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PubMed2005

MALDI-TOF MS and TaqMan assisted SNP genotyping of DNA isolated from formalin-fixed and paraffin-embedded tissues (FFPET).

Formalin-fixed paraffin-embedded tissues (FFPET) from archived clinical samples provide an invaluable source for large-scale molecular genetic studies. Pharmacogenetic investigations that require long-term clinical follow-up data of patients may particularly benefit from FFPET analysis. Matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and TaqMan-based (Thermus aquaticus polymerase) methodologies have become standard genotyping procedures. However, no data are available on the applicability of MALDI-TOF MS to the genotyping of low quality DNA, as it is usually obtained from FFPET, and data from TaqMan genotyping are limited. We isolated constitutional DNA from 274 FFPET samples (229 patients with breast cancer and 45 patients with benign breast diseases) and genotyped 15 polymorphic loci in 10 genes. Nine SNPs were genotyped by MALDI-TOF MS, and six were genotyped by the TaqMan methodology. We established rates for successful allele assignment for all FFPET, for FFPET prepared prior to 1990, and for FFPET prepared post-1990. Both methodologies showed high success rates ranging between 70.9 and 99.6% (mean: 91.8%) for MALDI-TOF MS and between 82.3 and 97.7% (mean: 91.0%) for TaqMan genotyping. No significant differences in genotyping performances for FFPET prepared prior to 1990 or post-1990 were observed. With the exception of one, all other genotype frequencies were in Hardy-Weinberg equilibrium. Furthermore, genotype frequencies matched those observed in a German breast cancer population and other Caucasian populations. Our study shows for the first time that MALDI-TOF MS and TaqMan genotyping procedures provide reliable data, and are therefore applicable in studies that require large scale FFPET genotyping.

Alleles↗

PubMed2006

A quality assessment survey of SNP genotyping laboratories.

To survey the quality of SNP genotyping, a joint Nordic quality assessment (QA) round was organized between 11 laboratories in the Nordic and Baltic countries. The QA round involved blinded genotyping of 47 DNA samples for 18 or six randomly selected SNPs. The methods used by the participating laboratories included all major platforms for small- to medium-size SNP genotyping. The laboratories used their standard procedures for SNP assay design, genotyping, and quality control. Based on the joint results from all laboratories, a consensus genotype for each DNA sample and SNP was determined by the coordinator of the survey, and the results from each laboratory were compared to this genotype. The overall genotyping accuracy achieved in the survey was excellent. Six laboratories delivered genotype data that were in full agreement with the consensus genotype. The average accuracy per SNP varied from 99.1 to 100% between the laboratories, and it was frequently 100% for the majority of the assays for which SNP genotypes were reported. Lessons from the survey are that special attention should be given to the quality of the DNA samples prior to genotyping, and that a conservative approach for calling the genotypes should be used to achieve a high accuracy.

Clinical Laboratory Techniques↗

PubMed2001

Genetic characterization of hypervariable region 1 in patients chronically infected with hepatitis C virus genotype 2.

The hypervariable region 1 (HVR1) has been most reliably identified in the genome of HCV genotype 1 isolates and thought to possibly play a role in immune evasion and development of chronic infection. There are few studies, however, of other HCV genotypes to determine if they also have such a hypervariable region present, and it is unclear whether or not there is any genotype-dependent difference in the genetic characteristics of HVR1. We determined the nucleotide sequence of 5' end of E2/NS1 region of the HCV genome spanning HVR1 of multiple genotype 1 and 2 HCV isolates and carried out a detailed genetic analysis. Similarity plots identified two hypervariable regions within the genotype 2 sequences, a larger one corresponding to HVR1 as well as a smaller 27-nucleotide region of hypervariability. The synonymous substitutions per synonymous site (ds) was greater than nonsynonymous substitutions per nonsynonymous site (dn) within genotype 1 group whereas dn and ds were similar in the genotype 2 group. Analysis of amino acid sequences revealed several conserved sites across genotype 1 and 2 (amino acid numbers 2,6, 20 and 26) and overall similar hydropathic profiles were found within two genotypes. Still, despite the hypervariability, the HVR1 showed a genotype-specific phylogenetic clustering. Thus, HVR1 appears to be conserved between genotypes in keeping with it having an important survival function. Genotype 2 appears to have a greater rate of nonsynonymous substitutions within HVR1, suggesting a greater positive evolutionary pressure.

Amino Acid Sequence↗

PubMed2004

Clade analysis and surface antigen polymorphism of hepatitis B virus American genotypes.

Eight genotypes (A-H) of hepatitis B virus (HBV) have been described, HBV genotypes F and H being autochthonous to America. HBV genotype F has been classified in four clusters. The objective of this study was to gain insight into the molecular epidemiology of HBV American genotypes, as well as to analyze the genotype-related polymorphism in some functional domains of the surface proteins. The sequences of the S region of 106 isolates genotype F and H were analyzed, out of which 47 isolates genotype F circulated in different Venezuelan populations. Most of the Venezuelan isolates genotype F were grouped in cluster III (n = 39) and 7 in cluster II. One isolate obtained from a blood donor could not be classified in any clade and harbored amino acid substitutions characteristic of a vaccine escape mutant (G145R) and a stop codon in the surface antigen. Amino acid analysis of the PreS and S gene products showed unique genetic characteristics in genotype F and H sequences in some important domains involved in the early steps of infection. Out of 30 available sequences, two complete genome sequences of HBV genotype F from Venezuela were obtained. Phylogenetic analysis of these complete genomes confirmed the presence of four clusters inside genotype F, differing in more than 4% nucleotide divergence. Our extended analysis showed that genotype F clades Ia, III, and IV exhibit a restricted geographic distribution (Central America, the North and the South of South America, respectively) while clades Ib and II are found in all the Americas except in the Northern South America and North America respectively.

Americas↗

PubMed2001

Genotype may correlate with liver carcinogenesis and tumor characteristics in cirrhotic patients infected with hepatitis B virus subtype adw.

To identify the influence of hepatitis B virus (HBV) genotype on development of hepatocellular carcinoma (HCC) and clinical outcome in chronic HBV infection, 26 consecutive cirrhotic patients infected with HBV subtype adw were investigated prospectively. HBV serology was undertaken using subtype-specific antibodies against hepatitis B surface antigens. The HBV genotype was determined by sequencing directly the polymerase chain reaction products of the HBV S gene. When HCC occurred, patients underwent transcatheter arterial embolization therapy. If tumor necrosis was incomplete, additional embolization therapy was carried out after a 3- to 4-month interval. At a median follow-up of 14.1 years (range 2.2 to 31.7), HCC occurred in 9 (35%) of 26 patients. Nineteen patients were infected with genotype B and 7 with genotype C. Four of the 19 genotype B patients (21%) and 5 of the 7 genotype C patients (71%) developed HCC (P = 0.058). Patient age (<45 years or 45 < or = ) at diagnosis of cirrhosis was the only significant independent factor influencing liver carcinogenesis by multiple logistic regression analysis and Cox's regression analysis (P = 0.0069 and 0.029, respectively). When analysis was limited to the age of 45 years or more at the last visit, genotype was the only contributory factor to HCC development by univariate analysis (P = 0.038). Whereas genotype B patients responded well to embolization therapy and had no recurrence of HCC for a prolonged period of time, genotype C patients showed poor responses and died of hepatic failure due to rapid HCC progression despite embolization therapy. The cumulative incidence of survival was significantly higher in the genotype B group (P = 0.0049). The HBV genotype correlated with the development of HCC, response to embolization therapy, and recurrence of HCC. Determination of HBV genotype may be useful in predicting outcomes in HBV subtype adw-related cirrhosis.

Adult↗

PubMed2002

Detection and genotyping of human papillomavirus DNA by SPF10 and MY09/11 primers in cervical cells taken from women attending a colposcopy clinic.

Human papillomavirus (HPV) is the main etiological agent of cervical cancer. There is a large number of HPV genotypes and therefore a need to distinguish the high risk HPV genotypes associated with invasive cancer from the low risk. Because persistence of high risk HPV infection is necessary for progression of a pre-invasive cervical change one needs to identify the individual genotype to see if it persists. PCR amplification of HPV DNA is described using two consensus primer systems from cervical cells. Amplified HPV DNA was genotyped using a reverse hybridization line probe assay (LiPA). HPV DNA was amplified from 42% of samples by MY09/11 and from 80% by SPF10. In 42 samples HPV DNA was detected by both primer sets and in 38 samples only the SPF10 primers detected HPV DNA. The LiPA detected 21 different HPV genotypes (13 high risk) in this cohort of samples. Forty-three percent contained a single HPV genotype and 24% contained multiple infections (2-5 genotypes). Overall, high risk HPV genotypes were detected in 48% of the cervical samples, the most frequent types were 16, 18, 31, and 51. The proportion of high risk HPV genotypes increased with more severe cytological abnormalities. This study demonstrates that the SPF10 primer set is more sensitive than the MY09/11 primer set and that genotyping by LiPA tells us if the HPV infection is caused by a high risk type and if the infection is mixed. Additionally LiPA provides information about the individual genotype when looking for persistence of infection. HPV DNA detection and genotyping is therefore a useful tool in the colposcopy clinic, used in conjunction with cytology.

Ambulatory Care↗

PubMed1999

Association of VDR and estrogen receptor genotypes with bone mass in postmenopausal Caucasian women: different conclusions with different analyses and the implications.

Much work has been done on the association between vitamin D receptor (VDR) genotypes and bone mineral density (BMD). Despite considerable effort, the results are inconsistent. While the VDR association remains unresolved, studies have expanded to other candidate genes (i.e., estrogen receptor (ER) genotypes), also yielding inconsistent results. A few studies have suggested that interaction effects between VDR and ER genotypes significantly affect BMD. We assessed associations of BMD with VDR BsmI genotypes, and ER XbaI and PvuII polymorphisms (denoted as ERX and ERP respectively) with spine, femoral neck, distal radius BMD, and with total body bone mineral content (tbBMC) in 108 US Mid-western postmenopausal Caucasian women. We statistically controlled for confounding factors such as height, weight, etc., in the analysis. No significant association was detected for ER genotypes with spine and radius BMD, or for VDR genotypes with femoral neck and radius BMD and tbBMC. No significant interaction between VDR and ER genotypes was detected in our sample. However, the VDR genotypes are significantly (p = 0.004) associated with approximately 5.8% spine BMD variation. Both ERX and ERP genotypes are significantly (p = 0.02) associated with approximately 3.5% femoral neck BMD variation. ERX genotypes are significantly (p = 0.03) associated with approximately 2.4% tbBMC variation. However, if the data were analyzed by simple ANOVA as in some previous studies, without adjusting statistically for confounding factors, all the significant results we found here would have gone undetected. Our findings suggest that: (1) VDR and ER genotypes may have different effects on BMD at different sites and on tbBMC; and (2) if significant factors influencing bone are not appropriately controlled, true significant associations can easily be missed. These findings may offer a partial explanation for some of the earlier inconsistent results of association studies on BMD with VDR and ER genotypes.

Absorptiometry, Photon↗

PubMed2005

No evidence for specificity between host and parasite genotypes in experimental Strongyloides ratti (Nematoda) infections.

A key requirement for several theories involving the evolution of sex and sexual selection is a specificity between host and parasite genotypes, i.e. the resistance of particular host genotypes to particular parasite genotypes and the infectivity of particular parasite genotypes for particular host genotypes. Determining the scope and nature of any such specificity is also of applied relevance, since any specificity for different parasite genotypes to infect particular host genotypes may affect the level of protection afforded by vaccination, the efficacy of selective breeding of livestock for parasite resistance and the long-term evolution of parasite populations in response to these control measures. Whereas we have some evidence for the role of specificity between host and pathogen genotypes in viral and bacterial infections, its role in macroparasitic infections is seldom considered. The first empirical test of this specificity for a vertebrate-nematode system is provided here using clonal lines of parasite and inbred and congenic strains of rat that differ either across the genome or only at the major histocompatibility complex. Although significant differences between the resistance of host genotypes to infection and between the fitness of different parasite genotypes are found, there is no evidence for an interaction between host and parasite genotypes. It is concluded that a specificity between host and parasite genotypes is unlikely in this system.

Animals↗

PubMed2006

Genotyping of hepatitis B virus (HBV) by oligonucleotides microarray.

Oligonuleotides (oligo) microarray is a promising method for virus genotyping. In this study, we developed an oligo microarray used for genotyping hepatitis B virus (HBV). It consists of 15 probes targeting HBV genotypes A-G and two genotypes of apes, and one conserved probe selected from the HBV pre-S region. To test a clinical sample, the gene targets of clinical samples were amplified and labelled with Cy5-dCTP in a PCR reaction using primers covering the flanking region of the HBV pre-S gene. Following purification, the labelled PCR products were hybridized to the microarray. In an analysis of 96 HBV patients' serum samples using our developed microarray, we identified 34 genotype B, 60 genotype C and 2 genotypes B/C coinfection samples. Sequencing results of 24 randomly selected samples agreed 100% with microarray data. Geographic distribution of genotypes C and B was also divergent, 95.7% (44/46) of genotype C and 64.0% (32/50) of genotype B samples were collected from Northern and Southern China, respectively. The accuracy of genotyping was confirmed by analyzing DNA sequences of 24 samples. It is demonstrated that low-density oligo microarray can serve as a reliable and time-saving method to HBV genotyping from patient's sera.

Genome, Viral↗

PubMed2005

Influence of apolipoprotein E genotype on the reliability of the Friedewald formula in the estimation of low-density lipoprotein cholesterol concentrations.

Lipoprotein data and apolipoprotein (apo) E genotype from 1302 participants, covering a wide range of total plasma cholesterol levels, were used to examine the impact of apo E genotype on the estimation of low-density lipoprotein cholesterol (LDL-C0 concentrations by the Friedewald formula using high-density lipoprotein cholesterol and triglyceride (TG) concentrations as compared with the beta -quantification reference procedure. The results showed that participants with apo E2/E2 genotype had significantly higher very low-density lipoprotein cholesterol (VLDL-C) concentrations and VLDL-C/TG ratio as well as lower LDL-C concentrations than participants with other apo E genotypes. Heterozygous carriers of the epsilon 2 allele had significantly higher VLDL-C than participants with apo E3/E3 and E4/E3 genotypes. The mean absolute error and the mean percentage of bias in calculated LDL-C according to all apo E genotypes, except E2/E2 genotype, were less than 0.16 mmol/L and 4.4%, respectively. Indeed, the mean error and the mean percentage of bias associated with the LDL-C calculated by the Friedewald formula in the apo E2/E2 group were 0.93 mmol/L and 40.6%, respectively. However, participants with the apo E2/E2 genotype and a type III phenotype showed a mean error and a mean percentage of bias reaching 1.53 mmol/L and 63.5%, respectively, whereas E2/E2 participants with a non-type III phenotype had a mean error and a mean percentage of bias of 0.18 mmol/L and 11.0%, respectively. Moreover, 41.9% to 57.1% of the participants had an absolute bias higher than 5% according to the apo E genotype, except for the apo E2/E2 genotypic group where 88.6% of the participants had an absolute bias higher than 5%. Stepwise multiple linear regression analyses revealed that the apo E genotype contributed to 39.0% of the VLDL-C/TG ratio variance, whereas sex, age, and high-density lipoprotein cholesterol explained between 0.5% and 3.2% of the variance. These results indicate that the apo E genotype exerts a significant influence on the estimation of LDL-C concentrations by the Friedewald formula as compared with the beta-quantification.

Adolescent↗

PubMed2005

Prevalence of hepatitis C virus genotypes in a Spanish liver transplant unit.

INTRODUCTION: Among the at least six major identified genotypes of HCV, genotype 1b, the one associated with a poorer prognosis, is the most prevalent in Spain. We aimed to compare the distribution of hepatitis C virus genotypes in our liver transplant unit with that of the other HCV patients at our institution (n = 413) in order to assess whether genotype 1b is more prevalent among patients with more severe liver disease. PATIENTS AND METHODS: One hundred eight patients of mean age 56 years included 81 (75%) OLT recipients and 27 (25%) with HCV cirrhosis. Determination of HCV genotypes was made with the Inno-LiPA HCV III. RESULTS: The overall distribution of genotypes was: 1b, 93 patients (86.1%); 1a; eight patients (7.4%); 3, four patients (3.7%); 4; two patients (1.9%), and 2; one patient (0.9%). The distribution was similar among patients with cirrhosis and OLT. Genotype 1b patients were older. Eleven (78.6%) of 14 patients with hepatocellular carcinoma had genotype 1b. In the control group the distribution was: 1b, 287 patients (69.5%); 1a, 54 patients (12.1%); 3, 41 patients (9.9%); 4, 20 patients (4.8%), and genotype 2, 11 patients (2.7%). This differences in the distribution of genotypes between our population and the control group was statistically significant (P < .001). CONCLUSIONS: Genotype 1b, the most prevalent genotype in our liver transplant unit, included older patients in whom hepatocellular carcinoma was common, perhaps due to their higher prevalence of cirrhosis.

Female↗

PubMed1999

Hepatitis C virus genotypes and quasispecies.

Genetic heterogeneity is a hallmark of the hepatitis C virus, as a result largely of the infidelity of viral RNA-dependent RNA polymerase. Random nucleotide substitutions are introduced at a very high rate. The existence of genotypes was confirmed by statistical and mathematical techniques, and the relation of the genotypes to each other has been determined. There are six major genotypes, each with multiple subtypes. Isolates of the same genotype have an average sequence homology of 95%, but different genotypes have sequence similarity of approximately 65% on average. The nucleotide sequence in portions of the hepatitis C viral genome, including the 5' noncoding region, part of the core gene, and other nonstructural proteins, is highly conserved. Genotype analysis typically utilizes these highly conserved regions. There are many techniques for determining viral genotype, and in general, concordance between techniques is good. Methods most commonly used for assigning hepatitis C virus (HCV) genotypes in clinical practice include restriction fragment length polymorphism analysis and the reverse hybridization line probe assay (LiPA; Innogenetics, Ghent, Belgium). The worldwide distribution of HCV genotypes has been determined; some genotypes are highly characteristic of certain areas. The most common subtypes, 1 and 2, are less genetically diverse than the others and are more widely distributed. The impact of genotype on disease course is controversial, but recent data suggest that there is a genotype-dependent differential response to therapy. Quasispecies refers to evolution of a highly related but genetically heterogeneous population of HCV isolates. The pathobiological and clinical implications of HCV quasispecies are poorly understood.

Genome, Viral↗

PubMedDate not supplied

Use of regularly scheduled albuterol treatment in asthma: genotype-stratified, randomised, placebo-controlled cross-over trial.

BACKGROUND: The issue of whether regular use of an inhaled beta2-adrenergic agonist worsens airflow and clinical outcomes in asthma is controversial. Retrospective studies have suggested that adverse effects occur in patients with a genetic polymorphism that results in homozygosity for arginine (Arg/Arg), rather than glycine (Gly/Gly), at aminoacid residue 16 of the beta2-adrenergic receptor. However, the existence of any genotype-dependent difference has not been tested in a prospective clinical trial. METHODS: Patients with mild asthma, not using a controller medication, were enrolled in pairs matched for forced expiratory volume in 1 s (FEV1) according to whether they had the Arg/Arg (n=37; four of 41 matches withdrew before randomisation) or Gly/Gly (n=41) genotype. Regularly scheduled treatment with albuterol or placebo was given in a masked, cross-over design, for 16-week periods. During the study, as-needed albuterol use was discontinued and ipratropium bromide was used as needed. Morning peak expiratory flow rate (PEFR) was the primary outcome variable. The primary comparisons were between treatment period for each genotype; the secondary outcome was a treatment by genotype effect. Analyses were by intention to treat. FINDINGS: During the run-in period, when albuterol use was kept to a minimum, patients with the Arg/Arg genotype had an increase in morning PEFR of 23 L/min (p=0.0162); the change in patients with the Gly/Gly genotype was not significant (2 L/min; p=0.8399). During randomised treatment, patients with the Gly/Gly genotype had an increase in morning PEFR during treatment with regularly scheduled albuterol compared with placebo (14 L/min [95% CI 3 to 25]; p=0.0175). By contrast, patients with the Arg/Arg genotype had lower morning PEFR during treatment with albuterol than during the placebo period, when albuterol use was limited (-10 L/min [-19 to -2]; p=0.0209). The genotype-attributable treatment difference was therefore -24 L/min (-37 to -12; p=0.0003). There were similar genotype-specific effects in FEV1, symptoms, and use of supplementary reliever medication. INTERPRETATION: Genotype at the 16th aminoacid residue of the beta2-adrenergic receptor affects the long-term response to albuterol use. Bronchodilator treatments avoiding albuterol may be appropriate for patients with the Arg/Arg genotype.

Administration, Inhalation↗

PubMed1995

Relationship of genotype to level of hepatitis C viraemia determined by competitive polymerase chain reaction.

To compare the levels of hepatitis C virus (HCV) viraemia in carriers of the same genotype in various stages of chronic HCV infection, we quantified the amount of HCV RNA by competitive polymerase chain reaction and determined HCV genotype using type-specific primers. The study population included 255 patients with chronic HCV infection (asymptomatic 33, chronic hepatitis 141, liver cirrhosis 50, hepatocellular carcinoma 31). Of these 255, the prevalence of HCV RNA genotype II was 67.8%, genotype III, 17.3% and genotype IV, 14.9%; no genotype I was found. The level of HCV RNA (logarithmic transformed copy numbers per 50 microliters of serum) was significantly higher in subjects of genotype II than in those of genotypes III or IV (mean titre 5.8 +/- 1.0 vs. 5.1 +/- 1.2 and 4.8 +/- 1.1, P < 0.05, respectively). There was no significant difference in the level of HCV RNA between genotypes III and IV. Of 173 patients of genotype II, there were no significant differences between the level of HCV RNA and the stage of liver disease or in the level of HCV RNA by age. Of the 129 with genotype II with a history of blood transfusion, there was no significant difference between the level of HCV RNA of patients with and without a history of transfusion or between that of patients with a history of blood transfusion and the time elapsed since blood transfusion. The level of HCV viraemia depended on the genotype of HCV RNA and did not correlate to age or to the stage of liver disease.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed2000

Differentiation of hepatitis B virus genotypes D and E by ELISA using monoclonal antibodies to epitopes on the preS2-region product.

An enzyme-linked immunosorbent assay (ELISA) has been described for serological determination of hepatitis B virus genotypes, using monoclonal antibodies (mAb) against seven distinct epitopes (b, m, k, s, u, f and g) on the preS2-region products of hepatitis B surface antigen (HBsAg). The usefulness of this method for serological detection of genotype E, however, was theoretical, because no HBsAg samples of this genotype were included in the original test panel. Moreover, the predicted serotype of genotype E (bksufg) closely resembled that of genotype D (bksu, bksuf or bksug). Four HBsAg samples of genotype E were tested by the original described ELISA. The epitope g, predicted to be present in these samples by amino acid sequences, was not detected when HBsAg of genotype E was captured on a solid phase by mAb to the common determinant 'a' of HBsAg and then reacted with mAb to g (5156) labeled with horseradish peroxidase. However, the four examples of HBsAg of genotype E were captured by mAb 5156 to g on a solid phase; they were then detected by labeled mAb to the common determinant 'a'. Since epitopes f and g co-occurred on HBsAg of genotype E, HBsAg samples of this genotype were also detected, by 'sandwiching' them between immobilized mAb to g and labeled mAb to f. By contrast, HBsAg of genotype D in 90 sera was not reactive when sandwiched between mAb to f and g. Thus, this modified ELISA enables the serological determination of all six genotypes of HBsAg and, by inference, of hepatitis B virus.

Africa↗

PubMed2001

HCV genotypes and age distribution in patients of Vienna and surrounding areas.

BACKGROUND: Chronic hepatitis C (CHC) can result in liver cirrhosis and hepatocellular carcinoma. Determination of the hepatitis C virus (HCV) genotype/subtype may be of prognostic value to estimate the risk of development of liver cirrhosis. OBJECTIVE: The HCV genotype/subtype was determined in patients with CHC and possible associations with age, source of HCV transmission, duration of HCV infection, and development of liver cirrhosis were investigated. STUDY DESIGN: A total of 250 consecutive patients with CHC were studied. HCV genotypes/subtypes were determined with a commercially available assay based on the reverse-hybridization principle. Source of HCV transmission and duration of HCV infection were taken from the patient documentation and liver cirrhosis was diagnosed by clinical, biochemical, and sonographic data. RESULTS: HCV genotypes 1, 2, 3, 4, and 5 were found in 74.8, 2.8, 16, 5.2, and 0.4% of the patients. Most frequent subtypes were 1b (54%), 1a (15.6%), and 3a (15.6%). Patients with genotype 1 (mean, 52.8 years) or 2 (mean, 51.0 years) were significantly older than patients with genotype 3 (mean, 37.2 years) or genotype 4 (mean, 37.2 years). Patients with subtype 1b (mean, 58.1 years) were significantly older than patients with subtype 1a (mean, 40.8 years) or 3a (mean, 37.5 years). The main sources of HCV infection were intravenous drug abuse in 30.0% of all patients (genotype 1 in 53.3%; genotype 3 in 40%) or transfusion of blood and blood products in 21.6% of all patients (genotype 1 in 83.4%). The source of transmission, however, remained unknown in 44.8% of all patients. The prevalence of genotype 1 was significantly higher in patients with long duration (more than 20 years) of CHC. In none of the patients with genotype 2 or 3, duration of CHC for more than 20 years was observed. The prevalence of genotype 4 was significantly higher in patients with short duration (less than 10 years) of CHC. Liver cirrhosis was diagnosed in 13.6% of all patients (97.1% of patients with genotype 1). Patients with liver cirrhosis were significantly older compared to asymptomatic patients (mean, 63.8 vs. 51.3 years). CONCLUSION: HCV subtype 1b was found to be the main subtype in the investigated population and is currently the major contributor to liver cirrhosis. Patients infected with subtype 1a, however, are at comparable risk for development of liver cirrhosis. In future, subtype 3a and genotype 4 may also become an increasing problem.

Adult↗

PubMed2001

Clinically relevant sequence-based genotyping of HBV, HCV, CMV, and HIV.

The term 'genotyping' describes the genetic characterization of a genome. The genotype analysis is performed to identify mutations that differentiate one individual or strain from another. The mutations may confer resistance to specific antiviral drugs or they may simply allow classification of a strain as to 'type' and 'subtype'. There are four human viruses for which genotype information is clinically useful. Hepatitis B virus (HBV) infections are being treated with antiretroviral drugs and resistance after prolonged treatment is common. Since HBV cannot be cultured, the only method of detecting resistance-conferring mutations in the genome is a genotypic analysis. Hepatitis C virus (HCV) infection can be cured by treatment with the combination of interferon and ribavirin but certain strains of virus are more resistant to treatment than others. The current recommendations are that all HCV type 1 infections be treated for 12 months whereas other types may be successfully treated in 6 months. Since interferon treatment may have significant side effects, the determination of HCV genotype is an important aspect of this therapeutic regimen. Treatment of cytomegalovirus (CMV) disease with nucleoside analogues occasionally results in resistant virus with mutations in the phosphotransferase gene (UL97) and/or the DNA polymerase gene (UL54) that can be tested with phenotypic or genotypic assays. Since CMV grows very slowly, it may be more clinically useful to perform a rapid genotypic assay although only the UL97 gene can be efficiently genotyped. Finally, the virus for which genotyping has become the standard of care, human immunodeficiency virus type 1 (HIV-1) can now be genotyped routinely by many clinical virology labs experienced with molecular amplification methods and automated DNA sequencing technology. All currently-available antiretroviral drugs are directed against either the protease or reverse transcriptase genes of HIV-1 and the mutations within these genes that confer resistance have been well described. Sequence-based genotyping methods are not necessarily the best approach for routine genotyping of these four viruses, but sequencing is the gold standard from which other methods are developed and against which they are compared.

Base Sequence↗

PubMed2006

Genotypes of hepatitis C virus (HCV) among positive Lebanese patients: comparison of data with that from other Middle Eastern countries.

Recently we identified hepatitis C virus (HCV) genotype 4 as the principle genotype among Lebanese thalassaemics. In an attempt to confirm the predominance of genotype 4 in Lebanon and perhaps in the Middle East, genotyping was attempted on 142 HCV-infected Lebanese patients from five different hospitals in the country. These included 38 HCV-positive patients with symptomatic liver disease who were referred to gastroenterologists and 104 HCV-positive patients with no symptoms of liver disease: 27 patients with thalassaemia, 30 patients on haemodialysis, 32 multi-transfused and 15 intravenous drug users. HCV genotyping was performed on PCR HCV RNA-positive samples using a commercial line probe assay (LiPA; Innogenetics, Ghent, Belgium). HCV genotype 4 is found to be the predominant genotype among HCV-infected Lebanese patients (ranging from 34.2% to 53.3%) followed by 1a (ranging from 12.5% to 43.3%) and 1b (ranging from 8.0% to 34.4%). In patients with symptomatic liver disease, however, genotype 4 (34.2%) was preceded by genotype 1a (39.5%). The predominance of HCV genotype 4 in our population (45.7%) confirms the predominance of HCV genotype 4 in Lebanon and most of the Arab countries in the Middle East but contrasts with data reported from non-Arab Middle Eastern Countries as can be seen from the literature review. Implications of genotyping for clinical outcome of HCV infection, response to treatment as well as for vaccine development are discussed.

Adult↗