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 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.

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 Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa

PLoS ONE ◽  
2016 ◽  
Vol 11 (4) ◽  
pp. e0153761 ◽  
Author(s):  
Mouna Rajhi ◽  
Kais Ghedira ◽  
Anissa Chouikha ◽  
Ahlem Djebbi ◽  
Imed Cheikh ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
North Africa ◽  
Virus Genotype ◽  
Genotype 2 ◽  
History Of

Molecular Epidemiology and Genetic History of Hepatitis C Virus Subtype 3a Infection in Thailand

Intervirology ◽  
2013 ◽  
Vol 56 (5) ◽  
pp. 284-294 ◽  
Author(s):  
Srunthron Akkarathamrongsin ◽  
Pitchaya Hacharoen ◽  
Pisit Tangkijvanich ◽  
Apiradee Theamboonlers ◽  
Yasuhito Tanaka ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Molecular Epidemiology ◽  
Genetic History ◽  
History Of ◽  
Virus Subtype

Genetic history of hepatitis C virus in Pakistan

2014 ◽  
Vol 27 ◽  
pp. 318-324 ◽  
Author(s):  
Irshad ur Rehman ◽  
Gilberto Vaughan ◽  
Michael A. Purdy ◽  
Guo-liang Xia ◽  
Joseph C. Forbi ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Genetic History ◽  
History Of

scholarly journals Epidemic history of hepatitis C virus infection in two remote communities in Nigeria, West Africa

2012 ◽  
Vol 93 (7) ◽  
pp. 1410-1421 ◽  
Author(s):  
Joseph C. Forbi ◽  
Michael A. Purdy ◽  
David S. Campo ◽  
Gilberto Vaughan ◽  
Zoya E. Dimitrova ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
20Th Century ◽  
Hypervariable Region ◽  
Hcv Infection ◽  
Genotype 1 ◽  
Remote Communities ◽  
African Countries ◽  
Genotype 2 ◽  
History Of

We investigated the molecular epidemiology and population dynamics of HCV infection among indigenes of two semi-isolated communities in North-Central Nigeria. Despite remoteness and isolation, ~15 % of the population had serological or molecular markers of hepatitis C virus (HCV) infection. Phylogenetic analysis of the NS5b sequences obtained from 60 HCV-infected residents showed that HCV variants belonged to genotype 1 (n = 51; 85 %) and genotype 2 (n = 9; 15 %). All sequences were unique and intermixed in the phylogenetic tree with HCV sequences from people infected from other West African countries. The high-throughput 454 pyrosequencing of the HCV hypervariable region 1 and an empirical threshold error correction algorithm were used to evaluate intra-host heterogeneity of HCV strains of genotype 1 (n = 43) and genotype 2 (n = 6) from residents of the communities. Analysis revealed a rare detectable intermixing of HCV intra-host variants among residents. Identification of genetically close HCV variants among all known groups of relatives suggests a common intra-familial HCV transmission in the communities. Applying Bayesian coalescent analysis to the NS5b sequences, the most recent common ancestors for genotype 1 and 2 variants were estimated to have existed 675 and 286 years ago, respectively. Bayesian skyline plots suggest that HCV lineages of both genotypes identified in the Nigerian communities experienced epidemic growth for 200–300 years until the mid-20th century. The data suggest a massive introduction of numerous HCV variants to the communities during the 20th century in the background of a dynamic evolutionary history of the hepatitis C epidemic in Nigeria over the past three centuries.

scholarly journals Phylogeography, Risk Factors and Genetic History of Hepatitis C Virus in Gabon, Central Africa

PLoS ONE ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. e42002 ◽  
Author(s):  
Richard Njouom ◽  
Mélanie Caron ◽  
Guillaume Besson ◽  
Guy-Roger Ndong-Atome ◽  
Maria Makuwa ◽  
...  
Keyword(s):  
Risk Factors ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Central Africa ◽  
Genetic History ◽  
History Of

scholarly journals Compartmentalization of Hepatitis C Virus Quasispecies in Blood Mononuclear Cells of Patients with Mixed Cryoglobulinemic Syndrome

2005 ◽  
Vol 79 (14) ◽  
pp. 9145-9156 ◽  
Author(s):  
Gianguglielmo Zehender ◽  
Chiara De Maddalena ◽  
Flavia Bernini ◽  
Erika Ebranati ◽  
Giuseppe Monti ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Positive Selection ◽  
Selection Pressure ◽  
Mononuclear Cells ◽  
Nonsynonymous Substitution ◽  
Substitution Rates ◽  
Hcv Genotype ◽  
Genotype 2 ◽  
Blood Mononuclear Cells

ABSTRACT The aim of this study was to investigate the quasispecies heterogeneity of hepatitis C virus (HCV) in the plasma, cryoprecipitate, and peripheral lymphocytes of chronically infected HCV patients with mixed cryoglobulinemia (MC). We studied 360 clones from 10 HCV-positive patients with MC and 8 age-, gender- and HCV genotype-matched subjects with chronic HCV infection but without MC. A partial nucleotide sequence encompassing the E1/E2 region, including hypervariable region 1 (HVR1), was amplified and cloned from plasma, cryoprecipitates, and peripheral blood mononuclear cells (PBMC), and the genetic diversity and complexity and synonymous and nonsynonymous substitution rates were determined. Heterogeneous selection pressure at codon sites was evaluated. Compartmentalization was estimated by phylogenetic and phenetic (Mantel's test) approaches. The patients with MC had 3.3 times lower nonsynonymous substitution rates (1.7 versus 5.7 substitutions/100 sites). Among the subjects with HCV genotype 1, the MC patients had significantly less complexity than the controls, whereas the diversity and complexity were similar in the genotype 2 patients and controls. Site-specific selection analysis confirmed the low frequency of MC patients showing positive selection. There was a significant correlation between positive selection and the infecting HCV genotype. The quasispecies were less heterogeneous in PBMC than in plasma. Significant compartmentalization of HCV quasispecies was observed in the PBMC of four of nine subjects (three with MC) and seven of nine cryoprecipitates. In one subject with MC, we detected a 5-amino-acid insertion at codons 385 to 389 of HVR1. Our results suggest reduced quasispecies heterogeneity in MC patients that is related to a low selection pressure which is probably due to an impaired immune response, the HCV genotype, and/or the duration of the infection. The frequent HCV quasispecies compartmentalization in patients' PBMC suggests a possible pathogenetic significance.

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