were designated according to geographical regions. The HPV16 variants classification was based on isolates derived from cancers. OBJECTIVES: Analysis of HPV16 LCR variants isolated from asymptomatic carriers for comparison with cervical cancer isolates to examine whether a correlation can be found between cervical epithelium state and variant of HPV16 it carries. MATERIALS AND METHODS: The HPV16 LCR fragments were amplified by PCR using DNA isolated from cervical swabs and tissue sections then screened for nucleotide changes by SSCP. Polymorphic sites were analysed for regulatory protein binding properties by EMSA. RESULTS: Comparison of the two groups revealed that isolates from cervical cancers predominantly carry changes in sequences of YY1 binding sites (especially at nucleotide 7519), while variants from asymptomatic carriers contained nucleotide changes within or close to transcription binding sites for AP-1, Oct-1, NF1, Tef-1, Tef-2, Sp1, YY1 and viral E2. EMSA study showed that sequence changes in the segment alter binding and formation of transcriptional complexes in quantitative and/or qualitative manner and so they may inflict viral activity. CONCLUSION: The results of our study show that there might be HPV16 variants of decreased oncogenic potential therefore infection with such variants can recede.

Binding Sites↗

Genetic, acquired, and related factors in the etiology of diabetes mellitus.

Diabetes mellitus is not a single disease entity, but a heterogenous group of disorders with a striking diversity of etiopathogenetic mechanisms as well as clinical manifestations. Lack of a known genetic marker for the disease(s) and variable influences of environmental factors on the expression of a putative diabetic genome have resulted in considerable debate over its etiology. Over the past few years, systematic epidemiologic studies, along with knowledge gained from a close association of certain human-leukocyte-antigens with the diabetic diathesis and possible role of host-immune factors, and gene-virus interaction have led to considerable advancement in the understanding of the disease-complex. Pending the availability of definite genetic marker(s), we propose a new, tentative classification based on the etiologic mechanisms. We also suggest that the term "prediabetes" be abandoned as a prospective entity, since as presently employed, this connotation carries a risk probability no different than the terms like prehypertension or precoronary thrombosis.

Adolescent↗

Immunodeficiency-related lymphoproliferative disorders: prospective data from the United Kingdom Children's Cancer Study Group Registry.

Clinical data and biological samples were prospectively collected in 42 children with lymphoproliferative disease (LPD) secondary to organ/bone marrow transplant-related immunosuppression (30: 11 liver, 10 heart/lung, 8 kidney and 1 bone marrow), other drug-induced immunosuppression (2), congenital immunodeficiency (8) or human immunodeficiency virus (HIV)-related immune dysfunction (2). Ages ranged from 10 months to 17 years and there were 15 girls. Pathology was centrally reviewed and showed polymorphic features in 5 cases, monomorphic in 23, mixed pattern in 5 patients and 9 other types. Using the Revised European-American Classification of Lymphoid Neoplasms, 5 were B lymphoblastoid, 24 were high-grade B and 14 were other subtypes. Using the Pittsburgh classification, 9 were lymphadenopathic, 10 were systemic, 25 were lymphomatous and, with the Murphy grouping for non-Hodgkin's lymphoma (NHL), 10 were localized and 32 non-localized. Twenty-four out of 38 evaluable cases were Epstein-Barr virus positive. Thirty-five patients were evaluable for clonality; 24 were monoclonal and 11 were polyclonal. Reduced immunosuppression in solid organ transplant patients resulted in resolution of disease in 14/24, which was sustained in 11. Nineteen patients received chemotherapy, 14/18 evaluable responded, which was sustained in 8 cases. Seven out of 29 solid organ transplant and 10/13 other immune-deficient patients died. In the largest group of patients, solid organ transplants, no significant clinical or biological characteristics that predicted outcome were identified. In the transplant group close monitoring of response during reduction in immunosuppression is essential and the early use of B NHL chemotherapy may be effective.

Adolescent↗

Reliable classification and recombination analysis of porcine endogenous retroviruses.

Prevention of cross-species infection with porcine endogenous retroviruses (PERV) is crucial for xenotransplantation. Previous studies described the potential risk of infection for the PERV gamma1 subfamilies A, B and C. Replication competent PERV gamma1 proviruses designated to a particular subfamily and hybrid viruses originating from retroviral recombination events between the subfamilies were observed. Future pig genome sequencing projects will reveal multiple novel PERV proviruses from additional breeds and animals. Evaluation of these viral genomes has to be carried out to assess the potential risk of retroviral cross-species infection. In this study, we tested common sequence comparison methods for the classification of PERV sequences and the detection of hybrid clones. The examination of the polymorphic nucleotide positions was found to be the most suitable procedure. We describe a fast and simple method using bioinformatic software tools which can also be applied to analogous analyses of other viral genomes.

Animals↗