Subtyping of hepatitis C virus isolates by a line probe assay using hybridization

Development and Comparison of In-house Line Probe Assay (LiPA) and SYBR Green Real-time PCR Regarding the Detection of Periodontal Pathogens

BACKGROUND

Periodontal disease, which can become a chronic condition, is an inflammatory disease that upsets the soft and hard structures supporting the teeth. The aim of the present study was to design and develop an in-house Line Probe Assay (LiPA), to detect putative periodontitis-related bacterial pathogens, and compare it with SYBR Green Real-time PCR.

METHODS

The LiPA method was launched using biotinylated 16s rRNA universal primers and specific probes for each of the five bacteria including Aggregatibacter acti-nomycetemcomitans, Prevotella intermedia, Tannerella forsythia, Porphyromonas gingivalis and Treponema denticola. For this, optimized quantities of the primers and specific probes were dotted onto nylon membrane stripes in a defined pattern. Hybridization was performed between the probes and the single-stranded biotinylated PCR products. The stripes were developed via biotin-streptavidin reaction. Ultimately, the analytical and diagnostic sensitivity and specificity of the in-house LiPA was evaluated and compared with SYBR Green Real-time PCR.

RESULTS

The detection limit of the LiPA was 2760 copies of targeted genes. In testing analytical specificity, only signals corresponding to the specific biotinylated products were produced. The calculated diagnostic sensitivity of the LiPA for the five bacterial targets ranged from 96.4 to 100%, whereas the diagnostic specificity was between 90.9 and 100%. Comparing the results, no noticeable difference (p=0.4795) was observed between the two methods.

CONCLUSION

To screen periodontal pathogens, a simple, inexpensive and accurate method is desirable. The in-house LiPA, having advantages such as high specificity and sensitivity, and the ability to detect five major periodontal pathogens, offers the option of evaluating samples without the need for a post-PCR platform.

Distribution of hepatitis C virus genotypes in Canada: Results from the LCDC Sentinel Health Unit Surveillance System

In a sentinel hepatitis surveillance study conducted by sentinel health units, 1469 patients were enrolled, and 959 (65.3%) were positive for antibody to hepatitis C virus (HCV). Samples from 387 patients (40.4%) were tested for HCV RNA, and 289 (74.7%) were positive for RNA. The major risk factor for HCV infection was injection drug use, reported in 71% of cases. The genotyping of HCV isolates showed that subtype 1a (48%) was predominant in Canada. The other subtypes detected were 1b (19%), 2a (6%), 2b (3%), 3a (22%) and 4a (1%). In Winnipeg, Manitoba, subtype 3a (47%) was more prevalent than subtype 1a (37%), and, in Guelph, Ontario, both subtypes 1a and 3a had equal (40%) distribution. The prevalence of subtype 3a was significantly higher in injection drug users (27%) than in nonusers (10%) (P<0.005). In Canada, injection drug use is the major risk factor for HCV infections, and subtype 1a is more prevalent.

Comparative performance evaluation of hepatitis C virus genotyping based on the 5' untranslated region versus partial sequencing of the NS5B region of brazilian patients with chronic hepatitis C

Background

Genotyping of hepatitis C virus (HCV) has become an essential tool for prognosis and prediction of treatment duration. The aim of this study was to compare two HCV genotyping methods: reverse hybridization line probe assay (LiPA v.1) and partial sequencing of the NS5B region.

Methods

Plasma of 171 patients with chronic hepatitis C were screened using both a commercial method (LiPA HCV Versant, Siemens, Tarrytown, NY, USA) and different primers targeting the NS5B region for PCR amplification and sequencing analysis.

Results

Comparison of the HCV genotyping methods showed no difference in the classification at the genotype level. However, a total of 82/171 samples (47.9%) including misclassification, non-subtypable, discrepant and inconclusive results were not classified by LiPA at the subtype level but could be discriminated by NS5B sequencing. Of these samples, 34 samples of genotype 1a and 6 samples of genotype 1b were classified at the subtype level using sequencing of NS5B.

Conclusions

Sequence analysis of NS5B for genotyping HCV provides precise genotype and subtype identification and an accurate epidemiological representation of circulating viral strains.

Differences between two real-time PCR-based hepatitis C virus (HCV) assays (RealTime HCV and Cobas AmpliPrep/Cobas TaqMan) and one signal amplification assay (Versant HCV RNA 3.0) for RNA detection and quantification

Hepatitis C virus (HCV) RNA detection and quantification are the key diagnostic tools for the management of hepatitis C. Commercially available HCV RNA assays are calibrated to the HCV genotype 1 (gt1)-based WHO standard. Significant differences between assays have been reported. However, it is unknown which assay matches the WHO standard best, and little is known about the sensitivity and linear quantification of the assays for non-gt1 specimens. Two real-time reverse transcriptase PCR-based assays (RealTime HCV and Cobas Ampliprep/Cobas TaqMan HCV [CAP/CTM]) and one signal amplification-based assay (the Versant HCV RNA, version 3.0, branched DNA [bDNA] assay) were compared for their abilities to quantify HCV RNA in clinical specimens (n = 65) harboring HCV isolates of gt1 to g5. The mean differences in the amounts detected by RealTime HCV in comparison to those detected by the bDNA assay and CAP/CTM were -0.02 and 0.72 log(10) IU/ml HCV RNA, respectively, for gt1; -0.22 and 0.03 log(10) IU/ml HCV RNA, respectively, for gt2; -0.27 and -0.22 log(10) IU/ml HCV RNA, respectively, for gt3; -0.19 and -1.27 log(10) IU/ml HCV RNA, respectively, for gt4; and -0.03 and 0.09 log(10) IU/ml HCV RNA, respectively, for gt5. The lower limits of detection for RealTime HCV and CAP/CTM were 16.8 and 10.3 IU/ml, respectively, for the WHO standard and in the range of 4.7 to 9.0 and 3.4 to 44.4 IU/ml, respectively, for clinical specimens harboring gt1 to gt6. Direct comparison of the two assays with samples of the WHO standard (code 96/798) with high titers yielded slightly smaller amounts by RealTime HCV (-0.2 log(10) at 1,500 IU/ml and -0.3 log(10) at 25,000 IU/ml) and larger amounts by CAP/CTM (0.3 log(10) at 1,500 IU/ml and 0.2 log(10) at 25,000 IU/ml). Finally, all three tests were linear between 4.0 x 10(3) and 1.0 x 10(6) IU/ml (correlation coefficient, >or=0.99). In conclusion, the real-time PCR based assays sensitively detected all genotypes and showed comparable linearities for the quantification of HCV RNA, with the exception of gt1 and gt4. The previously reported differences in the absolute quantification of samples harboring gt1 were confirmed and may be explained by different calibrations to the WHO standard.

Evaluation of Versant hepatitis C virus genotype assay (LiPA) 2.0

Hepatitis C virus (HCV) genotyping is a tool used to optimize antiviral treatment regimens. The newly developed Versant HCV genotype assay (LiPA) 2.0 uses sequence information from both the 5' untranslated region and the core region, allowing distinction between HCV genotype 1 and subtypes c to l of genotype 6 and between subtypes a and b of genotype 1. HCV-positive samples were genotyped manually using the Versant HCV genotype assay (LiPA) 2.0 system according to the manufacturer's instructions. For the comparison study, Versant HCV genotype assay (LiPA) 1.0 was used. In this study, 99.7% of the samples could be amplified, the genotype of 96.0% of samples could be determined, and the agreement with the reference method was 99.4% when a genotype was determined. The reproducibility study showed no significant differences in performance across sites (P = 0.43) or across lots (P = 0.88). In the comparison study, 13 samples that were uninterpretable or incorrectly genotyped with Versant HCV genotype assay (LiPA) 1.0 were correctly genotyped by Versant HCV genotype assay (LiPA) 2.0. Versant HCV genotype assay (LiPA) 2.0 is a sensitive, accurate, and reliable assay for HCV genotyping. The inclusion of the core region probes in Versant HCV genotype assay (LiPA) 2.0 results in a genotyping success rate higher than that of the current Versant HCV genotype assay (LiPA) 1.0.

Improvement of hepatitis C virus (HCV) genotype determination with the new version of the INNO-LiPA HCV assay

Hepatitis C virus (HCV) isolates have been classified into six main genotypes. Genotyping methods, and especially the widely used line probe assay (LiPA), are frequently based on the 5'-untranslated region (5'UTR). However, this region is not appropriate for discriminating HCV strains at the subtype level and for distinguishing many genotype 6 samples from genotype 1. We investigated the capacity of a novel LiPA (Versant HCV Genotype 2.0 assay) based on the simultaneous detection of 5'UTR and Core regions for genotypes 1 and 6 to provide correct HCV genotypes (characterized with a phylogenetic analysis) in a set of HCV strains mainly encountered in Western countries. The improvement was assessed by comparing the results to those obtained with the previous version of the assay. Of the 135 tested samples, 64.7% were concordant for genotype group and subtype with sequencing reference results using the Versant HCV Genotype 2.0 assay versus 37.5% with the previous version. The yield was mainly related to a better characterization of genotype 1, since the accuracy, tested in 62 genotype 1 samples, increased from 45.2% with the first version to 96.8% with the new one. However, this new version necessitates a specific PCR and could no longer be used after 5'UTR PCR used for current HCV infection diagnosis. Moreover, the information provided by 5'UTR hybridization is not reliable for correctly identifying the diversity within genotypes 2 and 4. Thus, the Versant HCV Genotype 2.0 assay remains a useful tool for clinical practice when only the discrimination between major HCV genotypes is necessary.

Molecular methods of hepatitis C genotyping

Hepatitis C virus is an RNA virus that is associated with chronic infection in the majority of people infected. Chronic infection with hepatitis C virus is the cause of significant morbidity and mortality worldwide and is associated with a large spectrum of liver disease including cirrhosis and hepatocellular carcinoma. End-stage liver disease due to chronic hepatitis C virus infection is currently the leading indication for liver transplantation in the USA. Hepatitis C virus genotyping of viral isolates circulating in the blood during chronic infection has become an important part of hepatitis C virus monitoring in chronically infected patients, and is useful as a prognostic indicator and to direct duration of therapy. This review will summarize information on hepatitis C genotyping, describe the limitations of current commercially available methods, give information on more recently developed methods, and provide a look to the future in terms of where advances in hepatitis C virus genotyping assays need to be made.

Estimating the prognosis of hepatitis C patients infected by transfusion in Canada between 1986 and 1990

OBJECTIVE

To develop a natural history model for chronic hepatitis C virus (HCV) infection to determine allocation of compensatory funds to Canadians who acquired HCV through the blood supply from 1986 through 1990.

METHODS

A Markov cohort simulation model for HCV prognosis was developed, using content experts, published data, posttransfusion look-back data, and a national survey.

RESULTS

The mortality rate in transfusees is high (46% at 10 years), although HCV-related deaths are rare. Only 14% develop cirrhosis at 20 years (95% confidence interval, 0%--44%), but 1 in 4 will eventually develop cirrhosis, and 1 in 8 will die of liver disease.

CONCLUSIONS

This unique application of Markov cohort simulation and epidemiologic methods provides a state-of-the-art estimate of HCV prognosis and has allowed compensation decisions to be based on the best available evidence.

Hepatitis C virus genotyping: interrogation of the 5' untranslated region cannot accurately distinguish genotypes 1a and 1b

Although the 5' untranslated region (5' UTR) is the most conserved region of the hepatitis C virus (HCV) genome, it has been suggested that interrogation of this region is sufficient for determination of the HCV genotype. We compared two methods of determination of the HCV genotype: (i) direct sequencing of the DNA of the NS-5b region and (ii) reverse line probe assay (LiPA; INNO-LiPA HCV II; Innogenetics N.V.) of the 5' UTR. There was 100% concordance between the two methods for genotype but only 80% concordance for subtype. A significant percentage of genotype 1a isolates were misclassified by LiPA as genotype 1b. Sequence analysis revealed that the only consistent difference in the 5' UTR for these genotype 1a isolates misclassified as genotype 1b was a single nucleotide (A/G) at position -99 of the HCV genome. All isolates with discordant results analyzed had a G at this position, consistent with LiPA determination of these samples as subtype 1b. However, sequence analysis of 222 nucleotides in the NS-5b region clearly identified all of these isolates as subtype 1a. Population distribution data from the University of Pittsburgh Medical Center of over 200 samples analyzed by sequencing of the NS-5b region and over 1,000 samples analyzed by LiPA also indicated that INNO-LiPA HCV II cannot accurately differentiate HCV genotype 1a isolates from HCV genotype 1b isolates. We provide evidence that the A/G at position -99 represents a sequence polymorphism in the HCV genome that cannot differentiate subtype 1a from subtype 1b isolates. In conclusion, the 5' UTR is not heterogeneous enough for use in determination of the HCV subtype and cannot be used for differentiation of HCV genotypes 1a and 1b.

Genotyping of hepatitis C virus types 1, 2, 3, and 4 by a one-step LightCycler method using three different pairs of hybridization probes

Determination of hepatitis C virus (HCV) genotypes has become increasingly important during the last years for prediction of the clinical course and the outcome of antiviral therapy. Therefore, numerous different methods have been developed to enable HCV genotyping. However, many of them are very laborious and expensive, leading to limited usage in daily routine diagnostics. We have established a method which combines the speed of the new LightCycler technology with the use of amplification products generated for diagnostic quantitative HCV RNA determination. Differentiation of HCV genotypes is performed with these amplicons in a single step by using fluorophore-labeled hybridization probes. Although currently only two different acceptor fluorophores are available for the LightCycler, types 1, 2, 3, and 4, which are by far the prevailing HCV genotypes in Europe and the United States, can be distinguished. Genotypes of specimens from 190 chronically HCV-infected patients were determined by the LightCycler method and compared with the results of nucleotide sequencing. Concordant results were obtained for all samples. This new method offers a fast and convenient possibility to determine the quantitative HCV RNA load and the genotype in large-scale settings within about 4 h.

Prevalence, genotype distribution and outcome of hepatitis C infections among the employees of the Hungarian Central Hospital for infectious diseases

Blood samples from 477 hospital workers (HWs) at the Central Hospital for Infectious Diseases, Budapest, Hungary were tested for hepatitis C virus (HCV) antibodies by enzyme immunoassay (EIA), and 13 (2.7%) of these were found to be HCV antibody positive. Ten (2.7%) were from nursing/housekeeping staff and three (2.9%) from medical staff. HCV antibody positive HWs were detected in 10 of 17 work places, and the prevalence rates in these departments or units varied between 1.2% and 6.5%. The prevalence increased gradually with increasing age, being 0% in these under 21 years of age and 9.5% in those above 50 years of age. Eleven (85%) of 13 HCV antibody positive HWs had HCV RNA in their sera, four of them intermittently during the follow-up period. HCV genotype 1 was present in two HWs, 1b in six HWs, 3a in one HW and 4 in two HWs. Chronic hepatitis C has developed in six (46%) HCV antibody positive HWs. Although the source of infection through needlestick could only be traced directly in one case, circumstantial evidence indicated that the majority of infections were occupationally acquired, originating from percutaneous or mucocutaneous exposure.

Comparison of three HCV genotyping assays: a serological method as a reliable and inexpensive alternative to PCR based assays

BACKGROUND

Determination of hepatitis C virus (HCV) genotypes and subtypes is of rising clinical importance. In times where also an increasing need for cost effectiveness can be observed, the demand for fast and easy performable assays grows.

OBJECTIVES

To evaluate and compare different genotyping methods regarding their reliability, practicability, and expense in the daily routine.

METHODS

Sera of 39 patients infected with different HCV subtypes were examined by a serological genotyping assay (NS-4 IBA), by the widely used INNO-LiPA HCV II, and by a nucleotide sequencing method.

RESULTS

The tests performed equally well in terms of HCV subtyping and no different results were obtained. However, the serotyping assay provided the results in less than half the time needed by the other two assays. Significant differences were also observed regarding the 'hands on' times and the costs. The technical equipment which was necessary to perform the assays is significantly reduced using the serological assay.

CONCLUSION

Our study demonstrates that the serological test offers the opportunity to determine HCV genotypes and subtypes reliably, fast, easy, and cost effective.

Serological determination of hepatitis C virus subtypes 1a, 1b, 2a, 2b, 3a, and 4a by a recombinant immunoblot assay

Serological determination of hepatitis C virus (HCV) subtypes has been hampered by the lack of suitable assays. Therefore, a recombinant immunoblot assay has been established for serological differentiation of HCV subtypes 1a, 1b, 2a, 2b, 3a, and 4a. It consists of recombinant HCV proteins from the NS-4 region propagated in Escherichia coli. To confirm the serotyping assay results, the results were compared with those obtained by nucleotide sequencing of the NS-5 region. Sera from 157 patients with chronic HCV infection were examined by this assay, and specific antibodies could be detected in 86% (n = 135) of them. The HCV genotype was determined correctly in all but one sample, and the subtypes determined by the serotyping assay corresponded to the HCV subtypes detected by nucleotide sequencing for 95% (n = 128) of the samples. These data indicate that HCV subtypes can be distinguished serologically. The assay that is described provides an easier means of identification of infection with different HCV subtypes for wider clinical and epidemiological applications.

Serological differentiation between HCV subtypes 1a and 1b by a recombinant immunoblot assay

Until now, no serological assay has been available for the differentiation of HCV subtypes. Since there is evidence that the subtypes differently influence the clinical course of HCV infection and the outcome of interferon therapy, we established a strip immunoblot assay (NS-4 IBA) with recombinant HCV proteins of the nonstructural 4 (NS-4) region propagated in Escherichia coli. Using this NS-4 IBA, we were able to distinguish HCV subtypes 1a and 1b, which are the most prevalent subtypes in Europe and the U.S.A. The results of the serotyping assay were compared with those obtained by nucleotide sequencing from the NS-5 region. Concordant results were observed to match 94.9% (n=100) by the NS-4 IBA and nucleotide sequencing. Discrepant results were obtained in only 5.1% (n=6). These data indicate that HCV subtypes can be serologically distinguished, providing the possibility for easier identification of infection with different HCV subtypes.

HCV genotypes in patients with chronic hepatitis C in Croatia

The determination of hepatitis C virus (HCV) genotype is an important epidemiological parameter in patients with chronic hepatitis C, while its clinical significance is still a matter of debate. The HCV genotypes in a group of 203 Croatian patients with chronic hepatitis C were examined. Genotypes were correlated to different risk factors, age, duration of the disease, liver histology activity and level of viremia. HCV-RNA was detected in each serum by means of reverse transcription PCR. Genotypes were determined from the amplificate by reverse hybridization in a line probe assay. The level of viremia was assessed by branched DNA (bDNA) signal amplification. The most common genotype was 1b (61.1% of patients), followed by 3a (26.1%), and 1a (10.8%). Other genotypes such as 2a and 4 were only rarely found in our patients (2%). Genotype 1b was most commonly acquired via blood transfusion, while genotype 3a was strongly related to intravenous drug use. Genotype 1b was associated with older age (mean 42.6 vs 29.3 years), longer duration of the disease (mean 6.0 vs 3.5 years), higher histologic activity score (mean 13.2 vs 10.6) and higher viremia (mean 9.06 vs 5.93 Meq/ml) at statistically significant levels (p < 0.001) when compared to genotype 3a. The prevalence of HCV genotypes follows the patterns of southeastern European countries, except for a lower prevalence of genotype 2. The observation that genotype 1b is associated with higher viremia and more severe liver injury is confirmed.

Comparison of DNA enzyme immunoassay and line probe assays (Inno-LiPA HCV I and II) for hepatitis C virus genotyping

Two methods for genotyping hepatitis C virus (DNA enzyme immunoassay [DEIA] and line probe assay [Inno-LiPA HCV I and II]) were compared on 120 samples and of these 87% were assigned to the same subtype by both assays. There were 15 subtyping discrepancies which involved 5% of type 1 isolates and 90% of type 2 isolates. Amplified products from the core and 5' untranslated regions (UTR) were sequenced to resolve conflicts. Type 1 discordant samples had a guanosine at position -99 in the 5' UTR, a characteristic of genotype 1b, and a core region typical of subtype 1a. The eight isolates classified as 2a/2c by LiPA and as subtype 2c by DEIA belonged to type 2.

Hepatitis C serotypes in nonalcoholic and alcoholic patients

Genotyping of the hepatitis C virus (HCV) RNA can be performed by a variety of methods following polymerase chain reaction amplification of a stable RNA portion of the genome. The gold standard is amplification of the RNA from the NS5 region, followed by direct sequencing and homology comparison. This method is extremely labor intensive. In this study, we compared an immunoblot serotyping technique (HCV SIA) to a reverse-hybridization line-probe assay (LiPA) for genotype classification among non-alcoholic HCV infected patients. We then compared and contrasted the response in this cohort to a population of alcoholic patients with HCV infection. To validate the serotype assay, sera from 110 patients with chronic HCV infection was utilized. Serotyping (Chiron SIA) and genotyping by the LiPA (Line Probe Assay, Innogenetics) reverse-hybridization technique was performed. Additionally, both methods were compared to sequence-derived genotyping in 26 patients based on PCR amplification of the NS5 region. After the validation phase, sera from 105 alcoholic patients was genotypically classified by the serologic method. The nonalcoholic and alcoholic groups were then compared with regard to serotype, demographics, and frequency of untypable test results. Among typable pairs, the overall concordance rate between serotyping and LiPA-based genotyping was 93.75%. Patients with genotype 1 by reverse hybridization demonstrated a 95.8% concordance with serotype. Untypable samples were present for both techniques, but since they occurred in different patients, the techniques were complementary. Alcoholic patients were significantly more likely to be infected with untypable serotypes than those without a pattern of alcohol abuse. These patients were also more likely to be HCV RNA negative than sera from typable patients. Serotype 1 was associated with high HCV RNA titer and poor interferon treatment response among both nonalcoholic and alcoholic patients. An immunoblot method for the evaluation of genotype classification was rapid and easily performed compared to sequence-based genotyping. There was a high degree of concordance compared to reverse-hybridization and sequence-based genotype characterization methods. Failure to detect HCV RNA in the serum is associated with a higher likelihood of classification failure. This problem was particularly prevalent in the alcoholic population. HCV RNA titers and treatment outcomes were strongly associated with serotype classification results, demonstrating clinical utility of this assay technique.

Unexpected high prevalence of hepatitis C virus genotype 4 in Southern Spain

BACKGROUND/AIMS

A unusually high rate of HCV-infected individuals in whom the HCV genotype cannot be ascertained by means of single PCR and LIPA procedures has recently been reported in our area. The aim of the present study was to investigate the epidemiological, clinical and molecular characteristics of these patients.

METHODS

Cross-sectional study. Eighty anti-HCV-positive patients with chronic liver disease, 45 (56.25%) of them intravenous drug users, were included. HCV genotyping was carried out in all patients using commercial single PCR and LIPA procedures. Samples where no HCV RNA amplification and/or indeterminate HCV genotype were found were also tested by means of a nested PCR. HCV viral load was measured in all patients.

RESULTS

HCV genotyping was not achieved in 23 (28.75%) individuals. No amplification of HCV RNA was found in 19 of them, and in four other cases the LIPA procedure did not allow identification of a distinct HCV genotype. After the use of nested PCR+LIPA, it was found that the HCV genotype 4 was found in 11 of those 23 individuals (47.82%). Ten of these 11 HCV genotype 4-harboring individuals were intravenous drug users. The HCV viral load was lower in HCV genotype 4-harboring individuals than in those whom the genotypes 1, 2 or 3 were found (p<0.001).

CONCLUSIONS

A high rate of HCV genotype 4-harboring cases has been found among HCV-infected individuals in Southern Spain. Had only single PCR been used, these individuals could have been wrongly regarded as non-viremic.

Comparative evaluation of five rapid methods for identifying subtype 1b and 2c hepatitis C virus isolates

A panel of 61 HCV isolates belonging to five different subtypes were used to evaluate five methods for rapid typing of HCV RNA: an in-house type-specific polymerase chain reaction based on the core region (type-specific PCR), a commercial amplification of the core region followed by hybridisation to probe coated wells (DEIA), a commercial amplification of the 5'-UTR region followed by hybridisation to probes immobilised on strips (LiPA), an in-house restriction fragment polymorphism analysis of the 5'UTR (RFLP), and a commercial serological method using synthetic peptides from the NS4 region (serotyping). The correct viral type was identified in 90% of cases by DEIA, in 82% of cases by type-specific PCR, in 80% of cases by LiPA and RFLP, and in 67% of cases by serotyping. Correct identification of the virus subtype was much less frequent and was beyond the performance characteristics of some assays. Major problems were found in the identification of isolates belonging to type 2. This was probably at least partly due to the fact that all type 2 isolates in the viral panel were of subtype 2c, which has been considered rare until recently.

cDNA sequencing of the 5' noncoding region (5' NCR) to determine hepatitis C genotypes in patients with chronic hepatitis C

Reports suggest that response to interferon-alpha therapy is influenced by both hepatitis C viral genotype and titer. Our aim was to determine if direct, automated, cycle sequencing of the PCR product from an HCV RNA detection assay could be used to reliably determine HCV genotype. In addition, the approach was used to determine the HCV genotype distribution in our patient population and to learn if there was a correlation between HCV genotype and RNA titer that could be used to predict response to treatment. In all 143 consecutive patients were tested for both HCV RNA titer and genotype. Automated, cycle sequencing of PCR product was highly effective and failed to yield a genotype in only 3 (2%) patients. The distribution of HCV genotypes was: 1a (40%), 1b (39%), 2a (2%), 2b (6%), 3a (4%). There were significant differences in the median HCV RNA titers between genotypes 1, 2, and 3. High HCV RNA titers >4.4 x 10(6) copies/ml were only seen in genotype 1. However, the HCV RNA level should not be used as a surrogate marker of genotype because of a significant overlap of titers within the genotypes.

Performance of the automated COBAS AMPLICOR system for the detection of hepatitis C virus RNA

BACKGROUND

The COBAS AMPLICOR (CA) instrument for the amplification and detection steps of the AMPLICOR molecular diagnostic assays has recently been introduced. The system contains a single thermal cycler with two independently controlled heating/cooling blocks, a pipettor, a magnetic particle washer, a photometer and an incubator.

OBJECTIVE

The performance of the CA instrument was evaluated in a routine diagnostic laboratory for the detection of hepatitis C virus (HCV) RNA. The new system was compared with the corresponding microwell plate assay (AMPLICOR HCV Test).

STUDY DESIGN

Routine clinical sera (350) from hemodialysis patients and patients with chronic HCV infection and interferon therapy were studied. If discrepant results were obtained, both assays were repeated (specimen preparation, amplification and detection); in addition, the HCV copy number was determined with the AMPLICOR HCV MONITOR Test.

RESULTS

There was a correlation between the CA HCV Test and the AMPLICOR HCV Test in 341 of 350 specimens (97%). After resolution of 9 discrepant results, the CA HCV Test gave a sensitivity of 97.8% and a specificity of 99.4%. The most common reason for discrepant results was a low HCV RNA copy number.

CONCLUSION

The CA system was found to be a labor-saving, fast and reliable instrument for the amplification and detection steps of a RT-PCR molecular assay for detection of HCV RNA.

Laboratory diagnosis of hepatitis C

In 1989 the hepatitis C virus was cloned, some 20 years after the first suggestion that hepatitis C virus(es) (HCV) existed. Since that time there has been rapid development of serological tests for detection of antibody to HCV and molecular tests for detection, quantitation, and characterization of HCV RNA. The development and performance characteristics of these test methods are reviewed and their implications for diagnosis, prognosis, and monitoring patients on therapy are discussed.

Second-generation line probe assay for hepatitis C virus genotyping

Because of the enormous variability of hepatitis C virus (HCV), the development of reliable genotyping assays is a formidable challenge. The optimal genotyping region appears to be the 5' untranslated region (UR) because of high conservation within, but considerable variability between, genotypes. In this study, 21 probes dispersed over seven variable 5' UR areas were applied to a line probe assay (LiPA) and used to analyze 506 HCV-infected sera from different geographical regions representing a multitude of subtypes. At least 31 different reactivity patterns emerged, with 404 (80%) of 506 distributed over 11 prototype patterns, in general corresponding to subtypes 1a, 1b, 2a/2c, 2b, 3a, 5a, and 6a and several type 4 subtypes. Subtyping specificity ranged from 97% in Hong Kong to 90% in Europe but was only 11% in West Africa, while typing specificity was always 100% when samples from Vietnam were excluded. In a second evaluation, the subtype prediction by LiPA of 448 GenBank 5' UR HCV sequences was scored. Of the 58 theoretically predicted patterns, 321 sequences (72%) were covered by the 11 prototype patterns. We concluded that (i) the selected probes detected the corresponding signature motifs in the seven variable regions with 100% reliability; (ii) these motifs allowed correct type interpretation of samples collected worldwide, with the exclusion of Vietnam, Thailand, or Vietnamese patients residing in European hospitals; and (iii) subtyping specificities vary according to geographical region, with 11 prototype subtyping patterns identifying the majority of samples from Europe and the Americas. These results indicate that the LiPA is a reliable assay applicable to routine typing and subtyping of HCV specimens.

Hepatitis C virus genotypes in the liver and serum of patients with chronic hepatitis C

OBJECTIVE: To evaluate the prevalence of hepatitis C virus (HCV) genotypes in a central area of Italy (Umbria); to analyze the correspondence of the genotypes detected in serum and liver samples; to study the relationship between HCV genotypes and severity of liver disease; to test whether co-infection with more than one HCV subtype could be influenced by the source of infection. METHODS: Genotyping by polymerase chain reaction with core-specific primers (Okamoto method) was performed in the serum and liver from 48 consecutive patients with histologically confirmed chronic C hepatitis. RESULTS: HCV genotype 1b was the prevalent strain and was not associated with more severe histologic damage. Data show a very good correspondence between genotypes identified in serum and liver specimens (91%). Mixed infections (with subtypes 1b and 2a) correlated significantly with intravenous drug abuse (p=0.001). CONCLUSION: We confirmed that subtype 1b is prevalent in central Italy. Co-infection with more than one subtype is not rare in intravenous drug abusers.

Hepatitis C plasma viral load is associated with HCV genotype but not with HIV coinfection

The influence of human immunodeficiency virus (HIV) coinfection and hepatitis C virus (HCV) genotype distribution on HCV viral load and alanine amino transferase (ALT) levels in chronically infected patients remains unclear. In the present study, serum samples from a group of haemophiliac patients were investigated retrospectively. HCV geno- and subtyping was carried out using the Inno line probe assay (Inno LIPA, Innogenetics, Zwijnaarde, Belgium) in 87 patients positive by HCV RT PCR. Of these patients, 31 (35.6%) were HIV coinfected. HCV RNA was quantified with the HCV Monitor kit (Roche, Basel, Switzerland) in 43 patients (22 HIV-negatives, 21 HIV-positives). The most prevalent genotypes were 1 (n = 52) and 3a (n = 16) followed by genotype 2 (n = 9) and 4 (n = 3). Mixed infections were detected in 7 patients. Of genotype 1 positive samples, 24 and 23 were classified as subtype a and b, respectively. Five samples could not be subtyped. Although higher mean values of ALT were observed in genotype 1 infected patients, there was no statistically significant association between HCV genotype or subtype and liver enzymes (P > 0.05). On the other hand, statistically significant higher HCV RNA titres were observed in haemophiliacs infected with HCV genotype 1 in comparison to those infected with other genotypes (P < 0.01). No relationship was found between the presence of HIV coinfection and viral load of HCV RNA. There was no evidence that HCV infection had a more severe outcome in HIV-positive patients who had been infected with HIV and HCV more than ten years ago, even in those with very low CD4+ cell counts. No clear association between high ALT levels and large amounts of viral RNA was observed. In conclusion, a large viral load is associated with HCV genotype 1 infection; HIV coinfection has no clear effect on the intensity of HCV replication. An ongoing prospective study will evaluate the respective role of viral load, genotype, HIV coinfection and ALT level in the response to interferon therapy.

Quantitation and genotyping of hepatitis C virus RNA in sera of hemodialysis and AIDS patients

BACKGROUND

Hepatitis C virus (HCV) infection is highly prevalent in hemodialysis and AIDS patients. Little information exists about the viral load in those patients.

OBJECTIVE

To characterize HCV infection in hemodialysis and AIDS patients, the viral load in the sera was measured. Results were compared with genotypes, gender of the patients, and biochemical markers of active hepatitis.

STUDY DESIGN

Sera from a total of 442 patients were screened with a third-generation EIA, and anti-HCV immunoreactivity was confirmed with the Wellcozyme HCV Western Blot. After qualitative PCR with the Amplicor PCR Test, positives were genotyped using a reverse hybridization test. Determination of HCV levels was done with the Amplicor HCV Monitor assay.

RESULTS

HCV RNA was detected in the sera of 95 (74.8%) EIA-positive patients. HCV RNA levels ranged from 1 x 10(4) to 1.4 x 10(6) molecules of HCV RNA/ml. Median HCV RNA levels of AIDS patients were slightly higher than those of hemodialysis patients. Male patients had higher median HCV RNA levels compared with female patients. No association between HCV RNA levels and both alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels was found. The most common genotypes were type 1b and type 1a, followed by type 3, type 4, and type 2a. There were no significant differences in HCV RNA levels among patients with genotypes 1a, 1b, and 2a. Patients infected with types 3 and 4, respectively, had significantly lower HCV RNA levels compared with other genotypes.

CONCLUSION

Because the Amplicor HCV Monitor assay allows quantitation of low-titer viremic patients, HCV RNA levels were distinctly lower compared with previous reports. HCV RNA levels of males did not differ significantly from those of females. ALT and AST are very poor indicators of ongoing HCV infection. Patients with chronic type 3 or type 4 HCV infection tended to have lower HCV RNA levels.