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PubMed1987

Studies on the classification of bovine enteroviruses.

Bovine enteroviruses isolated from cattle and other ruminants in various areas of the world were classified into three distinct serotypes by cross-neutralization tests using criteria established for the differentiation of human enteroviruses. According to Western blot analysis, however, immunodominant structural polypeptides VP1 of the viruses tested have common epitopes, recognized by antisera to each of the three serotypes. These findings indicate that non-neutralizing epitopes on VP1 are generally conserved. It is, therefore, conjectured that bovine enteroviruses were derived from a common ancestor.

Animals↗
PubMed2003

Genomic sequence of C1, the first streptococcal phage.

C(1), a lytic bacteriophage infecting group C streptococci, is one of the earliest-isolated phages, and the method of bacterial classification known as phage typing was defined by using this bacteriophage. We present for the first time a detailed analysis of this phage by use of electron microscopy, protein profiling, and complete nucleotide sequencing. This virus belongs to the Podoviridae family of phages, all of which are characterized by short, noncontractile tails. The C(1) genome consists of a linear double-stranded DNA molecule of 16,687 nucleotides with 143-bp inverted terminal repeats. We have assigned functions to 9 of 20 putative open reading frames based on experimental substantiation or bioinformatic analysis. Their products include DNA polymerase, holin, lysin, major capsid, head-tail connector, neck appendage, and major tail proteins. Additionally, we found one intron belonging to the HNH endonuclease family interrupting the apparent lysin gene, suggesting a potential splicing event yielding a functional lytic enzyme. Examination of the C(1) DNA polymerase suggests that this phage utilizes a protein-primed mechanism of replication, which is prominent in the phi29-like members of Podoviridae. Consistent with this evidence, we experimentally determined that terminal proteins are covalently attached to both 5' termini, despite the fact that no homology to known terminal proteins could be elucidated in any of our open reading frames. Likewise, comparative genomics revealed no close evolutionary matches, suggesting that the C(1) bacteriophage is a unique member of the Podoviridae.

Animals↗
PubMed2000

[Clinicopathological differential diagnosis of mycosis fungoides/Sézary syndrome from the cutaneous type of adult T-cell leukemia/lymphoma].

Mycosis fungoides/Sézary syndrome(MF/SS) is considered as a distinct clinical entity in the latest classifications, including the revised European-American classification of lymphoid neoplasm(REAL), and the ones by the WHO and the European Organization for Research and Treatment of Cancer(EORTC). In Japan, where is an endemic area for human T-cell lymphotropic virus type 1(HTLV-1), we have been facing some problems concerning the differential diagnosis of MF/SS. We have observed many cutaneous types of adult T-cell leukemia/lymphoma(cATL/L) that can initiate as erythematous infiltrating plaques similar to MF or as an erythrodermic lesion similar to SS and also as tumoral and nodular lesions, solitary or multiple that resemble d'emblée type MF. The importance of the differential diagnosis between MF/SS and cATL/L lies on the significant difference on the prognosis. It is worth to differentiate MF/SS from cATL/L, especially in MF patients positive for HTLV-1 antibody. We emphasize on the characteristics that differentiate MF/SS from cATL/L as well as on the new findings regarding clinical, histopathological, phenotypical and genotypical aspects of MF/SS.

Antibodies, Viral↗
PubMed1991

Canadian multicenter azidothymidine trial: AZT pharmacokinetics.

The study objective was to describe the pharmacokinetics of azidothymidine (AZT) in a large population of early, asymptomatic human immunodeficiency virus (HIV)-infected individuals. The study design was a multicenter, prospective, descriptive single-dose pharmacokinetic study. Each of 66 fasting, male, HIV-infected homosexuals older than 18 years of age and in CDC classifications II, III, and IVC2 received a single 400-mg oral dose of AZT with subsequent pharmacokinetic measurements performed during an 8-h period for AZT and its major metabolite, glucuronylazidothymidine (GAZT). Results were obtained in 65 patients (36 smokers, 29 nonsmokers), of whom 3 were noted to have hepatic dysfunction. In those with normal hepatic function, the following parameters were described: AZT, area under the curve (AUC) +/- SD, 9.9 +/- 5.7 microM.h, maximum concentration (Cmax) +/- SD, 7.3 +/- 4.7 microM; time to maximum concentration (Tmax) +/- SD, 0.93 +/- 0.42 h, and half-life (t1/2) +/- SD, 1.0 +/- 0.8 h. Corresponding values for GAZT were: AUC +/- SD 35.7 +/- 10.3 microM.h, Cmax +/- SD 21.3 +/- 7.3 microM, Tmax +/- SD 1.2 +/- 0.50 h, t1/2 +/- SD 0.98 +/- 0.62 h, No significant differences were found in comparisons of study site, CDC classification of disease, smokers versus nonsmokers, and in patients with hepatic dysfunction, although a higher AUC and earlier Cmax for AZT was noted in the latter group. It is concluded that AZT pharmacokinetics are similar in patients with early asymptomatic HIV disease when compared with previous reports in patients with later disease.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1995

[Gene therapy of blood disorders].

In the article the basic knowledge concerning genes and genetic disorders necessary to understand the methods utilized in contemporary attempts of gene therapy has been reviewed. Then, a classification of gene therapy methods was presented and approaches to somatic gene therapy were discussed with particular attention to the utilization of retroviral vectors and packaging cell lines. Other vector systems such as adenovirus, vaccinia virus, and herpes virus derived have also been mentioned as well as antisense strategy. Reviewed applications concerned mainly inborn gene errors, but strategy of gene-directed, gene-forced suicide of leukemic cells has also been mentioned.

Animals↗
PubMed2002

Complete genome sequence, taxonomic assignment, and comparative analysis of the untranslated regions of the Modoc virus, a flavivirus with no known vector.

We recently developed a model for flavivirus infection in mice and hamsters using the Modoc virus (MODV), a flavivirus with no known vector (P. Leyssen, A. Van Lommel, C. Drosten, H. Schmitz, E. De Clercq, and J. Neyts, 2001, Virology 279, 27-37). We now present the coding and noncoding sequence of MODV. The Modoc virus genome was determined to be 10,600 nucleotides in length with a single open reading frame extending from nucleotides 110 to 10,234, encoding 3374 amino acids. The deduced gene order of the single open reading frame is C-prM-E-NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5, which is exactly the same as that of the mosquito- and tick-borne flaviviruses. It is flanked by a 5'- and 3'-untranslated region (UTR) of 109 and 366 nucleotides, respectively. Alignment of the MODV amino acid sequence with that of 20 other flaviviruses revealed several regions with high sequence similarity corresponding to functionally important domains (e.g., the serine protease/helicase/NTPase of NS3 and the methyltransferase/RNA-dependent RNA polymerase of NS5) and conserved sites for proteolytic cleavage by viral and cellular proteases. Phylogenetic analysis of the entire coding region confirmed the classification of MODV within the flaviviruses with no known vector, which is in agreement with previous findings based on partial NS5 sequences. A detailed comparative analysis of the putative folding patterns of the 5'- and 3'-UTR of MODV and of the tick- and mosquito-borne viruses was carried out. Structural elements in the 5'- and 3' UTR of MODV that are preserved among vector-borne flaviviruses were noted and so were structural elements distinguishing the MODV UTRs from mosquito-borne and tick-borne flaviviruses. Also the putative secondary structure of circularized MODV RNA is presented.

3' Untranslated Regions↗
PubMed1981

A 27-nm virus isolated during an outbreak of acute infectious nonbacterial gastroenteritis in a convalescent hospital: a possible new serotype.

An outbreak of acute infectious nonbacterial gastroenteritis began among elderly patients in a convalescent hospital in Marin County in northern California in March 1978 and persisted through May 1978. The overall clinical attack rate was 51% of 187 residents and 12% of 180 employees. A 27-nm viruslike particle was observed by immune electron microscopy in stools obtained at or near the onset of illness from four of 32 patients. Seroresponses to the 27-nm particles were found by immune electron microscopy in 16 of 18 patients. In addition, serologic evidence of infection with this or a related agent was demonstrated in persons who developed illness in another large outbreak of acute infectious nonbacterial gastroenteritis which occurred in a nearby county. This agent is morphologically similar to but serologically unrelated to the Norwalk and Hawaii gastroenteritis agents and has been designated the Marin agent pending further classification.

Acute Disease↗
PubMed1993

Oncogenes of DNA and RNA tumor viruses and the origin of cellular oncogenes.

Oncogenes were first described as the genes of DNA tumor viruses responsible for in vivo and in vitro neoplastic transformation induced by such viruses. The first oncogenes described were the oncogenes of polyoma, SV40 and papilloma viruses. The polyoma virus oncogene has been designated the 'middle' T (tumor) antigen, whereas the SV40 oncogene is designated the 'large' T antigen. The large T of the polyoma virus can also be considered an oncogene, because it is capable of 'immortalizing', but not transforming primary cell cultures. Other oncogenes of DNA tumor viruses are the E1A of adenoviruses and the E7 gene of papilloma viruses. It has been proposed that some of the oncogenes of DNA tumor viruses act by binding the products of tumor suppressor genes, such as the retinoblastoma gene product Rb. In general, the products of the oncogenes of DNA tumor viruses need the cooperation of other oncogenes to establish a completely transformed phenotype. Oncogenes have been discovered in all replication defective RNA tumor viruses, whereas they are not present in the genomes of replication competent RNA tumor viruses, which can also give rise to a neoplastic phenotype, in vivo, but by a different mechanism. The discovery of oncogenes in RNA tumor viruses has led to the concept that these oncogenes are actually present in the genomes of all eucaryotic organisms and have been transduced and, in some cases, modified by a retrovirus. The characterization of the oncogenes of acute transforming retroviruses has led to the present classification of oncogenes, which include genes coding for proteins having different functional properties, but all characterized by having some role in the pathway which regulates cell proliferation. The experimental approach of DNA transfection has led to the discoveries of some oncogenes already known from the genomes of retroviruses and also of some new oncogenes which had never been transduced by retroviruses. The knowledge derived from retrovirus research and from the use of the DNA transfection technique has opened a whole new field of science thereby contributing greatly to our understanding of the mechanisms underlying neoplastic transformation and also to the understanding of normal cell physiology.

Animals↗
PubMed2006

Exogenous nitric oxide inhibits Crimean Congo hemorrhagic fever virus.

Crimean Congo hemorrhagic fever virus (CCHFV) is a geographically widespread pathogen that causes severe hemorrhagic fever with high mortality. Even though one of the main objectives focuses on the progress of antiviral agents, the research on CCHFV is strongly hampered due to its BSL-4 classification. Nitric oxide (NO), a mediator with broad biological effects, has been shown to possess inhibitory properties against various pathogens. The molecule constitutes a component of the innate immunity and serves to assist in the early immunological events where it contributes to clearance of microorganisms. In this study, we investigated the inhibitory properties of exogenous NO on CCHFV. We found that NO had a significant antiviral activity against CCHFV replication. By using the NO-donor S-nitroso-N-acetylpenicillamine (SNAP) we were able to show up to 99% reduction in virion progeny yield. In contrast, 3-morpholinosydnonimine hydrochloride (SIN-1), a peroxynitrite donor, had no significant antiviral activity against CCHFV. Furthermore the expression of viral proteins; the nucleocapsid protein and the glycoprotein, were clearly reduced with increasing concentrations of SNAP. We have also shown that the amount of total vRNA in SNAP-treated cells was reduced by about 50% compared to the controls.

Dose-Response Relationship, Drug↗
PubMed1993

Sequence determination of the nucleocapsid protein gene of the porcine epidemic diarrhoea virus confirms that this virus is a coronavirus related to human coronavirus 229E and porcine transmissible gastroenteritis virus.

The nucleotide sequence of 1.7 kbp cDNA, comprising the region nearest the 3' end of the genome of the porcine epidemic diarrhoea virus (PEDV), has been independently determined for two European isolates of PEDV. Almost identical results were obtained for the two isolates, which were derived from cases of PEDV infection in Belgium and Britain in 1977 and 1987, respectively. The sequences contained a 1323 nucleotide (nt) open reading frame (ORF), which showed moderate identity to the nucleocapsid (N) gene of other coronaviruses. The greatest similarity at both the nucleic acid and protein levels was to the human coronavirus 229E. The PEDV N gene was, however, notably larger than that of the human 229E and porcine transmissible gastroenteritis viruses. This reflects the presence of a putative insertion of approximately 135 nt located towards the middle of the N gene. A second 336 nt ORF, which might encode a leucine-rich protein similar to, but shorter than, the bovine coronavirus internal protein was found within the PEDV N gene. Several RNA motifs typical of coronaviruses were also observed. These results confirm the earlier provisional classification of PEDV as a coronavirus.

Amino Acid Sequence↗
PubMed1990

Identification of a viral gene encoding a ubiquitin-like protein.

The baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV, which is representative of the MNPV subtype in which the virions may contain many nucleocapsids within a single viral envelope) encodes a protein, v-ubi, that has 76% identity with the eukaryotic protein ubiquitin. Transcriptional mapping indicated that the gene for v-ubi was transcribed during the late phase of viral infection. Two transcriptional start sites potentially encoding v-ubi were identified. Both sites were contained within a sequence motif common to baculovirus late genes. A recombinant virus, AcUbi-beta Gal, encoding a ubiquitin-beta-galactosidase fusion protein was constructed to monitor the temporal regulation of v-ubi gene during viral infection. The fusion protein was expressed maximally at 14-18 hr postinfection, consistent with its classification as a late protein. The amount of ubiquitin-beta-galactosidase fusion protein that accumulated in AcUbi-beta Gal-infected cells by 48 hr postinfection was approximately 14% of the level of beta-galactosidase that was synthesized under control of the polyhedrin promoter. Transcriptional analysis confirmed that synthesis of the fusion protein was directed by the v-ubi gene promoter. AcUbi-beta Gal also produced normal levels of authentic viral ubiquitin message. Southern blot analysis of AcUbi-beta Gal and 15 additional isolates revealed that the fusion sequences had not recombined at the ubiquitin locus. A polyubiquitin gene was isolated and sequenced from Spodoptera frugiperda, a lepidopteran host cell line for AcMNPV. The predicted amino acid sequence of the product of the host gene is identical to animal ubiquitin.

Amino Acid Sequence↗
PubMed1993

The problem of antiviral therapy for chronic hepadnavirus infections.

Attempts at antiviral therapy of patients with active liver disease as a consequence of chronic hepatitis B virus infection have been moderately successful. The molecular and cellular basis for a successful outcome in these patients is not understood and the same therapies do not appear to benefit carriers that still have fairly normal livers and only a moderate hepatitis as a result of the immune response to the infection. Most carriers fall into this latter classification, at least during the early years of infection, and a therapy that could be successfully applied before extensive liver damage had occurred would presumably reduce the risk of subsequent liver damage and the progression to primary hepatocellular carcinoma. Traditionally, it has been assumed that the primary reason that individuals become chronically infected is that the cytotoxic T-cell response and/or antibody-dependent killing of infected hepatocytes is insufficient to clear the infection. Less attention has been focused on the role of the antibody response in the generation of virus-neutralizing antibodies as the possible major deficiency predisposing some individuals to become carriers. However, carriers normally are antigenemic for HBsAg and virus, and carriers with only antibodies to these structures in their circulation are virtually unknown. In addition, it is usually assumed that the hepatocyte, the major target of infection, does not spontaneously turn over and that, in the absence of an immune response to the infected cell, hepatocellular viability is unaffected.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed2002

HPV antibody detection by ELISA with capsid protein L1 fused to glutathione S-transferase.

An alternative enzyme linked immunosorbent assay (ELISA) system was developed to analyze antibodies to human papillomavirus capsid antigens. The assay uses glutathione crosslinked to casein to capture the major capsid protein L1 from human papillomavirus (HPV) types 6b, 16 and 18 fused to glutathione S-transferase (GST) as antigen. The method allows efficient one-step purification of L1 fusion protein from crude bacterial lysates on ELISA plates coated with glutathione casein. The GST-L1 capture ELISA detected HPV 16 antibodies with high type specificity. Comparison with the current "gold-standard" for L1-serology that uses virus-like particles (VLP) as antigen demonstrated similar assay sensitivity. Pairwise comparison of the absorbance values of 105 human sera obtained in the two ELISA formats for HPV 16 showed a R(2) value of linear regression of 0.68. Conformity of the two ELISAs in classification of sera as HPV 16 L1 antibody-positive or -negative was verified with Cohen's kappa test, yielding a value of 0.62. These data indicate that the GST-L1 capture ELISA is similar in performance to the VLP ELISA. The ease of antigen production and purification in the GST-based ELISA will be advantageous to screen large sample numbers in vaccine trials or epidemiological studies examining immune responses to many HPV types in parallel.

Animals↗
PubMed1989

Host-independent evolution and a genetic classification of the hepadnavirus family based on nucleotide sequences.

An analysis of molecular phylogeny was undertaken to examine whether the evolution of the hepadnavirus family is host-dependent. Using the nucleotide sequences of 18 strains, we constructed phylogenetic trees. The trees obtained show that all 12 strains of hepatitis B virus can be classified into four subgroups that are not compatible with conventional subtypes. We estimated the rate of synonymous (silent) substitution for hepatitis B virus to be 4.57 x 10(-5) per site per year. Applying this rate to the phylogenetic tree, we estimated that duck hepatitis B virus diverged from a common ancestor about 30,000 years ago at the earliest, that woodchuck hepatitis virus and ground squirrel hepatitis virus diverged about 10,000 years ago, and that hepatitis B virus diverged within the last 3000 years. Because these divergence times of the viruses are much more recent than those of the host species, it suggests that the hepadnavirus family evolved independently of host-species divergence.

Animals↗
PubMed1990

Clinical use of selective decontamination: the concept.

Infections can be classified according to: (1) the type of offending microorganism (virus, bacteria, fungi, parasites), (2) according to the clearance by the defence system (T cell dependent/independent) and (3) in case bacteria are the causative agents in Gram-positive and Gram-negative infections. The latter classification in Gram-positive and Gram-negative infections has appeared to have a practical consequence. Gram-negative bacteria, often involved in major infections and yeasts, appear to play practically no role in the intestinal ecological system. Consequently, it is nowadays increasingly attempted to eliminate Gram-negative bacteria and yeasts selectively from the digestive tract with antimicrobial agents. Selective suppression of Gram-positive bacteria may severely affect the ecosystem of the digestive tract. This selective suppression of Gram-negatives must be continued as long as patients are immunocompromised (locally or systemically) and is called selective decontamination of the digestive tract.

Anti-Bacterial Agents↗
PubMed1999

Molecular phylogeny of phi29-like phages and their evolutionary relatedness to other protein-primed replicating phages and other phages hosted by gram-positive bacteria.

The phi29-like phage genus of Podoviridae family contains phages B103, BS32, GA-1, M2, Nf, phi15, phi29, and PZA that all infect Bacillus subtilis. They have very similar morphology and their genomes consist of linear double-stranded DNA of approximately 20 kb. The nucleotide sequences of individual genomes or their parts determined thus far show that these phages evolved from a common ancestor. A terminal protein (TP) that is covalently bound to the DNA 5'-end primes DNA replication of these phages. The same mechanism of DNA replication is used by the Cp-1 related phages (also members of the Podoviridae family) and by the phage PRD1 (member of the Tectoviridae family). Based on the complete or partial genomic sequence data of these phages it was possible to analyze the evolutionary relationship within the phi29-like phage genus as well as to other protein-primed replicating phages. Noncoding regions containing origins of replication were used in the analysis, as well as amino acid sequences of DNA polymerases, and with the phi29-like phages also amino acid sequences of the terminal proteins and of the gene 17 protein product, an accessory component of bacteriophage DNA replicating machinery. Included in the analysis are also results of a comparison of these phage DNAs with the prophages present in the Bacillus subtilis genome. Based on this complex analysis we define and describe in more detail the evolutionary branches of phi29-like phages, one branch consisting of phages BS32, phi15, phi29, and PZA, the second branch composed of phages B103, M2, and Nf, and the third branch having phage GA-1 as its sole member. In addition, amino acid sequences of holins, proteins involved in phage lysis were used to extend the evolutionary study to other phages infecting Gram-positive bacteria. The analysis based on the amino acid sequences of holins showed several weak points in present bacteriophage classification.

Amino Acid Sequence↗
PubMed1994

Complete nucleotide sequence of the RNA 3 from subgroup II of cucumber mosaic virus (CMV) strain: Trk7.

The complete nucleotide sequence (2209 nucleotides) of the RNA 3 of the cucumber mosaic virus strain Trk7 was determined. Trk7-CMV possesses two open reading frames which encode the 3a protein (279 amino acids) and the coat protein (218 amino acids). Sequence analysis proved the earlier biological and serological classification of the RNA 3 molecule of Trk7-CMV in subgroup II. A high degree of homology was found in the strains Q and Kin of CMV, while the average similarity between the two different subgroups is much lower.

Amino Acid Sequence↗
PubMed1978

A method for classification of 5' termini of retroviruses.

A new method for the classification of retroviruses is presented. The scheme is based on the length and sequence of a DNA transcript of the 5' end of the genome. The method can be used to detect similarities between distantly related viruses as well as to discriminate between very closely related viruses. The method is applied to viruses isolated from mice, baboons, gibbons, a woolly monkey and chickens.

Alpharetrovirus↗