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PubMed2006

Genotyping of the lactase-phlorizin hydrolase -13910 polymorphism by LightCycler PCR and implications for the diagnosis of lactose intolerance.

BACKGROUND: Hypolactasia and lactose intolerance are common conditions worldwide. Hypolactasia seems to be strongly correlated with genotype C/C of the genetic variant C-->T(-13910) upstream of the lactase phlorizin hydrolase (LPH) gene. We developed a rapid genotyping assay for LPH C-->T(-13910) and investigated the relationship of positive lactose breath hydrogen test (LBHT) results suggesting lactose intolerance with LPH C-->T(-13910) genotype. METHODS: Using automated DNA purification on the MagNA Pure LC and real-time PCR on the LightCycler, we examined samples from 220 individuals to estimate genotype frequencies; we then determined LPH C-->T(-13910) genotype in samples from 54 Caucasian patients with a positive LBHT result and symptoms of lactose intolerance. RESULTS: Genotyping of 220 individuals revealed frequencies of 21.4%, 41.8%, and 36.8% for genotypes C/C, C/T, and T/T. Of the patients with positive LBHT results, only 50% had the C/C genotype suggestive of primary adult hypolactasia in our study population. The other patients had various degrees of secondary hypolactasia or symptoms of lactose intolerance. Patients with C/C genotype had a mean (SD) peak H2 increase in the LBHT [108 (58) ppm] that was significantly higher than in patients with the C/T [65 (54) ppm] and T/T [44 (34) ppm] genotypes. CONCLUSIONS: The new real-time PCR assay provides a rapid, labor-saving means for the genotyping of LPH C-->T(-13910). Use of the assay may assist in differentiating patients with primary hypolactasia from those with secondary hypolactasia and lactose intolerance, who may need further clinical examinations to diagnose their underlying primary diseases.

Adolescent↗
PubMed2006

CFTR genotype as a predictor of prognosis in cystic fibrosis.

STUDY RATIONALE: Certain CFTR genotypes are associated with reduced mortality. The accuracy of using CFTR genotype as a predictor of survival and the mechanisms through which CFTR genotype influences survival are unknown. PARTICIPANTS: All patients with cystic fibrosis (CF) enrolled in the US Cystic Fibrosis Foundation national registry between 1993 and 2002. DESIGN: We examined the prognostic value of CFTR genotype, grouped into "high-risk" and "low-risk" categories based on the effect of their CFTR genotype on phenotype and protein production. MEASUREMENTS AND RESULTS: Clinical and genetic data were available from 15,651 patients with CF. Patients with a high-risk CFTR genotype had a greater than twofold increased risk of death compared to patients with a low-risk CFTR genotype (relative risk, 2.25; 95% confidence interval [CI], 1.77 to 2.84; p < 0.001). This association was partly explained by lung function, nutritional status, pancreatic insufficiency, and Pseudomonas aeruginosa colonization. Of the 1,672 patients who died, median age at death for the high-risk CFTR genotype was 24.2 years (interquartile range, 18.4 to 32.0 years) and for the low-risk CFTR genotype was 37.6 years (interquartile range, 28.8 to 47.9 years; p < 0.001). The positive predictive value of this classification method as a test to identify patients who died before or after their 30th birthday was 69% (95% CI, 67 to 72%) with a negative predictive value of 71% (95% CI, 60 to 80%). CONCLUSIONS: Grouping patients into high-risk and low-risk CFTR genotype categories is associated with significant differences in survival and median age at death. These differences are not fully explained by lung function, nutritional measures, pancreatic insufficiency, or P aeruginosa colonization. Modest reassurance about the likelihood of a milder than average course can be provided for CF patients with a low-risk CFTR genotype, although it should be acknowledged that substantial phenotypic variability exists.

Adolescent↗
PubMed2004

Comparison of cytochrome P450 2C9 genotyping methods and implications for the clinical laboratory.

STUDY OBJECTIVE: To compare the accuracy, speed, and cost of two methodologies used for genotyping known variants in the cytochrome P450 (CYP) 2C9 metabolizing enzyme gene. DESIGN: Comparative study. SETTING: University research center. SAMPLES: Fifteen-milliliter mouthwash samples collected from 253 subjects participating in a warfarin pharmacogenomic study. INTERVENTION: Genotyping for the isoleucine-to-leucine change at codon 359 (Ile359Leu [*3] polymorphism) was performed by using the Pyrosequencing and polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) methods in all 253 samples. Genotyping for the arginine-to-cysteine change at codon 144 (Arg144Cys [*2] polymorphism) was performed by using Pyrosequencing in all samples and by PCR-RFLP in a random subset of 136 samples. MEASUREMENTS AND MAIN RESULTS: Comparisons of genotyping success rates, time efficiency, and cost analyses were conducted for Pyrosequencing and PCR-RFLP at each variant site. Pyrosequencing and PCR-RFLP produced similar success rates on the first genotyping attempt for the Arg144Cys variant (93.3% vs 90.4%, respectively) and the Ile359Leu variant (83.8% vs 79.1%, respectively). With Pyrosequencing, genotyping 96 samples for either polymorphism could be performed in 1 hour. In contrast, genotyping 96 samples by RFLP took 10 hours for the Arg144Cys variant and 20 hours for the Ile359Leu variant. Total cost/sample for Arg144Cys genotyping was dollars 1.90 with PCR-Pyrosequencing and dollars 3.14 with PCR-RFLP. Total cost/sample for Ile359Leu genotyping was dollars 1.88 with PCR-Pyrosequencing and dollars 10.18 with PCR-RFLP CONCLUSION: Compared with RFLP, genotype determination by Pyrosequencing is a more time-efficient, cost-effective, and robust method for CYP2C9 genotyping. Because of its wide applicability and ease of use, Pyrosequencing is a promising technology for future pharmacogenomic investigations.

Alleles↗
PubMed1999

Prognosis versus actual outcome. IV. The effectiveness of clinical parameters and IL-1 genotype in accurately predicting prognoses and tooth survival.

BACKGROUND: Recently, a genetic marker (IL-1 genotype) that identifies individuals at higher risk for developing severe periodontal disease was discovered. A subgroup of the population reported on earlier was evaluated to determine if knowledge of the patient's IL-1 genotype would improve accuracy in assignment of prognoses and prediction of tooth loss. METHODS: This subgroup consisted of 42 patients (1,044 teeth) in maintenance care for 14 years; 16 tested IL-1 genotype-positive (IL-1GP). Nine were smokers, and 30 had a history of smoking, with an average of 29.44 pack years. A multiple Cox regression model and Kaplan-Meier survival plots were fit to the subset of patients to evaluate tooth loss. RESULTS: Both IL-1GP and heavy smoking were significantly related to tooth loss. A positive IL-1 genotype increased the risk of tooth loss by 2.7 times, and heavy smoking by 2.9 times. The combined effect of IL-1GP and heavy smoking increased the risk of tooth loss by 7.7 times. The value of clinical parameters traditionally used to assign prognosis was found to be dependent on IL-genotype and smoking status. In the model that included IL-1 genotype and heavy smoking, none of the clinical parameters added significantly to the model for tooth loss while mobility, probing depth, crown-to-root ratio, and percent bone loss added significantly to the model, which included IL-1 genotype in non-smokers. IL-1GP patients and patients who smoked heavily demonstrated a much worse tooth survival rate when compared to IL-1 genotype-negative patients and non-smokers, respectively. CONCLUSIONS: Knowledge of the patient's IL-1 genotype and smoking status will improve the clinician's ability to accurately assign prognosis and predict tooth survival. Clinical implications are as follows. Investigators were unable to judge which patients would be IL-GP or negative based on their clinical presentation or family history of tooth loss due to periodontal disease. Since periodontal diseases are multifactorial, knowledge of the patient's genotype is more important in predicting future risk than explaining past disease. Knowledge of IL-1 genotype status would be important in developing a treatment plan and predicting tooth survival for a new patient who smokes and presents with periodontal disease, especially if restorative care is needed. Knowledge of a maintenance patient's IL-1 status would help target therapy for non-responding areas; one would be less likely to take a "wait and see approach" with IL-1GP patients. IL-1 positive non-smokers can be successfully treated and maintained over long periods of time.

Adult↗
PubMed2003

Mix-infections with different genotypes of HCV and with HCV plus other hepatitis viruses in patients with hepatitis C in China.

AIM: Clinical therapy and prognosis in HCV infections are not good, and mix-infections with different HCV genotypes or quasispecies and mix-infections with HCV plus other hepatitis viruses are important concerns worldwide. The present report describes the sequence diversity and genotying of the 5'NCR of HCV isolates from hepatitis patients mix-infected with different HCV genotypes or variants, and the conditions of mix-infections with HCV plus other hepatitis viruses, providing important diagnostic and prognostic information for more effective treatment of HCV infections. METHODS: The 5' non-coding region (5'NCR) of HCV was isolated from the patients sera and sequenced, and sequence variability and genotypes of HCV were defined by nucleotide sequence alignment and phylogenetic analysis, and the patients mix-infected with HCV plus other hepatitis viruses were analyzed. The conditions and clinical significance of mix-infections with HCV plus other hepatitis viruses were further studied. RESULTS: Twenty-four out of 43 patients with chronic hepatitis C were defined as mix-infected with different genotypes of HCV. Among these 24 patients, 9 were mix-infected with genotype 1 and 3, 7 with different variants of genotype 1, 2 with different variants of genotype 2, 6 with different variants of genotype 3. No patients were found mix-infected with genotype 1 and 2 or with genotype 2 and 3. The clinical virological analysis of 60 patients mix-infected with HCV plus other hepatitis viruses showed that 45.0 % of the patients were mix-infected with HCV plus HAV, 61.7 % with HCV plus HBV, 6.7 % with HCV plus HDV/HBV, 8.4 % with HCV plus HEV, 3.3 % with HCV plus HGV. Infections with HCV plus other hepatitis viruses may exacerbate the pathological lesion of the liver. CONCLUSION: The findings in the present study imply that mix-infections with different HCV genotypes and mix-infections with HCV plus other hepatitis viruses were relatively high in Yunnan, China, providing important diagnostic and prognostic information for more effective treatment of HCV infections.

5' Untranslated Regions↗
PubMed2000

Frequent genotype changes at -308, and 488 regions of the tumor necrosis factor-alpha (TNF-alpha) gene in patients with prostate cancer.

PURPOSE: Tumor necrosis factor-alpha (TNF-alpha) is involved in oncogenesis of several cancers. The purpose of this study was to investigate whether genotype changes of TNF-alpha promoter regions (-238, -308) and at the 488 region are associated with human prostate cancer. MATERIALS AND METHODS: The DNA from 73 cases of human prostate cancer was analyzed by allele-specific polymerase chain reaction to characterize the genotype changes of three regions of the TNF-alpha gene in prostate cancer patients. We also determined the genotype frequency in these patients. The relative risk of variant genotype was calculated by comparing with our previous data from healthy controls. RESULTS: Genetic changes were detected in 15.1% (11/73) of prostate cancer samples at 488 region of TNF-alpha. Seventy-three percent (53/73) of the patients showed genotype GA at -308 region of TNF-alpha. Genotype GA at 488 region in TNF-alpha was observed in 73% (53/73) of the cancer and 71% (52/73) of the normal tissue. The relative risks of incidence for prostate cancer was 14-fold higher in people with genotype GA at -308 region of TNF-alpha. The relative incidence for prostate cancer was a 17-fold higher in-patient with genotype GA at 488 region of TNF-alpha. Genotype GA at -308 of TNF-alpha was related to higher clinical tumor stage of prostate cancer than genotype G (p <0.05). CONCLUSIONS: The present study demonstrates, for the first time, that the genotype changes in -308 and 488 regions of TNF-alpha are associated with prostate cancer.

Alleles↗
PubMed2001

Evaluation of a new hepatitis C virus sequencing assay as a routine method for genotyping.

The determination of HCV genotypes, subtypes and isolates has been helpful in understanding the evolution and the epidemiology of the virus, and is an important factor in the pre-treatment evaluation. A new simpler and automated sequencing based system has been developed recently, the Visible Genetics TruGene Hepatitis C Assay. The aim of the study was to compare this new genotyping assay with reverse hybridization based Innogenetics INNO-LiPA HCV II assay that is used most commonly. Eighty-eight HCV-RNA positive patients were enrolled and divided in four groups: 26 hemodialysed patients, 30 untreated patients with chronic HCV hepatitis, 12 IFN non-responder patients with chronic HCV hepatitis, 20 asymptomatic HCV positive subjects. The 5'-UTR region was amplified by RT-PCR and the nucleotide sequences determined by the TruGene assay. In parallel, the amplicons were also tested by INNO-LiPA. Concordant results were obtained in 80 out of 88 cases (90.9%). The new assay allowed to genotype 2 samples not typed by LiPA as 1b and 2a/c. The new system also allowed the subtyping of 3 untypable samples, classified as genotype 1 by INNO-LiPA, as genotype 1b (1 sample) and, as genotype 4 (2 samples). The difference between these genotype 4 isolates and the closest genotype 1 isolate was 6 nucleotides. One LiPA genotype 1a sample was typed as 1b and 2 genotype 1b samples were all typed as 1a by the sequence analysis. In conclusion, the new assay is a sensitive and rapid method that is suitable for accurate large-scale genotyping.

5' Untranslated Regions↗
PubMed2002

In situ RT-PCR detection of hepatitis C virus genotypes in Chinese patients with hepatocellular carcinoma.

The correlation of hepatitis C virus genotypes and the development of hepatocellular carcinoma is still controversial. The most pertinent studies are conducted by seroepidemiological methods. It has been suggested that tissue RT-PCR may be more efficient than serological testing for hepatitis C virus RNA. The purpose of this study was to investigate the infectious status of hepatitis C virus genotypes in hepatocellular carcinoma tissue for revealing the role of hepatitis C virus genotypes in carcinogenesis of hepatocellular carcinoma. Hepatitis C virus genotypes in cancerous and noncancerous liver tissues of 95 Chinese patients with hepatocellular carcinoma were analyzed by a modified type-specific in situ reverse transcription polymerase chain reaction (RT-PCR) method. Hepatitis C virus genotypes were simultaneously examined by Okamoto's method using extracts from hepatocellular carcinoma tissues. The hepatitis C virus genotypes in hepatocellular carcinoma tissues were found including 1b, 2a, mixed type (1b+2a) and 3a in 13, 23, 2 and 4 samples respectively. There was no significant difference in either the positivities between 1b (13.7%, 13/95) and 2a (24.2%, 23/95) (P>0.05) or the staining intensity and distribution of positive cells between 1b and 2a (p>0.05). No statistically significant difference was found between the two virus genotypes in main clinico-pathologic parameters of hepatocellular carcinoma. The localizations of hepatitis C virus RNA-positive signals were mainly cytoplasmic (22/36) in noncancerous regions, but nucleocytoplasmic (19/36) or nuclear (3/36) in cancerous regions. The positive nucleocytoplasmic/nuclear signals of genotype 1b (11/13) in hepatocellular carcinoma were seen more frequently than those of genotype 2a (11/23) (P<0.05). The discordant hepatitis C virus 2a and 1b positivities in serum samples and in cancerous tissues of hepatocellular carcinoma patients were also found, suggesting that the detection of serum hepatitis C virus genotypes in the patients with hepatocellular carcinoma may not reflect the actual status of hepatitis C virus genotypes in cancerous tissue. The pathogenetic significance of existence of hepatitis C virus gene in the nucleus of hepatocytes and malignant cells needs further investigation.

Asian People↗
PubMed2004

Molecular biological analysis of genotyping and phylogeny of severe acute respiratory syndrome associated coronavirus.

BACKGROUND: SARS-CoV is the causative agent of severe acute respiratory syndrome (SARS) which has been associated with outbreaks of SARS in Guangdong, Hong Kong and Beijing of China, and other regions worldwide. SARS-CoV from human has shown some variations but its origin is still unknown. The genotyping and phylogeny of SARS-CoV were analyzed and reported in this paper. METHODS: Full or partial genomes of 44 SARS-CoV strains were collected from GenBank. The genotype, single nucleotide polymorphism and phylogeny of these SARS-CoV strains were analyzed by molecular biological, bioinformatic and epidemiological methods. RESULTS: There were 188 point mutations in the 33 virus full genomes with the counts of mutation mounting to 297. Further analysis was carried out among 36 of 188 loci with more than two times of mutation. All the 36 mutation loci occurred in coding sequences and 22 loci were non-synonymous. The gene mutation rates of replicase 1AB, S2 domain of spike glycoprotein and nucleocapsid protein were lower (0.079% - 0.103%). There were 4 mutation loci in S1 domain of spike glycoprotein. The gene mutation rate of ORF10 was the highest (3.333%) with 4 mutation loci in this small domain (120 bp) and 3 of 4 loci related to deletion mutation. By bioinformatics processing and analysis, the nucleotides at 7 loci of genome (T:T:A:G:T:C:T/C:G:G:A:C:T:C) can classify SARS-CoV into two types. Therefore a novel definition is put forward that according to these 7 loci of mutation, 40 strains of SARS-CoV in GenBank can be grouped into two genotypes, T:T:A:G:T:C:T and C:G:G:A:C:T:C, and named as SARS-CoV Yexin genotype and Xiaohong genotype. The two genotypes can be further divided into some sub-genotypes. These genotypes can also be approved by phylogenetic tree of three levels of 44 loci of mutation, spike glycoprotein gene and complete genome sequence. Compared to various strains among SARS-CoV Yexin genotype and Xiaohong genotype, GD01 strain of Yexin genotype is more closely related to SARS-CoV like-virus from animals. CONCLUSION: The results mentioned above suggest that SARS-CoV is responding to host immunological pressures and experiencing variation which provide clues, information and evidence of molecular biology for the clinical pathology, vaccine developing and epidemic investigation.

Evolution, Molecular↗
PubMed2004

[Distribution of HBV genotypes in the Czech population--pilot study].

A compact structure of the hepatitis B virus genome does not provide much space for development of mutations capable of further replication. In spite of that, 7 genotypes have been described so far. Discovery of the hepatitis B virus (HBV) genome diversity led to a range of further questions. Individual genotypes are subjects of investigation these days as for the pattern of disease transmission, course of disease, and consequences of an infection. The aim of this pilot study was to describe genotype distribution in the infected population of the Czech Republic. Moreover, epidemiological and clinical characteristics were monitored in our sample. We studied a group of 65 patients with positive HBsAg from which 48 samples of patients were genotyped. PCR (polymerase chain reaction) method was used in order to amplify S region of the HBV genome. Direct sequencing of PCR products was used, this is the most accurate method for genotype identification. A relatively uniform genotypic distribution was identified within the study population--only 2 genotypes, A and D, were found. Genotype A was identified in 35 (73%) patients and genotype D in 13 (27%) patients. No statistically significant association between the particular genotype and epidemiological and clinical parameters was proved in this pilot study. This study brings basic information on genotype distribution. A possible proof of correlation with clinical and epidemiological characteristics will require examination of a larger sample of patients.

Adult↗
PubMed2004

Egyptian genotyping of Giardia lamblia.

Out of 105 patients infected with Giardia, 38 patients have Genotype I (36.19%), 13 have Genotype II (12.38%), 10 have Genotype III (9.52%), 16 have mixed Genotype infection (15.24%) and 28 with undetermined Giardia infection by PCR (26.67%). None of the control group gave positive results for Giardia in stool by PCR. So, the sensitivity of the test for detection and identification of Giardia Genotypes from the original stool samples was 73.33% and specificity was 100%. Out of 61 cases in the symptomatic group, the prevalence of Giardia Genotype I was 32.79%, Genotype II was 16.39%, Genotype III was 9.84%, mixed Genotype infection was 16.39% and undetermined Genotype was 24.59% as compared to 40.91%, 6.82%, 9.09%, 13.64% & 29.55% in the asymptomatic group respectively. There is statistically insignificant difference between both groups as regarding the prevalence of the different Giardia Genotypes. (P < or = 0.05). The use of PCR as a routine work for diagnosis of giardiasis is not accepted at least in the developing and under-developing countries due to its high cost, the high quality of technical staff and advanced laboratory equipments required for PCR performance. Its application is usually limited to research activities, the detection of water sources contamination and for the detection of a potential source of Giardia infection in epidemics.

Adolescent↗
PubMed2004

Distribution of hepatitis C virus genotypes in patients with chronic hepatitis C infection in India.

BACKGROUND & OBJECTIVES: Hepatitis C virus (HCV), an important cause of chronic hepatitis, cirrhosis and hepatocellular carcinoma, shows a considerable genetic heterogeneity among hepatitis C virus isolates from all over the world. At least six main groups of sequence variants are recognized. The natural history of disease and response to treatment may be related to the genotype of HCV in a particular patient. Antigenic differences between genotypes also have implications for optimal design of serological sequencing and confirmatory assays for HCV. The present study was undertaken with the objective to find out various genotypes of hepatitis C virus prevalent in Indian patients with chronic hepatitis C infection. METHODS: Thirty six consecutive newly diagnosed patients with chronic hepatitis C infection were included in the study. HCV RNA was extracted from the serum by standard guanidinium thiocyanate method. Following reverse transcription and amplification, the HCV genotypes were determined by line probe assay (INNO-LiPA HCV II). RESULTS: Of the 36 patients, genotype 3 was found in 24 (66.6%). Of these 24 patients, 3a was seen in 5 patients (13.8%), 3b in two (5.5%) and mixed subtype 3a and 3b in 17 patients (47.2%). Genotype 1 was found in 5 patients (13.8%), with 1b in 1 and 1a in rest four cases. Two patients (5.5%) were infected with genotype 2 (subtype 2a and mixed subtype 2a, 2b respectively). One (2.7%) was infected with genotype 4 (4a). Mixed genotype infection was found in 4 patients (11.1%). INTERPRETATION & CONCLUSION: The present findings showed that genotype 3 of hepatitis C virus was the most prevalent genotype in patients with chronic hepatitis C in this part of India.

DNA, Viral↗
PubMed2004

Distribution of HBV genotypes and mutants among hepatitis B infected patients from northern Poland.

Hepatitis B virus (HBV) infection is one of the major global epidemiological problems. The aim of our study was to determine the distribution of HBV genotypes in Poland since the data concerning the spread of HBV viruses in the central-eastern region of Europe is still very limited. HBV DNA was extracted from 58 serum samples. To quantify the level of HBV DNA the Roche Amplicor HBV Monitor Assay was used. To genotype and assign HBV subtypes DNA sequencing methods were performed. The HBV virus from 43 serum samples from hepatitis B infected patients was genotype A (74.1%), 12 cases had genotype D (20.7%), and 3 had the rare in Europe genotype F (5.2%). Prediction of HBV serological subtypes based on HBsAg sequencing showed almost 100% occurrence of subtype adw2 in the group of genotype A samples, three different subtypes in genotype D (ayw2, ayw3, and ayw4), and equal distribution of subtype adw4q- in all 3 cases of genotype F, also the most prevalent subtype in the Amerindians. Our results coincide with the general European HBV prevalence. However, HBV genotype F, which is not a common genotype in European countries, was detected and so was relatively high occurrence of genotype D, which may reflect historical and ethnical migration events in Poland in the past.

Adolescent↗
PubMed2004

Genotyping of human giardiasis in relation to anti-Giardia secretory IgA and mucosal histopathology.

Comparative study between the prevalence of pathological grading and Giardia genotypes revealed that, in patients infected with Giardia group I and II, out of patients having Giardia genotype I the prevalence of grade 0 was 13.16%, grade I was 21.05%, grade II was 47.37%, grade III was 13.16% and grade IV was 2.26% in comparison to 0%, 30.77%, 46.15%, 7.69% and 15.38% in genotype II (13 patients) and 10%, 40%, 20%, 20% and 10% in group III (10 patients) also in relation to 25%, 43.75%, 18.75%, 6.25% and 6.25% in mixed genotype infections group (16 patients) and 25%, 25%, 35.71%, 10.71% and 3.57% in undetermined infection group (28 patients) for grade 0, I, II, III & IV pathology respectively. There was no statistically significant difference regarding the prevalence of pathological grading in different Giardia genotypes in Gs I & II (P > 0.05). The mean OD of anti-Giardia secretory IgA in relation to Giardia genotypes in patients infected with Giardia Gs I & II was significantly different in the mean OD values of anti-Giardia secretory IgA in patients with different Giardia genotypes which were 1.091 +/- 0.377, 1.079 +/- 0.474, 1.524 +/- 0.503, 1.292 +/- 0.472 & 1.004 +/- 0.31 groups of genotype I, II, III, mixed genotypes infection and undetermined infection group respecttively (P > 0.05), being more increased in patients infected with Giardia genotype III and in mixed genotype infection.

Adolescent↗
PubMed2005

Response to interferon-based therapies in HIV-infected patients with chronic hepatitis C due to genotype 4.

BACKGROUND: The hepatitis C virus (HCV) genotype is the main predictor of response to interferon (IFN)-based therapies. HCV genotype 4 is spreading among European intravenous drug users, who are frequently coinfected with HIV. Information about treatment response in this subset of patients is scarce and conflicting results have been reported. METHODS: All HIV-infected patients treated for chronic hepatitis C at our institution with a minimum follow-up of 6 months after discontinuing therapy were retrospectively analysed. They had received one of three HCV treatment modalities: IFN monotherapy, IFN plus ribavirin (RBV) or pegylated interferon (PEG-IFN) plus RBV. Treatment responses were stratified according to HCV genotype. RESULTS: A total of 390 patients were analysed. Sustained virological response (SVR) to HCV therapy had been reached by 90 (23.1%): 22/119 (18.5%) with IFN monotherapy; 17/106 (16%) with IFN plus RBV; and 51/165 (30.9%) with PEG-IFN plus RBV. SVR was significantly higher among those with HCV genotypes 2 or 3 (40.4%; 61/151) than in patients with either HCV genotype 1 (11.2%; 22/197) or HCV genotype 4 (16.7%; 7/42) (P<0.0001). In contrast, there were no significant differences in the response rate comparing HCV genotypes 1 and 4 (P=0.53). CONCLUSIONS: Response to IFN-based therapies in HIV-positive patients with hepatitis C due to HCV genotype 4 is poor, similar to that obtained for HCV genotype 1 and much lower than for HCV genotypes 2 and 3. Therefore, HIV-infected patients with hepatitis C due to genotype 4 should be considered as a particular subset of difficult-to-treat patients. New treatment strategies and drugs for these patients are eagerly awaited.

Adult↗
PubMedDate not supplied

Is HBV genotyping of clinical relevance?

The hepatitis B virus, as is the case of the hepatitis C virus, can be categorized in several genotypes. The genotyping of HBV is based on the nucleotide sequence divergence encoding the amino acids constituting the HBV surface proteins. Since the genotype of the hepatitis C virus is shown to be related to epidemiology and response to interferon therapy, one wonders whether this also holds for the hepatitis B virus. HBV genotypes clearly are found to be different in various geographical areas of infection. In Europe, genotypes A and D are predominant, whereas in Asian patients genotypes B and C are more frequent, and in the Middle-East the genotype D. Data concerning the clinical relevance are less clear but it seems that in Europe, the genotype A has a higher HBeAg clearance rate and a better outcome. In Asia, genotype B (and especially the genotype Bj) is associated with a higher HBeAg clearance and with less development of cirrhosis and HCC. The impact on spontaneous or therapy induced viral resolution is not yet clearly identified. Further evaluation in different countries is needed to delineate the impact of the genotype relative to other factors such as age at infection, level of serum transaminases and viral load, on the course of infection, complication, outcome of treatment and prognosis.

Antiviral Agents↗
PubMed2005

Determination of hepatitis B genotypes in patients with chronic hepatitis B virus infection in Turkey.

BACKGROUND/AIMS: There are significant variations in the geographic distribution of hepatitis B virus genotypes throughout the world, and some genotypes are associated with different clinical outcomes. Eight genotypes of human hepatitis B virus (designated A-H) have been described to date. To determine the hepatitis B virus genotypes in Turkish patients with chronic liver disease and compare the results with clinical characteristics of the patients. METHODS: Fifty-four (pediatric: n=25 and adult: n=29) patients with chronic hepatitis B virus infection and with an hepatitis B virus DNA level above 5 pg/ml were entered into the trial. Restriction fragment length polymorphism method was used to determine hepatitis B virus genotype and their restriction fragment length polymorphism patterns. Hepatitis B virus DNA samples of 13 patients were sequenced automatically for further confirmation of restriction fragment length polymorphism results. RESULTS: Genotype D was the dominant genotype in all of our cases. Among six restriction fragment length polymorphism patterns of genotype D reported in the literature, three (D1, D2, D6) were present in our series and D2 was the most frequent restriction fragment length polymorphism pattern (81.5%). No significant differences were observed among different genotype D restriction fragment length polymorphism patterns with respect to patients' serum ALT, AST, and hepatitis B virus DNA titer, but D2 restriction fragment length polymorphism pattern was significantly more common in younger adults compared to D1 restriction fragment length polymorphism pattern. CONCLUSION: Genotype D with D2 restriction fragment length polymorphism pattern is the dominant hepatitis B virus genotype in all age groups in Turkey.

Adolescent↗
PubMed2006

[Identification of hepatitis B virus genotypes in patients with chronic hepatitis B from different nationalities in ethnic minority areas in Yunnan Province, China].

OBJECTIVE: To determine whether there is evolutionary difference in hepatitis B virus (HBV) genotypes among the patients with chronic hepatitis B (CHB) of different nationalities and its clinical significance. METHODS: Peripheral blood samples were collected from 50 CHB patients, 25 of diverse nationalities and 25 of Han nationality from the ethnic minority regions in Yunnan Province, China, The HBV preS2/S (pre S2/S) and C genes were amplified by PCR. The PCR products were inserted into the vector pBluescriptIISK (pBS). The cloned preS2/S and C genes were sequenced. RESULTS: The sequences of HBV preS2/S and C genes from the 50 patients were 846 (with 49.1% of GC) and 552 (with 46.1% of GC) nucleotides (nt) in length, and encoded 281 and 183 amino acids (aa) respectively. These findings were registered in GenBank Accession Numbers: AY517619, AY517620, AY517488, AY517489, AY517598, AY517599. Compared with the HBV and subtype sequences in the GenBank database, the HBV preS2/S and C genes among all the subjects were homologous to ayw1 in sequence by 97.5% - 98.6% and 94.5% - 97.8% respectively. The "a" determinant region of S genes in all cases were found to be Arginine (AGA) and Lysine (AAA) at corresponding aa 122nd and 160th respectively. HBV genotype B was identified in all patients with CHB (ayw1 subtype). Genotypes A, C, D, E, F, G, and H were not detected in any of them. The quasi-species nature of the HBV in the sera was observed in 2 of the 50 samples examined (4%). There was not a significant difference in the prevalence of HBV genotype B between the 25 diverse nationality patients and the 25 control Han nationality patients (P > 0.05). In the 50 CHB patients, the preS2/S genes were identified to have aa substitutions at the positions R124K (1.1%), L172P (1.3%), M306T (1.5%), and I361M (1.6%), with a frequency of more than 1%. In all subjects, the frequency of aa G145R (0.4%) substitutions was less than 1%. In all subjects, nt variations of C genes caused aa substitutions among aa 27 - 63, 80 - 110, and 135 - 153 involved in T and B cell epitopes. In 45 CHB patients, C genes was identified to have aa substitutions at the positions V 27, N38, V63, Q135, and A147, due to nt variations of 1979A to G, 2012T to A, 2088G to T, 2304C to A, and 2339A to G transitions respectively. The frequency of aa substitutions of C genes was more than 1%. Whereas as for the other 5 severe CHB patients, the C gene variations of A to G, and A to C transitions at nt positions 2159 and 2189 led to aa substitutions of S to G and I to L at positions G87 and L97. No insertion or deletion was found in preS2/S and C regions. HBV genotype B was not relevant to different nationalities (all P > 0.05). CONCLUSION: It is the first time that the genotype of the HBV epidemic strains in the ethnic minority areas of Yunnan Province has been identified as genotype B subtype ayw1. The HBV genotype B is not related with nationality. A novel genotyping method by using PCR, gene cloning, followed by DNA sequencing that can identify all major genotypes has been developed. HBV genotype B is the geographic original strain in this area and is correlated with the severity of liver diseases and curative effect. HBV viral is the only significant variable associated with the CHB patients' prognosis.

Adolescent↗