[Hepatitis C virus genotyping: comparison of the Abbott RealTime HCV Genotype II assay and NS5B sequencing]. / Génotypage du virus de l'hépatite C : comparaison du test Abbott RealTime HCV Genotype II au séquençage de la région NS5B.

PURPOSE OF THE STUDY: Hepatitis C virus genotyping is needed for treatment decision and monitoring. The results of a genotyping assay based on real-time PCR and TaqMan chemistry were compared with the results of NS5B region sequencing. MATERIALS AND METHODS: One hundred and two sera (genotypes 1-6) were tested. Amplification and detection of viral RNA were performed with the Abbott RealTime HCV Genotype II assay targeting 5'non-coded region (5'NC) for the identification of genotypes 1 to 6 and NS5B, for 1a and 1b subtypes detection. Sequencing of 5'NC fragment was used to resolve discrepant results. RESULTS: No indeterminate results were obtained. Concordance with NS5B sequencing was 93% (95 on 102), 96% at the genotype level (98 on 102) and 93% for genotype 1 subtyping (40 on 43). Discordant genotyping results were a 2f subtype identified as 5, a 6a typed as 1, a 3a identified as a 1-3 co-infection and a 4r identified as a 1-4 co-infection. Discordant subtyping results were 2 1b subtypes only typed as 1 and a 1e identified as 1a. CONCLUSION: Abbott RealTime HCV Genotype II assay is a rapid, automated and simple to interpret method for HCV genotyping. It allows the detection of possible mixed infections which might have a negative impact on therapeutic response. However, the discrepant results found in this small series underline the need for assay optimization.

Natural history of serum HIV-1 RNA levels in 330 patients with a known date of infection. The SEROCO Study Group.

OBJECTIVE: To describe the spontaneous course, before the introduction of highly active antiretroviral therapy (HAART), of HIV-1 RNA during the AIDS-free period of the disease. To assess the predictive value of changes in HIV-1 RNA levels. DESIGN: A total of 330 patients with a known date of infection followed in the SEROCO cohort. METHODS: HIV-1 RNA levels (threshold, 200 copies/ml) were evaluated from 2243 frozen sera obtained from enrolment until the onset of AIDS or until February 1996. Lowess curves were used to describe the variations of viraemia during follow-up. A Cox regression model was used to assess the predictive value of early and updated CD4 cell count and viral load. RESULTS: In addition to a lower early viral load, patients who remained AIDS-free had, on average, a longer period of viral load decrease after infection (36 versus 18 months), followed by a slower viral load increase compared with those who progressed to AIDS. A true plateau-phase after the seroconversion period, lasting approximately 4 years, was identified only in patients who remained AIDS-free for at least 90 months. In multivariate analysis, both early viral load and later changes were significant predictors of progression to AIDS. A decrease in the CD4 cell count to less than 200 cells/microl and the onset of a group B condition remained significant predictors of progression. CONCLUSION: Our study extends to the early post-seroconversion phase the prognostic value of extracellular HIV-1 RNA levels. Moreover, our data suggest that, in most HIV-infected individuals, a progressive loss of control of viral replication arises during the early years of HIV-1 infection.

Performance of TRUGENE hepatitis C virus 5' noncoding genotyping kit, a new CLIP sequencing-based assay for hepatitis C virus genotype determination.

The performance of the recently developed, standardized direct sequencing assay for hepatitis C virus (HCV) genotyping [TRUGENE HCV 5'-NC (noncoding)] was assessed in comparison with the reverse hybridization-based assay INNO-LIPA HCV II. Both assays allow HCV genotyping starting from amplification products generated by the diagnostic Roche AMPLICOR HCV test. HCV amplicons from 205 patients were used for this study: 34 were tested prospectively by both methods, while 171 had been stored at -20 degrees C for up to 2 years after LiPA genotyping. The TRUGENE procedure failed to determine a genotype in six low-titered samples (3.5 +/- 0.3 log UI/mL vs. 5.2 +/- 0.5 UI/mL for typable samples). Type and subtype could be determined by sequencing for 199 samples (97%). Among them, five were considered as coinfections by the LiPA method. Three LiPA patterns suggesting type 1 and 4 coinfection were not supported by sequence analysis while one 1a/2b and one 1a/3a coinfection was backed up by direct sequencing. For the remaining 194 samples, type assignment was concordant in 100% of the cases. LiPA subtyping was available for 162 samples (83.5%). Sub-typing results concurred in 128 cases (79%). NS5B sequencing of discrepant samples underscored the limitation of the 5'-noncoding region (NCR) in correct subtype assignment. In conclusion, the TRUGENE HCV 5'-NC genotyping kit appeared to be a specific and reliable method that can be used in the current indication of HCV genotyping.

Hepatocellular carcinoma with lymphoid stroma: a tumour with good prognosis after liver transplantation.

AIMS: Carcinomas with lymphoid stroma arising in non-liver-organs have a better prognosis than other carcinomas and may be associated with Epstein-Barr virus. We determined the frequency, characteristics and prognosis of hepatocellular carcinomas with lymphoid stroma. METHODS AND RESULTS: Histology of the livers of 162 patients with hepatocellular carcinoma, who underwent an orthotopic liver transplantation, was reviewed independently by three pathologists. Hepatocellular carcinoma with lymphoid stroma was diagnosed when all tumour samples contained more lymphocytes than tumour cells. Epstein-Barr virus was detected by in-situ hybridization and by polymerase chain reaction. Five patients (3.6%) were classified as hepatocellular carcinomas with lymphoid stroma. All patients were males. Cirrhosis was present in four/five patients. Serum alpha-fetoprotein levels were normal. Inter-observer histological reproducibility was good. Tumour cells did not contain Epstein-Barr virus. The five patients were alive without tumour at three years, although two of them had adverse prognostic factors at the time of transplantation (more than one tumour with a diameter > or = 40 mm). Only one patient had tumour recurrence, but he survived 7.6 years post-transplantation. The 5-year survival of patients with hepatocellular carcinoma with lymphoid stroma was better than that of the patients with other types of hepatocellular carcinomas (P = 0.04). CONCLUSIONS: Hepatocellular carcinoma with lymphoid stroma should be considered as a distinct clinicopathological and prognostic entity.

Prognostic value of JC virus load in cerebrospinal fluid of patients with progressive multifocal leukoencephalopathy.

JC virus (JCV) load was determined by using quantitative polymerase chain reaction in cerebrospinal fluid (CSF) of 12 patients with AIDS-associated progressive multifocal leukoencephalopathy (PML) and compared with clinical outcome. JCV loads varied widely (3-7 log10 JCV equivalents/mL of CSF) and were apparently not related to absolute CD4 cell counts or CSF and plasma human immunodeficiency virus type 1 loads. A significant correlation was observed between JCV load and survival time (Spearman's rank correlation, -0.83; P<. 01). Moreover, CSF JCV load decreased and then became undetectable in 1 PML patient receiving cidofovir treatment, and this was associated with clinical improvement. These results show that CSF JCV load may be useful as a prognostic parameter and in monitoring the effectiveness of anti-JCV therapies in PML patients.

Multicenter evaluating of a commercially available PCR assay for diagnosing enterovirus infection in a panel of cerebrospinal fluid specimens.

Thirteen laboratories participated in blind tests of a panel of 20 coded cerebrospinal fluid specimens (7 uninfected samples, 3 samples infected with 1 50% tissue culture infective dose [TCID50]/0.1 ml [nonenterovirus strains], and 10 samples infected with 10, 1, or 0.1 TCID50/0.1 ml [three different enterovirus serotypes]) on the Amplicor enterovirus PCR assay (Roche Diagnostic Systems). The panel was also evaluated by in-house PCR (two nested-PCR and three one-step PCR assay) or tissue culture (eight laboratories). The viral load was shown to influence greatly the sensitivity of the assay. The average sensitivity of the Amplicor test ranged from 67 to 98% for viral titers of 1 to 10 TCID50/0.1 ml, respectively; titers of 0.1 TCID50/0.1 ml resulted in a sensitivity of only 16%. The overall specificity of the Amplicor test was 98%. The Amplicor assay compared favorably to the five in-house PCR tests (no significant difference in either sensitivity or specificity) and was much more sensitive than tissue culture (P < 0.001), even for high viral loads. It was easy to perform, rapid (about 6 h), well-standardized, and appeared to be suitable for the diagnosis of enterovirus meningitis on a routine basis in laboratories trained in molecular biology techniques.