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PubMed1988

Sequence and secondary structure analysis of the 5'-terminal region of flavivirus genome RNA.

The 5'-terminal noncoding region sequences were determined for the genome RNAs of seven strains of St. Louis encephalitis virus (SLEV) and one strain of West Nile virus (WNV) using a single synthetic cDNA primer complementary to the 5'-terminus of the coding region of a strain of WNV RNA. The 5'-terminal sequences obtained for the SLEV and WNV RNAs were compared with published sequences for yellow fever virus (YFV), Murray Valley encephalitis virus (MVEV), and dengue virus. While only short regions within the 5'-noncoding sequence were conserved among different flavivirus RNAs, significant homology was observed in this region among members of the same flavivirus subgroup and almost complete conservation was observed between different strains of the same virus. For example, seven strains of SLE, isolated from different geographic locations over a 17-year period and differing in their neurovirulence phenotype, contained only two to four nucleotide changes in the 5'-noncoding region. Interestingly, each of three low-virulence strains shared the same unique base substitution at position 16. Secondary structures predicted to be formed by the 5'-termini of each of the different flavivirus genome RNAs were of similar size and shape, in each case consisting of a stem with a small top loop and a larger side loop. The prediction of a common structure among a number of different flaviviruses, despite the lack of extensive sequence homology, suggests that this secondary structure is functionally important. An additional stem and loop structure is predicted to be formed in the region spanning the translation initiation codon. This structure showed significantly less conservation of size and shape than the 5'-terminal secondary structure.

Base Sequence↗
PubMed1995

Mutations within noncoding terminal sequences of model RNAs of Sendai virus: influence on reporter gene expression.

A reverse-genetics system employing the chloramphenicol acetyltransferase (CAT) reporter gene has been established previously for Sendai virus. We utilized PCR-directed mutagenesis to introduce nucleotide additions, deletions, and/or substitutions within terminal Sendai virus RNA sequences. The influence of these mutations on replication-transcription of these model Sendai-CAT RNAs was analyzed by assaying CAT activity. Results from these experiments indicate that (i) Sendai-CAT RNAs expressing wild-type levels of CAT activity conform to the Sendai virus rule of six, (ii) apparent exceptions to the rule of six exist in that the 5' terminus of the Sendai-CAT RNA is more tolerant than the 3' terminus of nucleotide additions or deletions, and (iii) the 3' leader region of Sendai-CAT RNA appears to be sensitive not only to mutagenesis (single-nucleotide addition or deletion) but also to changes in its total nucleotide length.

Base Sequence↗
PubMed1997

Insertion of 2 kb of bacteriophage DNA between an immunoglobulin promoter and leader exon stops somatic hypermutation in a kappa transgene.

Somatic hypermutation in rearranged immunoglobulin variable genes occurs in a 2kb region of DNA that is delimited on the 5' side by the promoter and on the 3' side by intron DNA. To identify sequence features that activate the mutation mechanism, we increased the distance between the promoter and the leader region to test whether the spacing of these elements was important. The promoter was separated from the leader sequence by inserting a 2 kb fragment of noncoding bacteriophage lambda DNA between the TATA box and ATG initiator codon in a kappa transgene. Mice from three founder lines were immunized, RNA and DNA were isolated from spleen and Peyer's patch B cells, and transcription of the transgene was confirmed. The frequency of mutation in endogenous heavy chain genes was high, indicating that some B cells underwent hypermutation. However, no hypermutation was found in the transgenic bacteriophage or variable region sequences. Hypermutation did occur in another kappa transgene that had a deletion of the VJ coding sequence, showing that the basic construct is functional and that the VJ exon is not necessary for the mutation mechanism. It is likely that the bacteriophage sequence is a potential substrate for mutation because other heterologous sequences have been shown to undergo mutation if placed downstream of the leader exon. The results suggest that the promoter should be contiguous with the leader exon for the mutation mechanism to function.

Animals↗
PubMed1997

GB virus C/hepatitis G virus infection among Korean patients with liver diseases and general population.

GB virus C and hepatitis G virus (GBV-C/HGV) have been identified from the patients with acute or chronic liver diseases as possible agents of non-B, non-C hepatitis by two different groups, independently. To investigate whether GBV-C/HGV plays a role among Korean patients with liver diseases, GBV-C/HGV RNA were evaluated in 337 sera by the reverse transcription polymerase chain reaction (RT-PCR) using specific primers derived from 5'-noncoding region of GBV-C/HGV genome. GBV-C/HGV RNA was identified in 11/337 (3.3%). They consisted of 1/160 (0.6%) and 10/177 (3.3%) among the general population and patients with liver diseases, respectively (P < 0.01). Nucleotide sequences of all PCR amplicons were determined by the dideoxy chain termination method and analyzed by molecular evolutionary methods. The phylogenetic tree showed all sequences could be divided into three genotypes. These results indicate that: (1) GBV-C/HGV already exist in Korea; (2) GBV-C/HGV may play some role as an etiologic factor among the Korean patients with liver diseases; (3) GBV-C/HGV infection is rare among Korean general population; and (4) there are at least three different types of GBV-C/HGV in Korea.

Adolescent↗
PubMed1989

Activation of the c-H-ras proto-oncogene by retrovirus insertion and chromosomal rearrangement in a Moloney leukemia virus-induced T-cell leukemia.

A rearrangement of the c-H-ras locus was detected in a T-cell line (DA-2) established from a Moloney leukemia virus-induced tumor. This rearrangement was associated with the high-level expression of H-ras RNA and the H-ras gene product, p21. DNA from DA-2 cells transformed fibroblasts in DNA transfection experiments, and the transformed fibroblasts contained the rearranged H-ras locus. The rearrangement involved one allele and was present in tissue from the primary tumor from which the cell line was isolated. Cloning and sequencing of the rearranged allele and comparison with the normal allele demonstrated that the rearrangement was complex and probably resulted from the integration of a retrovirus in the H-ras locus between a 5' noncoding exon and the first coding exon and a subsequent homologous recombination between this provirus and another newly acquired provirus also located on chromosome 7. These events resulted in the translocation of the coding exons of the H-ras locus away from the 5' noncoding exon region to a new genomic site on chromosome 7. Sequencing of the coding regions of the gene failed to detect mutations in the 12th, 13th, 59th, or 61st codons. The possible reasons for the complexity of the rearrangement and the significance of the activation of the H-ras locus to T-cell transformation are discussed.

Alleles↗
PubMed1992

Correlation of RNA secondary structure and attenuation of Sabin vaccine strains of poliovirus in tissue culture.

Part of the 5' noncoding regions of all three Sabin vaccine strains of poliovirus contains determinants of attenuation that are shown here to influence the ability of these strains to grow at elevated temperatures in BGM cells. The predicted RNA secondary structure of this region (nt 464-542 in P3/Sabin) suggests that both phenotypes are due to perturbation of base-paired stems. Ts phenotypes of site-directed mutants with defined changes in this region correlated well with predicted secondary structure stabilities. Reversal of base-pair orientation had little effect whereas stem disruption led to marked increases in temperature sensitivity. Phenotypic revertants of such viruses displayed mutations on either side of the stem. Mutations destabilizing stems led to intermediate phenotypes. These results provided evidence for the biological significance of the predicted RNA secondary structure.

Base Sequence↗
PubMed1994

Hepatitis C virus infection in spouses of patients with type C chronic liver disease.

OBJECTIVE: Survey for markers of hepatitis C virus (HCV) infection in spouses of patients with HCV-related chronic liver disease. DESIGN: Cross-sectional clinical, serologic, and molecular biological study of spouses of patients with HCV viremia and chronic liver disease. SETTING: University and city hospitals. PARTICIPANTS: Spouses (52 men and 102 women; mean age, 56 +/- 11 years) of 154 patients with HCV viremia (102 men and 52 women; mean age, 58 +/- 10 years), of whom 66 had chronic hepatitis, 49 had liver cirrhosis, and 39 had primary hepatocellular carcinoma. METHODS: Tests for HCV-associated antibodies were done using a second-generation enzyme immunoassay and immunoassays with synthetic oligopeptides deduced from the HCV core gene. Hepatitis C virus RNA was detected by polymerase chain reaction with primers deduced from the 5'-noncoding region and HCV genotypes by reaction with type-specific primers deduced from the HCV core gene. RESULTS: Hepatitis C virus-associated antibodies were detected in 42 (27%) spouses, of whom 25 were also positive for HCV RNA. Of 112 (73%) spouses without detectable antibodies, 2 had chronic liver disease. The development of markers of HCV infection in spouses increased with the duration of marriage, ranging from 1 to 60 years (30 +/- 11 years). CONCLUSIONS: Spouses of patients with HCV viremia and chronic liver disease have an increased risk for acquiring HCV, which is proportional to the duration of marriage. They should be followed routinely for markers of HCV infection and liver disease.

Aged↗
PubMed1981

Preferential codon usage in genes.

We present a method which permits comparison of the preferential use of degenerate codons within any gene. The method makes use of the triplet frequencies in the noncoding frames to assess whether a preference is specific to the reading frame. Preference is given a statistical meaning by use of the analysis of variance coupled to Duncan's multiple range test. Preferential use of degenerate codons is gene-specific and independent of gene size. The data suggest that any correlation between codon frequency distribution and tRNA levels is unreliable. In those animal genes examined, codons ending in C or G are preferred; in animal viruses tested, codons ending in U or A are preferred. Similarly, the bacterial genes and the genes of single-stranded DNA phages that we analyzed differed from each other as well as from eukaryotic genes in the third base of the codon.

Animals↗
PubMed1998

Molecular biological characterization of enterovirus variant isolated from patients with aseptic meningitis.

In Korea, there was a big outbreak of aseptic meningitis in 1993. Six clinical isolates of enterovirus were obtained from patients with aseptic meningitis and were identified as echovirus type 9 by serotyping with a pool of neutralizing antisera. For molecular characterization of the isolates, the nucleotide sequences of 5'-noncoding region (NCR), VP4, VP2, VP1, 2A and 2C regions of the isolates were compared with the corresponding regions of echovirus type 9 Hill and Barty strains. Unlike Hill strain, Barty strain contained a C-terminal extension to the capsid protein VP1 with an RGD (argnine-glycine-aspartic acid) motif. To determine whether similar structural features were present in our isolates, their nucleotide sequences including the VP1 region were analyzed. All isolates exhibited the VP1 extension with the RGD motif. We concluded the Korean isolates in the year of 1993 as the echovirus type 9 Barty strain although the isolates showed 15-20% nucleotide sequence differences in the several genomic regions.

5' Untranslated Regions↗
PubMed1991

Effect of prior immunity on the shedding of virulent revertant virus in feces after oral immunization with live attenuated poliovirus vaccines.

Groups of infants were immunized with one or two doses of orally inoculated live attenuated Sabin poliovirus vaccine (OPV group) or with one or two doses of enhanced-potency inactivated poliovirus vaccine (EIPV) administered parenterally followed by one or two doses of OPV (EIPV-OPV group). The fecal specimens from both groups were tested for poliovirus shedding 1-2 months after OPV. The virus isolates were examined for nucleic acid sequences in the 5' noncoding regions (bases 480, 481, and 472 for serotypes 1, 2, and 3, respectively) to determine whether the viruses shed represented nonattenuated revertants, attenuated parent vaccine strains (nonrevertants), or both. In the OPV group, 4 of the 6 virus isolates recovered 30-60 days after the first immunization dose and 1 of the 3 isolates obtained after the second dose were found to be nonrevertants (parent vaccine strain). In contrast, 11 of the 12 isolates in the EIPV-OPV group were of the nonvaccine revertant virus types. The frequency for reversion appeared to differ for different poliovirus serotypes. However, all revertant type 3 isolates were recovered from subjects previously immunized with EIPV.

Antibodies, Viral↗
PubMed1998

Usefulness of nested PCR and sequence analysis in a nosocomial outbreak of neonatal enterovirus infection.

BACKGROUND: Non-polio enterovirus infections are recognized in children during summer-fall seasons and they sometimes cause large outbreaks. We experienced a nosocomial infection in the neonatal nursery and echovirus type 7 was isolated from samples of four patients. OBJECTIVES: We diagnosed the horizontal infection of four neonates by reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) and the nucleotide sequence. STUDY DESIGN: Total RNA was extracted from clinical isolates, serum samples and cerebrospinal fluid (CSF). We amplified enterovirus genome in the 5'-noncoding region by nested PCR and determined the nucleotide sequences. RESULTS: Enterovirus genome was detected in all isolates, in the acute-phase sera in all four patients and in the CSF in one patient by the first PCR. By using nested PCR, the genome was detected from convalescent-phase sera in two patients. All enterovirus genome obtained from the nursery outbreak showed the same sequences with 100% homology. CONCLUSION: We demonstrated the clinical advantages of RT-nested PCR from serum samples and the analysis of nucleotide sequencing gave the supportive evidence of identification of transmission pathway.

5' Untranslated Regions↗
PubMed2003

Hepatitis C virus genotypes in Córdoba, Argentina. Unexpected high prevalence of genotype 2.

To determine hepatitis C virus (HCV) genotypes circulating in the central region of Argentina, 96 consecutive anti-HCV positive subjects were studied. The presence of HCV RNA was detected in 60 samples by RT-nested PCR of the 5' noncoding region (5' NCR). Genotyping was performed by restriction fragment length polymorphism analysis of 5' NCR region combined with PCR using type-specific primers of the core region. The groups of individuals in this study included hemophilia and hemodialysis patients, injecting drug users, screened blood donors, and patients with acute or chronic liver disease, all from Córdoba, Argentina. Overall, genotype 2 was the most prevalent (55.0%), followed by genotypes 1 (38.3%), and 3 (5.0%). Within genotype 1, subtype 1b was the most prevalent. An unexpected high prevalence of genotype 2 (61.9%) was found among patients with acute or chronic HCV infection (without known risk factors). These figures differ from other cohorts from East-Argentina where genotype 1 has been found as the most prevalent. This indicates that regional differences of genotype distribution might exist between Central and East Argentina.

Adolescent↗
PubMed1989

Structure of the human lck gene: differences in genomic organisation within src-related genes affect only N-terminal exons.

Although cDNA sequences coding for several Rous sarcoma virus Src-related protein tyrosine kinases (PTKs) have been reported for several years, knowledge of the structure and organisation of genes of the src family is still limited. In this work, a detailed structure and organisation of the human lck gene is reported. A 17-kb genomic clone encoding human p56 Lck, a lymphocyte-specific PTK of the Src-related subfamily, has been isolated. The human lck gene is organized in 13 exons, one more than in the human cellular (c)-src gene. The twelve coding exons are located in this clone, whereas the putative 5'-noncoding exon is probably located very far upstream from the second exon. Splicing sites for exons 4 to 12, which encode both conserved phospholipase-C-like and catalytic domains of the Src-like PTKs, arise exactly at the same position for the human lck, human c-src and c-fgr genes. The only differences concern the splice sites of exons 1' and 2, which encode the unique N-terminal domain of human Lck. These results give further evidence that the different PTKs of the Src-like family have probably evolved through the mechanism of exon shuffling.

Amino Acid Sequence↗
PubMed1999

High-throughput real-time reverse transcription-PCR quantitation of hepatitis C virus RNA.

We describe a rapid and reproducible method for assessment of the hepatitis C virus (HCV) load in serum samples. The method combines Taqman technology (Roche) and the ABI Prism 7700 (Perkin Elmer) real-time sequence detection system. We have optimized a single-tube reverse transcription-PCR (RT-PCR) that contains a dual-labeled fluorogenic probe to quantify the 5' noncoding region (5' NCR) of HCV. The probe contains a fluorescent reporter at the 5' end and a fluorescent quencher at the 3' end. The use of such a probe combined with the 5'-3' nuclease activity of Taq polymerase allows direct quantitation of the PCR product by the detection of a fluorescent reporter released in the course of the exponential phase of the PCR. For accurate quantitation of the number of copies of HCV in samples containing unknown quantities, we have used serial dilutions of a synthetic 5' NCR RNA standard of HCV that was previously quantified with an isotopic tracer. The method has a 5-log dynamic range (10(3) to 10(7)). The coefficient of regression of the standard curve was, on average, 0.98. The intra-assay and the interassay coefficients of variation of the threshold cycle were 1% and 6.2%, respectively. Seventy-nine RNA samples from the sera of infected patients were quantified by this method. Comparison of the results with those obtained by other quantitation methods (the Quantiplex 2.0 branched-DNA assay and the Superquant assay from the National Genetics Institute) revealed a significant correlation with all of the results. The mean values were also statistically comparable. In conclusion, the high sensitivity, simplicity, and reproducibility of the real-time HCV RNA quantitation which allows the screening of large numbers of samples, combined with its wide dynamic range, make this method especially suitable for monitoring of the viral load during therapy and tailoring of treatment schedules.

Adult↗
PubMed1993

Hepatitis C virus plus- and minus- strand RNA in hepatocellular carcinoma and adjoining nontumorous liver.

The presence of hepatitis C virus (HCV) RNA in serum and liver tissue was examined in seven patients with hepatocellular carcinoma (HCC), using the reverse transcriptase-polymerase chain reaction method with primers for the 5'-noncoding region. Plus-strand HCV-RNA was detected in the serum and liver tissue (both cancerous and noncancerous tissue) of all five patients who were positive for anti-HCV antibodies (C100-3 and P22) and was not detected in both of two patients who were negative for anti-HCV antibodies. Minus-strand HCV-RNA was only detected in the liver tissue (cancerous and noncancerous portion) of the five anti-HCV antibody-positive patients. The relative liver tissue content of minus-strand HCV-RNA ranged from 1 to 100 time less than that of plus strand HCV-RNA in cancerous and noncancerous tissue in each patient, respectively. There was no similar tendency in the HCV-RNA content between the cancerous and noncancerous portions of the liver in each patient. These results suggest that HCV exists and replicates in HCC tissue and may have some role in the development of HCC.

Alcoholism↗
PubMed2002

Quantification and duration of viraemia during hepatitis A infection as determined by real-time RT-PCR.

Human transmission studies and molecular techniques have provided evidence that transient viraemia occurs during infection with hepatitis A virus (HAV). However, the duration of its presence and levels during the phases of clinical disease and convalescence has not yet been well studied in human patients. Real-time RT-PCR techniques are increasingly used to quantify RNA viruses for diagnosis and/or research purposes. We have optimized a one-step RT-PCR that contains a dual-labelled fluorogenic probe to quantify the 5' noncoding region (5' NCR) of HAV. This method has a dynamic range (5-5 x 10(6) copies). The coefficient of regression of the standard curve was, on average 0.978. Intra-assay CVs% varied from 6.1% to 0.98%, and interassay CVs% from 6.46% to 2.1%. In the currently reported study 41 HAV IgM positive serum samples and 200 serum samples from healthy blood donors were tested by the quantitative RT-PCR method. The mean values on the first day of diagnosis found was 6.38 x 10(5) copies/mL. In a longitudinal study, viraemia persisted for an average of 60 days after clinical onset. These results show that viraemia in HAV infection lasts for many weeks.

Adolescent↗
PubMed2002

Role of picornaviruses in flu-like illnesses of adults enrolled in an oseltamivir treatment study who had no evidence of influenza virus infection.

The primary objective of this study was to determine the role of picornavirus in flu-like episodes (temperature of > or =38.0 degrees C plus one respiratory and one constitutional symptom) among otherwise healthy adults enrolled in a placebo-controlled, double-blind, randomized oseltamivir treatment study. Combined nasal and pharyngeal swabs were collected at baseline for influenza cultures and picornavirus reverse transcription (RT)-PCR. In addition, acute- and convalescent-serum samples were obtained for serological studies of common respiratory pathogens. From a total of 719 subjects enrolled in the clinical trial within 36 h of the onset of symptoms, 475 (66%) had evidence of recent influenza A or B virus infections by means of culture and/or serological testing. Of the 244 remaining patients, 36 (15%) presented a seroconversion for at least one of the common respiratory viruses or atypical pathogens. An RT-PCR assay for the picornavirus 5" noncoding region (NCR) was positive in a subset of 15 (19%) of 78 patients with flu-like illnesses of undetermined etiology. Sequence analysis of the picornavirus 5" NCR amplicons revealed that 14 (93%) of them had greater homology to rhinoviruses, whereas 1 (7%) was related to enteroviruses. Interestingly, median total symptom scores and oral temperatures of picornavirus-positive patients (n = 15) and placebo-treated influenza virus-positive patients (n = 161) were similar over a 3-week period. We conclude that, among the influenza virus-negative preselected cases of this study, rhinoviruses were relatively frequent pathogens associated with important respiratory and systemic symptoms.

Acetamides↗
PubMed1998

Generation of infectious pancreatic necrosis virus from cloned cDNA.

We developed a reverse genetics system for infectious pancreatic necrosis virus (IPNV), a prototype virus of the Birnaviridae family, with the use of plus-stranded RNA transcripts derived from cloned cDNA. Full-length cDNA clones of the IPNV genome that contained the entire coding and noncoding regions of RNA segments A and B were constructed. Segment A encodes a 106-kDa precursor protein which is cleaved to yield mature VP2, nonstructural protease, and VP3 proteins, whereas segment B encodes the RNA-dependent RNA polymerase VP1. Plus-sense RNA transcripts of both segments were prepared by in vitro transcription of linearized plasmids with T7 RNA polymerase. Transfection of chinook salmon embryo (CHSE) cells with combined transcripts of segments A and B generated infectious IPNV particles 10 days posttransfection. Furthermore, a transfectant virus containing a genetically tagged sequence was generated to confirm the feasibility of this system. The presence and specificity of the recovered virus were ascertained by immunofluorescence staining of infected CHSE cells with rabbit anti-IPNV serum and by nucleotide sequence analysis. In addition, 3'-terminal sequence analysis of RNA from the recovered virus showed that extraneous nucleotides synthesized at the 3' end during in vitro transcription were precisely trimmed or excluded during replication, and hence these were not incorporated into the genome. An attempt was made to determine if RNA-dependent RNA polymerase of IPNV and infectious bursal disease virus (IBDV), another birnavirus, can support virus rescue in heterologous combinations. Thus, CHSE cells were transfected with transcripts derived from IPNV segment A and IBDV segment B and Vero cells were transfected with transcripts derived from IBDV segment A and IPNV segment B. In either case, no infectious IPNV or IBDV particles were generated even after a third passage in cell culture, suggesting that viral RNA-dependent RNA polymerase is species specific. However, the reverse genetics system for IPNV that we developed will greatly facilitate studies of viral replication and pathogenesis and the design of a new generation of live attenuated vaccines.

Animals↗