[Molecular evolutionary analysis of hepatitis C virus--phylogenetic tree and divergence time].
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Hepacivirus↗
Biomedical subjects
M Mizokami
Publications and source records attributed to M Mizokami.
Neutrophil chemotactic N-acetyl peptides from the calpain small subunit are also chemotactic for immunocytes.
N-terminal peptides from the calpain small subunit were shown to have dose-dependent chemotactic activity toward several types of leukemia cells: T cell, B cell, monocyte and granulocyte/monocyte line leukemia cells. In order to prove that chemotaxis is mediated via receptors, a fluorescein-labeled probe was prepared from one of the N-terminal peptides and its interaction with peripheral leukocytes was estimated by means of flow cytometry, resulting in staining not only of neutrophils but also of most of the monocytes and more than half of the T and B lymphocytes. The results indicate that calpain-derived N-terminal peptides may be involved in defense mechanisms, inducing chemotaxis of immunocytes as well as that of neutrophils.
Amino Acid Sequence↗
New genotype of hepatitis C virus in South Africa.
Partial nucleotide sequences in the core region of the hepatitis C viral genome were determined by reverse transcription followed by polymerase chain reaction, in a patient with chronic hepatitis from South Africa. These nucleotide sequences showed a low degree of homology with known types of HCV: the degree of homology between the nucleotide sequences of these clones with HC-J1, J4, J6, J7, Tr, and Eb-1 were 86.1-87.3%, 87.3-87.9%, 83.0-83.9%, 81.1-82.0%, 81.0-82.2%, and 82.8-83.4%, respectively, and that the deduced amino acid sequence homologies between these clones and HC-J1, J4, H6, J7, Tr, and Eb-1 were 90.7-91.6%, 89.7-91.6%, 91.6-93.5%, 90.7-91.6%, 81.5-82.4%, and 89.2-90.2%, respectively. The nucleotide sequence homologies of these clones with HC-J1, J4, J6, J7, Tr, and Eb-1 were very low, compared to those between the same genotype. Further comparison using molecular evolutionary methods suggested that this sequences should be classified in a new genotype.
Amino Acid Sequence↗
Nucleotide sequence of the core region of hepatitis C virus in Pakistan and Bangladesh and the geographic characterisation of hepatitis C virus in south Asia.
A large number of complete and partial hepatitis C virus (HCV) sequences have been reported and classified into several genotypes, although none have been reported from South Asia. We have determined and evaluated partial sequences in the core region of HCV obtained from patients with chronic hepatitis in Pakistan and Bangladesh. Nucleotide sequences from these viruses show significant homology with the Japanese HCV-TR isolate (91.7%-97.9%) and low homology with other Japanese, American, and UK isolates including HCV-1, HC-J4, HC-J6, HC-J8, and E-b1 (79.3%-86.2%). The homologies of their deduced amino acids sequence with HCV-1, HC-J4, HC-J6, HC-J8, E-b1, and HCV-TR were 84.3%-89.8%, 85.0-87.9%, 84.1%-86.9%, 84.3%-87.0%, 90.2%-93.1%, and 89.8%-93.5%, respectively. These results suggest that our clones might be classified into the same genotype as HCV-TR. Further analysis using molecular evolutionary methods strongly supported the classification of these sequences with the HCV-TR genotype. Moreover, we could not detect any isolates which were closely related to our clones or HCV-TR in countries outside the South Asian area. These data further support the association of HCV genotypes with distinct geographic regions.
Amino Acid Sequence↗
Serum hepatitis C virus RNA level as a predictor of subsequent response to interferon-alpha therapy in Japanese patients with chronic hepatitis C.
Serum hepatitis C virus (HCV) RNA level has been shown to be a good predictor of subsequent response to interferon-alpha (IFN) therapy in US patients in whom genotype 1a/1b are both predominant. To determine whether serum HCV RNA level is a predictor of subsequent response to IFN in Japanese patients or not, appropriately collected pre-IFN therapy serum samples from 35 Japanese patients with chronic HCV infection were studied. Serum HCV RNA level and HCV genotype were determined and correlated with the subsequent response to IFN. Response to IFN was defined by serum alanine transaminase level: complete and sustained response (n = 15), complete response followed by relapse (n = 10), and no response (n = 10). Patients with complete and sustained response had lower pre-IFN serum HCV RNA level (median: RT-PCR+, bDNA-) compared to the complete response to relapse group (median: 5.25 x 10(6) genome equivalent/ml [eq/ml], P < 0.001) and the no response group (median: 10.63 x 10(6) eq/ml, P < 0.001). Seven (46.7%) of the complete and sustained response patients had HCV genotype 2a and three patients had a mixture of genotypes 1b and 2a. In contrast, all 10 patients in the complete response to relapse group had genotype 1b whereas 8 of 10 patients in the non-response group had genotype 1b and 2 had genotype 2b. The patients with HCV genotype 2a had lower serum HCV RNA level than those with 1b (P = 0.002).(ABSTRACT TRUNCATED AT 250 WORDS)
Adult↗
Reduction of synonymous substitutions in the core protein gene of hepatitis C virus.
Molecular evolutionary analyses were carried out to elucidate the phylogenetic relationships, the evolutionary rate, and the divergence times of hepatitis C viruses. Using the nucleotide sequences of the viruses isolated from various locations in the world, we constructed phylogenetic trees. The trees showed that strains isolated from a single location were not necessarily clustered as a group. This suggests that the viruses may be transferred with blood on a worldwide scale. We estimated the evolutionary rates at synonymous and nonsynonymous sites for all genes in the viral genome. We then found that the rate (1.35 x 10(-3) per site per year) at synonymous sites for the C gene was much smaller than those for the other genes (e.g., 6.29 x 10(-3) per site per year for the E gene). This indicates that a special type of functional constraint on synonymous substitutions may exist in the C gene. Because we found an open reading frame (ORF) with the C gene region, the possibility exists that synonymous substitutions for the C gene are constrained by the overlapping ORF whose reading frame is different from that of the C gene. Applying the evolutionary rates to the trees, we also suggest that major groups of hepatitis C viruses diverged from their common ancestor several hundred years ago.
Biological Evolution↗
Analysis of the core and E1 envelope region sequences of a novel variant of hepatitis C virus obtained in Indonesia.
Hepatitis C virus (HCV) is currently classified into 6 major types, HCV-1 through -6, each of which can be further divided into a few subtypes, e.g., HCV-1a, -1b, -1c, etc., on the basis of sequence variation of the viral genome. The core and E1 envelope regions of HCV genome were amplified from sera of Indonesian patients using reverse transcription-polymerase chain reaction. Sequence analysis of both core and E1 regions followed by molecular evolutionary phylogenetic analysis identified a novel sequence variant of HCV-1 (Td-6). Antibodies in the serum from which Td-6 was isolated reacted only marginally to the core protein of HCV-J, a representative strain of HCV-1b, despite strong antibody response against a mixture of the core, NS3 and NS4 proteins of HCV-1a. The possible mechanism for the diminished reactivity of the antibodies in the serum to the core protein of HCV-J is discussed.
Amino Acid Sequence↗
Variations of hepatitis B virus precore/core gene sequence in acute and fulminant hepatitis B.
Variations of the hepatitis B virus (HBV) precore/core sequence has been shown to play a role in the development of active liver disease in chronic hepatitis B. Whether this is also an important viral factor in the pathogenesis of acute and fulminant hepatitis B is unknown. To determine the precore/core gene sequence in patients with acute and fulminant hepatitis B, 11 patients with fulminant hepatitis B and seven patients with acute hepatitis B were studied. The sequences of precore/core gene were determined by direct sequencing of the polymerase chain reaction amplicons generated from the HBV isolated from patients' serum. For the 11 patients with fulminant hepatitis B, the precore/core regions were successfully amplified in 10 patients. Eight patients exhibited precore stop codon mutations. In addition, nine of the 10 fulminant hepatitis B patients had frequent nucleotide substitutions with corresponding changes in the predicted amino acid sequences in the mid-core and the 5' terminus region of the core gene. In contrast, precore stop codon mutants were not detected, and variations of the HBV core gene were minimal in patients with acute hepatitis B. The association of HBV precore mutants and HBV core gene variations with fulminant hepatitis B and not acute hepatitis B suggested that these variations may be important in modulating the clinical course of HBV infection.
Acute Disease↗
Molecular evolutionary virology: its application to hepatitis C virus.
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Animals↗
Cellular and humoral immune reactions against autoantigens and hepatitis C viral antigens in chronic hepatitis C.
BACKGROUND/AIMS: Previous reports have suggested that the hepatitis C virus (HCV) may induce autoimmune hepatitis. The aim of this study was to examine this hypothesis by investigating humoral and cellular immune responses to HCV-related antigens and various autoantigens in patients with chronic HCV infections. METHODS: Lymphoproliferative responses in vitro and/or circulating antibodies to an HCV core peptide, the putative autoantigen GOR, the liver-specific hepatic asialoglycoprotein receptor (ASGP-R), and other autoantigens were investigated in 27 adults with chronic hepatitis C. RESULTS: Five patients with HCV (18.5%) showed cellular immune responses to ASGP-R and two others had antibodies to ASGP-R, whereas 6 of 14 patients (42.8%) showed cellular responses to GOR and 7 of 14 patients (50%) showed responses to HCV core. Other autoantibodies were detected in three patients (11%). Nine patients with autoimmune hepatitis studied concurrently for comparison showed cellular and/or humoral responses to ASGP-R but not to GOR. Only 2 of 11 patients with other chronic liver disorders showed immune responses to any antigen tested. CONCLUSIONS: Specific immunocompetence against HCV-related antigens can often be shown in patients with chronic hepatitis C but is infrequently accompanied by autoreactions against liver-specific or nonspecific antigens. A reported association between T-cell responses to HCV core and lack of liver damage could not be confirmed.
Adult↗
Optimization for the detection of hepatitis C virus antigens in the liver.
To optimize the detection of hepatitis C viral antigens in liver tissue, cryostat and formalin-fixed, paraffin-embedded liver sections from 21 patients with chronic hepatic C viral infection were studied. For cryostat sections, six different fixatives were compared. Sixteen primary antibodies were tested: nine different mouse monoclonal anti-hepatitis C virus-core antibodies, a human monoclonal anti-hepatitis C virus-non-structural 4, and six rabbit polyclonals directed against synthetic peptides of the hepatitis C virus core, envelope, and non-structural 3, non-structural 4, non-structural 5. Three detection systems, 3- and 5-step peroxidase-antiperoxidase and avidin-biotin complex, were examined. In cryostat sections, acetone/chloroform formation consistently produced the best signal-to-background ratio. Five anti-hepatitis C virus-core monoclonals which recognize amino acid sequence 26-45 of the hepatitis C virus-core region consistently detected the viral antigen, but not the monoclonals directed against 39-74 of the hepatitis C virus-core region. The human anti-hepatitis C virus-non-structural 4, which reacts to amino acid sequence 1700-1705, also regularly detected viral antigen. The rabbit polyclonals produced either negative or nonspecific staining. The 5-step peroxidase-antiperoxidase provided the strongest signal and the avidin-biotin system produced high background consistently. Overall, hepatitis C virus core and non-structural 4 antigens were detected in 71% and 57% of the patients studied. Of the 16 patients seropositive for hepatitis C virus RNA, 75% and 69% had detectable hepatitis C virus core and non-structural 4, in contrast to 60% and 20% of the five hepatitis C virus RNA seronegative patients.(ABSTRACT TRUNCATED AT 250 WORDS)
Antigens, Viral↗
Hepatitis C virus serotype II responds more favorably to interferon-alpha therapy.
To determine whether serological typing of hepatitis C virus correlated with the response to interferon-alpha therapy, hepatitis C virus serotypes were determined by subtype-specific antibody to NS4 polypeptide by enzyme-linked immunosorbent assay in 55 Japanese patients with chronic active hepatitis C who subsequently received recombinant interferon-alpha 2a therapy. Response to interferon-alpha was defined as complete and sustained (n = 12), complete response followed by relapse (n = 26), and no response (n = 17). There was no difference in the clinical biochemical parameters between these patients groups. However, a higher proportion (50.0%) of patients with hepatitis C virus serotype II showed complete and sustained response to interferon-alpha, compared to serotype I (11.1%, p < 0.01). These data indicate that this simple hepatitis C virus serotyping assay is a useful predictor of response to interferon-alpha therapy in patients with chronic hepatitis C virus infection.
Adult↗
Differential sensitivity of hepatitis C virus quasispecies to interferon-alpha therapy.
The quasispecies nature of hepatitis C virus was investigated in a patient with chronic hepatitis C virus infection who underwent interferon-alpha therapy. The hepatitis C virus E2/NS1 region was amplified and cloned, and multiple clones were sequenced before and after interferon-alpha therapy. The hepatitis C virus quasispecies can be grouped into three groups by phylogenetic tree analysis. Quasispecies from all the groups were present before interferon-alpha therapy. However, only group 3 remained after interferon-alpha therapy. In addition, only group 3 hepatitis C virus quasispecies were present during the early biochemical relapse. These data indicate that various groups of hepatitis C virus quasispecies may have different sensitivity to interferon-alpha.
Adult↗
Confirmation of hepatitis C virus transmission through needlestick accidents by molecular evolutionary analysis.
To document the transmission of hepatitis C virus (HCV) through needlestick accidents, 3 health workers who acquired HCV through such accidents and their HCV donor patients were studied using molecular evolutionary analysis based on the HCV E2 region. At least six clones were sequenced from each subject. Nucleotide substitutions were estimated by the six-parameter method, and a phylogenetic tree was constructed by the neighbor-joining method. HCV isolates from the donor patient and the recipient were nested in one monophyletic cluster; this clustering was confirmed to be statistically significant by bootstrap analysis. The nucleotide divergence among the isolates from the recipient was always smaller than that from the donor, supporting the notion that the direction of transmission was from the donor to the recipient. These findings provide evidence, at a molecular evolutionary level, that HCV was transmitted through needlestick accidents.
Adult↗
Full-length sequence of the genome of hepatitis C virus type 3a: comparative study with different genotypes.
Hepatitis C virus (HCV) type K3a (type 3a), which represents a minor genotype in Europe, the U.S.A. and Asia, appears to be significantly distributed throughout Australia and Brazil. We amplified the HCV-K3a/650 genome by reverse transcription polymerase chain reaction in ten overlapping fragments and determined the nucleotide sequences. The total sequence was 9454 bases in length and contained an open reading frame of 3021 amino acids, which is 10 or 11 amino acids longer than in HCV type 1 and 12 amino acids shorter than the sequence of type 2. These differences were due to the different lengths of both the putative envelope protein E2 and the NS5A regions, whose nucleotide lengths differ between types 1 and 2 also. Phylogenetic analysis of the putative core region and a portion of NS5B encoding the Gly-Asp-Asp motif indicated that HCV-K3a closely matched the corresponding type 3a group. The deletion and addition of amino acids in both E2 and NS5A may be associated with their pathobiological features.
Amino Acid Sequence↗
Effects of ruminal protozoa on cellulose degradation and the growth of an anaerobic ruminal fungus, Piromyces sp. strain OTS1, in vitro.
An anaerobic rumen fungus, Piromyces sp. strain OTS1, was incubated in the presence or absence of a mixed, A-type, protozoal population obtained from a goat, in a medium containing filter paper cellulose as energy source and antibiotics to suppress bacterial growth. Fermentation end products, cellulose degradation, and chitin as an indicator of fungal biomass were examined. In the presence of protozoa, total volatile fatty acids, notably propionate and butyrate, increased, and lactate decreased. In fungus-protozoan coincubations, formate was not detected at the end of the experiment and the amount of reducing sugars remained low throughout the incubation period. The fungal growth in the coincubations was negatively affected. While protozoal predation on zoospores was one mechanism of inhibition, mature fungal cells were also affected. Total cellulose degradation was greater in fungal monocultures, but the amount of cellulose degraded per unit of fungal biomass was 25% larger in the coincubations. The negative effects that the protozoal predatory activity had on the fungal growth and subsequently on the amount of cellulose degraded by Piromyces sp. strain OTS1 were partially attenuated by the protozoal fibrolytic activity or by an enhanced fungal activity due to a more favorable environment.
Anaerobiosis↗
Evolution of pathogenic viruses with special reference to the rates of synonymous and nonsynonymous substitutions.
For pathogenic viruses such as human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), human influenza A virus, and human T-cell leukemia virus type I (HTLV-I), the evolutionary features were briefly reviewed with special reference to the rates of synonymous and nonsynonymous substitutions. In particular, these rates were discussed in connection with the neutral theory of molecular evolution. It was common to all the five pathogenic viruses that the rate of synonymous substitution was higher than that of nonsynonymous substitution particularly when the entire gene regions were compared between different isolates. This suggests that the viral proteins are quite conservative to functional and structural changes even though most of these viral genomes are evolving at a speed extraordinarily higher than their host genomes. Thus, this feature is consistent with the neutral theory. However, it is also pointed out that positive selection may be operating on some specific sites such as antigenic sites in order for the pathogenic viruses to escape from the host immune system.
Base Sequence↗
Chronic hepatitis C complicated by Coombs-negative hemolytic anemia during interferon treatment.
Autoimmune hemolytic anemia is an autoimmune diseases which is reported to be caused by interferon treatment. A 33-year-old male with chronic hepatitis C developed Coombs-negative hemolytic anemia, probably due to administration of interferon-alpha 2b. This is, to our knowledge, the first report of chronic hepatitis C complicated by Coombs-negative hemolytic anemia during interferon treatment.
Acute Kidney Injury↗