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Khan MA, Khan SA, Hamayun M, Ali M, Idrees M. Sequence variability of HCV 3a isolates based on core gene in patients from Lahore, Pakistan. Future Virol 2019. [DOI: 10.2217/fvl-2019-0086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Aim: To investigate the HCV 3a core sequence variation and amino acid substitutions of patients from Lahore, Pakistan. Materials & methods: Blood samples from HCV positive patients (n = 232) were collected for viral genotypes. Moreover, the nucleotide sequencing was performed for core gene of 20 samples. Results: Viral genotyping showed that 69.82% (n = 162) belonged to 3a genotype, 9.05% (1a; n = 21), 2.15% (3b; n = 5) and 18.98% were untypable (n = 44). Phylogenetic analyses suggest majority of our isolates clustered with previously reported reference isolates from Pakistan. The remaining isolates clustered with HCV-core sequences reported from Vietnam, Japan, Thailand, Iran, USA, Bangladesh, Malaysia and Morocco. Conclusion: We report HCV-core substitutions (G60E, R70Q, C91A, A94Q and Q63E/D) that could be associated with treatment response in Pakistani patients.
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Affiliation(s)
- Muhammad Ajmal Khan
- Center for Biotechnology & Microbiology (COBAM), University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Sumera Afzal Khan
- Center for Biotechnology & Microbiology (COBAM), University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Hamayun
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Idrees
- National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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Impacts and Challenges of Advanced Diagnostic Assays for Transplant Infectious Diseases. PRINCIPLES AND PRACTICE OF TRANSPLANT INFECTIOUS DISEASES 2019. [PMCID: PMC7121269 DOI: 10.1007/978-1-4939-9034-4_47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The advanced technologies described in this chapter should allow for full inventories to be made of bacterial genes, their time- and place-dependent expression, and the resulting proteins as well as their outcome metabolites. The evolution of these molecular technologies will continue, not only in the microbial pathogens but also in the context of host-pathogen interactions targeting human genomics and transcriptomics. Their performance characteristics and limitations must be clearly understood by both laboratory personnel and clinicians to ensure proper utilization and interpretation.
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Abstract
INTRODUCTION Hepatitis C virus (HCV) is divided into 7 genotypes and 67 subtypes. HCV genotype studies reflect the viral transmission patterns as well as human migration routes. In a clinical setting, HCV genotype is a baseline predictor for the sustained virological response (SVR) in chronic hepatitis C patients treated with peginterferon or some direct acting antivirals (DAAs). The Versant HCV genotype 2.0 assay has been globally used for HCV genotyping over a decade. Areas covered: The assay is based on reverse hybridization principle. It is evolved from its former versions, and the accuracy and successful genotyping/subtyping rate are substantially improved. It shows an accuracy of 99-100% for genotypes 1-6. It can also reliably identify subtypes 1a and 1b. However, the assay does not allow a high resolution for many other subtypes. Reasons for indeterminate or inaccurate genotyping/subtyping results are discussed. Expert commentary: Genotyping helps to find the most efficacious and cost-effective treatment regimen. The rapid development of anti-HCV treatment regimens, however, is greatly simplifying laboratory tests. In the near future, the need for HCV genotyping and frequent serial on-treatment HCV RNA tests will decrease along with the wide use of the more potent and pan-genotypic DAA regimens.
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Affiliation(s)
- Ruifeng Yang
- a Peking University People's Hospital, Peking University Hepatology Institute , Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases , Beijing , China
| | - Lai Wei
- a Peking University People's Hospital, Peking University Hepatology Institute , Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases , Beijing , China
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Némoz B, Roger L, Leroy V, Poveda JD, Morand P, Larrat S. Evaluation of the cobas® GT hepatitis C virus genotyping assay in G1-6 viruses including low viral loads and LiPA failures. PLoS One 2018; 13:e0194396. [PMID: 29566005 PMCID: PMC5864039 DOI: 10.1371/journal.pone.0194396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/04/2018] [Indexed: 12/19/2022] Open
Abstract
Direct-acting antiviral (DAA) drug performances depend on the viral genotype. So international recommendations give typing of the virus a prerequisite for treatment choice and patient management. Commercially available HCV genotyping kits are scarce and this analysis is often in-house using tedious PCRs and Sanger sequencing, leading to a lack of standardization. A newly commercialized HCV genotyping assay based on real-time PCR has been developed by Roche Diagnostics (Mannheim, Germany). We compared this new assay with our in-house PCRs -sequencing technique on 101 regular samples and 81 LiPA failures or low viral load samples. No genotype or 1a/1b subtype mismatch was observed. Two samples were misidentified at the subtype level without clinical impact. Three genotype 1b and two genotype 1a samples with low viral load could not be subtyped. Nevertheless, 13 (13%) samples from the regular panel and 35 (43%) from the more difficult-to-type panels failed to give results on first pass with the Roche kit. Failures were mostly associated with genotype 3 subtype a, with genotype 4 subtype non-a, or with viral loads <200 IU/mL (p = 0.0061). The workflow allowed a non-specialized technician to obtain results in less than 4 hours whereas 2 to 3 days and experienced staff were required with the in-house assay. In conclusion, the Roche cobas® HCV GT kit is easy and rapid to use and provides reliable results. The high rate of uninterpretable results particularly for low viral load samples and less frequent genotypes, and the absence of subtyping for non-genotype 1 could require sending complex samples to a specialized laboratory.
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Affiliation(s)
- Benjamin Némoz
- Laboratory of Virology, Institute for Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
| | - Léa Roger
- Laboratory of Virology, Institute for Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
| | - Vincent Leroy
- Department of Hepatology, Grenoble Alpes University Hospital, Grenoble, France
| | | | - Patrice Morand
- Laboratory of Virology, Institute for Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
- Institut of Structural Biology (IBS) –Mixed Research Unit 5075 (CEA-CNRS-UGA), Grenoble, Grenoble, France
| | - Sylvie Larrat
- Laboratory of Virology, Institute for Biology and Pathology, Grenoble Alpes University Hospital, Grenoble, France
- Institut of Structural Biology (IBS) –Mixed Research Unit 5075 (CEA-CNRS-UGA), Grenoble, Grenoble, France
- * E-mail:
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5
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EL Hadad S, Al-Hamdan H, Linjawi S. Partial sequencing analysis of the NS5B region confirmed the predominance of hepatitis C virus genotype 1 infection in Jeddah, Saudi Arabia. PLoS One 2017; 12:e0178225. [PMID: 28552946 PMCID: PMC5446157 DOI: 10.1371/journal.pone.0178225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/10/2017] [Indexed: 02/06/2023] Open
Abstract
Chronic hepatitis C virus (HCV) infection and its progression are major health problems that many countries including Saudi Arabia are facing. Determination of HCV genotypes and subgenotypes is critical for epidemiological and clinical analysis and aids in the determination of the ideal treatment strategy that needs to be followed and the expected therapy response. Although HCV infection has been identified as the second most predominant type of hepatitis in Saudi Arabia, little is known about the molecular epidemiology and genetic variability of HCV circulating in the Jeddah province of Saudi Arabia. The aim of this study was to determine the dominance of various HCV genotypes and subgenotypes circulating in Jeddah using partial sequencing of the NS5B region. To the best of our knowledge, this is the first study of its kind in Saudi Arabia. To characterize HCV genotypes and subgenotypes, serum samples from 56 patients with chronic HCV infection were collected and subjected to partial NS5B gene amplification and sequence analysis. Phylogenetic analysis of the NS5B partial sequences revealed that HCV/1 was the predominant genotype (73%), followed by HCV/4 (24.49%) and HCV/3 (2.04%). Moreover, pairwise analysis also confirmed these results based on the average specific nucleotide distance identity: ±0.112, ±0.112, and ±0.179 for HCV/1, HCV/4, and HCV/3, respectively, without any interference between genotypes. Notably, the phylogenetic tree of the HCV/1 subgenotypes revealed that all the isolates (100%) from the present study belonged to the HCV/1a subgenotype. Our findings also revealed similarities in the nucleotide sequences between HCV circulating in Saudi Arabia and those circulating in countries such as Morocco, Egypt, Canada, India, Pakistan, and France. These results indicated that determination of HCV genotypes and subgenotypes based on partial sequence analysis of the NS5B region is accurate and reliable for HCV subtype determination.
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Affiliation(s)
- Sahar EL Hadad
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Research Center of Genetic Engineering and Bioinformatics, VACSERA, Cairo, Egypt
- * E-mail:
| | - Hesa Al-Hamdan
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sabah Linjawi
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Fevery B, Verbinnen T, Peeters M, Janssen K, Witek J, Jessner W, De Meyer S, Lenz O. Virology analyses of HCV genotype 4 isolates from patients treated with simeprevir and peginterferon/ribavirin in the Phase III RESTORE study. J Viral Hepat 2017; 24:28-36. [PMID: 27696653 DOI: 10.1111/jvh.12614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 08/05/2016] [Indexed: 01/08/2023]
Abstract
Simeprevir is a hepatitis C virus NS3/4A protease inhibitor. Hepatitis C virus baseline NS3/4A polymorphisms and emerging mutations were characterized in treatment-naїve and treatment-experienced genotype 4-infected patients treated with simeprevir+peginterferon/ribavirin in the RESTORE study. Population sequencing of the NS3/4A region was performed and in vitro simeprevir activity against site-directed mutants or chimeric replicons with patient-derived NS3 protease sequences was assessed in a transient replicon assay. Simeprevir remained active against most (83/91 [91%]) baseline isolates tested in the chimeric replicon assay. Eight baseline isolates reduced simeprevir activity; these carried I132L or D168E substitutions reducing simeprevir median activity by 4.6- and 39-fold, respectively. Six of these eight isolates were from patients achieving sustained virologic response. Baseline NS3 Q80K polymorphism was not observed in the genotype 4-infected patients. Of the 107 simeprevir-treated patients, 37 did not achieve sustained virologic response for any reason. Of the 32 patients who failed treatment and had sequencing information, 28 (88%) had emerging mutations at NS3 positions 80, 122, 155, 156 and/or 168 at time of failure, similar to those in genotype 1. Emerging mutations were mainly D168V and D168E alone or combined with mutations at position 80. In general, isolates obtained at time of failure displayed high-level in vitro resistance to simeprevir (fold change ≥50) in a chimeric replicon assay with a median simeprevir fold change value of 440, consistent with observed mutations. In conclusion, emerging mutations in genotype 4 patients failing simeprevir+peginterferon/ribavirin treatment were similar to those in genotype 1 and conferred high-level resistance to simeprevir.
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Affiliation(s)
- B Fevery
- Janssen Pharmaceutica NV, Beerse, Belgium
| | | | - M Peeters
- Janssen Pharmaceutica NV, Beerse, Belgium
| | - K Janssen
- Janssen Pharmaceutica NV, Beerse, Belgium
| | - J Witek
- Janssen Research & Development LLC, Titusville, NJ, USA
| | - W Jessner
- Janssen Pharmaceutica NV, Beerse, Belgium
| | - S De Meyer
- Janssen Pharmaceutica NV, Beerse, Belgium
| | - O Lenz
- Janssen Pharmaceutica NV, Beerse, Belgium
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Mukherjee R, Burns A, Rodden D, Chang F, Chaum M, Garcia N, Bollipalli N, Niemz A. Diagnosis and Management of Hepatitis C Virus Infection. ACTA ACUST UNITED AC 2015; 20:519-38. [PMID: 25609256 DOI: 10.1177/2211068214563794] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Indexed: 01/03/2023]
Abstract
The hepatitis C virus (HCV) infects more than 200 million people globally, with increasing incidence, especially in developing countries. HCV infection frequently progresses to chronic liver disease, creating a heavy economic burden on resource-poor countries and lowering patient quality of life. Effective HCV diagnosis, treatment selection, and treatment monitoring are important in stopping disease progression. Serological assays, which detect anti-HCV antibodies in the patient after seroconversion, are used for initial HCV diagnosis. Qualitative and quantitative molecular assays are used to confirm initial diagnosis, determine viral load, and genotype the dominant strain. Viral load and genotype information are used to guide appropriate treatment. Various other biomarker assays are performed to assess liver function and enable disease staging. Most of these diagnostic methods are mature and routinely used in high-resource countries with well-developed laboratory infrastructure. Few technologies, however, are available that address the needs of low-resource areas with high HCV prevalence, such as Africa and Southeast Asia.
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Affiliation(s)
- Ronita Mukherjee
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Andrew Burns
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Diane Rodden
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Frances Chang
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Manita Chaum
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Nancy Garcia
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | | | - Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
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Sarrazin C, Lathouwers E, Peeters M, Daems B, Buelens A, Witek J, Wyckmans Y, Fevery B, Verbinnen T, Ghys A, Schlag M, Baldini A, De Meyer S, Lenz O. Prevalence of the hepatitis C virus NS3 polymorphism Q80K in genotype 1 patients in the European region. Antiviral Res 2015; 116:10-6. [PMID: 25614456 DOI: 10.1016/j.antiviral.2015.01.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/19/2014] [Accepted: 01/11/2015] [Indexed: 12/12/2022]
Abstract
Hepatitis C virus (HCV) NS3 polymorphism Q80K is mainly found in patients with HCV genotype (G) 1a, and has been associated with a reduced treatment response to simeprevir with pegylated interferon (P) and ribavirin (R). Prevalence of Q80K among G1 patients may vary geographically. Q80K prevalence in the North-American G1 population in a recent study was 34%. We conducted a post hoc meta-analysis of Q80K polymorphism prevalence among HCV G1-infected patients enrolled in simeprevir and telaprevir Phase II/III studies. Baseline HCV NS3/4A protease sequences were analysed by population sequencing to determine Q80K prevalence. Overall, of 3349 patients from 25 countries in the European region analysed, 35.8%, 63.8% and 0.3% of patients had G1a, G1b and other/unknown HCV G1 subtypes, respectively. Q80K was detected at baseline in 7.5% of HCV G1 patients overall. Examination by subtype showed that 19.8%, 0.5% and 18.2% of patients with G1a, G1b and other/unknown HCV G1 subtypes had the Q80K polymorphism, respectively. Among countries in the European region with sequencing data available for either ⩾20 patients with G1a and/or ⩾40 G1 patients overall, the Q80K prevalence in G1 ranged from 0% in Bulgaria to 18.2% in the UK. Q80K prevalence also varied within G1a across different countries. HCV subtype 1a was correctly determined in 99% of patients by the LiPA v2 assay. A low overall prevalence of Q80K was observed in HCV G1-infected patients in the European region, compared with North America. However, the prevalence varied by country, due to differing ratios of G1a/G1b and differing Q80K prevalence within the G1a populations.
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Affiliation(s)
- Christoph Sarrazin
- Johann Wolfgang Goethe University Hospital, Medical Department 1, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Erkki Lathouwers
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Monika Peeters
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Bjorn Daems
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Annemie Buelens
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - James Witek
- Janssen Research & Development LLC, 1125 Trenton Harbourton Rd, Titusville, NJ 08560, United States.
| | - Yves Wyckmans
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Bart Fevery
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Thierry Verbinnen
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Anne Ghys
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Michael Schlag
- Janssen-Cilag, Vorgartenstraße 206B, 1020 Vienna, Austria.
| | - Alessandra Baldini
- Janssen Cilag, 1 Rue Camille Desmoulins, 92130 Issy-les-Moulineaux, France.
| | - Sandra De Meyer
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Oliver Lenz
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
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Thu Thuy PT, Bunchorntavakul C, Tan Dat H, Rajender Reddy K. A randomized trial of 48 versus 24 weeks of combination pegylated interferon and ribavirin therapy in genotype 6 chronic hepatitis C. J Hepatol 2012; 56:1012-1018. [PMID: 22266603 DOI: 10.1016/j.jhep.2011.12.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 10/28/2011] [Accepted: 12/14/2011] [Indexed: 12/26/2022]
Abstract
BACKGROUND & AIMS Genotype 6 chronic hepatitis C (HCV) is encountered predominantly in Southeast Asia and data on optimal treatment strategy is limited. This study was aimed at assessing the rate and predictors of sustained virological response (SVR) in genotype 6 chronic HCV following 48 and 24 weeks of pegylated interferon and ribavirin therapy. METHODS This investigator-initiated, open-label randomized trial was conducted in Vietnam between 2008 and 2010. One hundred and five treatment-naïve HCV genotype 6 patients were randomized to either 48-week (N=70) or 24-week (N=35) duration of pegylated interferon (PEG-IFN) alfa-2a 180 mcg/week and ribavirin (RBV) 15mg/kg/day; 92 patients completed the study (63 in the 48-week and 29 in the 24-week group, respectively). Primary outcome was sustained virological response (SVR) as intention-to-treat analysis. RESULTS There was no statistical difference in SVR between 48-week and 24-week treated groups (71% vs. 60%, respectively; p=0.24). In the 48-week and 24-week treatment groups, 81% and 80% of cases achieved rapid virological response (RVR) (p=0.86), and 86% and 80% achieved complete early virological response (p=0.45). Among those patients with RVR, SVR was in 86% (48-weeks), and 75% (24-weeks) of cases, whereas following non-RVR, only 8% of cases had an SVR with 48-week treatment duration. CONCLUSIONS Overall, RVR was achieved in the majority of genotype 6 patients and, in those patients, similar and high rates of SVR were noted following 24-week and 48-week therapy. This observation, however, needs validation in a larger study to demonstrate non-inferiority of the shorter duration therapy. In non-RVR patients, even 48-week therapy achieved low SVR rates.
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Affiliation(s)
| | - Chalermrat Bunchorntavakul
- Rajavithi Hospital, Ministry of Public Health, Bangkok, Thailand; Division of Gastroenterology and Hepatology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ho Tan Dat
- Medic Medical Center, Ho Chi Minh City, Viet Nam
| | - K Rajender Reddy
- Division of Gastroenterology and Hepatology, University of Pennsylvania, Philadelphia, PA, USA.
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Ansari MA, Lingaiah R, Irshad M. HCV-Core Region: Its Significance in HCV-Genotyping and Type Dependent Genomic Expression. ACTA ACUST UNITED AC 2012. [DOI: 10.3889/mjms.1857-5773.2011.0208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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Bacon BR, Gordon SC, Lawitz E, Marcellin P, Vierling JM, Zeuzem S, Poordad F, Goodman ZD, Sings HL, Boparai N, Burroughs M, Brass CA, Albrecht JK, Esteban R. Boceprevir for previously treated chronic HCV genotype 1 infection. N Engl J Med 2011; 364:1207-17. [PMID: 21449784 PMCID: PMC3153125 DOI: 10.1056/nejmoa1009482] [Citation(s) in RCA: 1288] [Impact Index Per Article: 99.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND In patients with chronic infection with hepatitis C virus (HCV) genotype 1 who do not have a sustained response to therapy with peginterferon-ribavirin, outcomes after retreatment are suboptimal. Boceprevir, a protease inhibitor that binds to the HCV nonstructural 3 (NS3) active site, has been suggested as an additional treatment. METHODS To assess the effect of the combination of boceprevir and peginterferon-ribavirin for retreatment of patients with chronic HCV genotype 1 infection, we randomly assigned patients (in a 1:2:2 ratio) to one of three groups. In all three groups, peginterferon alfa-2b and ribavirin were administered for 4 weeks (the lead-in period). Subsequently, group 1 (control group) received placebo plus peginterferon-ribavirin for 44 weeks; group 2 received boceprevir plus peginterferon-ribavirin for 32 weeks, and patients with a detectable HCV RNA level at week 8 received placebo plus peginterferon-ribavirin for an additional 12 weeks; and group 3 received boceprevir plus peginterferon-ribavirin for 44 weeks. RESULTS A total of 403 patients were treated. The rate of sustained virologic response was significantly higher in the two boceprevir groups (group 2, 59%; group 3, 66%) than in the control group (21%, P<0.001). Among patients with an undetectable HCV RNA level at week 8, the rate of sustained virologic response was 86% after 32 weeks of triple therapy and 88% after 44 weeks of triple therapy. Among the 102 patients with a decrease in the HCV RNA level of less than 1 log(10) IU per milliliter at treatment week 4, the rates of sustained virologic response were 0%, 33%, and 34% in groups 1, 2, and 3, respectively. Anemia was significantly more common in the boceprevir groups than in the control group, and erythropoietin was administered in 41 to 46% of boceprevir-treated patients and 21% of controls. CONCLUSIONS The addition of boceprevir to peginterferon-ribavirin resulted in significantly higher rates of sustained virologic response in previously treated patients with chronic HCV genotype 1 infection, as compared with peginterferon-ribavirin alone. (Funded by Schering-Plough [now Merck]; HCV RESPOND-2 ClinicalTrials.gov number, NCT00708500.).
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Affiliation(s)
- Bruce R Bacon
- Saint Louis University School of Medicine, St. Louis, MO 63110-0250, USA.
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12
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Hepatitis C virus genotyping using an oligonucleotide microarray based on the NS5B sequence. J Clin Microbiol 2010; 48:3910-7. [PMID: 20844214 DOI: 10.1128/jcm.01265-10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The genotype of the hepatitis C virus (HCV) is essential for determining treatment duration in clinical practice and for epidemiological and clinical studies. Currently, few genotyping assays that determine the HCV subtype are available. This report describes a microarray-based molecular technique for identifying the HCV genotype and subtype. It uses low-density hydrogel-based biochips containing genotype- and subtype-specific oligonucleotides based on the sequences of the NS5B region of the HCV genome. The biochip contains 120 oligonucleotides that identify genotypes 1 to 6 and 36 (1a, 1b, 1c, 1d, 1e, 2a, 2b, 2c, 2d, 2i, 2j, 2k, 2l, 2m, 3a, 3b, 3k, 4a, 4c, 4d, 4f, 4h, 4i, 4k, 4n, 4o, 4p, 4r, 4t, 5a, 6a, 6b, 6d, 6g, 6h, and 6k) subtypes. The procedure included amplification of a 380-nucleotide (nt) fragment of NS5B and its hybridization on the biochip. Tests on 345 HCV-positive samples showed that the assay agreed with NS5B sequencing 100% for the genotype and 99.7% for the subtype. The hybridization on the microarray and the NS5B sequence were in 100% agreement for identifying the most common subtypes, 1a, 1b, 4a, 4d, and 3a. This approach is a promising tool for HCV genotyping, especially for implementing the new anti-HCV drugs that require accurate identification of clinically relevant subtypes.
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13
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de Paula Cavalheiro N, de la Rosa A, Elagin S, Tengan FM, Barone AA. Hepatitis C virus: molecular and epidemiological evidence of male-to-female transmission. Braz J Infect Dis 2010. [DOI: 10.1016/s1413-8670(10)70088-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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14
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Abstract
Hepatitis C (HCV) is the disease that has affected around 200 million people globally. HCV is a life threatening human pathogen, not only because of its high prevalence and worldwide burden but also because of the potentially serious complications of persistent HCV infection. Chronicity of the disease leads to cirrhosis, hepatocellular carcinoma and end-stage liver disease. HCV positive hepatocytes vary between less than 5% and up to 100%, indicating the high rate of replication of viral RNA. HCV has a very high mutational rate that enables it to escape the immune system. Viral diversity has two levels; the genotypes and Quasiaspecies. Major HCV genotypes constitute genotype 1, 2, 3, 4, 5 and 6 while more than 50 subtypes are known. All HCV genotypes have their particular patterns of geographical distribution and a slight drift in viral population has been observed in some parts of the globe.
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Affiliation(s)
- Nazish Bostan
- Department of Biological Sciences, Quaid-i-Azam University, Islamabad-45320, Pakistan
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15
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Simultaneous Quantification and Genotyping of Hepatitis C Virus RNA by a Two-Step Real-Time PCR Assay on the Lightcycler Instrument. Folia Med (Plovdiv) 2010; 52:21-30. [DOI: 10.2478/v10153-010-0003-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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16
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Qiu P, Cai XY, Ding W, Zhang Q, Norris ED, Greene JR. HCV genotyping using statistical classification approach. J Biomed Sci 2009; 16:62. [PMID: 19586537 PMCID: PMC2720937 DOI: 10.1186/1423-0127-16-62] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Accepted: 07/08/2009] [Indexed: 01/24/2023] Open
Abstract
The genotype of Hepatitis C Virus (HCV) strains is an important determinant of the severity and aggressiveness of liver infection as well as patient response to antiviral therapy. Fast and accurate determination of viral genotype could provide direction in the clinical management of patients with chronic HCV infections. Using publicly available HCV nucleotide sequences, we built a global Position Weight Matrix (PWM) for the HCV genome. Based on the PWM, a set of genotype specific nucleotide sequence "signatures" were selected from the 5' NCR, CORE, E1, and NS5B regions of the HCV genome. We evaluated the predictive power of these signatures for predicting the most common HCV genotypes and subtypes. We observed that nucleotide sequence signatures selected from NS5B and E1 regions generally demonstrated stronger discriminant power in differentiating major HCV genotypes and subtypes than that from 5' NCR and CORE regions. Two discriminant methods were used to build predictive models. Through 10 fold cross validation, over 99% prediction accuracy was achieved using both support vector machine (SVM) and random forest based classification methods in a dataset of 1134 sequences for NS5B and 947 sequences for E1. Prediction accuracy for each genotype is also reported.
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Affiliation(s)
- Ping Qiu
- Molecular Design and Informatics, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
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Cavalheiro NDP, De La Rosa A, Elagin S, Tengan FM, Araújo ESAD, Barone AA. Hepatitis C: sexual or intrafamilial transmission? Epidemiological and phylogenetic analysis of hepatitis C virus in 24 infected couples. Rev Soc Bras Med Trop 2009; 42:239-44. [DOI: 10.1590/s0037-86822009000300001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 04/14/2009] [Indexed: 11/22/2022] Open
Abstract
The role of sexual or intrafamilial transmission of hepatitis C is controversial. A phylogenetic analysis was performed on the non-structural region 5B of the hepatitis C virus (NS5B-HCV). High percentages of homology (mean of 98.3%) were shown between the couples. Twenty (83.3%) of the 24 men but only two of the women (8.3%) reported having had sexually transmitted diseases during their lives. The risk factors for HCV acquisition were blood transfusion (10 couples), use of illegal injected drugs (17), use of inhalants (15), acupuncture (5) and tattoos (5). The shared use of personal hygiene items included toothbrushes between six couples (25%), razor blades between 16 (66.7%), nail clippers between 21 (87.5%) and manicure pliers between 14 (58.3%). The high degree of similarity of the hepatitis C virus genome supports the hypothesis of hepatitis C virus transmission between these couples. The shared use of personal hygiene items suggests the possibility of intrafamilial transmission of infection.
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Maylin S, Martinot-Peignoux M, Moucari R, Boyer N, Ripault MP, Cazals-Hatem D, Giuily N, Castelnau C, Cardoso AC, Asselah T, Féray C, Nicolas-Chanoine MH, Bedossa P, Marcellin P. Eradication of hepatitis C virus in patients successfully treated for chronic hepatitis C. Gastroenterology 2008; 135:821-9. [PMID: 18593587 DOI: 10.1053/j.gastro.2008.05.044] [Citation(s) in RCA: 247] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 04/17/2008] [Accepted: 05/15/2008] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS It is unclear whether hepatitis C virus (HCV) is eradicated in patients with chronic hepatitis C who achieved a sustained virologic response (SVR). METHODS In this long-term follow-up study, including chronic hepatitis C patients who achieved SVR after interferon-based therapy, the presence of residual HCV RNA in serum, liver, and peripheral blood mononuclear cells (PBMCs) was assessed, using transcription-mediated amplification (sensitivity, <9.6 IU/mL). The benefit of SVR on liver fibrosis was evaluated using the METAVIR score. RESULTS A total of 344 patients were followed up for a median duration of 3.27 years (range, 0.50-18 y; interquartile range [IQR], 1.68-5.35 y). A total of 114 patients had a posttreatment liver tissue (median, 0.50 y; range, 0-14 y; IQR, 0-3.5 y) and a total of 156 had one PBMC (median, 3.0 y; range, 0.50-18 y; IQR, 1.25-5.50 y). Serum HCV RNA remained undetectable (1300 samples), indicating that none of the patients had a relapse. HCV RNA was detectable in 2 of 114 (1.7%) liver specimens, and in none of 156 PBMC specimens. Histologic analysis of 126 paired pretreatment and posttreatment liver biopsy specimens (median, 0.50 y; range, 0-14 y; IQR, 0-3.5 y) showed that fibrosis stage was improved in 56%, stable in 32%, deteriorated in 12%. Regression of cirrhosis was observed in 9 of 14 (64%) (95% confidence interval, 39-89) patients. No cirrhosis decompensation was observed, and 3 patients developed hepatocellular carcinoma. CONCLUSIONS In this large cohort of chronic hepatitis C patients, SVR was durable up to 18 years after treatment cessation, in addition to fibrosis stability/improvement (88%) and cirrhosis regression (64%). The presence of residual HCV RNA was observed only in liver tissue (1.7%). This result strongly suggests that SVR may be considered to show eradication of HCV infection.
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Affiliation(s)
- Sarah Maylin
- Université Paris VII, Hôpital Beaujon, Clichy, France
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Bracho MA, Saludes V, Martró E, Bargalló A, González-Candelas F, Ausina V. Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses. Virol J 2008; 5:72. [PMID: 18533988 PMCID: PMC2438343 DOI: 10.1186/1743-422x-5-72] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 06/05/2008] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Hepatitis C virus isolates have been classified into six main genotypes and a variable number of subtypes within each genotype, mainly based on phylogenetic analysis. Analyses of the genetic relationship among genotypes and subtypes are more reliable when complete genome sequences (or at least the full coding region) are used; however, so far 31 of 80 confirmed or proposed subtypes have at least one complete genome available. Of these, 20 correspond to confirmed subtypes of epidemic interest. RESULTS We present and analyse the first complete genome sequence of a HCV subtype 1g isolate. Phylogenetic and genetic distance analyses reveal that HCV-1g is the most divergent subtype among the HCV-1 confirmed subtypes. Potential genomic recombination events between genotypes or subtype 1 genomes were ruled out. We demonstrate phylogenetic congruence of previously deposited partial sequences of HCV-1g with respect to our sequence. CONCLUSION In light of this, we propose changing the current status of its subtype-specific designation from provisional to confirmed.
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Affiliation(s)
- Maria A Bracho
- Institut "Cavanilles" de Biodiversitat i Biologia Evolutiva, Universitat de València, Paterna (València), Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Verónica Saludes
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Elisa Martró
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Ana Bargalló
- Servei d'Aparell Digestiu, Hospital Universitari Germans Trias i Pujol, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain
| | - Fernando González-Candelas
- Institut "Cavanilles" de Biodiversitat i Biologia Evolutiva, Universitat de València, Paterna (València), Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Vicent Ausina
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain
- CIBER en Enfermedades Respiratorias (CIBERES), Spain
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Evaluation of a new assay in comparison with reverse hybridization and sequencing methods for hepatitis C virus genotyping targeting both 5' noncoding and nonstructural 5b genomic regions. J Clin Microbiol 2007; 46:192-7. [PMID: 17989191 DOI: 10.1128/jcm.01623-07] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We report the evaluation of a new real-time PCR assay for hepatitis C virus (HCV) genotyping. The assay design is such that genotype 1 isolates are typed by amplification targeting the nonstructural 5b (NS5b) subgenomic region. Non-genotype 1 isolates are typed by type-specific amplicon detection in the 5' noncoding region (5'NC) (method 1; HCV genotyping analyte-specific reagent assay). This method was compared with 5'NC reverse hybridization (method 2; InnoLiPA HCV II) and 5'NC sequencing (method 3; Trugene HCV 5'NC). Two hundred ninety-five sera were tested by method 1; 223 of them were also typed by method 2 and 89 by method 3. Sequencing and phylogenetic analysis of an NS5b fragment were used to resolve discrepant results. Suspected multiple-genotype infections were confirmed by PCR cloning and pyrosequencing. Even though a 2% rate of indeterminates was obtained with method 1, concordance at the genotype level with results with methods 2 and 3 was high. Among eight discordant results, five mixed infections were confirmed. Genotype 1 subtyping efficiencies were 100%, 77%, and 74% for methods 1, 2, and 3, respectively; there were 11/101 discordants between methods 1 and 2 (method 1 was predominantly correct) and 2/34 between methods 2 and 3. Regarding genotype 2, subtyping efficiencies were 100%, 45%, and 92% by methods 1, 2, and 3, respectively; NS5b sequencing of discordants (16/17) revealed a putative new subtype within genotype 2 and that most subtype calls were not correct. Although only sequencing-based methods provide the possibility of identifying new variants, the real-time PCR method is rapid, straightforward, and simple to interpret, thus providing a good single-step alternative to more-time-consuming assays.
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Navarro Ortega D, Jiménez Mayordomo M, Desamparados Martínez Aparicio M. Métodos moleculares para la determinación del genotipo del virus de la hepatitis C. Enferm Infecc Microbiol Clin 2007. [DOI: 10.1157/13111840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Laskus T, Wilkinson J, Karim R, Mack W, Radkowski M, deGiacomo M, Nasseri J, Chen Z, Xu J, Kovacs A. Hepatitis C virus quasispecies in HIV-infected women: role of injecting drug use and highly active antiretroviral therapy (HAART). Hepatology 2007; 46:359-70. [PMID: 17659581 PMCID: PMC3508063 DOI: 10.1002/hep.21715] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
UNLABELLED Despite the high frequency of HCV and HIV coinfection, little is known about HCV quasispecies in HIV-positive patients. The current analysis included 236 HIV+/anti-HCV+ women enrolled in the Women's Interagency HIV Study (WIHS). Hypervariable region 1 of the second envelope gene was analyzed by single-strand conformation polymorphism (SSCP). The relationship between the HCV quasispecies and clinical and demographic features were analyzed in multivariate models. Age over 40 years and high HCV RNA load were the only factors significantly associated with quasispecies complexity, assessed as the number of SSCP bands. High HIV and HCV plasma loads were associated with quasispecies stability over time, as reflected by stable SSCP band patterns. However, women who were actively injecting drugs were 3 times more likely to experience quasispecies changes than their noninjecting counterparts. No affect on HCV quasispecies dynamics was noted in relation to CD4 count or highly active antiretroviral therapy (HAART). CONCLUSION among HIV/HCV coinfected patients, HCV quasispecies complexity and dynamics correlate more closely with HIV and HCV plasma loads than with CD4+ cell counts. Active drug use is associated with quasispecies changes probably due to repeated superinfections with new HCV strains. This needs to be considered when planning treatment and prevention strategies for HCV in coinfected individuals.
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Affiliation(s)
- Tomasz Laskus
- St. Joseph's Hospital and Medical Center, Phoenix, AZ 85013, USA.
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Abstract
Hepatitis C virus is an RNA virus that is associated with chronic infection in the majority of people infected. Chronic infection with hepatitis C virus is the cause of significant morbidity and mortality worldwide and is associated with a large spectrum of liver disease including cirrhosis and hepatocellular carcinoma. End-stage liver disease due to chronic hepatitis C virus infection is currently the leading indication for liver transplantation in the USA. Hepatitis C virus genotyping of viral isolates circulating in the blood during chronic infection has become an important part of hepatitis C virus monitoring in chronically infected patients, and is useful as a prognostic indicator and to direct duration of therapy. This review will summarize information on hepatitis C genotyping, describe the limitations of current commercially available methods, give information on more recently developed methods, and provide a look to the future in terms of where advances in hepatitis C virus genotyping assays need to be made.
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Affiliation(s)
- Karen Weck
- University of North Carolina, Campus Box 7525, Chapel Hill, NC 27599-7525, USA.
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Laskus T, Operskalski EA, Radkowski M, Wilkinson J, Mack WJ, deGiacomo M, Al-Harthi L, Chen Z, Xu J, Kovacs A. Negative-strand hepatitis C virus (HCV) RNA in peripheral blood mononuclear cells from anti-HCV-positive/HIV-infected women. J Infect Dis 2006; 195:124-33. [PMID: 17152016 PMCID: PMC3319123 DOI: 10.1086/509897] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2006] [Accepted: 08/31/2006] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) has been reported to replicate in peripheral blood mononuclear cells (PBMCs), particularly in patients coinfected with HCV and human immunodeficiency virus (HIV). However, there are limited data regarding the prevalence of and the factors associated with extrahepatic replication. METHODS The presence of negative-strand HCV RNA in PBMCs was evaluated by a strand-specific assay for 144 anti-HCV-positive/HIV-infected women enrolled in the Women's Interagency HIV Study. One to 5 PBMC samples obtained from each woman were tested. Multivariate analyses were used to assess for associations with the clinical and demographic characteristics of the women. RESULTS Negative-strand HCV RNA was detected in 78 (25%) of 315 specimens, and, for 61 women (42%), > or = 1 specimen was found to have positive results. The presence of negative-strand HCV RNA in PBMCs was significantly positively associated with an HCV RNA plasma level of > or = 6.75 log copies/mL (P=.04) and consumption of > or = 7 alcoholic drinks per week (P=.02). It was also negatively associated with injection drug use occurring in the past 6 months (P=.03). A negative association with a CD4+ CD38+ DR+ cell percentage of > 10% and a positive association with acquired immunodeficiency syndrome were borderline significant (P=.05). CONCLUSIONS HCV replication in PBMCs is common among HIV-coinfected women and appears to be a dynamic process related to lifestyle, virologic, and immunologic factors.
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Affiliation(s)
- Tomasz Laskus
- Department of Medicine, St. Joseph's Hospital and Medical Center, Phoenix, AZ 85013, USA.
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Schutzbank TE, Sefers SE, Kahmann N, Li H, Tang YW. Comparative evaluation of three commercially available methodologies for hepatitis C virus genotyping. J Clin Microbiol 2006; 44:3797-8. [PMID: 17021114 PMCID: PMC1594808 DOI: 10.1128/jcm.01159-06] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We compared the performances of three hepatitis C virus genotyping methodologies supplied by Bayer, Abbott, and Third Wave Technologies. Genotypes were determined for 136 of 137 specimens by the Bayer method, 121 of 137 specimens by the Invader assay, and only 77 of 137 specimens by the Abbott assay. All reported genotypes were concordant by all three methods.
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Affiliation(s)
- Ted E Schutzbank
- CompuNet Clinical Laboratories, 2308 Sandridge Rd., Dayton, OH 45439, USA.
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Cantaloube JF, Laperche S, Gallian P, Bouchardeau F, de Lamballerie X, de Micco P. Analysis of the 5' noncoding region versus the NS5b region in genotyping hepatitis C virus isolates from blood donors in France. J Clin Microbiol 2006; 44:2051-6. [PMID: 16757597 PMCID: PMC1489428 DOI: 10.1128/jcm.02463-05] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The 5' noncoding region (5' NCR) of the hepatitis C virus (HCV) has become the standard for genotyping even though several reports show that its use can result in classification errors. The purpose of this study was to perform genotyping based on sequence analysis of the NS5b region in a set of 357 HCV strains isolated from blood donors in France in 2002 and 2003. Results were compared with those previously obtained using 5' NCR analysis, and HCV subtype distribution was reevaluated. Twenty-six of 120 strains (approximately 22%) initially identified as genotype 1b by 5' NCR region sequence analysis were reclassified as genotype 1a by NS5b region sequence analysis. Similarly, 14 of 23 strains (approximately 61%) initially identified as 2a/2c were reclassified as non-2a and non-2c subtypes, and 12 of 22 strains (approximately 45%) initially identified as 4c/4d subtypes were reclassified as non-4c and non-4d subtypes. Sequence analysis of the NS5b region also revealed 5 putative new subtype 2 variants and 2 putative new subtype 4 variants. Although these findings demonstrated full agreement between 5' NCR and NS5b sequence analysis with regard to type classification, genotyping based on phylogenetic analysis of the NS5b region is more accurate for subtype determination than genotyping based on analysis of the 5' NCR. Sequence analysis of the NS5b region is mandatory for epidemiologic studies.
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Affiliation(s)
- Jean-François Cantaloube
- Unité des Virus Emergents EA3292, Etablissement Français du Sang Alpes-Méditerranée, 149 bd Baille, 13005 Marseille, France.
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Antonishyn NA, Ast VM, McDonald RR, Chaudhary RK, Lin L, Andonov AP, Horsman GB. Rapid genotyping of hepatitis C virus by primer-specific extension analysis. J Clin Microbiol 2005; 43:5158-63. [PMID: 16207978 PMCID: PMC1248436 DOI: 10.1128/jcm.43.10.5158-5163.2005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Quick and accurate genotyping of hepatitis C virus (HCV) is becoming increasingly important for clinical management of chronic infection and as an epidemiological marker. Furthermore, the incidence of HCV infection with mixed genotypes has clinical significance that is not addressed by most genotyping methods. We have developed a fluorescence-based genotyping assay called primer-specific extension analysis (PSEA) for the most prevalent HCV genotypes and have demonstrated the capacity of PSEA-HCV for detecting mixed-genotype HCV infections. PSEA-HCV detects genotype-specific sequence differences in the 5' untranslated region of HCV in products amplified by the COBAS AMPLICOR HCV Test, v2.0. Simulated mixed HCV infection of plasma with RNase-resistant RNA controls demonstrates that PSEA-HCV can detect as many as five genotypes in one specimen. Furthermore, in dual-genotype simulations, PSEA-HCV can unequivocally detect both genotypes, with one genotype representing only 3.1% of the mixture (313/10,000 IU in starting plasma). Compared to INNO-LiPA HCV II, both assays determined the same genotype for 191/199 (96%) patient specimens (175 subtype and 16 genotype-only identifications). Following the initial evaluation, PSEA-HCV was used routinely to genotype HCV from patient specimens submitted to our laboratory (n=312). Seventeen (5.4%) mixed infections were identified. The distribution of single-infection HCV genotypes in our population was 60.9% type 1 (n=190), 12.8% type 2 (n=40), 20.2% type 3 (n=63), 0.3% type 4 (n=1), and 0.3% other (n=1). In conclusion, PSEA-HCV provides an inexpensive, high-throughput screening tool for rapid genotyping of HCV while reliably identifying mixed HCV infections.
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Affiliation(s)
- Nick A Antonishyn
- Saskatchewan Health, Provincial Laboratory, Regina, Saskatchewan S4S 5W6, Canada.
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Chevaliez S, Pawlotsky JM. Use of virologic assays in the diagnosis and management of hepatitis C virus infection. Clin Liver Dis 2005; 9:371-82, v. [PMID: 16023971 DOI: 10.1016/j.cld.2005.05.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
This article discusses the use of virologic assays in the diagnosis and management of hepatitis C virus (HCV) infection. The use of virologic tests has become essential in the management of HCV infection to diagnose HCV infection, guide treatment decisions, and assess the virologic response to antiviral therapy. The continuing development of test systems accompanied by new antiviral drugs and novel therapeutic approaches should lead to an optimization of the treatment of HCV infection.
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Affiliation(s)
- Stéphane Chevaliez
- Department of Virology, INSERM U635, Henri Mondor Hospital, University of Paris XII, 51 Avenue du Maréchal de Lattre de Tassigny, 94010 Créteil, France
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