scholarly journals Performance of Three Common Hepatitis C Virus (HCV) Genotyping Assays for Identification of HCV Genotype 2/1 Chimeras

2019 ◽  
Vol 57 (7) ◽  
Author(s):  
Kai-Henrik Peiffer ◽  
Lisa Kuhnhenn ◽  
Evelyn Stelzl ◽  
Julia Dietz ◽  
Simone Susser ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Real Time ◽  
Real Time Pcr ◽  
Hcv Genotype ◽  
Hcv Genotypes ◽  
The Real ◽  
Genotype 2 ◽  
Hcv Genotype 2 ◽  
Genotype Ii

ABSTRACT Besides seven major hepatitis C virus (HCV) genotypes (GT), a number of intergenotypic recombinant strains have been described. These so-called chimeras combine genetic characteristics of different HCV genotypes. However, correct genotype classification is important, as choice and duration of direct-acting antiviral (DAA) treatment is mainly based on the viral genotype. Therefore, misclassification of chimeras might lead to suboptimal treatment of patients infected with these strains. For example, 2k/1b chimeras are typically described as HCV genotype 2 strains by commercially available hybridization assays, but real-time PCR-based tests recognizing another HCV region might be more suitable for correct chimera detection. In this study, the analytic capacity of the hybridization-assay Versant HCV Genotype 2.0 (LiPA 2.0) and the real-time PCR-based-assays cobas HCV GT and Abbott RealTime HCV Genotype II were tested in a selected cohort of 230 patients infected with HCV genotype 1 (n = 53) and 2 (n = 177) and 48 patients infected with HCV 2/1 chimeric strains. While the Versant HCV Genotype 2.0 (LiPA 2.0) assay failed to identify chimeras in all of the patients (48/48, 100%), cobas HCV GT and Abbott HCV Genotype II assays identified chimeras correctly in 90% (43/48) and 65% (31/48) of the cases, respectively. In conclusion, while the hybridization-based Versant HCV Genotype 2.0 (LiPA 2.0) assay seems to be unsuitable for detection of HCV 2/1 chimeras, use of the real-time PCR-based assays cobas HCV GT and Abbott RealTime HCV Genotype II led to a higher rate of chimera detection.

scholarly journals High-Resolution Hepatitis C Virus Subtyping Using NS5B Deep Sequencing and Phylogeny, an Alternative to Current Methods

2014 ◽  
Vol 53 (1) ◽  
pp. 219-226 ◽  
Author(s):  
Josep Quer ◽  
Josep Gregori ◽  
Francisco Rodríguez-Frias ◽  
Maria Buti ◽  
Antonio Madejon ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Real Time ◽  
Deep Sequencing ◽  
Direct Sequencing ◽  
Treatment Strategies ◽  
Dual Infection ◽  
Genotype 1 ◽  
Hcv Genotype ◽  
Genotype Ii

Hepatitis C virus (HCV) is classified into seven major genotypes and 67 subtypes. Recent studies have shown that in HCV genotype 1-infected patients, response rates to regimens containing direct-acting antivirals (DAAs) are subtype dependent. Currently available genotyping methods have limited subtyping accuracy. We have evaluated the performance of a deep-sequencing-based HCV subtyping assay, developed for the 454/GS-Junior platform, in comparison with those of two commercial assays (Versant HCV genotype 2.0 and Abbott Real-time HCV Genotype II) and using direct NS5B sequencing as a gold standard (direct sequencing), in 114 clinical specimens previously tested by first-generation hybridization assay (82 genotype 1 and 32 with uninterpretable results). Phylogenetic analysis of deep-sequencing reads matched subtype 1 calling by population Sanger sequencing (69% 1b, 31% 1a) in 81 specimens and identified a mixed-subtype infection (1b/3a/1a) in one sample. Similarly, among the 32 previously indeterminate specimens, identical genotype and subtype results were obtained by direct and deep sequencing in all but four samples with dual infection. In contrast, both Versant HCV Genotype 2.0 and Abbott Real-time HCV Genotype II failed subtype 1 calling in 13 (16%) samples each and were unable to identify the HCV genotype and/or subtype in more than half of the non-genotype 1 samples. We concluded that deep sequencing is more efficient for HCV subtyping than currently available methods and allows qualitative identification of mixed infections and may be more helpful with respect to informing treatment strategies with new DAA-containing regimens across all HCV subtypes.

Evidence for two phylogenetic clusters within hepatitis C virus (HCV) genotype 2 inferred from analysis of complete coding sequences of 15 HCV strains

2013 ◽  
Vol 85 (10) ◽  
pp. 1754-1764 ◽  
Author(s):  
François Jordier ◽  
Marie-Laurence Deligny ◽  
Romain Barré ◽  
Philippe De Micco ◽  
Jean-François Cantaloube
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Coding Sequences ◽  
Hcv Genotype ◽  
Genotype 2 ◽  
Hcv Genotype 2

scholarly journals Frequent Recovery and Broad Genotype 2 Diversity Characterize Hepatitis C Virus Infection in Ghana, West Africa

2003 ◽  
Vol 77 (14) ◽  
pp. 7914-7923 ◽  
Author(s):  
Daniel Candotti ◽  
Jillian Temple ◽  
Francis Sarkodie ◽  
Jean-Pierre Allain
Keyword(s):  
United Kingdom ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
West Africa ◽  
Blood Donors ◽  
Hcv Infection ◽  
High Rate ◽  
Hcv Genotype ◽  
Genotype 2 ◽  
Hcv Genotype 2

ABSTRACT Hepatitis C virus (HCV) infection is thought to mostly become chronic and rarely resolves. HCV infection was serologically screened in 4,984 samples from Ghanaian blood donors, and 1.3% prevalence was found. At least 53% of confirmed anti-HCV carriers had no detectable viral RNA and were considered to have cleared the virus and recovered from the infection. Confirmation was authenticated by the presence of antibodies specific to at least two viral antigens, mostly NS3 and E2. Reactivity to HCV core antigens was lower in Ghanaian than United Kingdom blood donors. The minority of chronically infected donors carried a viral load significantly lower than an unselected comparative group of United Kingdom blood donors (2.5 × 105 versus 2.9 × 106 IU/ml; P = 0.004). HCV genotype 2 was largely predominant (87%). Sequence clustering was similarly broad in the E1/E2 and NS5 regions. The phylogenetic diversity and the incapacity to distinguish subtypes within genotype 2 in our and others' West African strains suggested that West Africa may be the origin of HCV genotype 2. The genetic diversity extended to the identification of strains clearly separated from known subtypes of genotype 2 and genotype 1. One strain appears to be part of a new HCV genotype. HCV infection in Ghana is characterized by a high rate of recovery and the predominance of broadly divergent genotype 2 strains.

scholarly journals Genetic History of Hepatitis C Virus in Venezuela: High Diversity and Long Time of Evolution of HCV Genotype 2

PLoS ONE ◽  
2010 ◽  
Vol 5 (12) ◽  
pp. e14315 ◽  
Author(s):  
Maria Z. Sulbarán ◽  
Federico A. Di Lello ◽  
Yoneira Sulbarán ◽  
Clarisa Cosson ◽  
Carmen L. Loureiro ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Hcv Genotype ◽  
Genetic History ◽  
Genotype 2 ◽  
Long Time ◽  
History Of ◽  
Hcv Genotype 2 ◽  
High Diversity

scholarly journals Distribution of hepatitis C virus genotypes and subtypes in a group of patients with chronic hepatitis C from Canton Sarajevo, 2012-2018

2019 ◽  
Vol 49 ◽  
Author(s):  
Irma Salimović- Bešić ◽  
Adna Kahriman ◽  
Suzana Arapčić ◽  
Amela Dedeić- Ljubović
Keyword(s):  
Chronic Hepatitis ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Chronic Hepatitis C ◽  
Hcv Rna ◽  
Genotype 3 ◽  
Hcv Genotype ◽  
Hcv Genotypes ◽  
Number Of Patients ◽  
Subtype 1B

Background: Hepatitis C virus (HCV) genotypes and subtypes exhibit significant geographic variations.Aim: To analyse the distribution of genotypes/subtypes of HCV in a group of patients with chronic hepatitis C from Canton Sarajevo during 2012-2018.Material and methods:The study enrolled 247 human plasma samples of HCV-RNA positive patients with available results of HCV genotyping test.Results: During 2012-2018, the domination of subtypes 1a (34.01%), 1b (28.34%) and genotype 3 (23.89%) was registered. In 2012 and 2013, HCV subtype 1a was the most common (27/63; 42.86% and 17/40; 42.50%, respectively). In 2014, the leading HCV genotype/subtype were 3 and 1b (17/57; 29.82%). In 2015, the dominance of HCV genotype 3 (14/39; 35.90%) continued, while in 2016, the same number of HCV subtypes 1a and 1b (11/30; 36.67%) was recorded. Although in a small number of tested, during 2017, HCV subtype 1b was the most prevalent (7/14; 50.00%), and in 2018, it was replaced by a HCV subtype 1a (3/4; 75.00%). Distribution of HCV genotypes/subtypes by age group of patients varied significantly (p=0.000). The largest number of patients (71/247; 28.74%) belonged to the age category 30-39 years and HCV genotypes/subtypes 1, 3, 4, 1a and 1b were identified. Except in 2017, male gender significantly dominated (p=0.000). In males, HCV subtype 1a (68/170; 40.00%) was the most common, while in women it was HCV subtype 1b (44/77; 57.14%).Conclusion: This six-year retrospective study showed the time variations of the circulating HCV genotypes/subtypes among patients with chronic hepatitis C in Canton Sarajevo. Genotyping of the HCV has an important implications for diagnosis and treatment of the patients.

scholarly journals Stability of hepatitis C virus RNA in blood samples by TaqMan real-time PCR

2010 ◽  
Vol 24 (3) ◽  
pp. 134-138 ◽  
Author(s):  
Kenan Sener ◽  
Mehmet Yapar ◽  
Orhan Bedir ◽  
Cem Gül ◽  
Ömer Coskun ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Real Time ◽  
Real Time Pcr ◽  
Hepatitis C Virus Rna ◽  
Blood Samples ◽  
Virus Rna
Sign in / Sign up

Export Citation Format

Share Document