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[Establishment of consensus sequence of PreS/S of hepatitis B virus with genotype B/serotype adw2 or genotype C/serotype adrq+ prevailing in Chongqing of China].

OBJECTIVE: To develop consensus sequence of HBV PreS/S with different subtype in Chongqing of China. METHODS: The gene of PreS/S of HBV in 18 AsC was sequenced. The genotype and serotype of HBV were determined. The main HBV strain prevailing in Chongqing was identified to establish its consensus sequence. RESULTS: It was found that 9 strains were genotype B/serotype adw2, 6 were genotype C/serotype adrq+ and 3 were genotype B/serotype ayw1. The consensus sequence of PreS/S of HBV with genotype B/serotype adw2 and genotype C/serotype adrq+ were established. There were 6 nucleotide variants which causing 4 amino acids change between consensus sequence of PreS/S with genotype B/serotype adw2 in Chongqing and in Southeast of China (homology showed 99.5% and 99.0% respectively). There were 13 different sites that caused 4 amino acids change between consensus sequence of PreS/S with genotype C/serotype adrq+ in Chongqing and in Northeast and South of China (homology showed 98.9% and 99.0% respectively). Comparing the two consensus sequence of PreS/S gene of different subtype HBV in Chongqing, there was 95 variants which caused 40 amino acids variants (the homology was 92.1% and 90.0% respectively). CONCLUSION: The consensus sequence of PreS/S of hepatitis B virus with genotype B/serotype adw2 and genotype C/serotype adrq+ prevailing in Chongqing was established.

Adolescent↗

Hepatitis B virus genotypes in acute and fulminant hepatitis patients from north India using two different molecular genotyping approaches.

Data from India on hepatitis B virus (HBV) genotype related differences in clinical progression and outcome of acute and fulminant hepatitis B are limited. Sera from patients with acute hepatitis B (AHB) (n=80), fulminant hepatitis B (FHB) (n=40) and asymptomatic HBsAg carriers (ASC) (n=40) were tested for HBV genotype using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and type-specific primers-based PCR (TSP-PCR). The genotype distribution for 160 patients with HBV related hepatitis/carriers were as follows: A, 3/80 (3.7%) in AHB, 2/40 (5%) in FHB and 7/40 (17.5%) in ASC; D, 77/80 (96.2%) in AHB, 38/40 (95%) in FHB and 33/40 (82.5%) in ASC. C, 0; B, 0; E, 0; F, 0 (p<0.01, genotype D versus A). Compared with genotype D, genotype A patients had no significant clinical or biochemical differences (p>0.05). HBV genotypes A and D were found to be prevalent in patients with HBV related acute and fulminant hepatitis from New Delhi, India. Genotype D was the dominant genotype prevalent in all patient categories while genotype A was solely responsible for AHB leading to chronic hepatitis B in 3.7% of the cases from this region.

Journal Article↗

Response to combined interferon and ribavirin is better in patients infected with hepatitis C virus genotype 6 than genotype 1 in Hong Kong.

Data on the treatment efficacy of interferon (IFN)-alpha and ribavirin in patients with chronic hepatitis infected with hepatitis C virus (HCV) of genotype 6 are lacking. A study has been reported from Hong Kong which compared the treatment efficacy of IFN-alpha and ribavirin in the treatment of chronic HCV infection with genotypes 1 and 6. Twenty-four patients with HCV genotype 1 and 16 patients with HCV genotype 6 were studied. The baseline demographic data including median age, gender ratio, alanine aminotransferase levels, bilirubin levels, HCV RNA levels and histological scores were comparable between the two groups of patients. All patients received IFN-alpha 5 million units three times per week and ribavirin (1,000 mg for those weighing </=75 kg and 1,200 mg for those weighing >75 kg) for 1 year. Patients infected with HCV genotype 6 achieved virological response significantly higher than those with HCV genotype 1 (67 vs. 33% at week 24, p = 0.02; 75 vs. 42% at the end of treatment, p = 0.05; 63 vs. 29% at 6 months after completion of treatment, p = 0.04). Histological improvement in inflammatory activity and fibrosis in the liver were observed in 25% and 25% of patients infected with HCV genotype 6 in contrast to only 13 and 8% in patients infected with HCV genotype 1; however, the differences were not statistically significant. In conclusion, patients with HCV genotype 6 gain a better response to combined treatment with IFN-alpha and ribavirin than those with HCV genotype 1 and achieve a significantly higher rate of sustained virological response.

Antiviral Agents↗

GBV-C/HGV genotypes: proposed nomenclature for genotypes 1-5.

The GB virus-C and hepatitis G virus (GBV-C/HGV) are variants of the same flavivirus. This proposal attempts to clarify the conflicting nomenclature for GBV-C/HGV genotypes. The first three genotypes described were genotype 1 (West Africa); genotype 2 (US/Europe) and genotype 3 (Asia). Subsequently, two groups published data from South Africa and Southeast Asia both stating the presence of a novel "4th genotype." These isolates are distinct phylogenetically. It is proposed that the nomenclature for genotypes 1-3 remains as per previous publications, and that the Southeast Asian isolates be known as genotype 4, and the South African isolates as genotype 5.

DNA, Viral↗

Hepatitis B virus genotypes in Uzbekistan and validity of two different systems for genotyping.

Hepatitis B virus (HBV) has been classified into seven genotypes, designated A-G. The HBV genotype has a characteristic geographical distribution. The Republic of Uzbekistan is located in the heart of Asia and has been considered to be a region with high endemicity of hepatitis viruses. However, the present distribution of hepatitis virus infection in this region is unknown. The aim of this study was to investigate the distribution of HBV genotypes and to elucidate the validity of two genotyping systems in Uzbekistan. Fifty-four patients with hepatitis B surface antigen were investigated. HBV genotypes were determined by two methods: one based on restriction fragment length polymorphism (RFLP) targeting to S region, and another on enzyme-linked immunosorbent assay (ELISA), using monoclonal antibodies to pre-S2 region. Seven (13%) and 47 (87%) of the 54 subjects were classified into genotypes A and D, respectively. Dual infection of two viral populations of the same genotype was observed in one subject. No significant difference of ALT level (203.3 +/- 244.7 vs. 190.6 +/- 39.5) and HBeAg (42.9% vs. 42.6%) were found between genotypes A and D. In this study, the validity of the genotyping systems in this region was confirmed.

Base Sequence↗

Co-circulation of two genotypes of measles virus and mutual change of the prevailing genotypes every few years in Osaka, Japan.

Genotypes of 44 wild-type measles virus (MV) strains isolated in Osaka, Japan, during 1997-2001, were determined based on phylogenetic analyses of a 456-nt 3' terminal nucleoprotein gene sequence with the reference MV strains designated by the World Health Organization. The wild-type MV strains were classified into two genotypes, D3 and D5, recognized as indigenous in Japan. Six of 12 strains isolated in 1997 were classified into genotype D3 and the other 6 into D5. Eleven of 13 strains were D3, and 2 were D5 in 1998. There were no measles epidemics, and no strains were isolated in 1999. Nine of 10 strains were genotype D5, and only one was D3 in 2000, and 9 of 9 were D5 in 2001. These results indicate that the wild-type MV strains classified into genotypes D3 and D5 co-circulated without the complete change of the MV genotype in Osaka, except in 2001. Furthermore, the prevailing genotype was different between 1998 and 2000-2001. Together with a previous report about MV genotype in this area during 1993-1995, these results suggest that the mutual change of the prevailing wild-type MV genotypes between D3 and D5 occurs every few years in Osaka, Japan.

Adolescent↗

Effects of GJB2 genotypes on the audiological phenotype: variability is present for all genotypes.

BACKGROUND AND AIM: Recent studies have revealed a genotype-phenotype correlation for mutations in the GJB2 gene. Since ethnic difference may have an effect for the degree of hearing loss due to background genes, we aimed to search for confirmation of previously suggested genotype-phenotype correlation in GJB2 deafness in the Turkish population. METHODS: Pure tone audiograms of 63 unrelated probands with GJB2-associated hearing loss having 15 different mutations were obtained and evaluated for correlation between the degree of hearing loss and genotypes. RESULTS: Three GJB2 genotypes identified in more than one family were homozygous c.35delG (44 probands), homozygous p.E120del (four probands) and c.[35delG]+[IVS1+1G>A] (two probands). No statistical difference for the degree of hearing loss was observed when the genotypes were compared individually or grouped according to their effects on the protein. The most likely explanation for this result is the relatively small size of the studied population. Degree of hearing loss was variable in c.35delG and p.E120del homozygotes. Intra-familial phenotypic variability was present for some genotypes. The detailed audiological data for homozygous p.E120del and c.[35delG]+[328delG] genotypes are reported for the first time in this study. CONCLUSION: Previously reported genotype-phenotype correlations for the GJB2 deafness should be cautiously interpreted during the clinical counseling since variability in the degree of hearing loss is present for all GJB2 genotypes.

Adolescent↗

Hepatitis C virus genotype 1b chimeric replicon containing genotype 3 NS5A domain.

Infections with hepatitis C virus (HCV) genotype 3 exhibit differences in clinical phenotype including an increase in response to interferon therapy and development of steatosis. To initiate studies on genotype 3, we created a chimeric genotype 1b replicon containing a genotype 3a NS5A domain. The chimera was capable of efficient colony formation after the selection of a novel dominant adaptive mutation. Thus, domains from highly different strains can interact to form a functional replicase. A new genotype 1a replicon was constructed as well. Genotype specific influence on interferon sensitivity was examined using genotype 1a, 1b and chimeric 1b-3a replicons. The genotype 3a NS5A domain did not increase the sensitivity of the chimeric replicon to IFNalpha. The results suggest that NS5A is not sufficient to convey the increased IFNalpha response by genotype 3 or the replicon model is not capable of mimicking the events involved in increased sustained viral response.

Amino Acid Sequence↗

An epidemiologic survey of methicillin-resistant Staphylococcus aureus by combined use of mec-HVR genotyping and toxin genotyping in a university hospital in Japan.

OBJECTIVE: To evaluate the usefulness of an assay using two polymerase chain reaction-based genotyping methods in the practical surveillance of methicillin-resistant Staphylococcus aureus (MRSA). METHODS: Nosocomial infection and colonization were surveyed monthly in a university hospital in Japan for 20 months. Genotyping with mec-HVR is based on the size of the mec-associated hypervariable region amplified by polymerase chain reaction. Toxin genotyping uses a multiplex polymerase chain reaction method to amplify eight staphylococcal toxin genes. RESULTS: Eight hundred nine MRSA isolates were classified into 49 genotypes. We observed differing prevalences of genotypes for different hospital wards, and could rapidly demonstrate the similarity of genotype for outbreak isolates. The incidence of genotype D: SEC/TSST1 was significantly higher in isolates causing nosocomial infections (49.5%; 48 of 97) than in nasal isolates (31.4%; 54 of 172) (P = .004), suggesting that this genotype may represent the nosocomial strains. CONCLUSION: The combined use of these two genotyping methods resulted in improved discriminatory ability and should be further investigated.

Bacterial Toxins↗

Evaluation of genotype data in clinical risk assessment: methods and application to BRCA1, BRCA2, and N-acetyl transferase-2 genotypes in breast cancer.

Associations of numerous susceptibility genes with disease risk have been reported. However, objective methods have not been developed to evaluate the conditions under which translation of knowledge about susceptibility genotypes may be clinically informative. We describe and apply a statistical approach to evaluate when genotype information may be clinically informative in disease risk assessment. We estimate an interval of cumulative cancer incidences where it may be appropriate to use these genes in disease risk assessment. We also estimate the magnitude of a log odds ratio (H) that measures genotype-disease association. We illustrate this method with three breast cancer susceptibility genotypes: population screening data evaluating the 185delAG mutation at BRCA1 and the 6174delT mutation at BRCA2 in a Ashkenazi Jewish population, and case control data for the slow acetylation genotype at the N-acetyl transferase 2 (NAT2) gene in combination with smoking. Knowledge of the 185delAG mutation in BRCA1 (HdelAG = 3.42; 95% CI: 3.04, 3.79) or the 6174delT mutation in BRCA2 (HdelT = 1.98; 95% CI: 1.16, 2.30) can be clinically informative in distinguishing individuals who are and are not at breast cancer risk in populations with cumulative breast cancer incidences of > or = 4% and > or = 13%, respectively. NAT2 genotypes alone are much less clinically informative in predicting breast cancer risk (HNAT2 = 0.10). However, knowledge of both heavy smoking 20 years ago and NAT2 genotype is a more clinically informative predictor of postmenopausal breast cancer risk with HNAT2 = 2.19, when the cumulative breast cancer incidence in the target population is at least 31%. These results indicate that knowledge of the 185delG mutation-status may be clinically informative even in populations with low cumulative breast cancer incidences, whereas the 6174delT mutation and NAT2 genotypes may only be clinically informative in a population with higher cumulative breast cancer incidence. The proposed approach can be used to objectively evaluate the conditions under which susceptibility genotypes may be applied for risk assessment or genetic screening.

Adult↗

Genotyping of hepatitis C virus: coinfection by multiple genotypes detected in children with chronic posttransfusion hepatitis C.

The distribution of genotypes of the hepatitis C virus (HCV) was studied in 24 children with chronic posttransfusion hepatitis C. Genotypes were determined by reverse transcription-nested polymerase chain reaction with type-specific primers. Twenty (83%) were infected by a single genotype: 14 by type II [1b], 3 by III [2a], and 3 IV [2b]. Four (17%) were coinfected by two genotypes. The amount of blood transfusion given to the patients infected by multiple genotypes was significantly larger than to those infected by a single genotype (mean +/- SD, 15.2 +/- 14.4 vs 78.6 +/- 42.0 U). Three of the four patients infected by multiple genotypes were considered to be immunocompromised by anticancer therapy for malignant disease. Eighteen patients showed a raised level of alanine aminotransferase throughout the follow-up, while the remaining six patients (three of type II [1b], two of IV [2b], and one of III [2a] + IV [2b]) achieved biochemical remission. Liver biopsy was performed on 19 patients. Compared to those with type III [2a] or IV [2b], those with type II [1b] appeared to show more severe histological changes with higher histological activity index scores, although there was no significant difference. The positive rates of antibody to C100-3 or 5-1-1 in patients with type III [2a] or IV [2b] were lower than in those with type II [1b] (33 and 33 vs 43 and 50%), whereas the antibody to C33C or C22-3 was detected in nearly all patients regardless of their genotypes. In the present study, we found a high incidence of multiple-genotype infection among children with chronic posttransfusion hepatitis C.

Adolescent↗

Molecular genotyping to distinguish between recrudescents and new infections in treatment trials of Plasmodium falciparum malaria conducted in Sub-Saharan Africa: adjustment of parasitological outcomes and assessment of genotyping effectiveness.

Molecular genotyping of baseline and post-treatment recurrent Plasmodium falciparum is recommended to distinguish recrudescent from new infections. However, genotyping performance and adjustment of treatment outcomes have not been evaluated in large field trials. Parasitological outcomes were assessed in nine double-blinded trials of uncomplicated P. falciparum malaria in African children treated with artesunate/placebo plus standard monotherapies. Day 28 failure rates were adjusted by stepwise genotyping the P. falciparum glutamate rich protein (glurp), merozoite surface protein 1 (msp1) and 2 (msp2). We calculated overall and laboratory genotyping performance and compared unadjusted (crude) and PCR-adjusted outcomes. 3455 (93.6%) of 3691 enrolled patients were evaluable by Day 28. 767 (22%) had post-Day 14 recurrent parasitemias of which 686 could be genotyped: 246 were recrudescences, 286 new infections and 154 unresolved. The overall and laboratory genotyping performance were 69 (12-100)% and 78 (50-100)%, respectively. The mean Day 28 crude parasitological failure rate was 44 (range 3-87)%. PCR-adjusted rates were 36 (range 2-86)% if unresolved infections were counted as failures or 33 (range 2-86)% if excluded from analysis. The overall difference between crude Day 28 and Day 14 failure rates was 22% (95% CI 20.3, 24.6) but decreased to 14% (95% CI 12.1, 16.3) if unresolved infections are counted as failures, or to 11% (95% CI 9.8, 16.3) if unresolved infections are excluded from the analysis. Genotyping refined treatment outcomes but diligence is needed in sample collection and analysis to improve its performance. Our findings support the WHO recommendation of PCR genotyping in malaria clinical trials and suggest that stepwise genotyping of only two loci (msp2 and msp1 or glurp) can reliably discriminate recrudescences from new infections.

Africa South of the Sahara↗

Simultaneous quantification and genotyping of hepatitis B virus for genotypes A to G by real-time PCR and two-step melting curve analysis.

Both the viral titer and the genotype significantly determine clinical outcomes and responses to antiviral treatment in chronic hepatitis B virus (HBV) infection. A method was developed for large-scale A-to-G genotyping with simultaneous viral quantification. The assay was run on a LightCycler instrument using hybridization probes. The genotype was determined from the melting points of the probes in a two-step manner. Set 1 amplicons differentiated genotypes B, E, and F from A, C, D, and G and simultaneously quantified viremia by real-time PCR. Melting curve analysis using the set 2-1 amplicon or the set 2-2 amplicon reaction mixture was then used to differentiate these genotype groups into single genotypes. HBV DNA quantification was consistent with that of the Amplicor assay and linear in a range from 10(2) to 10(13) copies/ml. By comparison with the restriction fragment length polymorphism method, 92.3% of 441 samples were accurately genotyped by the current assay. The method should be useful for genotyping and quantification of HBV DNA in areas where all genotypes exist.

DNA Primers↗

Effect of genotyping error on type-I error rate of affected sib pair studies with genotyped parents.

OBJECTIVE: In affected sib pair studies without genotyped parents the effect of genotyping error is generally to reduce the type I error rate and power of tests for linkage. The effect of genotyping error when parents have been genotyped is unknown. We investigated the type I error rate of the single-point Mean test for studies in which genotypes of both parents are available. METHODS: Datasets were simulated assuming no linkage and one of five models for genotyping error. In each dataset, Mendelian-inconsistent families were either excluded or regenotyped, and then the Mean test applied. RESULTS: We found that genotyping errors lead to an inflated type I error rate when inconsistent families are excluded. Depending on the genotyping-error model assumed, regenotyping inconsistent families has one of several effects. It may produce the same type I error rate as if inconsistent families are excluded; it may reduce the type I error, but still leave an anti-conservative test; or it may give a conservative test. Departures of the type I error rate from its nominal level increase with both the genotyping error rate and sample size. CONCLUSION: We recommend that markers with high error rates either be excluded from the analysis or be regenotyped in all families.

Family↗

Distribution of hepatitis B virus genotypes: phylogenetic analysis and virological characteristics of genotype C circulating among HBV carriers in Kolkata, Eastern India.

AIM: To evaluate the genotype distribution of hepatitis B virus (HBV) in Eastern India and to clarify the phylogenetic origin and virological characteristics of the recently identified genotype C in this region. METHODS: Genotype determination, T1762/A1764 mutation in the basal core promoter (BCP) and A1896 mutation in the precore region of 230 subjects were determined by restriction fragment length polymorphism method (RFLP) and the result was confirmed by direct sequencing. RESULTS: The predominant genotypes D (HBV/D) and A (HBV/A) were detected in 131/230 (57%) and 57/230 (25%) samples. In addition, genotype C (HBV/C) was detected in 42/230 (18%) isolates. Surface gene region was sequenced from 45 isolates (27 HBV/C, 9 HBV/A and 9 HBV/D). Phylogenetic analysis revealed that all of the HBV/C sequences clustered with South East Asian subgenotype (HBV/Cs). The sequence data showed remarkable similarity with a Thai strain (AF068756) (99.5% +/- 0.4% nucleotide identities) in 90% of the genotype C strains analyzed. T1762/A1764 mutation in BCP region, associated with high ALT was significantly higher in HBeAg negative isolates than HBeAg positive isolates. Frequency of A1896 mutation leading to HBeAg negativity was low. CONCLUSION: The present study reports the genotypic distribution and the characteristics of partial genome sequences of HBV/C isolates from Eastern India. Low genetic diversity and confinement of HBV/C in Eastern India possibly indicate a recent, limited, spread in this region. Genotype C with T1762/A1764 mutation has been reported to increase the risk for hepatocellular carcinoma; therefore genotype C carriers in Eastern India should be carefully monitored.

Adolescent↗

Reference values and biological variation for tumor marker CA 19-9 in serum for different Lewis and secretor genotypes and evaluation of secretor and Lewis genotyping in a Caucasian population.

The concentration of the tumor marker CA 19-9 is influenced by the patient's secretor status and Lewis genotype. The aim of this study was to establish novel reference intervals for CA 19-9 in serum based on secretor and Lewis genotypes, to investigate the biological variation of CA 19-9, and to evaluate the utility of Lewis and secretor genotyping on a group of individuals with serologically defined Lewis phenotypes. CA 19-9 was measured in serum of 500 healthy individuals. Secretor and Lewis genotypes were determined by sequencing and PCR-cleavage methods. Significant differences were found between subgroups with different Lewis and secretor genotypes. Genotype-based reference intervals for CA 19-9 are presented. The upper reference limit for all individuals was 28.7 kilounits/L; for secretors and nonsecretors, the upper reference limits were 12.4 and 61.2 kilounits/L, respectively. The analytical imprecision (CVA) was 9.8%, the within-subject variability (CVI) was 15.8%, and the between-subject variability (CVG) was 102.2%. Good agreement was found between Lewis and secretor genotyping and conventional blood grouping. Genotype-based reference intervals may be a way to increase the clinical utility of CA 19-9. On the basis of the calculation of a critical difference for sequential values (significant at P </=0.05) of 51.5%, a 40-50% change in marker concentration is suggested as the limit for significant change when the marker is used for follow up. PCR-based genotyping is a reliable method for secretor and Lewis histo-blood grouping.

Adult↗

A genotype 2b NS5B polymerase with novel substitutions supports replication of a chimeric HCV 1b:2b replicon containing a genotype 1b NS3-5A background.

HCV diversity suggests that evaluation of HCV inhibitors for broad genotypic efficacy is warranted. The replicon system enables cell-culture compound efficacy evaluation against an active replication complex, and a functional replicon dependent upon a genotype 2b polymerase would augment existing cell-culture efficacy studies that are presently limited to genotype 1a, 1b, and 2a replicons. We made a chimeric Neo(r) 1b:2b replicon where genotype 2b NS5B was inserted into a genotype 1b NS3-5A background and transfected replicon RNA to generate Neo(r) cell lines. All cell lines contained novel substitutions within NS5B which were subsequently engineered into the parental 1b:2b replicon and shown to enhance replication to various degrees. A single NS5B M31I substitution enhanced replication to levels sufficiently robust to quantify sensitivity to HCV inhibitors in a transient replication assay. The M31I 1b:2b replicon was similarly sensitive to an active-site nucleoside inhibitor of NS5B as genotype 1b replicons, but was insensitive to two non-nucleoside inhibitors which were otherwise efficacious against the genotype 1b replicons. This work describes a novel HCV replicon sustained by a genotype 2b polymerase that is sufficiently robust for quantifiable analysis in a transient replication assay, and demonstrates its utility in characterizing anti-HCV compounds for cross-genotypic efficacy.

Adenosine↗

Detecting genotype combinations that increase risk for disease: maternal-fetal genotype incompatibility test.

Biological mechanisms that involve gene-by-environment interactions have been hypothesized to explain susceptibility to complex familial disorders. Current research provides compelling evidence that one environmental factor, which acts prenatally to increase susceptibility, arises from a maternal-fetal genotype incompatibility. Because it is genetic in origin, a maternal-fetal incompatibility is one possible source of an adverse environment that can be detected in genetic analyses and precisely studied, even years after the adverse environment was present. Existing statistical models and tests for gene detection are not optimal or even appropriate for identifying maternal-fetal genotype incompatibility loci that may increase the risk for complex disorders. We describe a new test, the maternal-fetal genotype incompatibility (MFG) test, that can be used with case-parent triad data (affected individuals and their parents) to identify loci for which a maternal-fetal genotype incompatibility increases the risk for disease. The MFG test adapts a log-linear approach for case-parent triads in order to detect maternal-fetal genotype incompatibility at a candidate locus, and allows the incompatibility effects to be estimated separately from direct effects of either the maternal or the child's genotype. Through simulations of two biologically plausible maternal-fetal genotype incompatibility scenarios, we show that the type-I error rate of the MFG test is appropriate, that the estimated parameters are accurate, and that the test is powerful enough to detect a maternal-fetal genotype incompatibility of moderate effect size.

Bias↗