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PubMed2003

An unusual type IB topoisomerase from African trypanosomes.

African trypanosomes are ancient eukaryotes that cause lethal disease in humans and cattle. Available drugs are inadequate and the need for new therapeutic targets is great. Trypanosoma brucei and related pathogens differ strikingly from higher eukaryotes in many aspects of nucleic acid structure and metabolism. We find yet another example of this in their unusual DNA topoisomerase IB. Type IB topoisomerases relieve the supercoils that accumulate during DNA and RNA synthesis, and are of considerable importance as the target for antitumor camptothecins. Dozens of type IB topoisomerases sequenced from eukaryotes, bacteria, and pox viruses are all encoded by a single gene that predictably contains a highly conserved DNA binding domain and C-terminal catalytic domain, linked by a nonconserved hydrophilic region. We find that topoisomerase IB in T. brucei is encoded by two genes: one for the DNA-binding domain and a second for the C-terminal catalytic domain. In keeping with this, highly purified fractions of native T. brucei topoisomerase IB catalytic activity contain two proteins, of 90 and 36 kDa. The native enzyme is conventional in its Mg2+-independence, ability to relax positive and negative supercoils, and inhibition by camptothecin. Camptothecin promotes the formation of a covalent complex between 32P-labeled substrate DNA and the small subunit. This unusual structural organization may provide a missing link in the evolution of type IB enzymes, which are thought to have arisen over time from the fusion of two independent domains. It also provides another basis for the design of selectively toxic drug candidates.

Amino Acid Sequence↗

PubMed2002

Cutaneous EBV-related lymphoproliferative disorder in a 15-year-old boy with AIDS: an unusual clinical presentation.

Lymphomas are a well-known malignancy in individuals with human immunodeficiency virus type 1 (HIV-1) infection. Most lymphomas are of B-cell lineage and cutaneous involvement is rare. Cutaneous T-cell lymphomas have been previously described in adults with HIV-1 infection but are exceptional in HIV-1 infected-children. The authors report here the extremely rare case of a large-cell cutaneous lymphoproliferation of T-cell lineage expressing Epstein-Barr virus (EBV) antigens in a 15-year-old boy with AIDS and his uncommon clinical presentation. The atypical clinical evolution with a nonaggressive treatment emphasizes that for immunosuppressed patients, the diagnosis of immunosuppression-related lymphoproliferative disorder should be considered before giving the diagnosis of malignant lymphoma when tumoral lymphoid cells express EBV antigens.

Acquired Immunodeficiency Syndrome↗

PubMed1992

Antigenic and genetic characterization of the haemagglutinins of recent cocirculating strains of influenza B virus.

The antigenic and genetic characteristics of the haemagglutinins of influenza type B viruses isolated since 1988 during periods of both widespread activity (1990/1991) and sporadic activity (1989/1990) were examined using microneutralization tests and direct RNA sequencing. During 1989/1990, influenza B viruses representative of two distinct lineages antigenically and genetically related to either B/Victoria/2/87 or B/Yamagata/16/88 were isolated, and a minor drift variant of B/Yamagata/16/88, B/Hong Kong/22/89, was identified. In 1990/1991, B/Hong Kong/22/89- or B/Yamagata/16/88-like viruses accounted for the majority of the influenza virus isolates in most countries. Sequence analysis of the HA1 domains of representative viruses confirmed the continued existence of two main lineages among recent strains of influenza B virus and identified unique amino acid changes that could account for the altered antigenic reactivity of some variants. Sequence analysis of the HA2 domains of some of the recent influenza B viruses allowed for a comparison of the evolutionary rates and patterns between the HA1 and HA2 domains.

Amino Acid Sequence↗

PubMed1999

Giant viruses infecting algae.

Paramecium bursaria chlorella virus (PBCV-1) is the prototype of a family of large, icosahedral, plaque-forming, double-stranded-DNA-containing viruses that replicate in certain unicellular, eukaryotic chlorella-like green algae. DNA sequence analysis of its 330, 742-bp genome leads to the prediction that this phycodnavirus has 376 protein-encoding genes and 10 transfer RNA genes. The predicted gene products of approximately 40% of these genes resemble proteins of known function. The chlorella viruses have other features that distinguish them from most viruses, in addition to their large genome size. These features include the following: (a) The viruses encode multiple DNA methyltransferases and DNA site-specific endonucleases; (b) PBCV-1 encodes at least part, if not the entire machinery to glycosylate its proteins; (c) PBCV-1 has at least two types of introns--a self-splicing intron in a transcription factor-like gene and a splicesomal processed type of intron in its DNA polymerase gene. Unlike the chlorella viruses, large double-stranded-DNA-containing viruses that infect marine, filamentous brown algae have a circular genome and a lysogenic phase in their life cycle.

Biological Evolution↗

PubMed2005

HCV and HIV co-infection in pregnant women attending St. Camille Medical Centre in Ouagadougou (Burkina Faso).

Five hundred and forty-seven pregnant women with less than 32 weeks of amenorrhoea, attending an antenatal clinic of St. Camille Medical Centre (SCMC) of Ouagadougou were enrolled for a hepatitis C virus (HCV) and HIV co-infection study. Fifty-eight (10.6%) were HIV positive and 18 (3.3%) were anti-HCV positive. Only seven pregnant women (i.e., 1.3%) had a documented HIV and HCV co-infection. HCV-RNA was found in 5 out of 18 (27.8%) patients, who had anti-HCV antibodies. The genotype analysis of these five patients showed that two were of 1b whereas three were of 2a genotype. Mother-to-infant transmission of the same HCV genotype (2a) was documented in only one case. High 1b prevalence has been reported in other parts of Africa, while 2a is the prevalent genotype (60%) in Burkina Faso. This genotype has a higher response rate to treatment. Serum transaminases were normal, also in presence of HCV-RNA. The higher than expected rate of co-infection in Burkina Faso seems to demonstrate a correlation between these two infections, which could influence the evolution of HIV and HCV diseases.

Adolescent↗

PubMed2003

Structural and functional genomics and evolutionary relationships in the cluster of genes encoding murine 2',5'-oligoadenylate synthetases.

2',5'-Oligoadenylate synthetases (2',5'-OASs) are interferon-inducible enzymes. Some of these proteins play an important role in cellular physiology, in particular, in the innate defense mechanisms against RNA virus infections. In the present publication we report the complete genomic structure of the cluster of genes encoding mouse 2',5'-OAS, with all its transcription units, their predicted functions, and their evolutionary relationships. We found that mouse Oas2/Oas3 genes have a genomic structure similar to that of human OAS2/OAS3, while the mouse equivalent of human OAS1 is composed of eight (Oas1a to Oas1h) tandemly arranged transcription units. For all these eight genes a specific inducible promoter controls transcription. The possible functions of this family of proteins are discussed.

2',5'-Oligoadenylate Synthetase↗

PubMed1997

Sequence variation and phylogenetic analysis of the 5' terminus of hepatitis G virus.

We determined the nucleotide and deduced amino acid sequence of the 5' terminus of the hepatitis G virus (HGV) genome from isolates of varied geographical origins. Our analysis showed that the putative 5' non-coding region (NCR) contains several blocks of highly conserved sequences that may be useful for the development of a reverse transcriptase-polymerase chain reaction (RT-PCR) assay for detection of HGV RNA. Overall, the degree of conservation within the 669-nucleotide (nt) 5'terminal sequence was found to range from 99.5% to 86% sequence identity. We also showed that the HGV NCR from some isolates contained conserved insertions or deletions that altered the translational reading frames at the 5'-end of the genome, resulting in different sizes of predicted polyproteins encoded by genomes of individual isolates. Specifically, the insertions/deletions affected the size of the peptide preceding the putative first envelope (E1) protein. Phylogenetic analysis of the nucleotide sequences suggested that the isolates examined can be classified into distinct groups that may be useful for studying the molecular evolution of HGV and possible relationships between isolate sequence characteristics and infection patterns.

Adenovirus E1 Proteins↗

PubMed1998

[Guidelines for implementing antiretroviral therapy].

The rapid evolution of new information has introduced extraordinary complexity into the treatment of HIV-infected persons. Therefore it is recommended that care should be supervised by an expert. With regard to specific recommendations, treatment should be offered to all patients with the acute HIV syndrome and all patients with symptoms ascribed to HIV infection. The strength of the recommendation to treat asymptomatic patients should be based on the patient's willingness to accept therapy, the probability of adherence with the prescribed regimen, and the prognosis in term of time to an AIDS-defining disease as predicted by plasma HIV RNA levels and CD4+ T-cell counts. Once the decision has been made to initiate antiretroviral therapy, the goal is maximum viral suppression for as long as possible. Results of therapy are evaluated primarily with plasma HIV RNA levels: these are expected to show a one-log (10-fold) decrease at 8 weeks and no detectable virus at 4 to 6 months after initiation of treatment. Failure of therapy may be ascribed to nonadherence, inadequate potency of drugs or suboptimal levels of antiretroviral agents, resistance, and other factors that are poorly understood. Patient education and involvement in therapeutic decisions is important for all medical conditions but is considered especially critical for HIV-infection and its treatment.

Acquired Immunodeficiency Syndrome↗

PubMed1991

Generation of virus genetic lineages during an outbreak of poliomyelitis.

Wild poliovirus type 3 isolates collected during the Finnish outbreak (1984 to 1985) in different geographical locations were compared by partial RNA sequencing. The entire 5' non-coding end and a discontinuous part of the capsid coding region were sequenced from 15 isolates. Combining the present sequence data with previously published data and analysing these by the maximum parsimony method showed that the epidemic strains had diverged in cocirculating lineages. Genetic comparison of strains isolated from a single person often revealed a branched structure in the phylogenetic tree indicating high potential for diversification. The extent of variation generated under immunological pressure during an infection lasting for weeks in one person was high as compared with the observed geographical variation.

Antigens, Viral↗

PubMed2006

Duration of peginterferon therapy in acute hepatitis C: a randomized trial.

Spontaneous resolution of acute hepatitis C virus infection cannot be predicted, and chronic evolution of the disease occurs in a majority of cases. To assess the efficacy and safety of peginterferon alpha-2b administered for 8, 12, or 24 weeks in patients with acute hepatitis C virus infection a total of 161 patients were identified with acute hepatitis C virus infection. Of these, 30 patients refused treatment but were retained in the study as a nonrandomized comparison group. Of the 131 patients who consented to treatment, 29 patients spontaneously resolved, leaving 102 patients randomly assigned to peginterferon alpha-2b (1.5 microg/kg) for 8 weeks (group A; n=34), 12 weeks (group B; n=34), and 24 weeks (group C; n=34). The primary end point was sustained virologic response. An intent-to-treat analysis was used for efficacy and safety end points. Sustained virologic response was achieved in 23/34 (67.6%), 28/34 (82.4%), and 31/34 (91.2%) of patients in groups A, B, and C, respectively; all had undetectable hepatitis C virus RNA 48 weeks after the end of therapy. Treatment for 8 or 12 weeks was effective in genotypes 2, 3, and 4, whereas genotype 1 required 24 weeks of therapy. The 8- and 12-week regimens were associated with fewer adverse events compared with the 24-week regimen. In conclusion, peginterferon alpha-2b effectively induces high sustained virologic response rates in patients with acute hepatitis C virus infection, thus preventing development of chronic hepatitis C. Duration of treatment should be further optimized based on genotype and rapid virologic response at week 4.

Acute Disease↗

PubMed1983

Characterization of the SS-B (La) antigen in adenovirus-infected and uninfected HeLa cells.

The molecular composition and subcellular localization of the antigens recognized by anti-SS-B (La or Ha) antibodies was investigated. Ten anti-SS-B sera were selected by indirect immunofluorescence and by their immunological identity in counter-immunoelectrophoresis (CIE) with an anti-SS-B reference serum. All sera precipitated virus-associated (VA) RNA from cellular extracts of adenovirus-infected HeLa cells. Earlier results had shown that in adenovirus-infected HeLa cells a cellular 50 000 mol. wt. protein was tightly associated with VA RNA in situ. Our present results indicate that this 50 000 protein is the only SS-B antigen present in adenovirus-infected as well as in uninfected cells. A major part (greater than 80%) of the SS-B antigen is present in a readily extractable, soluble form. The rest is found in an insoluble form tightly associated with an internal nuclear structure that is mostly referred to as the nuclear matrix. Both forms are very susceptible to proteolytic degradation resulting in at least two distinct breakdown products of mol. wts. 40 000 and 25 000. The cellular 50 000 polypeptide is present in extracts of various types of cells and tissues, indicating that this antigen is very well conserved during evolution. The association of the 50 000 mol. wt. antigen with host- as well as viral-coded RNA polymerase III products also suggests an important function for this protein in the metabolism of these small RNAs.

Adenoviruses, Human↗

PubMed2001

Substrate sequence selection by retroviral integrase.

Integration of retrovirus DNA is a specific process catalyzed by the integrase protein acting to join the viral substrate DNA (att) sequences of about 10 bases at the ends of the long terminal repeat (LTR) to various sites in the host target cell DNA. Although the interaction is sequence specific, the att sequences of different retroviruses are largely unrelated to one another and usually differ between the two ends of the viral DNA. To define substrate sequence specificity, we designed an "in vitro evolution" scheme to select an optimal substrate sequence by competitive integration in vitro from a large pool of partially randomized substrates. Integrated substrates are enriched by PCR amplification and then regenerated and subjected to subsequent cycles of selection and enrichment. Using this approach, we obtained the optimal substrate sequence of 5'-ACGACAACA-3' for avian sarcoma-leukosis virus (ASLV) and 5'-AACA(A/C)AGCA-3' for human immunodeficiency virus type 1, which differed from those found at both ends of the viral DNA. Clonal analysis of the integration products showed that ASLV integrase can use a wide variety of substrate sequences in vitro, although the consensus sequence was identical to the selected sequence. By a competition assay, the selected nucleotide at position 4 improved the in vitro integration efficiency over that of the wild-type sequence. Viral mutants bearing the optimal sequence replicated at wild-type levels, with the exception of some mutations disrupting the U5 RNA secondary structure important for reverse transcription, which were significantly impaired. Thus, maximizing the efficiency of integration may not be of major importance for efficient retrovirus replication.

Alpharetrovirus↗

PubMed1999

Little evidence for synergism among deleterious mutations in a nonsegmented RNA virus.

Several models have been proposed to account for the segmentation of RNA viruses. One of the best known models suggests that segmentation, and mixing of segments during coinfections, is a way to eliminate deleterious mutations from the genome. However, for validity, this model requires that deleterious mutations interact in a synergistic way. That is, two mutations together should have a more deleterious effect than the result of adding their individual effects. Here I present evidence that deleterious mutations in foot-and-mouth disease virus produce a decline in fitness but that the relationship between the number of mutations fixed and the magnitude of fitness decline is compatible mainly with a nonsynergistic model. However, the statistical uncertainties associated with the data still give some room for the existence of very weak synergistic epistasis.

Aphthovirus↗

PubMed2004

[Successful treatment of chronic hepatitis C in hemophiliacs based on historical development of therapeutic protocols].

Chronic infection with hepatitis C virus is very frequent among hemophilic patients in all developed counties, including the Czech Republic. Because of a possibility of developing serious terminal stages of infection, liver cirrhosis and hepatocellular carcinoma, the tendency in treatment of patients with chronic hepatitis C is to start it as soon as possible and thus reduce the probability of developing these advanced stages of disease which are difficult to treat. Treatment of hemophilic patients with chronic hepatitis C started in the Department of Infectious Diseases, University Hospital Brno Bohunice, in 1996. Used treatment schemes have reflected historical evolution of treatments used to treat chronic hepatitis C. Initially, alpha-interferon (IFN) was administered in monotheraphy (6 patients), later, since 1999, a combination of alpha-IFN and ribavirin was administered (13 patients), and since 2001 a combination of pegylated interferon (PEG-IFN) and ribavirin (3 patients) was administered. In all the patients the individual treatments took 12 month. Sustained negativization of HCV RNA in serum has not been achieved in any patient treated only with alpha-IFN. In patients who were administered the combination of alpha-IFN and ribavirin this effect appeared in 4 from 7 cases without history of treatment with alpha-IFN (57%), one from 2 relapses and one from 3 non-responders. The combination PEG-IFN and ribavirin was effective in the only one patient who relapsed after alpha-IFN and ribavirin and in one from the two non-responders to this combination. The tolerance and safety of treatment was good in haemophilia patients and could be fully compared to those in other patients with chronic hepatitis C.

Antiviral Agents↗

PubMed2004

A chimeric bovine enteric calicivirus: evidence for genomic recombination in genogroup III of the Norovirus genus of the Caliciviridae.

The Norovirus genus of the Caliciviridae encompasses viruses that cause outbreaks of gastroenteritis in human and viruses that have been associated with diarrhea in cattle. The two bovine noroviruses, Bo/Newbury2/76/UK and Bo/Jena/80/DE, represent two distinct genetic clusters in the newly described genogroup III. In the present study, Jena-like polymerase sequences were identified for the first time in the UK, but one of these, Bo/Thirsk10/00/UK, was a chimeric virus. Bo/Thirsk10/00/UK had a Jena-like polymerase gene but Newbury2-like capsid and ORF3 genes by comparison of their genome organization, nucleotide, and amino acid identities and phylogenetic analyses. The present study is one of few studies to clearly demonstrate the existence of chimeric genomes in the Norovirus genus and the first, to our knowledge, to identify a chimeric genome in genogroup III. It provides additional support that genomic recombination is part of the natural evolution of noroviruses and is relevant to the diagnosis and immunological control of norovirus diarrhea outbreaks.

Amino Acid Sequence↗

PubMed2003

Molecular characterization of a novel astrovirus associated with disease in mink.

Pre-weaning diarrhoea is a well-known problem in mink farming in Europe, causing morbidity that varies between farms, regions and season. Different causalities for the disease have been proposed, but only most recently has a novel astrovirus been identified as an important risk factor. In this report, the molecular characterization, origin and evolution of this novel astrovirus of mink are discussed. The polyadenylated, positive-stranded RNA genome was sequenced and found to contain 6610 nt, organized into three ORFs and two short UTRs. A ribosomal frameshift sequence links the 5' two ORFs, containing sequence motifs for a serine protease (ORF1a) and an RNA-dependent RNA polymerase (ORF1b). The structural proteins are encoded by ORF2 and, presumably, are expressed as a polyprotein precursor to be cleaved into the mature capsid proteins. These results indicate that mink astrovirus (MiAstV) has all of the features typical of members of the Astroviridae. Phylogenetic analyses revealed that MiAstV is distantly related to established astroviruses, showing less than 67 % similarity at the nucleotide level with its closest relative, ovine astrovirus, and even lower identities at the predicted amino acid level. Nevertheless, sequence analysis of MiAstV isolates from geographically distinct Swedish and Danish farms showed much less diversity. This suggests either the spread in the mink population of a virus that has evolved a long time ago or the recent introduction of an ancient virus into a new host species.

Amino Acid Sequence↗

PubMedDate not supplied

The Pur protein family: clues to function from recent studies on cancer and AIDS.

The Pur protein family consists of four known members in humans, the prototype gene for which is strongly conserved throughout evolution. Several investigations have now implicated Pur alpha in pathways of inhibition of oncogenic transformation. Clues to the potential importance of Pur family members in cancer are derived from observations of genetic alterations of both Pur alpha and Pur beta in myelodysplastic syndrome progressing to acute myelogenous leukemia. A role for newly-discovered Pur gamma in neoplasia is also beginning to emerge as studies have indicated that cellular levels of two Pur gamma isoforms are elevated in certain tumors. A variety of studies have now implicated Pur alpha in development of blood cells and cells of the central nervous system. Clues to the functions of Pur alpha, a key family member, have recently been derived from studies of the interactions of HIV-1 and JC virus (JCV) in AIDS. JCV causes an opportunistic infection in the brains of certain HIV-1-infected individuals. Pur alpha can influence this viral interaction through functional associations with the Tat protein and TAR RNA of HIV-1, and with large T-antigen and DNA regulatory regions of JCV. Evidence is now strong that Pur alpha interacts with both DNA and RNA and that an important aspect of its function is to recruit regulatory proteins to specific nucleic acid sequences in processes as diverse as DNA replication, gene transcription, RNA transport in the cytoplasm and compartmentalized mRNA translation.

Acquired Immunodeficiency Syndrome↗

PubMed1983

Structural comparisons of some small spherical plant viruses.

The structures of tomato bushy stunt virus, southern bean mosaic virus and satellite tobacco necrosis virus have been compared quantitatively. The organization of the shell domains of tomato bushy stunt virus and southern bean mosaic virus within the icosahedral envelope is identical. The wedge-shaped end of the subunit is closer to the fivefold or quasi-sixfold axes in all three viruses but the packing about the three- and twofold axes is quite different in satellite tobacco necrosis virus as compared to tomato bushy stunt virus or southern bean mosaic virus. The polypeptide folds of these viruses have greatest similarity in the beta-sheet region of the eight-stranded anti-parallel beta-barrel. The largest differences occur in the connecting segments. There is no clear indication of homologous amino acid sequences between southern bean mosaic virus and satellite tobacco necrosis virus. However, there is some conservation of the following functional groups. (1) Threonines and serines at the hexagonal-pentagonal wedge-shaped end of the subunit. (2) Lysines and arginines at the protein-RNA interface. (3) Hydrophobic residues in the cavity within the anti-parallel beta-barrel. (4) An aspartic acid near a site which binds Ca in tomato bushy stunt virus. (5) Ionic interactions in the contacts between fivefold-related subunits. These virus coat protein structures are not as similar to each other as the alpha and beta chains of hemoglobin but have greater likeness to one another than the NAD-binding domains of dehydrogenases or lysozymes from hen egg-white and T4 phage. The surface domains of tomato bushy stunt virus and southern bean mosaic virus are more like each other than like satellite tobacco necrosis virus. A divergent evolutionary tree is proposed on the basis of these observations.

Amino Acids↗