Search PubMed⌕ Search

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.

At least 1,441 records · Page 80Linked to original sources
PubMed1991

An ELISA procedure for the diagnosis of dengue infections.

Although the hemagglutination-inhibition (HI) test has been the standard test used by the World Health Organization (WHO) for the classification of serologic response in dengue infections, it is slow, requiring paired specimens. Furthermore, not all investigators have accepted the classification. Thus, there is an urgent need to develop a rapid test which employs a single specimen. We developed an enzyme-linked immunosorbent assay (ELISA) for rapid classification of serologic responses in dengue infections based on the ratio of IgM and IgG in a single specimen. Using the criteria established by the WHO (1986) for comparison, concordant results were obtained in 81% and 95% of primary and secondary infections, respectively, when serum specimens were tested as pairs. When tested as single specimens, the diagnoses by ELISA and HI agreed in 41% and 52% of acute specimens of primary and secondary infections, respectively. The lower rate of concordance in acute-phase samples was due to the absence of detectable IgM in acute specimens collected at outpatient clinics. On the other hand, diagnoses by ELISA and HI agreed in 79% and 95% of primary and secondary infections when single convalescent specimens were used. Analysis of the discordant results between the two tests revealed that the interpretation by the IgM-IgG ratio agreed better with HI classifications practised by some investigators than it did with the WHO.

Antibodies, Viral↗
PubMed2003

Acute pancreatitis following kidney transplantation - role of viral infections.

Acute pancreatitis following renal transplantation is an unusual complication that carries a high mortality. Over the last 10 yr, five of 185 patients at our center developed acute pancreatitis. All had live related donors and were on conventional triple drug immunosuppression. Pancreatitis was classified according to the computed tomography scan based on Atlanta Classification. All five patients who developed acute pancreatitis had evidence of symptomatic or serologically active viral infection (chicken pox in two, cytomegalovirus infection in two, hepatitis E virus in one) and no patient without viral infection developed pancreatitis. Overall, 45 patients developed symptomatic or serologically active viral infection. There was a significant association between viral infection and pancreatitis (chi-square test, p < 0.001). Three patients with severe acute pancreatitis died while both patients with mild pancreatitis survived. An active search for viral infections should be made in all patients with acute pancreatitis. Specific antiviral measures may help reduce the mortality of acute pancreatitis in these patients. Consideration must be given to varicella immunization in patients with renal failure.

Acute Disease↗
PubMed2005

The effect of paralogous lineages on the application of reconciliation analysis by cophylogeny mapping.

Paralogy defines similarity caused by duplication rather than common descent and is well known in the case of paralogous gene copies within a single genome. The term is here extended to paralogous lineages of associates within a single host. The phylogenies of four genera within the Herpesviridae were reconciled with host phylogenies using cophylogenetic mapping. The observed correspondence for each pair of phylogenies was evaluated through randomization of the viral phylogeny and demonstrated to be greater than expected by chance. A simulation study was then carried out to assess the influence of paralogous lineages on the efficacy of reconciliation analysis. Combining viral taxa from different genera that infected common hosts introduced incongruence into the cophylogenies and reduced both the minimum and maximum observed number of codivergence events relative to the initial analysis of orthologous clades. However, at an average sample size this did not alter the fundamental significance of observed correspondence. With smaller sample sizes, the number of orthologous taxa selected at random from the pool of taxa was reduced. False-negative results then increased in proportion from 0.02 to 0.33. These results demonstrated that reconciliation analysis is robust under conditions of paralogy at "normal" sample sizes but is adversely affected by a combination of paralogy and low sample size. Consideration of phylogenies for Papillomavirus, Atadenovirus, and Mastadenovirus suggest that paralogous lineages may be a widespread phenomenon among DNA viruses and that duplication irrespective of host speciation is an important cause of viral diversification.

Animals↗
PubMed2005

Weighted least-squares likelihood ratio test for branch testing in phylogenies reconstructed from distance measures.

A variety of analytical methods is available for branch testing in distance-based phylogenies. However, these methods are rarely used, possibly because the estimation of some of their statistics, especially the covariances, is not always feasible. We show that these difficulties can be overcome if some simplifying assumptions are made, namely distance independence. The weighted least-squares likelihood ratio test (WLS-LRT) we propose is easy to perform, using only the distances and some of their associated variances. If no variances are known, the use of the Felsenstein F-test, also based on weighted least squares, is discussed. Using simulated data and a data set of 43 mammalian mitochondrial sequences we demonstrate that the WLS-LRT performs as well as the generalized least-squares test, and indeed better for a large number of taxa data set. We thus show that the assumption of independence does not negatively affect the reliability or the accuracy of the least-squares approach. The results of the WLS-LRT are no worse than the results of the bootstrap methods, such as the Felsenstein bootstrap selection probability test and the Dopazo test. We also show that WLS-LRT can be applied in instances where other analytical methods are inappropriate. This point is illustrated by analyzing the relationships between human immunodeficiency virus type 1 (HIV-1) sequences isolated from various organs of different individuals.

Animals↗
PubMed2000

Therapeutic application of zinc in human immunodeficiency virus against opportunistic infections.

The relevance of zinc in resistance to infections by virus, fungi and bacteria is recognized because of its pivotal role in the efficiency of the entire immune system, in particular in conferring biological activity to a thymic hormone called thymulin, which has differentiation properties on T-cell lines. In infection with human immunodeficiency virus (HIV), the zinc-bound form of thymulin (active thymulin, ZnFTS) is strongly reduced in stage IV of the disease (Centers for Disease Control and Prevention classification) with concomitant decrements in CD4(+) cell count and zincemia values. The zinc-unbound form of thymulin (inactive thymulin, FTS) is, in contrast, very high. The in vitro addition of zinc to plasma samples induces a recovery of the thymulin active form, suggesting low zinc bioavailability as the cause of impaired thymic functions with consequent CD4(+) depletion. An analysis of risk factors for the incidence of recidivism opportunistic infections shows CD4(+) depletion and zinc deficiency to have significant scores. Supplementation with zinc for 1 mo (45 mg Zn(2+)/d) associated with zidovudine (AZT) therapy in stage IV induces recovery of active zinc-bound thymulin, of zincemia, of CD4(+) cells with concomitant reduction (50%) of recidivism opportunistic infections compared with the AZT-treated group. Complete disappearance of recidivism by Candida aesophagea or Pneumocystis carinii is observed after supplementation with zinc. The relative risk factors (CD4(+) depletion and zinc-deficiency) have lower scores in the HIV-positive zinc-treated group, confirming, as such, the relevance of zinc in opportunistic infections that involve extracellular matrix. Such an assumption is indirectly confirmed with new HAART, where no opportunistic infections occur. Indeed, HIV RNA is inversely correlated with both CD4(+) and zincemia values (r = -0.73, P<0.01) in HAART-treated subjects. Lower scores for the same relative factors for the appearance of opportunistic infections are present in HAART-treated subjects compared with those treated with AZT. These findings, on the one hand, show the poor efficacy of AZT therapy compared with HAART therapy for the progression of HIV, but on the other hand, they suggest that the lack of occurrence of opportunistic infections by HAART may also result from major zinc bioavailability. This further supports the key role played by zinc against opportunistic infections in HIV with a possible independent effect by either HIV or the pathogens involved.

AIDS-Related Opportunistic Infections↗
PubMed2004

Post-transplant lymphoproliferative disorder limited to the skin.

BACKGROUND: Post-transplant lymphoproliferative disorder (PTLD) is a condition affecting immunosuppressed transplant patients and has a variety of clinical presentations. It is rarely found in the skin, and cases of PTLD in the skin are usually linked with lymph node or other organ involvement. METHODS: We report a case of plasmacytoid PTLD that is limited to the skin. A 63-year-old man with a history of cardiac transplant presented with exophytic tumors involving the lower extremity. The diagnosis and classification of the various forms of PTLD are discussed. RESULTS: Histology, immunohistochemical stains, and in situ hybridization revealed an aggressive plasmacytoid tumor that was Epstein-Barr virus positive. The patient's tumors resolved with decreased immunosuppression and localized radiation. CONCLUSION: This case is unusual for several reasons including involvement limited to the skin, presentation 15 years following transplant, and plasmacytoid phenotype of the tumor. This disorder will likely be seen by dermatologists and dermatopathologists with the increasing use of immunosuppressive medications in the dermatologist's patient population.

Epstein-Barr Virus Infections↗
PubMed1983

Regional blood-to-tissue transport in avian sarcoma virus (ASV)-induced brain tumors.

Regional blood-to-tissue transport of 14C-alpha-aminoisobutyric acid (AIB) was measured in avian sarcoma virus (ASV)-induced rat brain tumors and expressed as a unidirectional transfer rate constant (K). The magnitude of K was variable and did not correlate with histologic classification or specific features of the tumors, with the possible exception of sarcomas. Averaged mean K was highest for anaplastic astrocytomas and lowest for gemistocytic astrocytomas (GA); however, the range of measurement within the individual tumor classifications (except GA) was broad. K was not consistently related to tumor size or tumor location; choroid plexus and subependymal tumors were exceptions and had higher K values. The averaged mean K of tumor-free brain in the contralateral hemisphere (CBA) was comparable to that of control animals. The averaged mean K in brain adjacent to tumor was greater than in CBA and generally one-third to one-half of the value in tumor periphery, indicating that these tumors affect the permeability characteristics of adjacent brain capillaries. Estimates of the fractional extraction (E) of AIB by the tumors ranged between 0.009 and 0.2; E's in this range indicate that tumor capillaries are not freely permeable to this solute.

Animals↗
PubMed1986

[Value of puncture biopsy of the liver during diagnostic and follow-up examinations (clinical aspects, immunological markers, images) in chronic hepatitis].

Chronic hepatitis is defined as chronic liver disease of at least 6 months' duration. Liver biopsy is essential for diagnosis and allows classification into chronic persistent hepatitis and chronic active hepatitis. Chronic persistent hepatitis is associated with hepatitis B infection or with infection with the non A non B viruses. The prognosis is good and it requires no treatment. Autoimmune chronic active hepatitis presents a very active clinical, biochemical and immunological picture. Prednisolone therapy is of benefit in prolonging life. Steroid therapy is disappointing in hepatitis B related chronic active hepatitis. Superinfection with delta agent may affect HBsAg positive patients: it appears to cause activation of disease and progression towards cirrhosis. Hepatocarcinoma is another complication of chronic B infection. Chronic active non A non B hepatitis is diagnosed by elimination since there is no specific diagnostic test.

Adolescent↗
PubMed1997

Histopathology and pathobiology of hepatotropic virus-induced liver injury.

The present report concerns current knowledge regarding immunopathogenesis that can be applied in the interpretation of histopathological changes in acute and chronic viral hepatitis. The histopathological features of viral hepatitis have not been changed and light microscopic examination remains essential for making a diagnosis and classification of chronic hepatitis and for the provision of objective parameters on grading and staging. However, new understanding and knowledge of viral pathogenesis, host immune responses, the biological behaviour of the causative viral agents and, in particular, viral interference in multiple hepatotropic viral infections must be taken into consideration in the interpretation of histopathological and immunopathological findings of liver tissues. This report also presents some histopathological analyses on multiple hepatotropic viral infections. It can be concluded that the diagnostic histological criteria for acute hepatitis remain applicable in such settings. However, the cause of acute flare up in chronic hepatitis could not be determined without clinical, virological and serological information. Routine histopathology cannot distinguish a new infection from an acute exacerbation due to a high level of viral replication or mutant virus. A repertoire of immunocytochemical stainings for viral antigens is helpful, but caution must be exercised in suggesting a specific viral aetiology due to the fact that suppression of pre-existing viral antigens can be pronounced when the new or concurrent infection is hepatitis C virus related.

Animals↗
PubMed2006

Sperm output in patients with primary infertility and hepatitis B or C virus; negative influence of HBV infection during concomitant varicocele.

AIM: The aim of this study was to evaluate the sperm abnormalities in young infertile patients with hepatitis B (HBV) or C (HCV) virus infection and to evaluate the additional negative influence of varicocele on sperm parameters in these patients. METHODS: Part I. Forty-two infertile patients in Child-Pugh classification A with HBV (n=23) or HCV (n=19) infection, underwent sperm analysis and quantitative detection of HBV-DNA or HCV-RNA in blood serum. Sperm parameters were compared to those of a group of 30 patients with primary infertility due to causes different from liver diseases and/or varicocele). Part II. Twenty-one infertile patients with varicocele associated to HBV (n=11) or HCV (n=10) infection were also enrolled and underwent semen analysis: a group of 39 patients without liver disease, but with varicocele alone served as matched-control group. RESULTS: Part I. HBV patients (with a median HBV-DNA load of 6x10(5) copies/mL, range 1x10(5)-10x10(6)) showed median sperm parameters (sperm density, total number, forward motility and morphology, viability) significantly worse than those found in patients with HCV (with a median HCV-RNA load of 2.3x10(6) copies/mL, range (2x10(5)-12x10(6)). Sperm parameters showed no significant correlation with the duration of infertility neither with the duration of viral infection. Sperm morphology only, exhibited a trend (P=0.06) of negative correlationship (r=-0.59) with the viral HBV-DNA load, whereas the other sperm parameters studied showed no correlation with the viral load. Part II. The group of infertile patients with HBV and varicocele showed median values of all sperm parameter evaluated significantly worse than those found in infertile patients with varicocele alone, or with HCV infection plus varicocele. CONCLUSIONS: Patients with HBV infection show worse sperm parameters compared with HCV patients. The additional presence of varicocele further impairs sperm output in HBV patients.

Adult↗
PubMed1990

SPECT gallium-67 scanning in early human immunodeficiency virus (HIV) infection. Failure of scanning abnormalities to correlate with immunologic staging.

The use of gallium scanning in the treatment of patients with AIDS has been well described. In this study, 27 HIV-infected patients (Walter Reed Staging Classification I-V) with normal chest roentgenograms were evaluated to determine the occurrence of thoracic gallium abnormalities in early HIV infection. SPECT was used for gallium scanning. Patients received gallium injection on day 1 and bronchoalveolar lavage on day 2, and scanning was performed on day 3. Twenty-eight scans in 27 patients were performed. Mean nodal SPECT activity was compared with corresponding values for lung parenchyma, bronchoalveolar lavage cell counts, and peripheral blood T4 lymphocyte counts. No relationship between nodal and parenchymal activity and cell counts was observed. Although visual scan interpretation was unaffected, gallium activity was significantly increased in the region of bronchoalveolar lavage compared with uptake in other lung regions. It is concluded that SPECT gallium scanning demonstrates significant gallium avidity in recently lavaged lung areas, although no impact on visual scan interpretation was seen. Further, no correlation was seen between the degree of nodal uptake and the immunologic status of these patients with early HIV infection.

Adult↗
PubMed2002

Viral, parasitic and prion diseases of farmed deer and bison.

The most important viral disease of farmed deer and bison is malignant catarrhal fever. The other herpesviruses which have been isolated from these species are briefly described. Other viral agents that are recognised in these animals, including adenovirus, parapox, foot and mouth disease, bluetongue, epizootic haemorrhagic disease, bovine virus diarrhoea, rotavirus and coronavirus, are also discussed. Ectoparasites of importance in this group in various parts of the world include a variety of ticks, as well as lice, keds, Oestridae, mange mites and fire ants. Helminth parasites include liver flukes (Fascioloides and Fasciola), gastrointestinal nematodes of the family Trichostrongylidae, pulmonary lungworms of the genus Dictyocaulus and extra-pulmonary lungworms of the family Protostrongylidae. Chronic wasting disease is principally important in North America, where the disease occurs in wild cervids in a limited area and has been reported in farmed deer in a small number of states in the United States of America and one province in Canada. These diseases are summarised in terms of their classification, epidemiology, clinical signs, pathology, diagnosis, treatment and control.

Animals↗
PubMed2006

Sequencing and characterisation of p74 gene in two isolates of Anticarsia gemmatalis MNPV.

P74 is a protein encoded in the genome of baculoviruses, associated with the envelopes of occluded virus. Its presence proved to be essential for per os infection. In first place, in this work we designed two universal primers to amplify a sequence region of the p74 ORF in baculoviruses from different classification groups. Then, by the use of these amplicons we obtained the complete sequence of the p74 locus from two isolates of AgMNPV, 2D (Brazil) and SF (Argentina). In the flanking regions we determined the complete sequence of p10 gene and a portion of p26 gene. Comparing both p74 sequence data (ORFs of 1935 bp) we found fifteen nucleotide changes that result in six amino acid changes. Comparisons of AgMNPV p74s with other baculovirus homologous genes indicate a close relationship with other group I Nucleopolyhedrovirus, in particular CfDEFNPV. These results were based on ORF sequence, amino acid sequence and gene order. The predictive studies about secondary structure and hydrophobic index point at six regions potentially associated to its function or native conformation. Finally, the detection of p74 mRNA after virus DNA replication confirms a late expression pattern.

Amino Acid Sequence↗
PubMed1993

Infectious diarrhoea. Viruses.

Increased knowledge has been gained into the aetiology and pathogenesis of viral gastroenteritis during the past two decades. There are now thought to be four major subclassifications of gastroenteritis-causing viruses; these include rotavirus, enteric adenovirus, calicivirus, including Norwalk and Norwalk-like viruses, and astrovirus. The association of these agents with gastroenteritis has been made by their electron microscopic detection in stool and intestinal biopsy specimens from affected patients, the inability to detect the viruses after recovery from disease, and the subsequent development of immunoglobulin responses after infection; in some instances disease transmission was achieved in human volunteers. The association of these viral agents with gastroenteritis has facilitated the study of classification, epidemiology, immunity, diagnostic tests, methods of treatment and, most importantly, disease prevention strategies such as vaccine development for rotavirus. This chapter highlights the major features of these agents, with special attention being given to the pertinent molecular biology as well as current and future prospects for vaccination. Enteric viral infections of the gastrointestinal tract in patients with AIDS are also discussed.

Diarrhea↗
PubMed2004

Correlation of mass spectrometry identified bacterial biomarkers from a fielded pyrolysis-gas chromatography-ion mobility spectrometry biodetector with the microbiological gram stain classification scheme.

A pyrolysis-gas chromatography-ion mobility spectrometry (Py-GC-IMS) briefcase system has been shown to detect and classify deliberately released bioaerosols in outdoor field scenarios. The bioaerosols included Gram-positive and Gram-negative bacteria, MS-2 coliphage virus, and ovalbumin protein species. However, the origin and structural identities of the pyrolysate peaks in the GC-IMS data space, their microbiological information content, and taxonomic importance with respect to biodetection have not been determined. The present work interrogates the identities of the peaks by inserting a time-of-flight mass spectrometry system in parallel with the IMS detector through a Tee connection in the GC module. Biological substances producing ion mobility peaks from the pyrolysis of microorganisms were identified by their GC retention time, matching of their electron ionization mass spectra with authentic standards, and the National Institutes for Standards and Technology mass spectral database. Strong signals from 2-pyridinecarboxamide were identified in Bacillus samples including Bacillus anthracis, and its origin was traced to the cell wall peptidoglycan macromolecule. 3-Hydroxymyristic acid is a component of lipopolysaccharides in the cell walls of Gram-negative organisms. The Gram-negative Escherichia coli organism showed significant amounts of 3-hydroxymyristic acid derivatives and degradation products in Py-GC-MS analyses. Some of the fatty acid derivatives were observed in very low abundance in the ion mobility spectra, and the higher boiling lipid species were absent. Evidence is presented that the Py-GC-ambient temperature and pressure-IMS system generates and detects bacterial biochemical information that can serve as components of a biological classification scheme directly correlated to the Gram stain reaction in microorganism taxonomy.

Biomarkers↗
PubMed1990

Antigenic homology among coronaviruses related to transmissible gastroenteritis virus.

The antigenic homology of 26 coronavirus isolates, of which 22 were antigenically related to transmissible gastroenteritis virus (TGEV), was determined with 42 monoclonal antibodies. Type, group, and interspecies specific epitopes were defined. Two group specific MAbs distinguished the enteric TGEV isolates from the respiratory variants. An antigenic subsite involved in neutralization was conserved in porcine, feline, and canine coronavirus. The classification of the human coronavirus 229E in a taxonomic cluster distinct from TGEV group is suggested.

Animals↗
PubMed2003

Molecular features of non-B, non-C hepatocellular carcinoma: a PCR-array gene expression profiling study.

BACKGROUND/AIMS: Hepatocellular carcinoma (HCC) usually develops following chronic liver inflammation caused by hepatitis C or B virus. Through expression profiling in a rare type of HCC, for which the causes are unknown, we sought to find key genes responsible for each step of hepatocarcinogenesis in the absence of viral influence. METHODS: We used 68 non-B, non-C liver tissues (20 HCC, 17 non-tumor, 31 normal liver) for expression profiling with PCR-array carrying 3072 genes known to be expressed in liver tissues. To select the differentially expressed genes, we performed random permutation testing. A weighted voting classification algorithm was used to confirm the reliability of gene selection. We then compared these genes with the results of previous expression profiling studies. RESULTS: A total of 220 differentially expressed genes were selected by random permutation tests. The classification accuracies using these genes were 91.8, 92.0 and 100.0% by a leave-one-out cross-validation, an additional PCR-array dataset and a Stanford DNA microarray dataset, respectively. By comparing our results with previous reports on virus-infected HCC, four genes (ALB, A2M, ECHS1 and IGFBP3) were commonly selected in some studies. CONCLUSIONS: The 220 differentially expressed genes selected by PCR-array are potentially responsible for hepatocarcinogenesis in the absence of viral influence.

Aged↗