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PubMed2005

Serotyping of hepatitis C virus in hemodialysis patients: comparison with a standardized genotyping assay.

The aims of this study were to investigate the prevalence of hepatitis C virus (HCV) genotypes and serotypes in anti-HCV-positive hemodialysis patients and determine the concordance between genotyping and serotyping methods. Sixty-two hemodialysis patients were included in this study. HCV RNA was determined using polymerase chain reaction assay and genotypes using a line probe assay. HCV serotyping was performed with competitive enzyme-linked immunosorbent assay. Genotype 4 (52 patients) was the most predominant genotype, followed by type 1 (10 patients). The most prevalent HCV serotype was type 4 (41 patients), followed by serotype 1 (6 patients). We detected multiple serotypes in 4 patients and untypeable strains in 11. The overall sensitivity of serotyping assay was 82% for the study patients. According to the genotyping results, the sensitivity of serotyping was 60% and 86.5% for HCV types 1 and 4, respectively. There was a 100% concordance between results of serotyping and genotyping in the identification of HCV type 1 and 91% concordance in HCV type 4. Serological typing method may be of great value in microbiology laboratories that require a simple assay for identification of HCV genotypes, although the sensitivity of this assay may be limited by the immunocompetence of infected hemodialysis patients.

Adult↗
PubMed2006

The influence of mode of delivery and ACE genotype on serum angiotensin converting enzyme (ACE) activity in the mother and infant at term.

OBJECTIVE: Angiotensin converting enzyme (ACE) and its genotype have been shown to play a role in the pathophysiology of pregnancy complications such as pre-eclampsia and intrauterine growth restriction and possibly in adult onset chronic diseases. The physiological changes of ACE and the influence of its genotype during the intrapartum period are not well known. Hence the aim of this study was to assess serum ACE activity and its genotype in mothers and infants at term in relation to labour and mode of delivery. STUDY DESIGN: A cross sectional study of 99 women who laboured and 27 women who delivered by elective caesarean section after 36 completed weeks gestation with uncomplicated pregnancies. Venous cord bloods were obtained immediately after delivery of the placenta for serum ACE activity, ACE genotype and acid-base status. Maternal venous samples were obtained just after delivery for analysis of ACE activity and ACE genotype. Univariate analyses were performed using parametric tests for normally distributed data and nonparametric tests for the data that were not normally distributed. A multiple regression model was developed to adjust for potential confounding factors. RESULTS: The umbilical venous ACE activity was similar for infants delivered following labour compared to those delivered by elective caesarean section, 47.2 U/L (35-64) versus 40.1 U/L (31-60) (adjusted p=0.21). Maternal ACE activities were 28.9 U/L (22-35) and 32.1 U/L (22-40) respectively (adjusted p=0.17). The ACE activity in infants was higher than that of mothers 46 U/L versus 22 U/L, respectively (p= or <0.001). Neither the mode of delivery nor the presence of suspected fetal compromise influenced maternal or infant ACE activity. There was no influence of the infants' genotype on ACE activity in relation to mode of delivery. The DD genotype was associated with higher ACE activity in mothers (p=0.001) but not in infants (p=0.56). CONCLUSIONS: This study shows that intrapartum events do not affect ACE activity. These results will enhance our ability to investigate the role of ACE and its genotype in abnormal fetal growth and in subsequent adult onset chronic disease.

Acidosis↗
PubMed2004

Detection of hepatitis C virus by a user-developed reverse transcriptase-PCR and use of amplification products for subsequent genotyping.

BACKGROUND: Detection, quantitation and genotyping of hepatitis C virus (HCV) are important in selecting appropriate therapy. Current commercially available HCV genotyping kits, including sequencing-based TRUGENE HCV 5'NC and hybridization-based INNO-LiPA HCV II assays, rely on amplification products (amplicons) generated by HCV reverse-transcriptase (RT)-PCR methods such as the Roche AMPLICOR HCV test. METHODS: We developed a one-step RT-PCR assay to amplify and detect HCV RNA, and the resulting amplicons were used for HCV genotyping (TRUGENE). A total of 142 clinical samples were used to compare results from the RT-PCR/TRUGENE assay and those generated by the COBAS AMPLICOR and INNO-LiPA tests. RESULTS: Eighty-seven of 108 plasma specimens which were positive by AMPLICOR were also positive by the user-developed RT-PCR, giving a sensitivity of 100.0%. The RT-PCR detected 2 of 21 AMPLICOR-negative specimens and none of 34 HCV-EIA-negative serum specimens, giving a specificity of 96.4%. The 87 amplicons from the RT-PCR yielded HCV genotypes. HCV genotype results from both TRUGENE and INNO-LiPA were all in agreement. The TRUGENE and INNO-LiPA assays identified 69 (79.3%) and 47 (54.0%) specimens, respectively at the subtype level. HCV subtype information agreed by both assays in 34 of 36 (99.4%) specimens. One specimen with HCV genotypes 2 and 4 by INNO-LiPA was classified as a single genotype 2 by TRUGENE. CONCLUSION: Our data showed that the user-developed RT-PCR has comparable sensitivity and specificity for the detection of HCV in clinical specimens. The amplicons generated by the RT-PCR can be used for HCV genotyping by the sequencing-based TRUGENE assay.

Base Sequence↗
PubMed2006

Prevalent HBV genotypes and subtypes in a South Indian population.

BACKGROUND: Genotypes or genetic subtypes describe genetically related strains and have been described for viruses belonging to several different families. The eight major genotypes of hepatitis B virus (HBV) have distinct geographic distribution. Recent studies suggest possible pathogenic and therapeutic differences among HBV genotypes. OBJECTIVES: To evaluate the HBV genotypes of 85 samples by RFLP analysis and sequence the desired region to look for variations and identify the subtypes of the surface region. STUDY DESIGN: We studied 85 patients with HBV in order to identify the most prevalent genotype and subtype. Patients with HBV-related liver disease attending the Department of Gastroenterology at Owaisi Hospital and Research Centre were studied. RESULTS AND CONCLUSIONS: Genotype D1 was most prevalent. Genotyping was carried out by RFLP analysis and confirmed by sequencing. Nucleotide sequences showed significant homology (96-97%) with the other genotypes that have been reported. Subtype ayw was the most prevalent subtype within the surface region. Construction of a phylogenetic tree incorporating these isolates and other published HBV sequences showed that the isolates are derived from the same evolutionary tree. The study adds to our understanding of the genetic diversity of HBV and the geographical distribution of its subtypes, and will be useful for reconstructing the evolutionary history of HBV.

Adult↗
PubMed2005

An in vitro model of hepatitis C virus genotype 3a-associated triglycerides accumulation.

BACKGROUND/AIMS: The hepatitis C virus (HCV) induces lipid accumulation in vitro and in vivo. Although clinical observations are consistent with a direct effect of HCV genotype 3a on lipid metabolism, experimental systems have focused on the expression of HCV proteins of genotype 1. To extend these observations, we established an in vitro model expressing the HCV core of different genotypes. METHODS: The HCV core protein from patients with severe (genotype 3a) or no (genotypes 1b, 2a, 3h, 4h and 5a) liver steatosis was expressed in Huh7 cells. Core protein expression (by immunohistochemistry and immunoblot) and triglycerides accumulation (by Oil Red O stain and enzymatic measurement) were evaluated 48h after transfection. RESULTS: Although triglyceride accumulation occurred with genotypes 1b, 3a and 3h, the genotype 3a core protein expression resulted in the highest level of accumulation (i.e. about 3-fold with respect to 1b, and 2-fold with respect to 3h). This effect was not related to core protein expression levels and was abolished by culturing cells in lipid-free medium. CONCLUSIONS: Consistent with observations in chronic hepatitis C patients, the in vitro expression of HCV genotype 3a core protein is the ideal candidate model for studying the mechanisms of HCV-associated steatosis.

Adult↗
PubMed2005

GNB3 C825T polymorphism and response to interferon-alfa/ribavirin treatment in patients with hepatitis C virus genotype 1 (HCV-1) infection.

BACKGROUND/AIMS: The outcome of infection with the hepatitis C virus (HCV) has been shown to be influenced by genetic host factors. The G protein beta3 subunit (GNB3) C825T polymorphism has been shown to determine immune cell functions in vitro. We investigated the association of GNB3 genotypes with treatment response in HCV-infected patients. METHODS: We genotyped 1781 HCV-free blood donors and 232 HCV-infected patients treated with interferon-alfa/ribavirin. Sustained virologic response (SVR) was defined by undetectable HCV-RNA 24 weeks after discontinuation of therapy. Non-response (NR) was defined by positive HCV-RNA at the end of at least 24 weeks of treatment. GNB3 genotypes were determined by DNA restriction enzyme analyses. RESULTS: Genotype distribution was not significantly different in healthy controls and HCV-infected patients. Only in HCV genotype 1-infected patients a significant correlation between GNB3 CC genotype and NR could be observed (6 TT, 42 TC, 54 CC) versus SVR (11 TT, 25 TC, 19 CC) patients (P = 0.004). In a logistic regression analysis including biochemical and virologic characteristics, only GNB3 CC genotype was significantly associated with NR (OR 4.9; 95% CI = 1.4-16.5; P = 0.011). CONCLUSIONS: The GNB3 825 CC genotype is associated with NR in HCV-1-infected patients.

Antiviral Agents↗
PubMed2004

Hepatitis B virus genotyping based on cluster analysis of the region involved in lamivudine resistance.

Hepatitis B virus (HBV) genotyping and treatment resistances analysis provide key information for the study of infected patients. Among the existing HBV genotyping methods, restriction fragment length polymorphism (RFLP) based methods are used widely, but HBV genetic variability may lead to wrong results. A simple method for HBV genotyping is described. This single assay provides information related to both genotyping and lamivudine resistance. measuring genotyping reliability. A short region including the YMDD motif of the polymerase gene was analyzed using cluster analysis of 55 isolates. To discriminate the seven HBV genotypes, a selected fragment was used as representative of each genotype (consensus sequences). Comparison between complete genomes from GenBank and from the YMDD analysis using PHILIP package was used for method testing. Sequencing of 102 different serum samples was carried out, and the results were compared with representative sequences. Consensus sequences were chosen corresponding to the different HBV genotypes. Statistical comparison between our method and others gives more than 90% of coincidences with a critical level of 0.056. Comparison between RFLP and the method described gives 3% of discordance results and 3% of untypables samples by RFLP. All the discordant results observed had a change in the pre-S sequence which introduced a new restriction site.

Amino Acid Motifs↗
PubMed2005

Possible interactions of the endothelial constitutive nitric oxide synthase genotype with alcohol drinking and walking time for high serum uric acid levels among Japanese.

A variable number of tandem repeat polymorphism located in intron 4 of the gene for endothelial constitutive nitric oxide synthase (ecNOS) is reported to be significantly associated with the nitric oxide level, which influences serum uric acid (SUA). To cast light on any association between the polymorphism and hyperuricemia, as well as gene-environment interactions, a cross-sectional study was conducted for 703 health checkup examinees (213 men and 490 women). The age-adjusted odds ratio (aOR) of hyperuricemia (> or =7 mg/dL) for ecNOS 4/4, 4/5, or 5/6 genotypes (non-5/5 group) as compared with the 5/5 genotype was 2.41 (95% confidence interval [CI], 1.09-5.30) in men. The aORs for drinking alcohol relative to never drinking were found to be 8.93 (95% CI, 1.02-78.16) among men with non-5/5 genotypes and 1.76 (95% CI, 0.59-5.26) for their 5/5 counterparts. Moreover, the aORs for heavy drinking (> or =50 mL/d) were 23.16 (95% CI, 2.14-250.35) and 2.48 (95% CI, 0.75-8.15), respectively. The interaction between the genotype and current drinking was 3.10 (95% CI, 0.45-21.41). The aORs for more than 30 minutes of daily walking relative to 30 minutes or less of daily walking were found to be 1.54 (95% CI, 0.40-5.95) among men with non-5/5 genotypes and 0.31 (95% CI, 0.12-0.81) for their 5/5 counterparts. The interaction between the genotype and more than 30 minutes of daily walking was 4.92 (95% CI, 0.95-25.64). This study indicated that the ecNOS variable number of tandem repeat polymorphism influences the SUA level in men. Although the interactions were not significant, alcohol intake may be more influential among men with non-5/5 genotypes and walking may be more effective among men with the 5/5 genotype. These findings would be informative for men with high SUA levels.

Adult↗
PubMed2004

Impact of donor and recipient cytokine genotypes on renal allograft outcome.

Allelic differences in gene promoter or codifying regions have been described to affect regulation of gene expression, consequently increasing or decreasing cytokine production and signal transduction responses to a given stimulus. This observation has been reported for interleukin (IL)-10 (-1082 A/G; -819/-592 CT/CA), transforming growth factor (TGF)-beta (codon 10 C/T, codon 25 G/C), tumor necrosis factor (TNF)-alpha (-308 G/A), TNF-beta (+252 A/G), interferon (IFN)-gamma (+874 T/A), IL-6 (-174 G/C), and IL-4R alpha (+1902 G/A). To evaluate the influence of these cytokine genotypes on the development of acute or chronic rejection, we correlated the genotypes of both kidney graft recipients and cadaver donors with the clinical outcome. Kidney recipients had 5 years follow-up, at least 2 HLA-DRB compatibilities, and a maximum of 25% anti-HLA pretransplantation sensitization. The clinical outcomes were grouped as follows: stable functioning graft (NR, n = 35); acute rejection episodes (AR, n = 31); and chronic rejection (CR, n = 31). The cytokine genotype polymorphisms were defined using PCR-SSP typing. A statistical analysis showed a significant prevalence of recipient IL-10 -819/-592 genotype among CR individuals; whereas among donors, the TGF-beta codon 10 CT genotype was significantly associated with the AR cohort and the IL-6 -174 CC genotype with CR. Other albeit not significant observations included a strong predisposition of recipient TGF-beta codon 10 CT genotype with CR, and TNF-beta 252 AA with AR. A low frequency of TNF-alpha -308 AA genotype also was observed among recipients and donors who showed poor allograft outcomes.

Cytokines↗
PubMed2006

Hepatitis C virus genotypes in southern Taiwan: prevalence and clinical implications.

The role of hepatitis C virus (HCV) genotypes in the development of hepatocellular carcinoma (HCC) is still controversial. To determine the distribution and clinical implications of HCV genotypes in southern Taiwan, we analysed 418 patients with chronic HCV infections. HCV genotypes were determined using an HCV Line Probe Assay. The predominant HCV genotype was 1b (45.5%), followed by 2a/2c (30.9%) and 2b (6.9%). The prevalence of genotype 1b in HCC patients (60.3%) was significantly higher than in those with liver cirrhosis (38.7%) and chronic hepatitis (38.7%) (P=0.003 and P<0.001, respectively). Patients with chronic HCV 2a/2c infection had higher alanine aminotransferase (ALT) levels than those with chronic HCV 1b infection (P<0.001). Univariate analysis revealed that disease severity was significantly correlated with older age, genotype 1b, lower ALT levels and lower viral load. Based on multiple logistic regression analysis, after adjusting for age and serum HCV RNA levels, HCV 1b infection was still a significant risk factor for HCC. In conclusion, the predominant genotypes in southern Taiwan were 1b and 2a/2c, and disease severity was associated with genotype 1b.

Aged↗
PubMed2005

Genotypes of TNF-alpha, VEGF, hOGG1, GSTM1, and GSTT1: useful determinants for clinical outcome of bladder cancer.

OBJECTIVES: To determine whether polymorphisms of tumor necrosis factor-alpha (TNF-alpha), vascular endothelial growth factor (VEGF), human 8-oxoguanine DNA glycosylase 1 (hOGG1), glutathione S-transferase-mu (GSTM1), and glutathione S-transferase-phi (GSTT1) are risk factors for bladder cancer among Koreans. METHODS: We performed polymerase chain reaction-restriction fragment length polymorphism and multiplex polymerase chain reaction in blood genomic DNA of 153 patients with primary bladder cancer and 153 control subjects. RESULTS: GSTM1-negative, GSTT1-positive, and hOGG1 Ser326Ser and Ser326Cys genotypes are risk factors for bladder cancer (P = 0.020, P = 0.044, and P = 0.012, respectively). The cancer stage was significantly associated with the TNF-alpha genotype (GG versus GA and AA; P = 0.036). A notable correlation was observed between the VEGF genotype and grade (P = 0.015). In patients with superficial bladder cancer, the hOGG1 genotype was related to recurrence. The hOGG1 Ser326Ser and Ser326Cys genotypes were risk factors for superficial bladder cancer recurrence compared with the Cys326Cys genotype (P = 0.033, adjusted odds ratio 5.580, 95% confidence interval 1.145 to 27.183). Patients with the GSTM1-positive genotype were at a 3.3-fold increased risk of cancer progression compared with those with the GSTM1-negative genotype (P = 0.009, adjusted odds ratio 0.303, 95% confidence interval 0.123 to 0.745). CONCLUSIONS: Our data collectively suggest that these genetic polymorphisms may be useful as prognostic markers for bladder cancer in the clinical setting.

Biomarkers, Tumor↗
PubMed2004

Estimation of genotype error rate using samples with pedigree information--an application on the GeneChip Mapping 10K array.

Currently, most analytical methods assume all observed genotypes are correct; however, it is clear that errors may reduce statistical power or bias inference in genetic studies. We propose procedures for estimating error rate in genetic analysis and apply them to study the GeneChip Mapping 10K array, which is a technology that has recently become available and allows researchers to survey over 10,000 SNPs in a single assay. We employed a strategy to estimate the genotype error rate in pedigree data. First, the "dose-response" reference curve between error rate and the observable error number were derived by simulation, conditional on given pedigree structures and genotypes. Second, the error rate was estimated by calibrating the number of observed errors in real data to the reference curve. We evaluated the performance of this method by simulation study and applied it to a data set of 30 pedigrees genotyped using the GeneChip Mapping 10K array. This method performed favorably in all scenarios we surveyed. The dose-response reference curve was monotone and almost linear with a large slope. The method was able to estimate accurately the error rate under various pedigree structures and error models and under heterogeneous error rates. Using this method, we found that the average genotyping error rate of the GeneChip Mapping 10K array was about 0.1%. Our method provides a quick and unbiased solution to address the genotype error rate in pedigree data. It behaves well in a wide range of settings and can be easily applied in other genetic projects. The robust estimation of genotyping error rate allows us to estimate power and sample size and conduct unbiased genetic tests. The GeneChip Mapping 10K array has a low overall error rate, which is consistent with the results obtained from alternative genotyping assays.

Computer Simulation↗
PubMed2002

Single Strand Conformation Polymorphism (SSCP) as a quick and reliable method to genotype M235T polymorphism of angiotensinogen gene.

OBJECTIVES: Conflicting results on the relationship between M235T polymorphism of angiotensinogen (AGT) gene and diabetic nephropathy are reported in the literature, probably due to the small number of subjects, to different inclusion criteria and the different genotype analysis methods used. The aim of the present study was to set up a fast, cheap and reliable method to allow the genotyping of M235T polymorphism in a large number of subjects. DESIGN AND METHODS: We developed in our laboratory a new specifically designed PCR-SSCP method for M235T genotyping whose specificity was compared with that of Allele Specific PCR (ASPCR) and Mutagenically Separated PCR (MS-PCR). The exact M235T genotype was estabilished by direct sequencing. The new PCR-SSCP method was then used to genotype a population of 1171 hypertensive, normoalbuminuric type II diabetes mellitus patients. The patients were also genotyped for ACE I/D polymorphism. For comparison a group of hypertensive non diabetic patients (n = 88) were also screened. RESULTS: The PCR-SSCP method identified the M235T polymorphism with no misinterpretation at variance with ASPCR and MS-PCR methods that showed a preferential amplification of the T allele. The rare Y248C polymorphism of the AGT gene was also detected by PCR-SSCP. In diabetic hypertensive patients the prevalence of TT genotype was higher than in normotensive healthy controls and equivalent to that found in hypertensive non diabetic patients. CONCLUSIONS: The PCR-SSCP method for detection of M235T polymorphism is a powerful and sensitive tool for rapid, cheap and efficient screening of a large number of samples. The results obtained with this method demonstrate an association of the TT genotype of AGT gene with hypertension, both in diabetic and non diabetic patients.

Adult↗
PubMed1999

A multiplex PCR for unequivocal differentiation of all encapsulated and non-encapsulated genotypes of Trichinella.

We have developed a single PCR test for the simple and unequivocal differentiation of all currently recognised genotypes of Trichilnella. Partial DNA sequence data were generated from internal transcribed spacers ITS1 and ITS2, and from the expansion segment V region of the ribosomal DNA repeat from five species of Trichinella and two additional genotypes, designated T5 and T6. Five different PCR primer sets were identified which, when used simultaneously in a multiplex PCR, produce a unique electrophoretic DNA banding pattern for each species and genotype including three distinct genotypes of Trichinella pseudospiralis. The banding patterns for each parasite genotype consist of no more than two well-defined DNA fragments, except isolates of T. pseudospiralis which generate multiple, closely migrating bands. The expansion segment V-derived primer set contributes at least one fragment to each genotypic pattern and, therefore, functions both as a means for differentiation as well as an internal control for the PCR. The reliability and reproducibility of each DNA banding pattern were verified using multiple geographical isolates of each Trichinella genotype. The technique was developed further to distinguish genotypes at the level of single muscle larvae using a nested, multiplex PCR, whereby the entire internal transcribed spacer region as well as the gap region of the expansion segment V of the large subunit ribosomal DNA are amplified concurrently in a first-round PCR using primer sets specific for each region, followed by the multiplex PCR for final diagnosis.

Animals↗
PubMed1996

Resting energy expenditure, pulmonary inflammation, and genotype in the early course of cystic fibrosis.

To further investigate the early course of cystic fibrosis (CF), specifically to examine factors contributing to energy imbalance, we examined resting energy expenditure (REE) (by indirect calorimetry) per unit body weight and metabolically active body cell mass (by total body potassium), in relation to CF genotype (by genomic DNA analysis), CF pancreatic phenotype, and markers of pulmonary inflammation (from bronchoalveolar lavage fluid). Eighteen subjects with presymptomatic CF who were less than 2 years of age (n = 11, delta F508/ delta F508 genotype; n = 15, pancreatic insufficiency phenotype), identified by newborn screening, were compared with age-, sex-, and length-matched control subjects (n = 13). Those with the delta F508/ delta F508 genotype had significantly higher mean REE expressed per unit body weight (125%) and body cell mass (115%; p < 0.03). Those with other genotypes (n = 7) did not, as a group, have significantly different mean REEs, but individuals with known "severe" genotypes had REEs in the high range and those with a pancreatic-sufficient phenotype had significantly lower REE than those with a pancreatic-insufficient phenotype (p < 0.05), and REEs were in the normal range. Examination of bronchoalveolar lavage fluid revealed positive culture results (7/10) but variable colony counts, neutrophil percentages, and concentrations of interleukin-8 and interleukin-1 beta equally in both CF genotype groups. These markers of pulmonary inflammation were not correlated, individually or collectively, with REE or genotype. We conclude that genotypic variations in energy balance are detectable early in CF unrelated to lung inflammation. Subclinical defects in body composition and pulmonary integrity occur early in CF and, in combination with increased cellular metabolic activity, have important clinical implications with respect to early diagnosis and management.

Body Composition↗
PubMed2003

Effect of genotype on phenotype and mortality in cystic fibrosis: a retrospective cohort study.

BACKGROUND: Over 1000 mutations of the cystic fibrosis transmembrane conductance regulator gene (CFTR) that cause cystic fibrosis have been identified. We examined the effect of CFTR genotype on mortality and disease phenotype. METHODS: Using the US Cystic Fibrosis Foundation National Registry, we did a retrospective cohort study to compare standardised mortality rates for the 11 most common genotypes heterozygous for DeltaF508 with those homozygous for DeltaF508. Of the 28455 patients enrolled in the registry at the time of our analysis, 17853 (63%) were genotyped. We also compared the clinical phenotype, including lung function, age at diagnosis, and nutritional measures, of 22 DeltaF508 heterozygous genotypes. Mortality rates and clinical phenotype were also compared between genotypes classified into six classes on the basis of their functional effect on CFTR production. FINDINGS: Between 1991 and 1999, genetic and clinical data were available for 17853 patients with cystic fibrosis, which was 63% of the total cohort. There were 1547 deaths during the 9 years of follow-up. In the analysis of the 11 most common genotypes, DeltaF508/R117H, DeltaF508/DeltaI507, DeltaF508/3849+10kbC-->T, and DeltaF508/2789+5G-->A had a significantly lower mortality rate (4.7, 8.0, 11.9, and 4.4, respectively) than the genotype homozygous for DeltaF508 (21.8, p=0.0060). DeltaF508/R117H, DeltaF508/DeltaI507, DeltaF508/ 3849+10 kbC-->T, DeltaF508/2789+5G-->A, and DeltaF508/A455E have a milder clinical phenotype. Outcomes for all functional classes were compared with that of class II (containing DeltaF508 homozygotes) and classes IV and V had a significantly lower mortality rate and milder clinical phenotype. INTERPRETATION: Patients with cystic fibrosis have distinct genetic subgroups that are associated with mild clinical manifestations and low mortality. These differences in phenotype are also related to the functional classification of CFTR genotype.

Adolescent↗
PubMed1997

Rapid and sensitive genotyping of hepatitis C virus by single-strand conformation polymorphism.

There is an increasing demand for genotyping hepatitis C virus (HCV) isolates due to the rapidly expanding list of distinct HCV genotypes and the mounting evidence of genotype-specific clinical consequences. We describe an SSCP-based assay for determining genotypes in HCV infections. HCV RNA extracted from serum was amplified by a sensitive nested-PCR assay producing a 287 bp fragment of the conserved 5' non-coding region (NCR) and analysed by non-denaturing polyacrylamide gel electrophoresis. Following empirical optimisation of the SSCP assay we identified distinct conformation polymorphisms (characteristic band patterns) corresponding to types 1a, 1b, 2a, 2b, 2c, 3 and 4 found in the Western Australian population. Seventy-three HCV RNA-positive samples were used to evaluate the SSCP genotyping assay for accuracy and efficiency by comparison with the previously established genotyping methods of manual direct sequencing and dideoxy fingerprinting. SSCP genotyping was in concord with control methods while performing more rapidly and at a fraction of the cost. Moreover, SSCP detected two co-infected samples that were not shown by the control methods. The PCR-SSCP assay provides an accurate and rapid method for genotyping of HCV RNA-positive samples at the 5' NCR by type-specific sequence polymorphisms which is applicable to large-scale screening.

DNA, Viral↗
PubMed1998

A novel method for pestivirus genotyping based on palindromic nucleotide substitutions in the 5'-untranslated region.

A simple and practical method was developed for pestivirus genotyping based on analysis of the secondary structures in the 5'-untranslated region (UTR). Three stable stem-loop structures, V1, V2 and V3, predicted by computer in the 5'-UTR, included strictly conserved consensus base-pairings which are shared by all the genotypes of pestivirus or are characteristic to each genotype of pestivirus. On the basis of the palindromic nucleotide substitution at the secondary structural level, six genotypes have been identified among pestivirus strains, irrespective of the cytopathic and non-cytopathic biotypes. They are genotypes Ia, Ib, Ic and II in bovine viral diarrhea virus, genotype III in border disease virus, and genotype IV in classical swine fever virus. The stable stem-loop structures, which were maintained by palindromic nucleotide substitutions in the stem region, may represent references for the classification and identification of pestivirus species and/or genotypes.

Animals↗