Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping

An Insight into Hepatitis C Virus: In Search of Promising Drug Targets

Hepatitis C Virus (HCV) is a global health concern, chronically infecting over 70 million people worldwide. HCV is a bloodborne pathogen that primarily affects the liver, and chronic HCV infection can lead to cirrhosis, liver cancer, and liver failure over time. There is an urgent need for more effective approaches to prevent and treat HCV. This review summarizes current knowledge on the virology, transmission, diagnosis, and management of HCV infection. It also provides an in-depth analysis of HCV proteins as promising targets for antiviral drug and vaccine development. Specific HCV proteins discussed as potential drug targets include the NS5B polymerase, NS3/4A protease, entry receptors like CD81, and core proteins. The implications of HCV proteins as diagnostic and prognostic biomarkers are also explored. Current direct-acting antiviral therapies are effective but have cost, genotype specificity, and resistance limitations. This review aims to synthesize essential information on HCV biology and pathogenesis to inform future research on improved preventive, diagnostic, and therapeutic strategies against this global infectious disease threat.

Comparative performance of two commercial sample-to-result systems for hepatitis C virus quantitation and genotyping

OBJECTIVES

Accurate assays for hepatitis C virus (HCV) quantitation and genotyping are important for the management of HCV infection. In this study, we evaluated the performance of cobas HCV and cobas HCV GT assays (Roche) for HCV quantitation and genotyping on the cobas 4800 System.

METHODS

We compared the performance of the cobas HCV assays with another commercial system (Abbott m2000) using a panel of well-characterized patient samples and proficiency testing samples.

RESULTS

The limit-of-detection of the cobas HCV assay in our center was higher (15 IU/mL) than the manufacturer claim (9.2 IU/mL). The assay showed high analytical specificity, accuracy, precision, and linearity. Performance was congruent with the RealTime HCV assay (Abbott). For genotyping, the cobas HCV GT assay only showed moderate agreement with the RealTime HCV Genotype II assay (kappa = 0.550). The cobas assay outperformed the RealTime assay for typing HCV genotypes 1b and 6 (p = 0.033).

CONCLUSION

Our results confirm that the cobas 4800 System is a reliable platform for HCV quantitation and genotyping. The cobas HCV GT assay is a good choice for genotype 1b/6 endemic areas in east Asia, clearly outperforming the RealTime HCV Genotype II assay.

Comparison of Sanger sequencing for hepatitis C virus genotyping with a commercial line probe assay in a tertiary hospital

BACKGROUND

The technique most frequently used to genotype HCV is quantitative RT-PCR. This technique is unable to provide an accurate genotype/subtype for many samples; we decided to develop an in-house method with the goal of accurately identifying the genotype of all samples. As a Belgium National Centre of reference for hepatitis, we developed in-house sequencing not only for 5'UTR and core regions starting from VERSANT LiPA amplicons but also for NS5B regions. The sequencing of VERSANT LiPA amplicons might be useful for many laboratories worldwide using the VERSANT LiPA assay to overcome undetermined results.

METHODS

100 samples from Hepatitis C virus infected patients analysed by the VERSANT HCV Genotype 2.0 LiPA Assay covering frequent HCV types and subtypes were included in this study. NS5B, 5'UTR and Core home-made sequencing were then performed on these samples. The sequences obtained were compared with the HCV genomic BLAST bank.

RESULTS

All the samples were characterised by the VERSANT LiPA assay (8 G1a, 17 G1b, 6 G2, 11 G3, 13 G4, and 10 G6). It was not possible to discriminate between G6 and G1 by the VERSANT LiPA assay for 8 samples and 27 had an undetermined genotype. Forty-one samples were sequenced for the three regions: NS5B, 5'UTR and Core. Twenty-three samples were sequenced for two regions: 5' UTR and Core and 36 samples were sequenced only for NS5B. Of the 100 samples included, 64 samples were analysed for 5'UTR and Core sequencing and 79 samples were analysed for NS5B sequencing. The global agreement between VERSANT LiPA assay and sequencing was greater than 95%.

CONCLUSIONS

In this study, we describe a new, original method to confirm HCV genotypes of samples not discriminated by a commercial assay, using amplicons already obtained by the screening method, here the VERSANT LiPA assay. This method thus saves one step if a confirmation assay is needed and might be of usefulness for many laboratories worldwide performing VERSANT LiPA assay in particular.

Epidemiological and Clinical Characteristics of Human Hepegivirus 1 Infection in Patients With Hepatitis C

Background

Transmission of human hepegivirus 1 (HHpgV-1), a novel human pegivirus, is closely associated with hepatitis C virus (HCV). The impact of HHpgV-1 viremia on HCV infection is unknown. This study aimed to (a) evaluate the impact of HHpgV-1 viremia on HCV viral load and liver injury and (b) elucidate the clinical and molecular epidemiology of HHpgV-1 infection.

Methods

Individuals with HHpgV-1 viremia (cases) were identified by screening plasma from 655 HCV-infected adults. HHpgV-1 isolates were sequenced for phylogenetic analysis, and viral load was quantified. Cases were age- and sex-matched to HCV-infected individuals without HHpgV-1 viremia (controls) in a 1:3 ratio. A retrospective case–control analysis was performed to identify differences in HCV viral load and parameters of liver injury.

Results

Among HCV-infected adults, 16/655 (2.4%) had HHpgV-1 viremia. Risk groups for HHpgV-1 infection included intravenous drug users, blood product recipients, tattoo recipients, and men who have sex with men. Viral sequences clustered into 2 distinct HHpgV-1 genogroups. Cases had a higher mean HCV viral load than controls, with difference between means of 0.58 log₁₀ IU/mL (P = .009). Cases were more likely to have an HCV viral load >5 log₁₀ IU/mL (P = .028). Multiple regression demonstrated the impact of HHpgV-1 viral load and infection status on HCV viral load. HHpgV-1 infection was not associated with higher liver function tests, fibrosis scores, or imaging abnormalities.

Conclusions

HHpgV-1 viremia is associated with a higher HCV viral load in co-infected patients. HHpgV-1 infection does not affect progression of HCV-related liver disease.

Using high-throughput sequencing for investigating intra-host hepatitis C evolution over long retrospective periods

Collections of biological samples held by hospitals represent invaluable resources for conducting retrospective evolutionary studies of chronic infections. Using high-throughput sequencing, those collections permit analysis of within-host genetic diversity over long follow-up periods, and allow a better understanding of resistance to treatment regimes during disease evolution. Here, we studied the evolution of hepatitis C virus (HCV) populations in two patients with an absence of response to dual therapies. We implemented amplicon sequencing to survey genomic variation at the Core and NS5B regions of HCV over a period of 13 years from blood samples obtained at multiple time points. We observed mixed infection by multiple HCV genotypes in both patients. Genetic heterogeneity and sample composition analysis provided information about the changes in viral population over the course of clinical treatment, with NS5B experiencing an increase in diversity after treatment initiation. Secondary infections were estimated to predate treatment year, and our results pointed towards diversifying selection occurring post-treatment, acting on standing genomic variation and maintaining high genetic heterogeneity during infection. For these two patients infected with multiple HCV genotypes, the maintenance of viral diversity was explained with the hypothesis of soft selective sweep started at the same time as antiviral treatment was initiated.

Nosocomial transmission of hepatitis C virus in a liver transplant center in Hong Kong: implication of reusable blood collection tube holder as the vehicle for transmission

BACKGROUND

A liver transplant recipient developed hospital-acquired symptomatic hepatitis C virus (HCV) genotype 6a infection 14 months post transplant.

OBJECTIVE

Standard outbreak investigation.

METHODS

Patient chart review, interviews of patients and staff, observational study of patient care practices, environmental surveillance, blood collection simulation experiments, and phylogenetic study of HCV strains using partial envelope gene sequences (E1-E2) of HCV genotype 6a strains from the suspected source patient, the environment, and the index patient were performed.

RESULTS

Investigations and data review revealed no further cases of HCV genotype 6a infection in the transplant unit. However, a suspected source with a high HCV load was identified. HCV genotype 6a was found in a contaminated reusable blood-collection tube holder with barely visible blood and was identified as the only shared item posing risk of transmission to the index case patient. Also, 14 episodes of sequential blood collection from the source patient and the index case patient were noted on the computerized time log of the laboratory barcoding system during their 13 days of cohospitalization in the liver transplant ward. Disinfection of the tube holders was not performed after use between patients. Blood collection simulation experiments showed that HCV and technetium isotope contaminating the tip of the sleeve capping the sleeved-needle can reflux back from the vacuum-specimen tube side to the patient side.

CONCLUSIONS

A reusable blood-collection tube holder without disinfection between patients can cause a nosocomial HCV infection. Single-use disposable tube holders should be used according to the recommendations by Occupational Safety and Health Administration and World Health Organization.