Comparison of Three Different Hepatitis C Virus Genotyping Methods: 5′<scp>NCR PCR</scp>‐<scp>RFLP</scp>, Core Type‐Specific <scp>PCR</scp>, and <scp>NS</scp>5b Sequencing in a Tertiary Care Hospital in South India

Daniel, Hubert Darius J.; David, Joel; Raghuraman, Sukanya; Gnanamony, Manu; Chandy, George; Sridharan, Gopalan; Abraham, Priya

doi:10.1002/jcla.22045

Cited by 3 publications

(2 citation statements)

References 38 publications

(45 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Genotyping of HCV was crucial for tailoring IFN-based therapy, and this involved utilization of reverse hybridization assays that amplify specific genomic regions ( 5′UTR or C ) to determine genotype and occasionally subtype [ 281 , 295 ]. However, the most reliable method for HCV genotype determination employs genomic sequencing and phylogenetic analysis of the E1 or NS5B regions [ 296 ]. The role of HCV genotyping following the availability of pan-genotypic DAA regimens remains an issue to be further investigated [ 135 ].…”

Section: Diagnosis Of Hcvmentioning

confidence: 99%

Contemporary Insights into Hepatitis C Virus: A Comprehensive Review

Sallam,

Khalil

2024

Microorganisms

View full text Add to dashboard Cite

Hepatitis C virus (HCV) remains a significant global health challenge. Approximately 50 million people were living with chronic hepatitis C based on the World Health Organization as of 2024, contributing extensively to global morbidity and mortality. The advent and approval of several direct-acting antiviral (DAA) regimens significantly improved HCV treatment, offering potentially high rates of cure for chronic hepatitis C. However, the promising aim of eventual HCV eradication remains challenging. Key challenges include the variability in DAA access across different regions, slightly variable response rates to DAAs across diverse patient populations and HCV genotypes/subtypes, and the emergence of resistance-associated substitutions (RASs), potentially conferring resistance to DAAs. Therefore, periodic reassessment of current HCV knowledge is needed. An up-to-date review on HCV is also necessitated based on the observed shifts in HCV epidemiological trends, continuous development and approval of therapeutic strategies, and changes in public health policies. Thus, the current comprehensive review aimed to integrate the latest knowledge on the epidemiology, pathophysiology, diagnostic approaches, treatment options and preventive strategies for HCV, with a particular focus on the current challenges associated with RASs and ongoing efforts in vaccine development. This review sought to provide healthcare professionals, researchers, and policymakers with the necessary insights to address the HCV burden more effectively. We aimed to highlight the progress made in managing and preventing HCV infection and to highlight the persistent barriers challenging the prevention of HCV infection. The overarching goal was to align with global health objectives towards reducing the burden of chronic hepatitis, aiming for its eventual elimination as a public health threat by 2030.

show abstract

Section: Diagnosis Of Hcvmentioning

confidence: 99%

Contemporary Insights into Hepatitis C Virus: A Comprehensive Review

Sallam,

Khalil

2024

Microorganisms

View full text Add to dashboard Cite

show abstract

“…DNA sequencing was performed through the ABI genetic analyzer 3500 and the results were analysed by BioEdit sequencing alignment software and submitted to the HCV BLAST sequence database to obtain the genotype results. The primer sequences are shown in S1 Table [15].…”

Section: Hcv Genotypingmentioning

confidence: 99%

Longitudinal assessment of HCV core antigen kinetics to monitor therapeutic response in the age of DAAs

et al. 2023

View full text Add to dashboard Cite

Background In the economy of therapeutic monitoring, an affordable viral marker is essential in the era of direct-acting antivirals (DAAs). We elucidated the kinetics of HCVcAg to delineate its precise role in monitoring therapeutic response. Methods In this longitudinal study, 3208 patients were tested for HCV RNA. A total of 423 patients were started on DAAs. Treatment response and kinetics of HCVcAg/RNA were assessed in treatment-naïve (n = 383) and previously treated (n = 40) patients with follow-up for 2 years. Results After the initiation of DAAs, the rate of relapse was significantly higher in the previously treated group than naive group [12.5% (5/40) Vs 2% (7/383), p<0.0001]. The response rate at RVR was significantly higher with HCVcAg than RNA in both groups (p<0.02). The kinetics of HCVcAg and RNA were significantly different at ETR and SVR12 in the naïve (p<0.04), but similar at all therapeutic points in the previously treated group. The correlation between HCVcAg and RNA was good at baseline, ETR and SVR, except RVR in both groups (r>0.6; p<0.0001). Furthermore, HCV genotypes, treatment regimen, CTP (<7/≥7) and MELD (<15/≥15) did not influence the therapeutic response and the viral replication kinetics (p>0.05). Conclusions It is the first longitudinal study from India shows that the response rate and kinetics of HCVcAg are comparable to HCV RNA for an extended duration, except at RVR, irrespective of the HCV genotypes, treatment regimen, and liver disease severity. Hence, HCVcAg can be considered as a pragmatic marker to monitor therapeutic response and predict relapse in the era of DAAs.

show abstract

On leveraging self-supervised learning for accurate HCV genotyping

Fahmy,

Hammad,

Mabrouk

et al. 2024

Sci Rep

View full text Add to dashboard Cite

Hepatitis C virus (HCV) is a major global health concern, affecting millions of individuals worldwide. While existing literature predominantly focuses on disease classification using clinical data, there exists a critical research gap concerning HCV genotyping based on genomic sequences. Accurate HCV genotyping is essential for patient management and treatment decisions. While the neural models excel at capturing complex patterns, they still face challenges, such as data scarcity, that exist a lot in computational genomics. To overcome this challenges, this paper introduces an advanced deep learning approach for HCV genotyping based on the graphical representation of nucleotide sequences that outperforms classical approaches. Notably, it is effective for both partial and complete HCV genomes and addresses challenges associated with imbalanced datasets. In this work, ten HCV genotypes: 1a, 1b, 2a, 2b, 2c, 3a, 3b, 4, 5, and 6 were used in the analysis. This study utilizes Chaos Game Representation for 2D mapping of genomic sequences, employing self-supervised learning using convolutional autoencoder for deep feature extraction, resulting in an outstanding performance for HCV genotyping compared to various machine learning and deep learning models. This baseline provides a benchmark against which the performance of the proposed approach and other models can be evaluated. The experimental results showcase a remarkable classification accuracy of over 99%, outperforming traditional deep learning models. This performance demonstrates the capability of the proposed model to accurately identify HCV genotypes in both partial and complete sequences and in dealing with data scarcity for certain genotypes. The results of the proposed model are compared to NCBI genotyping tool.

show abstract

Comparison of Three Different Hepatitis C Virus Genotyping Methods: 5′NCR PCR‐RFLP, Core Type‐Specific PCR, and NS5b Sequencing in a Tertiary Care Hospital in South India

Cited by 3 publications

References 38 publications

Contemporary Insights into Hepatitis C Virus: A Comprehensive Review

Contemporary Insights into Hepatitis C Virus: A Comprehensive Review

Longitudinal assessment of HCV core antigen kinetics to monitor therapeutic response in the age of DAAs

On leveraging self-supervised learning for accurate HCV genotyping

Contact Info

Product

Resources

About