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Byrne A, Bissonnette N, Ollier S, Tahlan K. Investigating in vivo Mycobacterium avium subsp. paratuberculosis microevolution and mixed strain infections. Microbiol Spectr 2023; 11:e0171623. [PMID: 37584606 PMCID: PMC10581078 DOI: 10.1128/spectrum.01716-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's Disease (JD) in ruminants, which is responsible for significant economic loss to the global dairy industry. Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with genetically distinct strains of a pathogen, whereas within-host changes in an infecting strain leading to genetically distinguishable progeny is called microevolution. The two processes can influence host-pathogen dynamics, disease progression and outcomes, but not much is known about their prevalence and impact on JD. Therefore, we obtained up to 10 MAP isolates each from 14 high-shedding animals and subjected them to whole-genome sequencing. Twelve of the 14 animals examined showed evidence for the presence of MSIs and microevolution, while the genotypes of MAP isolates from the remaining two animals could be attributed solely to microevolution. All MAP isolates that were otherwise isogenic had differences in short sequence repeats (SSRs), of which SSR1 and SSR2 were the most diverse and homoplastic. Variations in SSR1 and SSR2, which are located in ORF1 and ORF2, respectively, affect the genetic reading frame, leading to protein products with altered sequences and computed structures. The ORF1 gene product is predicted to be a MAP surface protein with possible roles in host immune modulation, but nothing could be inferred regarding the function of ORF2. Both genes are conserved in Mycobacterium avium complex members, but SSR1-based modulation of ORF1 reading frames seems to only occur in MAP, which could have potential implications on the infectivity of this pathogen. IMPORTANCE Johne's disease (JD) is a major problem in dairy animals, and concerns have been raised regarding the association of Mycobacterium avium subsp. paratuberculosis (MAP) with Crohn's disease in humans. MAP is an extremely slow-growing bacterium with low genome evolutionary rates. Certain short sequence repeats (SSR1 and SSR2) in the MAP chromosome are highly variable and evolve at a faster rate than the rest of the chromosome. In the current study, multiple MAP isolates with genetic variations such as single-nucleotide polymorphisms, and more noticeably, diverse SSRs, could simultaneously infect animals. Variations in SSR1 and SSR2 affect the products of the respective genes containing them. Since multiple MAP isolates can infect the same animal and the possibility that the pathogen undergoes further changes within the host due to unstable SSRs, this could provide a compensative mechanism for an otherwise slow-evolving pathogen to increase phenotypic diversity for overcoming host responses.
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Affiliation(s)
- Alexander Byrne
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
| | - Séverine Ollier
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
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HCV Genotype Distribution of Patients with Chronic Hepatitis C in Istanbul. MEDICAL BULLETIN OF SISLI ETFAL HOSPITAL 2021; 55:86-92. [PMID: 33935541 PMCID: PMC8085459 DOI: 10.14744/semb.2020.66990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 12/06/2020] [Indexed: 11/20/2022]
Abstract
Objectives: Hepatitis C virus (HCV), which has no protective vaccine, is a common cause of chronic hepatitis, which is a severe public health threat. There are differences in nucleotide and amino acid sequences in different regions of the HCV genome. As a result of these differences, HCV has been shown to have at least seven major genotypes and many subtypes. In Turkey, the prevalence of genotype 1 is between 51.7% and 97.1%, the highest rate among all genotypes, while subtype 1b is the genotype with the highest rate. It is important to detect mixed genotype infection reliably as it causes treatment failure. This study aims to reveal the distribution of the HCV genotypes in our hospital in Istanbul over the years and to contribute to the epidemiological data of Turkey. Methods: For this purpose, 385 patient samples sent to Sisli Hamidiye Etfal Training and Research Hospital, Clinical Microbiology Laboratory for HCV genotype determination between January 2016 and June 2019 were evaluated retrospectively. Anti-HCV was screened by enzyme immunoassay and confirmation was performed by Line immunoassay. HCV genotyping assays targeting highly conserved 5’UTR and most variable region NS5B regions were used. Results: The most common genotype was genotype 1 (81.3%) with 313 cases and subtypes 1a and 1b were detected at the rates of 10.9% and 67.8%, respectively. In addition, genotype 3, 2, 4, 5 were detected at the rates of 8.8%, 3.4%, 2.9%, 0.8%, respectively and mixed genotype was found in 2.9% of cases. Although genotype 5 is seen in South Africa, it is found in the Middle East region, albeit at a low rate. In our study, it was observed that genotype 5 was detected in different years from patients of Syrian origin. Conclusion: In this study, genotype 1 was the most common genotype with a rate of 81.3% and subtype 1b was 67.8%, in accordance with the literature. However, genotypes 3, 2, 4 and 5 were also present at low rates. It is important to monitor these rare genotypes since some of them are dominant in surrounding countries. In addition, 2.9% of HCV mixed genotype was detected and this should be considered concerning management of HCV infection.
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3
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Jandovitz N, Nair V, Grodstein E, Molmenti E, Fahmy A, Abate M, Bhaskaran M, Teperman L. Hepatitis C-positive donor to negative recipient kidney transplantation: A real-world experience. Transpl Infect Dis 2021; 23:e13540. [PMID: 33259125 DOI: 10.1111/tid.13540] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 11/03/2020] [Accepted: 11/22/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND Several studies have shown that transplanting a hepatitis C virus (HCV)-negative recipients with a HCV-positive donor is feasible in a research setting. In February 2018, we began transplanting HCV-negative recipients with HCV-positive donors as standard of care. METHODS All patients, except those with previously cured HCV and those with cirrhosis, were consented for HCV NAT-positive donor kidneys. After transplantation, patients were tested for HCV RNA until viremic. A direct-acting antiviral (DAA) agent was prescribed based on genotype and insurance approval. Sustained virologic response (SVR) at weeks 4 and 12 was recorded. Renal function and death censored graft survival at 1 year were evaluated and compared to recipients of HCV NAT-negative kidneys. RESULTS A total of 25 HCV NAT-positive donor kidney transplants from February to October 2018 were performed. All patients received basiliximab and maintained with tacrolimus, mycophenolate mofetil, and prednisone. Median time from viremia to start of DAA was 13 (8-22) days. The most common genotype was 1a (60%), followed by 3a (28%). The most commonly prescribed DAA was ledipasvir/sofosbuvir (56%), followed by velpatasvir/sofosbuvir (32%), and then glecaprevir/pibrentasvir (12%). All patients achieved initial SVR12, except one. One patient had a mixed-genotype infection requiring retreatment to achieve SVR12. Death censored graft survival was 96%. Recipients of HCV NAT-positive organs compared to HCV NAT-negative organs received younger donors (mean 35 ± 8.9 vs 45.1 ± 15.7 years; P < .01) and spent less time on the waitlist (median 479 (93-582) vs 1808 (567-2263) days; P = .02). CONCLUSION HCV NAT-negative recipients can be safely and successfully transplanted with HCV NAT-positive donor kidneys outside of a research protocol. Access to DAA and timely administration of therapy is important and an insurance approval process within the transplant center can be beneficial to patients. A case of mixed-genotype infection was presented, and although not as common, can be successfully treated. HCV organs can expand the organ pool and should no longer be considered experimental. The use of these organs in HCV-negative recipient's decreases waiting time, have excellent outcomes, and should be considered standard of care.
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Affiliation(s)
- Nicholas Jandovitz
- Department of Pharmacy, North Shore University Hospital -Northwell Health, Manhasset, NY, USA.,Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Vinay Nair
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Elliot Grodstein
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Ernesto Molmenti
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Ahmed Fahmy
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Mersema Abate
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Madhu Bhaskaran
- Department of Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Lewis Teperman
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
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Manso CF, Bibby DF, Lythgow K, Mohamed H, Myers R, Williams D, Piorkowska R, Chan YT, Bowden R, Ansari MA, Ip CLC, Barnes E, Bradshaw D, Mbisa JL. Technical Validation of a Hepatitis C Virus Whole Genome Sequencing Assay for Detection of Genotype and Antiviral Resistance in the Clinical Pathway. Front Microbiol 2020; 11:576572. [PMID: 33162957 PMCID: PMC7583327 DOI: 10.3389/fmicb.2020.576572] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/14/2020] [Indexed: 01/05/2023] Open
Abstract
Choice of direct acting antiviral (DAA) therapy for Hepatitis C Virus (HCV) in the United Kingdom and similar settings usually requires knowledge of the genotype and, in some cases, antiviral resistance (AVR) profile of the infecting virus. To determine these, most laboratories currently use Sanger technology, but next-generation sequencing (NGS) offers potential advantages in throughput and accuracy. However, NGS poses unique technical challenges, which require idiosyncratic development and technical validation approaches. This applies particularly to virology, where sequence diversity is high and the amount of starting genetic material is low, making it difficult to distinguish real data from artifacts. We describe the development and technical validation of a sequence capture-based HCV whole genome sequencing (WGS) assay to determine viral genotype and AVR profile. We use clinical samples of known subtypes and viral loads, and simulated FASTQ datasets to validate the analytical performances of both the wet laboratory and bioinformatic pipeline procedures. We show high concordance of the WGS assay compared to current "gold standard" Sanger assays. Specificity was 92.3 and 96.1% for AVR and genotyping, respectively. Discordances were due to the inability of Sanger assays to assign the correct subtype or accurately call mixed drug-resistant variants. We show high repeatability and reproducibility with >99.8% sequence similarity between sequence runs as well as high precision for variant frequency detection at >98.8% in the 95th percentile. Post-sequencing bioinformatics quality control workflows allow the accurate distinction between mixed infections, cross-contaminants and recombinant viruses at a threshold of >5% for the minority population. The sequence capture-based HCV WGS assay is more accurate than legacy AVR and genotyping assays. The assay has now been implemented in the clinical pathway of England's National Health Service HCV treatment programs, representing the first validated HCV WGS pipeline in clinical service. The data generated will additionally provide granular national-level genomic information for public health policy making and support the WHO HCV elimination strategy.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Rory Bowden
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - M. Azim Ansari
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Camilla L. C. Ip
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | | | - Jean L. Mbisa
- Public Health England, London, United Kingdom
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
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5
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Sallam M, Batarseh R, Natsheh A, Abbadi J, Al-Fraihat E, Yaseen A, Kaddomi D, Khamees N, Mahafzah A, Şahin GÖ. An update on hepatitis C virus genotype distribution in Jordan: a 12-year retrospective study from a tertiary care teaching hospital in Amman. BMC Infect Dis 2019; 20:3. [PMID: 31892307 PMCID: PMC6938611 DOI: 10.1186/s12879-019-4735-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/24/2019] [Indexed: 11/16/2022] Open
Abstract
Background Nucleic acid hybridization (NAH) of hepatitis C virus (HCV) is a practical and reliable tool for virus genotyping. Genotype assignment is an important factor in the prediction of treatment success in chronic hepatitis C patients. The aim of this study was to determine the genotype distribution among HCV clinical isolates in Jordan between 2007 and 2018. Methods Electronic and paper-based clinical data registry records from 2007 to 2018 at the Jordan University Hospital (JUH) were retrospectively examined for individuals with HCV genotype, HCV viral load, and alanine aminotransferase (ALT) testing results. Genotype determination was based on NAH technique using the HCV 5′ untranslated region (5′ UTR) with 386 requests available from 342 unique individuals. Results A total of 263 out of 342 unique individuals (76.9%) had genotyping results available for final analysis with 259 individuals each having a single genotyping result. The most common HCV genotypes in the study were: genotype 4 (n = 142, 54.0%), genotype 1 (n = 87, 33.1%), genotype 3 (n = 16, 6.1%), genotype 2 (n = 9, 3.4%), other undetermined genotypes (n = 5, 1.9%) and mixed infections (n = 4, 1.5%). Sub-genotyping results were available for 46 individuals as follows: sub-genotype 4c/d (n = 13, 28.3%), sub-genotype 1a (n = 11, 23.9%), sub-genotype 1b (n = 10, 21.7%), sub-genotype 4a (n = 8, 17.4%), sub-genotype 3a (n = 2, 4.3%), sub-genotypes 2a/c and 4 h (n = 1, 2.2% for both). Individuals infected with genotype 1 showed higher viral load when compared to those infected with genotype 4 (p = 0.048, t-test). Younger HCV-infected individuals (< 52 years) had higher ALT levels compared to older individuals (p = 0.036, t-test). Self-reported risk factors for HCV acquisition included: history of previous surgery, invasive dental procedures, and blood transfusion, delivery at home, circumcision at home and wet cupping therapy (hijama). Conclusions High genetic diversity of HCV was found in Jordan, with genotypes 4 and 1 as the most prevalent genotypes co-circulating in the country. Potential impact of virus genotype on disease markers (viral load, ALT) was detected and needs further assessment. The study can be helpful to plan for future prevention and management of HCV infection in Jordan.
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Affiliation(s)
- Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan. .,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan. .,Department of Translational Medicine, Faculty of Medicine, Lund University, 22100, Malmö, Sweden.
| | - Rawan Batarseh
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Anas Natsheh
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Jumana Abbadi
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Esraa Al-Fraihat
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Alaa' Yaseen
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Doaa Kaddomi
- Gastroenterology and Liver Division, Department of Internal Medicine, Jordan University Hospital, Amman, 11942, Jordan
| | - Nadia Khamees
- Gastroenterology and Liver Division, Department of Internal Medicine, Jordan University Hospital, Amman, 11942, Jordan
| | - Azmi Mahafzah
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, the University of Jordan, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan.,Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Queen Rania Al-Abdullah Street-Aljubeiha, /P.O. Box: 13046, Amman, 11942, Jordan
| | - Gülşen Özkaya Şahin
- Department of Translational Medicine, Faculty of Medicine, Lund University, 22100, Malmö, Sweden.,Department of Clinical Microbiology, Laboratory Medicine, Skåne University Hospital, 22100, Lund, Sweden
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6
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Molnar MZ, Nair S, Cseprekal O, Yazawa M, Talwar M, Balaraman V, Podila PSB, Mas V, Maluf D, Helmick RA, Campos L, Nezakatgoo N, Eymard C, Horton P, Verma R, Jenkins AH, Handley CR, Snyder HS, Cummings C, Agbim UA, Maliakkal B, Satapathy SK, Eason JD. Transplantation of kidneys from hepatitis C-infected donors to hepatitis C-negative recipients: Single center experience. Am J Transplant 2019; 19:3046-3057. [PMID: 31306549 DOI: 10.1111/ajt.15530] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 07/02/2019] [Accepted: 07/05/2019] [Indexed: 01/25/2023]
Abstract
Our aim was to evaluate the safety of transplanting kidneys from HCV-infected donors in HCV-uninfected recipients. Data collected from 53 recipients in a single center, observational study included donor and recipient characteristics, liver and kidney graft function, new infections and de novo donor-specific antibodies and renal histology. Treatment with a direct-acting antiviral regimen was initiated when HCV RNA was detected. The mean ± SD age of recipients was 53 ± 11 years, 34% were female, 19% and 79% of recipients were white and African American, respectively. The median and interquartile range (IQR) time between transplant and treatment initiation was 76 (IQR: 68-88) days. All 53 recipients became viremic (genotype: 1a [N = 34], 1b [N = 1], 2 [N = 3], and 3 [N = 15]). The majority (81%) of recipients did not experience clinically significant increases (>3 times higher than upper limit of the normal value) in aminotransferase levels and their HCV RNA levels were in the 5 to 6 log range. One patient developed fibrosing cholestatic hepatitis with complete resolution. All recipients completed antiviral treatment and 100% were HCV RNA-negative and achieved 12-week sustained virologic response. The estimated GFRs at end of treatment and 12-week posttreatment were 67 ± 21 mL/min/1.73 m2 and 67 ± 17 mL/min/1.73 m2 , respectively. Four recipients developed acute rejection. Kidney transplantation from HCV-infected donors to HCV-negative recipients should be considered in all eligible patients.
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Affiliation(s)
- Miklos Z Molnar
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee.,Division of Nephrology, Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee.,Department of Transplantation and Surgery, Semmelweis University, Budapest, Hungary
| | - Satheesh Nair
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Orsolya Cseprekal
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee.,Department of Transplantation and Surgery, Semmelweis University, Budapest, Hungary
| | - Masahiko Yazawa
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee.,Divison of Nephrology and Hypertension, St. Marianna University School of Medicine, Tokyo, Japan
| | - Manish Talwar
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Vasanthi Balaraman
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Pradeep S B Podila
- Faith & Health Division, Methodist Le Bonheur Healthcare, Memphis, Tennessee.,Division of Health Systems Management & Policy, School of Public Health, The University of Memphis, Memphis, Tennessee
| | - Valeria Mas
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Daniel Maluf
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Ryan A Helmick
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Luis Campos
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Nosratollah Nezakatgoo
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Corey Eymard
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Peter Horton
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Rajanshu Verma
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Ann Holbrook Jenkins
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee
| | - Charlotte R Handley
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee
| | - Heather S Snyder
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee
| | - Carolyn Cummings
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee
| | - Uchenna A Agbim
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Benedict Maliakkal
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Sanjaya K Satapathy
- Sandra Atlas Bass Center for Liver Diseases & Transplantation, Zucker School of Medicine at Hofstra, Department of Medicine, Northshore University Hospital/Northwell Health, Manhasset, New York
| | - James D Eason
- James D. Eason Transplant Institute, Methodist University Hospital, Memphis, Tennessee.,Division of Transplant Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, Tennessee
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7
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Abdel Ghaffar TY, El Naghi S, Abdel Gawad M, Helmy S, Abdel Ghaffar A, Yousef M, Moafy M. Safety and efficacy of combined sofosbuvir/daclatasvir treatment of children and adolescents with chronic hepatitis C Genotype 4. J Viral Hepat 2019; 26:263-270. [PMID: 30380158 DOI: 10.1111/jvh.13032] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/03/2018] [Indexed: 12/16/2022]
Abstract
Direct-acting antivirals have become available for treating chronic HCV (hepatitis C virus) infection in adults and, recently, in children at least 12 years old. Our aim was to investigate the safety and efficacy of combined sofosbuvir (SOF)/daclatasvir (DCV) for HCV Genotype 4 in children aged 8 to 18 years or weighing 17 kg or more. A total of 40 chronic HCV-infected, treatment-naïve children with well compensated livers were recruited from two sites. Patients received combined therapy of SOF (400 mg/d for patients weighing greater than 45 kg; 200 mg/d for patients weighing 17 to 45 kg) and DCV (60 mg/d for patients weighing greater than 45 kg; 30 mg/d for patients weighing 17 to 45 kg) for 12 weeks. They were followed up regularly by clinical examination and laboratory tests during treatment (weekly in the first month then monthly to the end of treatment), every 3 months for 6 months post-treatment, and at 48 weeks post-treatment. In our cohort, which included 45% of children below the age of 12 years (72.5% genotype 4 and 27.5% mixed genotype 4 and 1), end of treatment response (ETR) was 97.5%. Sustained virologic response for weeks 12 and 24 post-treatment (SVR12 and SVR24) were 97.5% and 95%, respectively, on an intention to treat basis, and 100% and 100% for those who completed the study protocol. Observed side effects were mild and none required drug cessation. Combined SOF/DCV was found to be effective and safe for treating HCV Genotype 4-infected children, 8 years of age and above.
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Affiliation(s)
- Tawhida Y Abdel Ghaffar
- Yassin Abdel Ghaffar Charity Center for Liver Disease and Research, Cairo, Egypt.,Department of Pediatrics, Ain Shams University, Cairo, Egypt
| | - Suzan El Naghi
- Yassin Abdel Ghaffar Charity Center for Liver Disease and Research, Cairo, Egypt.,Department of Pediatrics, National Hepatology & Tropical Medicine Research Institute, Cairo, Egypt
| | | | - Sarah Helmy
- Yassin Abdel Ghaffar Charity Center for Liver Disease and Research, Cairo, Egypt
| | | | | | - Mohamad Moafy
- Department of Pediatrics, Ain Shams University, Cairo, Egypt
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8
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Olmstead AD, Montoya V, Chui CK, Dong W, Joy JB, Tai V, Poon AFY, Nguyen T, Brumme CJ, Martinello M, Matthews GV, Richard Harrigan P, Dore GJ, Applegate TL, Grebely J, Howe AYM. A systematic, deep sequencing-based methodology for identification of mixed-genotype hepatitis C virus infections. INFECTION GENETICS AND EVOLUTION 2019; 69:76-84. [PMID: 30654177 DOI: 10.1016/j.meegid.2019.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 01/10/2019] [Accepted: 01/13/2019] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) mixed genotype infections can affect treatment outcomes and may have implications for vaccine design and disease progression. Previous studies demonstrate 0-39% of high-risk, HCV-infected individuals harbor mixed genotypes however standardized, sensitive methods of detection are lacking. This study compared PCR amplicon, random primer (RP), and probe enrichment (PE)-based deep sequencing methods coupled with a custom sequence analysis pipeline to detect multiple HCV genotypes. Mixed infection cutoff values, based on HCV read depth and coverage, were identified using receiver operating characteristic curve analysis. The methodology was validated using artificially mixed genotype samples and then applied to two clinical trials of HCV treatment in high-risk individuals (ACTIVATE, 114 samples from 90 individuals; DARE-C II, 26 samples from 18 individuals) and a cohort of HIV/HCV co-infected individuals (Canadian Coinfection Cohort (CCC), 3 samples from 2 individuals with suspected mixed genotype infections). Amplification bias of genotype (G)1b, G2, G3 and G5 was observed in artificially mixed samples using the PCR method while no genotype bias was observed using RP and PE. RP and PE sequencing of 140 ACTIVATE and DARE-C II samples identified the following primary genotypes: 15% (n = 21) G1a, 76% (n = 106) G3, and 9% (n = 13) G2. Sequencing of ACTIVATE and DARE-C II demonstrated, on average, 2% and 1% of HCV reads mapping to a second genotype using RP and PE, respectively, however none passed the mixed infection cutoff criteria and phylogenetics confirmed no mixed infections. From CCC, one mixed infection was confirmed while the other was determined to be a recombinant genotype. This study underlines the risk for false identification of mixed HCV infections and stresses the need for standardized methods to improve prevalence estimates and to understand the impact of mixed infections for management and elimination of HCV.
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Affiliation(s)
| | | | - Celia K Chui
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Winnie Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Jeffrey B Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada; Faculty of Medicine, Department of Medicine, Division of AIDS, University of British Columbia, Vancouver, BC, Canada
| | - Vera Tai
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Art F Y Poon
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Thuy Nguyen
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | | | | | - P Richard Harrigan
- Faculty of Medicine, Department of Medicine, Division of AIDS, University of British Columbia, Vancouver, BC, Canada
| | - Gregory J Dore
- UNSW Sydney, The Kirby Institute, Sydney, NSW, Australia
| | | | - Jason Grebely
- UNSW Sydney, The Kirby Institute, Sydney, NSW, Australia
| | - Anita Y M Howe
- BC Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
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9
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Foster GR, Dore GJ, Wang S, Grebely J, Sherman KE, Baumgarten A, Conway B, Jackson D, Asselah T, Gschwantler M, Tomasiewicz K, Aguilar H, Asatryan A, Hu Y, Mensa FJ. Glecaprevir/pibrentasvir in patients with chronic HCV and recent drug use: An integrated analysis of 7 phase III studies. Drug Alcohol Depend 2019; 194:487-494. [PMID: 30529905 DOI: 10.1016/j.drugalcdep.2018.11.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND Injection drug use is the primary mode of transmission for hepatitis C virus (HCV), and treatment guidelines recommend treating HCV-infected people who use drugs; however, concerns about adherence, effectiveness, and reinfection have impeded treatment uptake. METHODS Data were pooled from seven phase III trials that evaluated the efficacy and safety of 8 or 12 weeks of glecaprevir/pibrentasvir (G/P) in patients chronically infected with HCV genotypes 1-6. Patients had compensated liver disease, with or without cirrhosis, and were HCV treatment-naïve or -experienced with interferon or pegylated interferon ± ribavirin, or sofosbuvir plus ribavirin ± pegylated interferon. Patients were grouped into recent drug users (injection drug use ≤12 months before screening, positive urine drug screen [UDS], and/or drug-related adverse event), former drug users (>12 months before screening and negative UDS), or non-drug users. Assessments included sustained virologic response at 12 weeks posttreatment (SVR12), treatment adherence, and safety. RESULTS Among 1819 patients, 5%, 34%, and 61% were recent, former, and non-drug users, respectively. Treatment adherence and completion were high (≥96%) regardless of drug use status. SVR12 was achieved by 93% (n/N = 91/98), 97% (n/N = 591/610), and >99% (n/N = 1106/1111) of recent, former, and non-drug users, respectively (intention-to-treat analysis). The overall rates of virologic failure were ≤1.5% across all three subpopulations, with no HCV reinfections among recent drug users. Drug-related serious adverse events and adverse events leading to treatment discontinuation were experienced by ≤1% of patients. CONCLUSIONS G/P is a well-tolerated and efficacious pangenotypic regimen for chronic HCV-infected people with recent or active drug use.
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Affiliation(s)
- Graham R Foster
- Hepatology Unit, Queen Mary University of London, Mile End Rd., London E1 4NS, UK.
| | - Gregory J Dore
- The Kirby Institute, UNSW Sydney, Wallace Wurth Building, High St., Kensington NSW 2052, Australia
| | - Stanley Wang
- AbbVie Inc., 1 North Waukegan Road, North Chicago, IL, USA
| | - Jason Grebely
- The Kirby Institute, UNSW Sydney, Wallace Wurth Building, High St., Kensington NSW 2052, Australia
| | - Kenneth E Sherman
- Division of Digestive Diseases, University of Cincinnati College of Medicine, CARE/Crawley Building, Suite E-870, 3230 Eden Avenue, Cincinnati, OH 45267, USA
| | - Axel Baumgarten
- Center for Infectiology, Driesener Str. 11, 10439 Berlin, Germany
| | - Brian Conway
- Vancouver Infectious Diseases Centre, 1200 Burrard St., Vancouver, BC V6Z 2C7, Canada
| | - Daniel Jackson
- Digestive Health Specialists of the Southeast, 480 Honeysuckle Rd., Dothan, AL 36305, USA
| | - Tarik Asselah
- Université Paris Diderot, INSERM UMR1149, AP-HP Hôpital Beaujon, 100 Boulevard du Général Leclerc, 92110 Clichy, France
| | - Michael Gschwantler
- Department of Internal Medicine IV, Wilhelminenspital, and Sigmund Freud University, Freudplatz, 1A-1020 Vienna, Austria
| | - Krzysztof Tomasiewicz
- Department of Infectious Diseases and Hepatology, Medical University of Lublin, Staszica 16, 20-081 Lublin, Poland
| | - Humberto Aguilar
- Louisiana Research Center, 1800 E 70th St, Shreveport, LA 71105, USA
| | - Armen Asatryan
- AbbVie Inc., 1 North Waukegan Road, North Chicago, IL, USA
| | - Yiran Hu
- AbbVie Inc., 1 North Waukegan Road, North Chicago, IL, USA
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10
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McNaughton AL, Sreenu VB, Wilkie G, Gunson R, Templeton K, Leitch ECM. Prevalence of mixed genotype hepatitis C virus infections in the UK as determined by genotype-specific PCR and deep sequencing. J Viral Hepat 2018; 25:524-534. [PMID: 29274184 PMCID: PMC5947153 DOI: 10.1111/jvh.12849] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/20/2017] [Indexed: 12/13/2022]
Abstract
The incidence of mixed genotype hepatitis C virus (HCV) infections in the UK is largely unknown. As the efficacy of direct-acting antivirals is variable across different genotypes, treatment regimens are tailored to the infecting genotype, which may pose issues for the treatment of underlying genotypes within undiagnosed mixed genotype HCV infections. There is therefore a need to accurately diagnose mixed genotype infections prior to treatment. PCR-based diagnostic tools were developed to screen for the occurrence of mixed genotype infections caused by the most common UK genotypes, 1a and 3, in a cohort of 506 individuals diagnosed with either of these genotypes. The overall prevalence rate of mixed infection was 3.8%; however, this rate was unevenly distributed, with 6.7% of individuals diagnosed with genotype 3 harbouring genotype 1a strains and only 0.8% of samples from genotype 1a patients harbouring genotype 3 (P < .05). Mixed infection samples consisted of a major and a minor genotype, with the latter constituting less than 21% of the total viral load and, in 67% of cases, less than 1% of the viral load. Analysis of a subset of the cohort by Illumina PCR next-generation sequencing resulted in a much greater incidence rate than obtained by PCR. This may have occurred due to the nonquantitative nature of the technique and despite the designation of false-positive thresholds based on negative controls.
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Affiliation(s)
- A. L. McNaughton
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK,Present address:
Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | - V. B. Sreenu
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK
| | - G. Wilkie
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK
| | - R. Gunson
- West of Scotland Specialist Virology CentreRoyal Infirmary of GlasgowGlasgowUK
| | | | - E. C. M. Leitch
- MRC‐University of Glasgow Centre for Virus ResearchGlasgowUK
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11
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Eckhardt BJ, Scherer M, Winkelstein E, Marks K, Edlin BR. Hepatitis C Treatment Outcomes for People Who Inject Drugs Treated in an Accessible Care Program Located at a Syringe Service Program. Open Forum Infect Dis 2018; 5:ofy048. [PMID: 29644246 PMCID: PMC5887278 DOI: 10.1093/ofid/ofy048] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/05/2018] [Indexed: 01/04/2023] Open
Abstract
Hepatitis C virus (HCV) is a significant public health problem that disproportionately afflicts people who inject drugs. We describe outcomes of HCV treatment co-located within a syringe services program (SSP). Fifty-three participants started therapy, and 91% achieved sustained virologic response. SSPs provide an effective venue for HCV treatment.
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Affiliation(s)
- Benjamin J Eckhardt
- Division of Infectious Diseases and Immunology, NYU School of Medicine, New York, New York.,Division of Infectious Diseases, Weill Cornell Medicine, New York, New York
| | - Matthew Scherer
- Division of Infectious Diseases, Columbia University Medical Center, New York, New York
| | | | - Kristen Marks
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York
| | - Brian R Edlin
- National Development and Research Institutes New York, New York.,Weill Cornell Medical College, New York, New York
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12
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Del Campo JA, Parra-Sánchez M, Figueruela B, García-Rey S, Quer J, Gregori J, Bernal S, Grande L, Palomares JC, Romero-Gómez M. Hepatitis C virus deep sequencing for sub-genotype identification in mixed infections: A real-life experience. Int J Infect Dis 2017; 67:114-117. [PMID: 29253705 PMCID: PMC5812776 DOI: 10.1016/j.ijid.2017.12.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/05/2017] [Accepted: 12/07/2017] [Indexed: 12/26/2022] Open
Abstract
Routine strategies for hepatitis C virus (HCV) genotyping have several limitations. Deep sequencing methods can solve this problem. Accurate determination of viral genotypes and subtypes would allow optimal patient management and the most effective therapy. Mixed infections may represent a key factor for efficient therapy. Patients infected with more than one HCV genotype (mixed infection) can be detected only by deep sequencing methods. These patients can fail treatment with direct-acting antiviral agents, hence next-generation sequencing methods are highly recommended in clinical practice.
Background The effectiveness of the new generation of hepatitis C treatments named direct-acting antiviral agents (DAAs) depends on the genotype, subtype, and resistance-associated substitutions present in individual patients. The aim of this study was to evaluate a massive sequencing platform for the analysis of genotypes and subtypes of hepatitis C virus (HCV) in order to optimize therapy. Methods A total of 84 patients with hepatitis C were analyzed. The routine genotyping methodology for HCV used at the study institution (Versant HCV Assay, LiPA) was compared with a deep sequencing platform (454/GS-Junior and Illumina MiSeq). Results The mean viral load in these HCV patients was 6.89 × 106 ± 7.02 × 105. Viral genotypes analyzed by LiPA were distributed as follows: 26% genotype 1a (22/84), 55% genotype 1b (46/84), 1% genotype 1 (1/84), 2.5% genotype 3 (2/84), 6% genotype 3a (5/84), 6% genotype 4a/c/d (5/84). When analyzed by deep sequencing, the samples were distributed as follows: 27% genotype 1a (23/84), 56% genotype 1b (47/84), 8% genotype 3a (7/84), 5% genotype 4d (4/84), 2.5% genotype 4f (2/84). Six of the 84 patients (7%) were infected with more than one subtype. Among these, 33% (2/6) failed DAA-based triple therapy. Conclusions The detection of mixed infection could explain some treatment failures. Accurate determination of viral genotypes and subtypes would allow optimal patient management and improve the effectiveness of DAA therapy.
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Affiliation(s)
- José A Del Campo
- UCM Digestive Diseases, Valme University Hospital, Seville, Spain; Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain.
| | - Manuel Parra-Sánchez
- UCM Infectious Diseases and Microbiology, Valme University Hospital, Seville, Spain
| | | | - Silvia García-Rey
- UCM Infectious Diseases and Microbiology, Valme University Hospital, Seville, Spain
| | - Josep Quer
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Liver Disease Laboratory - Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR-HUVH), Universitat Autonoma Barcelona, Barcelona, Spain
| | - Josep Gregori
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Liver Disease Laboratory - Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR-HUVH), Universitat Autonoma Barcelona, Barcelona, Spain; Roche Diagnostics SL, Sant Cugat del Vallès, Barcelona, Spain
| | - Samuel Bernal
- UCM Infectious Diseases and Microbiology, Valme University Hospital, Seville, Spain
| | - Lourdes Grande
- UCM Digestive Diseases, Valme University Hospital, Seville, Spain
| | - José C Palomares
- UCM Infectious Diseases and Microbiology, Valme University Hospital, Seville, Spain
| | - Manuel Romero-Gómez
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain; Hospital Universitario Virgen del Rocío, Instituto de Investigación Biomédica de Sevilla (IBiS), Seville, Spain
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13
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Cabezas J, Llerena S, Puente Á, Fábrega E, Crespo J. Causes of treatment failure for hepatitis C in the era of direct-acting antiviral therapy. REVISTA ESPANOLA DE ENFERMEDADES DIGESTIVAS 2017; 108:421-30. [PMID: 26666379 DOI: 10.17235/reed.2015.3894/2015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hepatitis C therapy in the era of the newer direct-acting antiviral agents has radically changed our treatment schemes by achieving very high rates of sustained virological response. However, treatment with direct antiviral agents fails in a subgroup of patients. This group of so-called difficult-to-treat individuals is the subject of this paper, which reviews the causes of virological failure, their clinical implications, and some final recommendations.
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Affiliation(s)
- Joaquín Cabezas
- Aparato Digestivo/Unidad de Hepatología, Hospital Universitario Marqués de Valdecilla, España
| | - Susana Llerena
- Aparato Digestivo/ Unidad de Hepatologia, Hospital Universitario Marqués de Valdecilla, España
| | - Ángela Puente
- Aparato Digestivo/Unidad de Hepatología, Hospital Universitario Marqués de Valdecilla, España
| | | | - Javier Crespo
- Servicio Aparato Digestivo, Hospital Universitario Marqués de Valdecilla, 39002
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14
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High HCV subtype heterogeneity in a chronically infected general population revealed by high-resolution hepatitis C virus subtyping. Clin Microbiol Infect 2017; 23:775.e1-775.e6. [DOI: 10.1016/j.cmi.2017.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 02/02/2017] [Accepted: 02/04/2017] [Indexed: 01/17/2023]
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15
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Eckhardt B. Hepatitis C Treatment in People Who Inject Drugs. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2016. [DOI: 10.1007/s40506-016-0091-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Abstract
Before starting chronic hepatitis C treatment, the viral genotype/subtype has to be accurately determined and potentially coupled with drug resistance testing. Due to the high genetic variability of the hepatitis C virus, this can be a demanding task that can potentially be streamlined by viral whole-genome sequencing using next-generation sequencing as demonstrated by an article in this issue of the Journal of Clinical Microbiology by E. Thomson, C. L. C. Ip, A. Badhan, M. T. Christiansen, W. Adamson, et al. (J Clin Microbiol. 54:2455-2469, 2016, http://dx.doi.org/10.1128/JCM.00330-16).
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17
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Cuypers L, Ceccherini-Silberstein F, Van Laethem K, Li G, Vandamme AM, Rockstroh JK. Impact of HCV genotype on treatment regimens and drug resistance: a snapshot in time. Rev Med Virol 2016; 26:408-434. [PMID: 27401933 DOI: 10.1002/rmv.1895] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/11/2016] [Accepted: 06/15/2016] [Indexed: 12/11/2022]
Abstract
The introduction of highly potent direct-acting antivirals (DAAs) has revolutionized hepatitis C virus treatment. Nevertheless, viral eradication worldwide remains a challenge also in the era of DAA treatment, because of the high associated costs, high numbers of undiagnosed patients, high re-infection rates in some risk groups and suboptimal drug efficacies associated with host and viral factors as well as advanced stages of liver disease. A correct determination of the HCV genotype allows administration of the most appropriate antiviral regimen. Additionally, HCV genetic sequencing improves our understanding of resistance-associated variants, either naturally occurring before treatment, acquired by transmission at HCV infection, or emerging after virological failure. Because treatment response rates, and the prevalence and development of drug resistance variants differ for each DAA regimen and HCV genotype, this review summarizes treatment opportunities per HCV genotype, and focuses on viral genetic sequencing to guide clinical decision making. Although approval of the first pan-genotypic DAA-only regimen is expected soon, HCV genetic sequencing will remain important because when DAA therapies fail, genotyping and resistance testing to select a new active DAA combination will be essential. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Lize Cuypers
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | | | - Kristel Van Laethem
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Guangdi Li
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.,Department of Metabolism and Endocrinology, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Anne-Mieke Vandamme
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.,Center for Global Health and Tropical Medicine, Microbiology Unit, Institute for Hygiene and Tropical Medicine, University Nova de Lisboa, Lisbon, Portugal
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18
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Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes. J Clin Microbiol 2016; 54:2470-84. [PMID: 27385709 PMCID: PMC5035407 DOI: 10.1128/jcm.00330-16] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/28/2016] [Indexed: 12/14/2022] Open
Abstract
Affordable next-generation sequencing (NGS) technologies for hepatitis C virus (HCV) may potentially identify both viral genotype and resistance genetic motifs in the era of directly acting antiviral (DAA) therapies. This study compared the ability of high-throughput NGS methods to generate full-length, deep, HCV sequence data sets and evaluated their utility for diagnostics and clinical assessment. NGS methods using (i) unselected HCV RNA (metagenomics), (ii) preenrichment of HCV RNA by probe capture, and (iii) HCV preamplification by PCR implemented in four United Kingdom centers were compared. Metrics of sequence coverage and depth, quasispecies diversity, and detection of DAA resistance-associated variants (RAVs), mixed HCV genotypes, and other coinfections were compared using a panel of samples with different viral loads, genotypes, and mixed HCV genotypes/subtypes [geno(sub)types]. Each NGS method generated near-complete genome sequences from more than 90% of samples. Enrichment methods and PCR preamplification generated greater sequence depth and were more effective for samples with low viral loads. All NGS methodologies accurately identified mixed HCV genotype infections. Consensus sequences generated by different NGS methods were generally concordant, and majority RAVs were consistently detected. However, methods differed in their ability to detect minor populations of RAVs. Metagenomic methods identified human pegivirus coinfections. NGS provided a rapid, inexpensive method for generating whole HCV genomes to define infecting genotypes, RAVs, comprehensive viral strain analysis, and quasispecies diversity. Enrichment methods are particularly suited for high-throughput analysis while providing the genotype and information on potential DAA resistance.
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19
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Yang L, Jiang C, Hu S, Diao Q, Li J, Si W, Chen M, Zhao RY. Evolving Diversity of Hepatitis C Viruses in Yunnan Honghe, China. Int J Mol Sci 2016; 17:403. [PMID: 26999127 PMCID: PMC4813258 DOI: 10.3390/ijms17030403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/26/2016] [Accepted: 03/09/2016] [Indexed: 12/23/2022] Open
Abstract
The Chinese Honghe Autonomous Prefecture (Honghe) in Yunnan Province is a unique ethnic area because it is inhabited by more than ten different minority ethnic groups. Geographically, Honghe directly shares a border with Vietnam. The objective of this study was to investigate genetic diversity and distribution of the Hepatitis C virus (HCV) in Honghe. Ninety nine subjects who were infected with HCV or HCV/HIV (Human Immunodeficiency Virus Type 1) were recruited into this study. HCV genotypes and subtypes were determined based on the sequences of the core/envelope 1 (C/E1) and the nonstructural protein 5B (NS5B) genomic regions. The viral diversity and origins of dissemination were examined by phylogenetic analyses. Three HCV genotypes (1, 3 and 6) with six subtypes (1b, 3b, 3a, 6a, 6n and 6v) were identified. The most predominant form was genotype 3 (54.6%) followed by 6 (34.3%), and 1 (9.1%). The HCV subtype 3b appeared to be the most frequent form (38.4%) followed by 6n (20.2%) and 3a (16.2%). Statistical analyses suggested a possible rise of the genotype 6a in Honghe among intravenous drug users with HCV/HIV co-infections. Further phylogenetic analyses suggested that similar HCV-6a viruses might have been circulating in the Honghe area for more than a decade, which likely originated from Vietnam or vice versa. Two HCV samples with single HCV infection (SC34 and SC45) were isolated that could represent new recombinant variants. Although the genetic prevalence of HCV in Honghe is in general agreement with that of Southwest China and Yunnan Province, the diversity of HCV genotypes and subtypes in Honghe is somewhat unique and evolving. Information presented here should provide useful information for future health surveillance and prevention of HCV infection in this area.
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Affiliation(s)
- Lanhui Yang
- Department of Clinical Laboratory, The First People's Hospital of Honghe, Mengzi 661100, China.
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, 21201 MD, USA.
| | - Chenyan Jiang
- Division of Life Science, College of Life Science and Technology, Honghe University, Mengzi 661100, China.
| | - Song Hu
- Department of Infectious Diseases, The First People's Hospital of Honghe, Mengzi 661100, China.
| | - Qiongni Diao
- Division of Life Science, College of Life Science and Technology, Honghe University, Mengzi 661100, China.
| | - Jia Li
- Department of Infectious Diseases, The First People's Hospital of Honghe, Mengzi 661100, China.
| | - Wei Si
- Department of Clinical Laboratory, The First People's Hospital of Honghe, Mengzi 661100, China.
| | - Mei Chen
- Department of Infectious Diseases, The First People's Hospital of Honghe, Mengzi 661100, China.
| | - Richard Y Zhao
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, 21201 MD, USA.
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20
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Gowin E, Bereszyńska I, Adamek A, Kowala-Piaskowska A, Mozer-Lisewska I, Wysocki J, Michalak M, Januszkiewicz-Lewandowska D. The prevalence of mixed genotype infections in Polish patients with hepatitis C. Int J Infect Dis 2016; 43:13-16. [DOI: 10.1016/j.ijid.2015.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/28/2015] [Accepted: 12/05/2015] [Indexed: 10/22/2022] Open
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21
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Spatiotemporal Reconstruction of the Introduction of Hepatitis C Virus into Scotland and Its Subsequent Regional Transmission. J Virol 2015; 89:11223-32. [PMID: 26311892 DOI: 10.1128/jvi.02106-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 08/19/2015] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED A more comprehensive understanding of hepatitis C virus (HCV) transmission dynamics could facilitate public health initiatives to reduce the prevalence of HCV in people who inject drugs. We aimed to determine how HCV sequences entered and spread throughout Scotland and to identify transmission hot spots. A Scottish data set with embedded demographic data was created by sequencing the NS5B of 125 genotype 1a (Gt1a) samples and 166 Gt3a samples and analyzed alongside sequences from public databases. Applying Bayesian inference methods, we reconstructed the global origin and local spatiotemporal dissemination of HCV in Scotland. Scottish sequences mainly formed discrete clusters interspersed between sequences from the rest of the world; the most recent common ancestors of these clusters dated to 1942 to 1952 (Gt1a) and 1926 to 1942 (Gt3a), coincident with global diversification and distribution. Extant Scottish sequences originated in Edinburgh (Gt1a) and Glasgow (Gt3a) in the 1970s, but both genotypes spread from Glasgow to other regions. The dominant Gt1a strain differed between Edinburgh (cluster 2 [C2]), Glasgow (C3), and Aberdeen (C4), whereas significant Gt3a strain specificity occurred only in Aberdeen. Specific clusters initially formed separate transmission zones in Glasgow that subsequently overlapped, occasioning city-wide cocirculation. Transmission hot spots were detected with 45% of samples from patients residing in just 9 of Glasgow's 57 postcode districts. HCV was introduced into Scotland in the 1940s, concomitant with its worldwide dispersal likely arising from global-scale historical events. Cluster-specific transmission hubs were identified in Glasgow, the key Scottish city implicated in HCV dissemination. This fine-scale spatiotemporal reconstruction improves understanding of HCV transmission dynamics in Scotland. IMPORTANCE HCV is a major health burden and the leading cause of hepatocellular carcinoma. Public health needle exchange and "treatment as prevention" strategies targeting HCV are designed to reduce prevalence of the virus in people who inject drugs (PWID), potentially mitigating the future burden of HCV-associated liver disease. Understanding HCV transmission dynamics could increase the effectiveness of such public health initiatives by identifying and targeting regions playing a central role in virus dispersal. In this study, we examined HCV transmission in Scotland by analyzing the genetic relatedness of strains from PWID alongside data inferring the year individuals became infected and residential information at a geographically finer-scale resolution than in previous studies. Clusters of Scotland-specific strains were identified with regional specificity, and mapping the spread of HCV allowed the identification of key areas central to HCV transmission in Scotland. This research provides a basis for identifying HCV transmission hot spots.
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Abstract
The majority of new and existing cases of HCV infection in high-income countries occur among people who inject drugs (PWID). Ongoing high-risk behaviours can lead to HCV re-exposure, resulting in mixed HCV infection and reinfection. Assays used to screen for mixed infection vary widely in sensitivity, particularly with respect to their capacity for detecting minor variants (<20% of the viral population). The prevalence of mixed infection among PWID ranges from 14% to 39% when sensitive assays are used. Mixed infection compromises HCV treatment outcomes with interferon-based regimens. HCV reinfection can also occur after successful interferon-based treatment among PWID, but the rate of reinfection is low (0-5 cases per 100 person-years). A revolution in HCV therapeutic development has occurred in the past few years, with the advent of interferon-free, but still genotype-specific regiments based on direct acting antiviral agents. However, little is known about whether mixed infection and reinfection has an effect on HCV treatment outcomes in the setting of new direct-acting antiviral agents. This Review characterizes the epidemiology and natural history of mixed infection and reinfection among PWID, methodologies for detection, the potential implications for HCV treatment and considerations for the design of future studies.
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Abdelrahman T, Hughes J, Main J, McLauchlan J, Thursz M, Thomson E. Next-generation sequencing sheds light on the natural history of hepatitis C infection in patients who fail treatment. Hepatology 2015; 61:88-97. [PMID: 24797101 PMCID: PMC4303934 DOI: 10.1002/hep.27192] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/29/2014] [Indexed: 12/18/2022]
Abstract
UNLABELLED High rates of sexually transmitted infection and reinfection with hepatitis C virus (HCV) have recently been reported in human immunodeficiency virus (HIV)-infected men who have sex with men and reinfection has also been described in monoinfected injecting drug users. The diagnosis of reinfection has traditionally been based on direct Sanger sequencing of samples pre- and posttreatment, but not on more sensitive deep sequencing techniques. We studied viral quasispecies dynamics in patients who failed standard of care therapy in a high-risk HIV-infected cohort of patients with early HCV infection to determine whether treatment failure was associated with reinfection or recrudescence of preexisting infection. Paired sequences (pre- and posttreatment) were analyzed. The HCV E2 hypervariable region-1 was amplified using nested reverse-transcription polymerase chain reaction (RT-PCR) with indexed genotype-specific primers and the same products were sequenced using both Sanger and 454 pyrosequencing approaches. Of 99 HIV-infected patients with acute HCV treated with 24-48 weeks of pegylated interferon alpha and ribavirin, 15 failed to achieve a sustained virological response (six relapsed, six had a null response, and three had a partial response). Using direct sequencing, 10/15 patients (66%) had evidence of a previously undetected strain posttreatment; in many studies, this is interpreted as reinfection. However, pyrosequencing revealed that 15/15 (100%) of patients had evidence of persisting infection; 6/15 (40%) patients had evidence of a previously undetected variant present in the posttreatment sample in addition to a variant that was detected at baseline. This could represent superinfection or a limitation of the sensitivity of pyrosequencing. CONCLUSION In this high-risk group, the emergence of new viral strains following treatment failure is most commonly associated with emerging dominance of preexisting minority variants rather than reinfection. Superinfection may occur in this cohort but reinfection is overestimated by Sanger sequencing.
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Affiliation(s)
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus ResearchGlasgow, UK
| | - Janice Main
- Department of Medicine, Imperial College NHS TrustLondon, UK
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus ResearchGlasgow, UK
| | - Mark Thursz
- Department of Medicine, Imperial College NHS TrustLondon, UK
| | - Emma Thomson
- MRC-University of Glasgow Centre for Virus ResearchGlasgow, UK
- Department of Medicine, Imperial College NHS TrustLondon, UK
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Mousavi SF, Moosavy SH, Alavian SM, Eghbali H, Mahboobi H. Distribution of hepatitis C virus genotypes among patients with hepatitis C virus infection in hormozgan, iran. HEPATITIS MONTHLY 2013; 13:e14324. [PMID: 24403914 PMCID: PMC3877657 DOI: 10.5812/hepatmon.14324] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 09/29/2013] [Accepted: 11/23/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND More than 170 million people in the world are infected with Hepatitis C virus (HCV). Determination of HCV genotype before starting the treatment is required, because HCV genotype affects the course of treatment and drug dosage. OBJECTIVES We aimed to evaluate HCV genotypes among patients with positive results for anti-HCV in Bandar Abbas from 2011 to 2012. PATIENTS AND METHODS Five hundred and nine consecutive patients with established chronic HCV infection referred to Behavioral Diseases Consultation Center, Blood Transfusion and Center for Special Diseases from March 2011 to March 2012 were enrolled in this cross sectional study. Five mL of peripheral blood was taken from precipitants and viral RNA extracted after plasma separation. Hepatitis C virus RNA was detected by reverse transcriptase-nested polymerase chain reaction (RT-nested PCR) assay and then HCV genotypes analyzed using restriction fragment length polymorphism (RFLP) method. RESULTS In overall, 509 patients enrolled to this study. The mean age of these patients was 38.87 ± 9.55 years ranging from 1 to 90 years. Routs of transmission were: 238 (46.7%) inject of substance, 149 (29.3%) unknown rout, 62 (12.2%) blood transfusion, 50 (9.8%) sexual contact, and 10 (2%) mother to child. Frequency of HCV genotypes were: 316 (62.1%) 1a, 117 (23%) 1b, and 76 (14.9%) 3a. there was no significant association between HCV genotypes and gender, educational degree, risk factor of Hepatitis C, job, monthly income, HIV infection, Hepatitis B virus (HBV) infection, Intravenous drug injection, and underlying disease (P > 0.05). CONCLUSIONS This results the same as many similar studies demonstrated that common HCV genotypes in Iranian patients were 1a, 3a and 1b, respectively. Patients with 1a and 1b genotypes have lower responses to interferon treatment, and it is reasonable to perform early screening to diagnose and determine HCV genotype for effective treatment and diagnose high-risk cases.
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Affiliation(s)
| | - Seyed Hamid Moosavy
- Shahid Mohammadi Hospital of Hormozgan, University of Medical Sciences, Bandar Abbas, IR Iran
- Corresponding Author: Seyed Hamid Moosavy, Shahid Mohammadi Hospital of Hormozgan, University of Medical Sciences, Bandar Abbas, IR Iran. Tel: +98-9177635854, Fax: +98-7613354056, E-mail:
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, IR Iran
- Middle East Liver Diseases Center (MELD Center), Tehran, IR Iran
| | - Hajar Eghbali
- Shahid Mohammadi Hospital of Hormozgan, University of Medical Sciences, Bandar Abbas, IR Iran
| | - Hamidreza Mahboobi
- Infectious and Tropical Diseases Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, IR Iran
- Department of Phychology, Payame Noor University, Tehran, IR Iran
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